Select genomic region:
Overview
1.1
1.2
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1.51

### Identified secondary metabolite regions using strictness 'relaxed'

NZ_CP025018.1 (Streptomyces sp. M56)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | NRPS | 1 | 36,796 |  |
Region 2 | terpene-precursor | 91,891 | 112,988 |
Region 3 | NRPS,T1PKS,NRPS-like | 341,395 | 447,350 | Low | rapamycin | NRPS:Type I+PKS
Region 4 | T1PKS | 531,612 | 580,137 |  |
Region 5 | arylpolyene,NRPS | 632,565 | 705,334 | High | coprisamide C/coprisamide D | NRPS:Type I
Region 6 | NRP-metallophore,NRPS | 958,607 | 1,016,941 | High | coelichelin | NRPS:Type I
Region 7 | NRPS-like,NRPS,betalactone,T1PKS,T3PKS | 1,038,389 | 1,152,616 | Medium | totopotensamide A/totopotensamide B | NRPS:Type I+PKS
Region 8 | butyrolactone | 1,264,710 | 1,275,705 |  |
Region 9 | NRPS,NRPS-like | 1,306,450 | 1,394,695 | Medium | glycinocin A | NRPS:Type I
Region 10 | T1PKS | 1,420,686 | 1,559,130 | High | azalomycin F3a | PKS
Region 11 | T1PKS | 1,774,909 | 1,948,524 | High | nigericin | PKS:Type I
Region 12 | T1PKS | 2,039,904 | 2,119,811 | High | efomycin K/efomycin L | PKS
Region 13 | redox-cofactor | 2,155,093 | 2,177,184 |  |
Region 14 | hserlactone | 2,287,395 | 2,308,153 |  |
Region 15 | butyrolactone | 2,319,042 | 2,329,977 |
Region 16 | T1PKS | 2,503,248 | 2,551,386 |
Region 17 | terpene | 2,889,388 | 2,915,841 | High | hopene | terpene
Region 18 | T2PKS | 3,111,295 | 3,183,810 | High | spore pigment | PKS
Region 19 | T1PKS | 3,294,877 | 3,357,541 |  |
Region 20 | RiPP-like | 3,421,522 | 3,433,093 |  |
Region 21 | NRPS,aminocoumarin,arylpolyene,terpene-precursor | 3,520,150 | 3,601,467 | High | cinnapeptin | NRPS:Type I
Region 22 | NI-siderophore | 3,669,966 | 3,700,128 |  |
Region 23 | NRPS-like | 4,287,332 | 4,330,178 | High | echoside A/echoside B/echoside C/echoside D/echoside E | NRPS:Type I
Region 24 | thioamitides | 4,632,899 | 4,655,465 |  |
Region 25 | NI-siderophore | 4,861,531 | 4,890,692 | High | legonoxamine A/desferrioxamine B/legonoxamine B | other:other
Region 26 | terpene | 5,951,394 | 5,973,679 | High | geosmin | terpene:Sesquiterpene
Region 27 | indole | 6,562,376 | 6,583,524 | Medium | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | other:other
Region 28 | NRPS | 6,786,863 | 6,830,873 | Medium | ochronotic pigment | other:other
Region 29 | HR-T2PKS | 6,880,819 | 6,931,023 | Medium | (2E,4E,6E,8E)-N-(2-hydroxy-5-oxocyclopent-1-en-1-yl)-9-(o-tolyl)nona-2,4,6,8-tetraenamide/(E)-N-(2-hydroxy-5-oxocyclopent-1-en-1-yl)-5-(o-tolyl)pent-4-enamide | PKS+NRPS:Type I
Region 30 | RiPP-like | 6,937,785 | 6,950,181 |  |
Region 31 | T1PKS,lanthipeptide-class-i | 7,086,447 | 7,271,689 | Medium | desulfoclethramycin/clethramycin | other:other
Region 32 | ectoine | 8,288,587 | 8,298,991 | High | ectoine | other:other
Region 33 | NI-siderophore | 8,455,701 | 8,487,532 | Low | peucechelin | NRPS:Type I
Region 34 | terpene | 8,522,312 | 8,551,458 | Low | aurachin C/aurachin D/aurachin SS | PKS+terpene
Region 35 | T1PKS,NRPS-like,2dos | 8,762,999 | 8,846,225 | Medium | macbecin/macbecin II | PKS
Region 36 | T1PKS,NRPS-like | 8,881,451 | 8,958,135 | Low | geldanamycin | PKS
Region 37 | PKS-like,terpene | 9,032,523 | 9,076,634 | Low | rustmicin | PKS:Iterative type I
Region 38 | T1PKS,NRPS-like,betalactone | 9,392,965 | 9,489,931 | Medium | geldanamycin | PKS
Region 39 | terpene | 9,545,856 | 9,567,855 | High | cyclooctatin | terpene:Diterpene
Region 40 | terpene | 9,576,395 | 9,597,585 | High | pristinol | terpene
Region 41 | NRPS,T1PKS | 9,795,135 | 9,912,586 | Medium | meridamycin | NRPS:Type I+PKS
Region 42 | T1PKS,NRPS-like | 9,916,695 | 10,000,645 | High | hygrocin A/hygrocin B | PKS
Region 43 | terpene-precursor | 10,029,151 | 10,050,233 |  |
Region 44 | T1PKS,hglE-KS,RiPP-like | 10,129,891 | 10,256,044 | High | hexacosalactone A | other:other
Region 45 | NRPS | 10,264,496 | 10,343,248 |  |
Region 46 | terpene | 10,366,147 | 10,389,936 | Low | brasilicardin A | terpene+saccharide
Region 47 | terpene,NRPS,T1PKS,lanthipeptide-class-ii | 10,498,358 | 10,573,363 |  |
Region 48 | NRPS-like | 10,607,706 | 10,650,444 |  |
Region 49 | NAPAA | 10,937,152 | 10,971,414 |  |
Region 50 | nucleoside,T1PKS,T3PKS | 11,203,965 | 11,407,643 | High | bafilomycin B1 | PKS:Type I
Region 51 | betalactone,NRP-metallophore,NRPS | 11,421,156 | 11,497,318 | High | coelibactin | NRPS:Type I

NZ_CP025018.1 - Region 1 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 36,796 nt. (total: 36,796 nt) Show pHMM detection rules used
Region on contig edge.
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CFP59_RS00100: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS00115: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS00135: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS00145: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase
CFP59_RS00140: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Ligases: ligase
CFP59_RS00030: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS00035: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
Additional weak hits (18):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.34 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.93 out of 27.78
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.61 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.77 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.19 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.08 out of 23.43
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.79 out of 30.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.70 out of 27.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.60 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.10 out of 29.65
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.08 out of 23.43
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.40 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.98 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.00 out of 29.65
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.09 out of 28.14
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 36796:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-X - Ser - Val)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS00030: X
AMP-binding (18..336): X
nrpys: Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    NRTPCNALVMSGSIITAAARQGYGLTEA-VNFSF
  Nearest Stachelhaus code(s):
    Tyr DAMSIGAVIK (38% 8Å match)
    Phe DAWTIAGVCK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

CFP59_RS00035: X - Ser - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (465..867): X
nrpys: Val, aIle

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDAFNLEVWLWTGGEVNGYGPTETTVFATR
  Nearest Stachelhaus code(s):
    Val or aIle DALWWGGVFK (88% 8Å match)
    Ile DALWWGGVFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1941..2335): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LVTHFDVSVWETNQVCAGEVNMYGITETTVHATY
  Nearest Stachelhaus code(s):
    Ser DVWNVAMVHK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2992..3368): Val
nrpys: Val

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LALAFDMCKPELQAVVGGELACYGPTETTVWSTA
  Nearest Stachelhaus code(s):
    D-Ala DMPQLGMVWK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

CFP59_RS00040: mmal
PKS_AT (155..340): mmal
ATSignature: (unknown)
No matches above 50%
minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 60.2
  Methoxymalonyl-CoA: 59.7
  Ethylmalonyl-CoA: 46.8
  Propionyl-CoA: 38.8
  CHC-CoA: 36.1
  2-Methylbutyryl-CoA: 36.1
  trans-1,2-CPDA: 29.1
  Isobutyryl-CoA: 9.7
  Acetyl-CoA: 9.4
  Benzoyl-CoA: 8.1
  Malonyl-CoA: 7.2
  3-Methylbutyryl-CoA: 1.5
  inactive: 0.0
  fatty_acid: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein

NZ_CP025018.1 - Region 2 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 91,891 - 112,988 nt. (total: 21,098 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: Monooxygenation
CFP59_RS50425: Monooxygenation

MITE
  MITE0000012Monooxygenation (identity: 85.70%)

Hydrolases: hydrolase
CFP59_RS00525: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: synthetase
CFP59_RS00495: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus
BGC0001456.3 |  | 0.38 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000664.5 |  | 0.38 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002013.4 |  | 0.37 | ribosomal | curacozole | Streptomyces curacoi
BGC0000633.3 |  | 0.37 | terpene | carotenoid | Streptomyces avermitilis
BGC0000393.5 |  | 0.37 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0000286.3 |  | 0.36 | PKS | viguiepinol | Streptomyces sp. KO-3988

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus
BGC0001456.3 |  | 0.38 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000664.5 |  | 0.38 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002013.4 |  | 0.37 | ribosomal | curacozole | Streptomyces curacoi
BGC0000633.3 |  | 0.37 | terpene | carotenoid | Streptomyces avermitilis
BGC0000393.5 |  | 0.37 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0000286.3 |  | 0.36 | PKS | viguiepinol | Streptomyces sp. KO-3988

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
CFP59_RS00495: PT_FPPS_like
Domain 1 (63 - 361): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31
Confidence: medium
Additional weak hits (7):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.30 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.81 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.38 out of 29.38
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.68 out of 30.98
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.31 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
HPP | Hexaprenyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor

NZ_CP025018.1 - Region 3 - NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 341,395 - 447,350 nt. (total: 105,956 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CFP59_RS01720: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS01745: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CFP59_RS01750: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

CFP59_RS01765: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CFP59_RS01800: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS01825: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CFP59_RS01855: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CFP59_RS01870: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS01875: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS01905: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CFP59_RS01920: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: aminotransferase
CFP59_RS01830: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: deaminase hydrolase peptidase
CFP59_RS01725: HAD-superfamily hydrolase, subfamily IA, variant

smcogs
  SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

CFP59_RS01775: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

CFP59_RS01860: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

CFP59_RS01930: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CFP59_RS01935: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Ligases: ligase synthase
CFP59_RS01730: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

CFP59_RS01790: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CFP59_RS01795: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS01805: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CFP59_RS01845: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS01850: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | T1PKS | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000342.4 |  |  |  |  | 1.39 | NRPS | enniatin | Fusarium equiseti
BGC0001250.4 |  |  |  |  | 1.34 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  |  |  | 1.34 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  |  |  |  | 1.34 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  |  | 1.30 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  |  |  |  | 1.25 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001833.4 |  |  |  |  | 1.25 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  |  |  |  | 1.23 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  |  |  |  | 1.22 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  | 1.20 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.70 | NRPS | enniatin | Fusarium equiseti
BGC0001250.4 |  | 0.68 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.68 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.66 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
Additional weak hits (7):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.69 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.43 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.73 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.43 out of 33.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.33 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.17 out of 32.93
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.34 out of 27.18
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 3, location 341394 - 447350:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (shikimic_acid - redemal - ccmal - ccmal - ccmal) + (Hpr) + (Me-redmal - Me-ccmal - ccmal - Me-redmal - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 341394 - 384637:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (shikimic_acid - redemal - ccmal - ccmal - ccmal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 354360 - 447350:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (shikimic_acid - redemal - ccmal - ccmal - ccmal) + (Hpr) + (Me-redmal - Me-ccmal - ccmal - Me-redmal - mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS01795: X
AMP-binding (9..433): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FEVFFDGSVSESMSLFGGETNCYGPTETTIVITG
  Nearest Stachelhaus code(s):
    Phe DVSTCGCIIK (62% 8Å match)
    bOH-Tyr DASTLGAICK (56% 8Å match)
  Stachelhaus code match:
    60% (weak)

CFP59_RS01805: X
AMP-binding (483..877): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQAFDVSFQEPFLCVSGEVNLYGPTETNAATVH
  Nearest Stachelhaus code(s):
    Aze DVQFISQIAK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

CFP59_RS01845: shikimic_acid - emal - mal - mal - mal
CAL_domain (34..439): shikimic_acid
minowa: shikimic_acid

Prediction, score:
  shikimic_acid: 503.8
  AHBA: 306.4
  fatty_acid: 0.0
  Acetyl-CoA: 0.0
  NH2: -1.8

PKS_AT (1754..2029): emal
ATSignature: Methylmalonyl-CoA, Ethylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Ethylmalonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 83.3%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 153.1
  Methylmalonyl-CoA: 142.3
  Methoxymalonyl-CoA: 112.8
  trans-1,2-CPDA: 67.9
  Propionyl-CoA: 61.2
  Malonyl-CoA: 59.4
  CHC-CoA: 58.2
  2-Methylbutyryl-CoA: 55.5
  Isobutyryl-CoA: 39.2
  Benzoyl-CoA: 29.6
  fatty_acid: 22.8
  Acetyl-CoA: 20.1
  inactive: 13.5
  3-Methylbutyryl-CoA: 12.2

PKS_AT (3679..3941): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 161.1
  Methoxymalonyl-CoA: 74.7
  inactive: 68.7
  Methylmalonyl-CoA: 50.4
  Isobutyryl-CoA: 32.7
  Acetyl-CoA: 23.4
  Ethylmalonyl-CoA: 20.4
  Propionyl-CoA: 15.8
  fatty_acid: 14.6
  Benzoyl-CoA: 12.0
  CHC-CoA: 11.4
  2-Methylbutyryl-CoA: 10.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5183..5443): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 160.2
  Methoxymalonyl-CoA: 73.0
  inactive: 68.2
  Methylmalonyl-CoA: 50.1
  Isobutyryl-CoA: 28.2
  Acetyl-CoA: 22.3
  Ethylmalonyl-CoA: 17.0
  Propionyl-CoA: 16.6
  fatty_acid: 14.3
  Benzoyl-CoA: 11.1
  CHC-CoA: 10.8
  2-Methylbutyryl-CoA: 9.5
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (6779..7042): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 162.7
  Methoxymalonyl-CoA: 75.2
  inactive: 68.4
  Methylmalonyl-CoA: 50.6
  Isobutyryl-CoA: 33.0
  Acetyl-CoA: 23.4
  Ethylmalonyl-CoA: 20.4
  Propionyl-CoA: 15.9
  fatty_acid: 14.6
  Benzoyl-CoA: 12.0
  CHC-CoA: 11.4
  2-Methylbutyryl-CoA: 10.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS01850: Hpr
Search NORINE for peptide: strict or relaxed
AMP-binding (487..883): Hpr
nrpys: Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pip (Hpr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQIFDYSVQESYACQGGEHNHYGPAESQLVTGY
  Nearest Stachelhaus code(s):
    Hpr DYQYLGHLVK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

CFP59_RS01855: mmal - mmal - mal - mmal - mal
PKS_AT (543..816): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 175.1
  Ethylmalonyl-CoA: 164.9
  Methoxymalonyl-CoA: 145.3
  2-Methylbutyryl-CoA: 88.0
  Propionyl-CoA: 83.1
  trans-1,2-CPDA: 81.4
  Malonyl-CoA: 78.2
  CHC-CoA: 74.9
  Isobutyryl-CoA: 60.9
  Benzoyl-CoA: 56.8
  Acetyl-CoA: 35.5
  fatty_acid: 20.6
  inactive: 18.7
  3-Methylbutyryl-CoA: 16.4

PKS_AT (2483..2776): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 204.8
  Ethylmalonyl-CoA: 203.7
  Methoxymalonyl-CoA: 161.0
  2-Methylbutyryl-CoA: 111.5
  Propionyl-CoA: 99.8
  Malonyl-CoA: 98.2
  trans-1,2-CPDA: 92.0
  Isobutyryl-CoA: 89.3
  CHC-CoA: 81.8
  Benzoyl-CoA: 63.0
  Acetyl-CoA: 39.0
  inactive: 30.3
  fatty_acid: 25.6
  3-Methylbutyryl-CoA: 24.9

PKS_AT (4172..4428): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 162.5
  Methoxymalonyl-CoA: 74.6
  inactive: 68.3
  Methylmalonyl-CoA: 50.1
  Isobutyryl-CoA: 31.5
  Acetyl-CoA: 21.6
  Ethylmalonyl-CoA: 20.7
  Propionyl-CoA: 18.9
  fatty_acid: 14.6
  Benzoyl-CoA: 11.7
  CHC-CoA: 11.4
  2-Methylbutyryl-CoA: 9.9
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5676..5949): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 175.1
  Ethylmalonyl-CoA: 163.1
  Methoxymalonyl-CoA: 144.7
  2-Methylbutyryl-CoA: 87.1
  Propionyl-CoA: 82.0
  trans-1,2-CPDA: 81.7
  Malonyl-CoA: 80.7
  CHC-CoA: 77.1
  Isobutyryl-CoA: 62.1
  Benzoyl-CoA: 59.5
  Acetyl-CoA: 35.2
  inactive: 21.6
  fatty_acid: 20.8
  3-Methylbutyryl-CoA: 18.3

PKS_AT (7641..7930): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 66.7%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 143.0
  Methoxymalonyl-CoA: 58.5
  Methylmalonyl-CoA: 54.6
  inactive: 50.0
  Isobutyryl-CoA: 28.8
  Propionyl-CoA: 27.5
  Ethylmalonyl-CoA: 27.1
  Benzoyl-CoA: 19.9
  fatty_acid: 14.0
  trans-1,2-CPDA: 11.1
  Acetyl-CoA: 9.7
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -0.3

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production

NZ_CP025018.1 - Region 4 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 531,612 - 580,137 nt. (total: 48,526 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CFP59_RS02325: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS02390: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS02415: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CFP59_RS02485: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: acetyltransferase
CFP59_RS02365: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Ligases: synthase
CFP59_RS02405: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS02410: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  | 0.63 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0000037.4 |  | 0.61 | PKS | cichorine | Aspergillus nidulans FGSC A4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  | 0.63 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0000037.4 |  | 0.61 | PKS | cichorine | Aspergillus nidulans FGSC A4

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.38 out of 23.79
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (13):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.80 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.81 out of 18.57
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 19.26
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.36 out of 27.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.13 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.66 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.61 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.06 out of 24.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.49 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 6, location 531611 - 580137:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS02405: mal
PKS_AT (1607..1902): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 181.3
  inactive: 139.8
  Methoxymalonyl-CoA: 69.4
  Methylmalonyl-CoA: 69.2
  Propionyl-CoA: 54.6
  Isobutyryl-CoA: 52.2
  Ethylmalonyl-CoA: 28.4
  Benzoyl-CoA: 26.2
  trans-1,2-CPDA: 20.4
  2-Methylbutyryl-CoA: 20.4
  Acetyl-CoA: 18.8
  CHC-CoA: 16.3
  fatty_acid: 12.5
  3-Methylbutyryl-CoA: 9.4

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism

NZ_CP025018.1 - Region 5 - NRPS,arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 632,565 - 705,334 nt. (total: 72,770 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CFP59_RS02775: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CFP59_RS02780: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

CFP59_RS02785: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

CFP59_RS02790: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CFP59_RS02820: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS02890: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS02965: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS52165: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: kinase
CFP59_RS02995: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: deacetylase deaminase
CFP59_RS02895: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

CFP59_RS02980: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Ligases: ligase synthase
CFP59_RS02865: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS02870: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS02875: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS02900: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

CFP59_RS02920: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CFP59_RS02925: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
CFP59_RS02805: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | arylpolyene | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002510.2 |  |  | 1.79 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0002378.3 |  |  | 0.65 | NRPS | coprisamide C, coprisamide D | Streptomyces sp.
BGC0002192.3 |  |  | 0.53 | PKS | FR901512 | fungal sp. No.14919
BGC0002547.2 |  |  | 0.45 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces youssoufiensis
BGC0002135.2 |  |  | 0.43 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.40 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.40 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.39 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.38 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  |  | 0.38 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002510.2 |  | 0.96 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002378.3 |  | 0.74 | NRPS | coprisamide C, coprisamide D | Streptomyces sp.
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001133.4 |  | 0.70 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.83 out of 26.33
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.26 out of 23.79
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.31 out of 27.04
Confidence: medium
Additional weak hits (16):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.07 out of 30.97
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.35 out of 25.75
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.69 out of 29.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.28 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.50 out of 21.55
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.82 out of 23.43
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.19 out of 25.75
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 39.62
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.45 out of 20.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.45 out of 20.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.09 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 7, location 632564 - 705334:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Ala - D-Ser) + (D-X - Val - X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 632564 - 673695:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-X - Val - X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 641119 - 705334:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Ala - D-Ser) + (D-X - Val - X - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS02920: X - Val - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (465..860): X
nrpys: 3OH-Leu, Leu

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAAAFDAAVLEMLIVVGGDVNAYGPTESTVAATM
  Nearest Stachelhaus code(s):
    3OH-Leu DALLVGAVAK (82% 8Å match)
    Leu DALLVGAVAK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2004..2408): Val
nrpys: Val

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDGSFDASTYEVWLWSGGDGDGYGPTETTTFAAY
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3070..3478): X
nrpys: Dpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISVWQSEVMVTGEVNAYGPTECSDDVTH
  Nearest Stachelhaus code(s):
    Dpr DIWEMTADDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4141..4548): X
nrpys: bMe-Asp

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    asp,asn (Asp, Asn)
  Single AA prediction:
    asn (Asn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YFASFDLSVTAVKALLGGELNMYGPTETTVNCSQ
  Nearest Stachelhaus code(s):
    bMe-Asp DLTKLGMVNK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

CFP59_RS02925: Ala - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (476..877): Ala
nrpys: Ala

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    ala (Ala)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWATFDVSVFEGSAVLAGEANIYGPTEATVYATA
  Nearest Stachelhaus code(s):
    Ala DVFSVAIVYK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1993..2399): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWTTFDVSVWEWHFLCSGEHNLYGPTEASVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 6 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 958,607 - 1,016,941 nt. (total: 58,335 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer oxidoreductase oxygenase
CFP59_RS04260: flavodoxin

smcogs
  SMCOG1134: flavodoxin

CFP59_RS04360: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

CFP59_RS04380: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CFP59_RS04395: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: formyltransferase
CFP59_RS04365: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: dehalogenase esterase hydrolase
CFP59_RS04320: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

CFP59_RS04370: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

CFP59_RS04410: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Isomerases: mutase
CFP59_RS04435: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase
CFP59_RS04330: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000325.5 |  |  | 1.10 | NRPS | coelichelin | Streptomyces coelicolor A3(2)
BGC0000357.5 |  |  | 0.69 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001825.4 |  |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  | 0.57 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  |  | 0.57 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  |  | 0.57 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.57 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  | 0.56 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001137.5 |  |  | 0.47 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0002476.2 |  |  | 0.42 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000325.5 |  | 0.82 | NRPS | coelichelin | Streptomyces coelicolor A3(2)
BGC0000357.5 |  | 0.68 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.62 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.62 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.61 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001137.5 |  | 0.57 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0002476.2 |  | 0.54 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 30.12 out of 30.12
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 27.49 out of 30.12
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.37 out of 30.12
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.90 out of 30.12
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.36 out of 36.53
Confidence: strong
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 22.40
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.30 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.84 out of 36.53
Confidence: medium
Additional weak hits (16):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.36 out of 29.51
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.14 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.87 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.02 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.24 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.25 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.40 out of 36.53
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.67 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.95 out of 39.62
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.12 out of 36.53
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.61 out of 23.43
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.27 out of 20.01
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.81 out of 21.84
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 10, location 958606 - 1016941:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Fo-OH-Orn - D-Thr - OH-Orn)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS04330: Fo-OH-Orn - Thr - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (144..542): Fo-OH-Orn
nrpys: Fo-OH-Orn

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWQAFDISINELYLWCGGEYHGYGPAETTIGVSH
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DINYWGGIGK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1625..2037): Thr
nrpys: Thr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNTHFDFAVWEGNQIFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3050..3450): OH-Orn
nrpys: OH-Orn

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    MNHVFDMSWEEWNVLLGGEYNLYGPTEYTINTLG
  Nearest Stachelhaus code(s):
    OH-Orn DMENLGLINK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
DmdR1 | Iron(II)-dependent repressor
HypR | L-hydroxyproline utilization repressor
OsdR | Development and stress management regulator

NZ_CP025018.1 - Region 7 - NRPS,NRPS-like,T1PKS,T3PKS,betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,038,389 - 1,152,616 nt. (total: 114,228 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
betalactone: (HMGL-like and AMP-binding)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CFP59_RS04635: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

CFP59_RS04640: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS04650: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

CFP59_RS04755: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS04790: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CFP59_RS04795: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

CFP59_RS04800: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CFP59_RS04865: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase halogenase methyltransferase sulfotransferase
CFP59_RS04625: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CFP59_RS04630: Sulfotransferase domain

extras
  Sulfotransfer_1: Sulfotransferase domain

CFP59_RS04645: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

CFP59_RS04660: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CFP59_RS04695: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase hydrolase
CFP59_RS04615: thioesterase

smcogs
  SMCOG1004: thioesterase

CFP59_RS04810: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: hydratase lyase
CFP59_RS04600: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

CFP59_RS04700: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

CFP59_RS04705: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Isomerases: racemase
CFP59_RS04855: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase synthase
CFP59_RS04590: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

CFP59_RS04605: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CFP59_RS04655: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS04675: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

CFP59_RS04775: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

CFP59_RS49975: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS51780: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS-like | NRPS | betalactone | T1PKS | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002341.2 |  |  |  |  |  | 1.45 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001128.4 |  |  |  |  |  | 1.38 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  |  |  | 1.38 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002608.2 |  |  |  |  |  | 1.35 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0001833.4 |  |  |  |  |  | 1.34 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  |  |  |  | 1.33 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  |  |  | 1.30 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  |  |  |  | 1.26 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  |  |  | 1.23 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  |  |  |  |  | 1.23 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002608.2 |  | 0.75 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.73 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.87 out of 29.72
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
Additional weak hits (10):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.00 out of 30.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.45 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.12 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.26 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.82 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.82 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.26 out of 26.06
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.36 out of 32.74
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.65 out of 29.25
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 11, location 1038388 - 1142175:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-ccmal - Me-ohmal - Me-redmal) + (Me-redmal - ohmal) + (Thr - Ala - Dab - Val - Ile) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 12, location 1038388 - 1081613:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly) + (Thr - Ala - Dab - Val - Ile)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 1041855 - 1100674:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal - ohmal) + (Thr - Ala - Dab - Val - Ile) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 14, location 1071435 - 1142175:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-ccmal - Me-ohmal - Me-redmal) + (Me-redmal - ohmal) + (Thr - Ala - Dab - Val - Ile)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 15, location 1111542 - 1152616:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-ccmal - Me-ohmal - Me-redmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS04650: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (147..550): Gly
nrpys: Gly

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISLWQSQVAVTGEVNCYGLTEVSDDSNH
  Nearest Stachelhaus code(s):
    Gly DIWQATCDDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

CFP59_RS04655: Thr - Ala - Dab - Val - Ile
Search NORINE for peptide: strict or relaxed
AMP-binding (470..887): Thr
nrpys: Thr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTAHFDFSVWEGSQVFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1592..1989): Ala
nrpys: Ala

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LFRAFDVATWETQLLVAGEGNAYGPTEITVIAAA
  Nearest Stachelhaus code(s):
    Ala DVWQLAAVIK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3292..3687): Dab
nrpys: Dab

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRAFDGSTVEVHMLTGADRSSYGPTEVTVIGTQ
  Nearest Stachelhaus code(s):
    Dab DGVHLGSVIK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4367..4770): Val
nrpys: Val

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LPAAFDCTTFEIVLLTGGDINGYGPTESTTYTHS
  Nearest Stachelhaus code(s):
    Dhpg or cl-me-dHpg DSFLLGGTYK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (5441..5855): Ile
nrpys: Ile

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    QWMAFDASVWEWQLLCIGEHNLYGPTEASVAVTS
  Nearest Stachelhaus code(s):
    Ile DAWQLLLVAK (91% 8Å match)
  Stachelhaus code match:
    90% (moderate)

CFP59_RS49975: mmal - mal
PKS_AT (557..851): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 189.7
  Ethylmalonyl-CoA: 179.0
  Methoxymalonyl-CoA: 153.6
  2-Methylbutyryl-CoA: 123.9
  trans-1,2-CPDA: 120.0
  Propionyl-CoA: 99.8
  CHC-CoA: 88.7
  Malonyl-CoA: 71.5
  Isobutyryl-CoA: 54.4
  Benzoyl-CoA: 46.4
  Acetyl-CoA: 23.6
  inactive: 22.3
  fatty_acid: 22.2
  3-Methylbutyryl-CoA: 17.0

PKS_AT (2674..2969): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 198.8
  inactive: 96.8
  Methoxymalonyl-CoA: 56.0
  Methylmalonyl-CoA: 43.6
  Propionyl-CoA: 37.8
  Isobutyryl-CoA: 19.5
  Acetyl-CoA: 16.9
  Ethylmalonyl-CoA: 15.3
  Benzoyl-CoA: 10.7
  fatty_acid: 10.4
  2-Methylbutyryl-CoA: 7.1
  trans-1,2-CPDA: 4.1
  CHC-CoA: 1.2
  3-Methylbutyryl-CoA: 0.0

CFP59_RS51780: mal - mmal - mmal - mmal
PKS_AT (549..798): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 66.7%
  inactive: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 44.9
  inactive: 9.7
  Acetyl-CoA: 9.6
  Propionyl-CoA: 4.4
  Methoxymalonyl-CoA: 0.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0
  Methylmalonyl-CoA: -0.2

PKS_AT (1511..1806): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 201.6
  Ethylmalonyl-CoA: 190.9
  Methoxymalonyl-CoA: 153.6
  trans-1,2-CPDA: 119.6
  2-Methylbutyryl-CoA: 115.9
  Propionyl-CoA: 105.7
  Malonyl-CoA: 100.7
  CHC-CoA: 100.1
  Isobutyryl-CoA: 72.9
  Benzoyl-CoA: 67.8
  Acetyl-CoA: 51.2
  inactive: 34.7
  fatty_acid: 25.0
  3-Methylbutyryl-CoA: 19.4

PKS_AT (3288..3583): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 208.9
  Ethylmalonyl-CoA: 205.0
  Methoxymalonyl-CoA: 160.9
  trans-1,2-CPDA: 130.7
  2-Methylbutyryl-CoA: 125.5
  Propionyl-CoA: 109.7
  CHC-CoA: 107.5
  Malonyl-CoA: 102.5
  Isobutyryl-CoA: 75.7
  Benzoyl-CoA: 73.6
  Acetyl-CoA: 55.9
  inactive: 39.9
  3-Methylbutyryl-CoA: 35.4
  fatty_acid: 28.4

PKS_AT (4837..5131): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 192.7
  Ethylmalonyl-CoA: 182.9
  Methoxymalonyl-CoA: 155.7
  2-Methylbutyryl-CoA: 128.1
  trans-1,2-CPDA: 122.6
  Propionyl-CoA: 102.3
  CHC-CoA: 88.5
  Malonyl-CoA: 73.2
  Isobutyryl-CoA: 56.0
  Benzoyl-CoA: 49.1
  Acetyl-CoA: 25.3
  inactive: 22.9
  fatty_acid: 22.2
  3-Methylbutyryl-CoA: 16.6

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
NtrC | Nitrogen regulatory protein C
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 8 - butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,264,710 - 1,275,705 nt. (total: 10,996 nt) Show pHMM detection rules used
butyrolactone: AfsA

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: dehydratase
CFP59_RS05350: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001458.4 |  | 0.53 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0000850.5 |  | 0.51 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.38 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002584.2 |  | 0.37 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002443.3 |  | 0.32 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0002386.2 |  | 0.32 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0002316.2 |  | 0.32 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000528.5 |  | 0.31 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000219.4 |  | 0.31 | PKS, saccharide | elloramycin | Streptomyces olivaceus
BGC0002805.2 |  | 0.31 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001458.4 |  | 0.53 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0000850.5 |  | 0.51 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.38 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002584.2 |  | 0.37 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002443.3 |  | 0.32 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0002386.2 |  | 0.32 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0002316.2 |  | 0.32 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000528.5 |  | 0.31 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000219.4 |  | 0.31 | PKS, saccharide | elloramycin | Streptomyces olivaceus
BGC0002805.2 |  | 0.31 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.62 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.58 out of 20.01
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP025018.1 - Region 9 - NRPS,NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,306,450 - 1,394,695 nt. (total: 88,246 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CFP59_RS05495: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

CFP59_RS05605: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CFP59_RS05620: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

CFP59_RS05695: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Hydrolases: deaminase hydrolase
CFP59_RS05560: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

CFP59_RS05570: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CFP59_RS05710: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: lyase
CFP59_RS05630: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

CFP59_RS49995: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
CFP59_RS05490: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

CFP59_RS05580: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS05585: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS05590: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS05610: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS05625: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS05640: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

Translocases: transport
CFP59_RS05565: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.85 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.85 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  | 0.83 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  |  | 0.81 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  |  | 0.81 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.81 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.80 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  |  | 0.78 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  |  | 0.78 | NRPS | enniatin | Fusarium equiseti
BGC0001641.4 |  |  | 0.77 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.77 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  | 0.74 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001825.4 |  | 0.74 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.88 out of 20.97
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.88 out of 27.04
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (12):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.32 out of 20.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.41 out of 36.54
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.81 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.60 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.81 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.59 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.52 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.79 out of 30.97
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.34 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 21.55
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.63 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 17, location 1306449 - 1394695:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - Pro) + (Gly - X - Gly - X - Gly - D-Thr) + (X - D-Hpr) + (Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 18, location 1306449 - 1384193:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - Pro) + (Gly - X - Gly - X - Gly - D-Thr) + (X - D-Hpr) + (Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 19, location 1351419 - 1394695:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - X - Gly - X - Gly - D-Thr) + (X - D-Hpr) + (Asp)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS05580: Leu - Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (468..864): Leu
nrpys: Leu

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDASTYEVFLWTGGEVDVYGPTETTTFAVR
  Nearest Stachelhaus code(s):
    Leu DAYFWGVTFK (94% 8Å match)
    Val DAYFWGVTFK (91% 8Å match)
    Ile DAYFWGVTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1539..1952): Pro
nrpys: Pro

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pro (Pro)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHTFDVSVQESYAVQAGEHNHYGPAETHVVTAC
  Nearest Stachelhaus code(s):
    Pro DVQYVAHVVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

CFP59_RS05585: Gly - X - Gly - X - Gly - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (466..865): Gly
nrpys: Gly

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    gly (Gly)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAMTFDIAGLEVQALVGGEMNMYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGMIWK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1532..1906): X
nrpys: Dpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    asp,asn (Asp, Asn)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRASFDLTVTATKVITGGEVNAYGPTEATVNCAD
  Nearest Stachelhaus code(s):
    Dpr DLTKIGAVNK (94% 8Å match)
    Asp DLTKIGAVNK (79% 8Å match)
    OH-Asp or OMe-Asp DLTKIGAVNK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2571..2971): Gly
nrpys: Gly

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    gly (Gly)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FSMTFDIAGLEVQALVGGETNLYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3637..4011): X
nrpys: Dpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    asp,asn (Asp, Asn)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRASFDLTVTATKVITGGEVNAYGPTEATVNCAD
  Nearest Stachelhaus code(s):
    Dpr DLTKIGAVNK (94% 8Å match)
    Asp DLTKIGAVNK (79% 8Å match)
    OH-Asp or OMe-Asp DLTKIGAVNK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4677..5075): Gly
nrpys: Gly

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    gly (Gly)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FSMTFDIAGLEVQALVGGETNLYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5793..6181): Thr
nrpys: Thr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSTHFDFSVWEGNQVFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
    Val DFWNVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

CFP59_RS05590: X - Hpr
Search NORINE for peptide: strict or relaxed
AMP-binding (476..850): X
nrpys: Dpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    asp,asn (Asp, Asn)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRASFDLTVTATKVITGGEVNAYGPTEATVNCAD
  Nearest Stachelhaus code(s):
    Dpr DLTKIGAVNK (94% 8Å match)
    Asp DLTKIGAVNK (79% 8Å match)
    OH-Asp or OMe-Asp DLTKIGAVNK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2186..2597): Hpr
nrpys: Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pip (Hpr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHLFDFAVQEQFAFQGGEHNIYGPAETHAATST
  Nearest Stachelhaus code(s):
    Hpr DFQFFGIAAK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

CFP59_RS05610: NH2
CAL_domain (42..470): NH2
minowa: NH2

Prediction, score:
  NH2: 128.6
  fatty_acid: 28.5
  Acetyl-CoA: 10.6
  AHBA: 9.7
  shikimic_acid: 0.0

CFP59_RS05625: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (241..648): Asp
nrpys: Asp

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISLWQAQVSVTGEVNAYGATETSDDPMH
  Nearest Stachelhaus code(s):
    Asp DIWQSTADDK (91% 8Å match)
    dnmeProp or Dab DIWQSTADDK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
DasR | N-acetylglucosamine dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 10 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,420,686 - 1,559,130 nt. (total: 138,445 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CFP59_RS05885: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

CFP59_RS05925: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS06020: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acylase
CFP59_RS05965: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CFP59_RS05995: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CFP59_RS50655: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Lyases: hydratase
CFP59_RS05915: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Ligases: ligase synthase
CFP59_RS05970: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS05975: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS06000: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS06005: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS06010: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS50660: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: permease
CFP59_RS05910: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001523.5 |  | 0.83 | PKS | azalomycin F3a | Streptomyces sp. 211726
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001700.5 |  | 0.69 | PKS | niphimycin C, niphimycin D, niphimycin E, 17-O-methylniphimycin, niphimycin Iα, 19-O-malonylniphimycin | Streptomyces sp. IMB7-145
BGC0000041.3 |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000018.5 |  | 0.68 | PKS | angolamycin | Streptomyces eurythermus
BGC0000067.5 |  | 0.66 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000166.5 |  | 0.66 | PKS | tylactone | Streptomyces fradiae
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001523.5 |  | 0.83 | PKS | azalomycin F3a | Streptomyces sp. 211726
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001700.5 |  | 0.69 | PKS | niphimycin C, niphimycin D, niphimycin E, 17-O-methylniphimycin, niphimycin Iα, 19-O-malonylniphimycin | Streptomyces sp. IMB7-145
BGC0000041.3 |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000018.5 |  | 0.68 | PKS | angolamycin | Streptomyces eurythermus
BGC0000067.5 |  | 0.66 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000166.5 |  | 0.66 | PKS | tylactone | Streptomyces fradiae
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.14 out of 23.79
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.24 out of 27.18
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.71 out of 23.79
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.04 out of 18.57
Confidence: medium
Additional weak hits (18):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.75 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.73 out of 29.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.88 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.42 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.48 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.14 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.50 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.22 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.65 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.45 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.28 out of 36.53
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.58 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.94 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.28 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 20, location 1420685 - 1559130:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (redmal) + (Me-ccmal - ohmal) + (Me-ccmal - pk - ccmal) + (ohmal - ohmal - ohmal) + (ohmal - ohmal - mal - pk - redmal) + (pk - ohmal) + (pk - ccmal) + (pk)
Non-colinear ordering:
  CFP59_RS05975 + CFP59_RS06005 + CFP59_RS06010 + CFP59_RS06000 + CFP59_RS05995 + CFP59_RS50660 + CFP59_RS50655 + CFP59_RS05980

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS05965: pk
PKS_AT (26..305): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

Prediction, score:
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Malonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

CFP59_RS05970: X
AMP-binding (10..375): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    NRNLHQYGLSMIDACSGAALDSYGSTEAGNVSFA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CFP59_RS05975: mal
PKS_AT (671..977): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 234.2
  inactive: 138.2
  Methoxymalonyl-CoA: 75.5
  Methylmalonyl-CoA: 63.8
  Isobutyryl-CoA: 36.8
  Ethylmalonyl-CoA: 29.9
  Propionyl-CoA: 26.0
  Benzoyl-CoA: 21.6
  Acetyl-CoA: 15.8
  trans-1,2-CPDA: 14.0
  2-Methylbutyryl-CoA: 12.3
  fatty_acid: 11.6
  CHC-CoA: 9.4
  3-Methylbutyryl-CoA: 0.0

CFP59_RS05980: pk
PKS_AT (576..874): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 228.3
  Methylmalonyl-CoA: 227.0
  Methoxymalonyl-CoA: 184.0
  2-Methylbutyryl-CoA: 159.5
  trans-1,2-CPDA: 129.6
  Propionyl-CoA: 114.0
  Malonyl-CoA: 109.8
  CHC-CoA: 103.9
  Isobutyryl-CoA: 79.2
  Benzoyl-CoA: 63.0
  3-Methylbutyryl-CoA: 48.9
  inactive: 47.7
  Acetyl-CoA: 39.5
  fatty_acid: 27.4

CFP59_RS50655: pk - mal
PKS_AT (569..867): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 232.4
  Methylmalonyl-CoA: 230.8
  Methoxymalonyl-CoA: 186.6
  2-Methylbutyryl-CoA: 158.7
  trans-1,2-CPDA: 137.6
  CHC-CoA: 118.5
  Malonyl-CoA: 117.4
  Propionyl-CoA: 117.3
  Isobutyryl-CoA: 84.2
  Benzoyl-CoA: 62.2
  3-Methylbutyryl-CoA: 49.0
  inactive: 44.6
  Acetyl-CoA: 44.5
  fatty_acid: 35.0

PKS_AT (2139..2442): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 246.3
  inactive: 117.8
  Methoxymalonyl-CoA: 78.9
  Methylmalonyl-CoA: 71.9
  Propionyl-CoA: 39.9
  Isobutyryl-CoA: 31.6
  Ethylmalonyl-CoA: 27.7
  2-Methylbutyryl-CoA: 21.0
  Acetyl-CoA: 20.5
  Benzoyl-CoA: 16.7
  CHC-CoA: 12.6
  fatty_acid: 10.0
  trans-1,2-CPDA: 9.2
  3-Methylbutyryl-CoA: 0.0

CFP59_RS50660: pk - mal
PKS_AT (566..864): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 231.0
  Methylmalonyl-CoA: 230.0
  Methoxymalonyl-CoA: 186.5
  2-Methylbutyryl-CoA: 156.8
  trans-1,2-CPDA: 135.0
  CHC-CoA: 118.5
  Malonyl-CoA: 118.2
  Propionyl-CoA: 117.2
  Isobutyryl-CoA: 84.9
  Benzoyl-CoA: 62.3
  3-Methylbutyryl-CoA: 49.9
  inactive: 49.8
  Acetyl-CoA: 40.7
  fatty_acid: 31.8

PKS_AT (2117..2418): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 241.3
  inactive: 112.4
  Methoxymalonyl-CoA: 70.8
  Methylmalonyl-CoA: 62.4
  Propionyl-CoA: 39.4
  Isobutyryl-CoA: 30.0
  Ethylmalonyl-CoA: 29.1
  Acetyl-CoA: 21.7
  Benzoyl-CoA: 18.6
  fatty_acid: 16.3
  2-Methylbutyryl-CoA: 13.5
  trans-1,2-CPDA: 12.3
  CHC-CoA: 11.2
  3-Methylbutyryl-CoA: 0.0

CFP59_RS05995: mal - mal - mal - pk - mal
PKS_AT (568..869): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 245.1
  inactive: 125.7
  Methoxymalonyl-CoA: 81.1
  Methylmalonyl-CoA: 69.2
  Propionyl-CoA: 36.7
  Isobutyryl-CoA: 32.0
  Ethylmalonyl-CoA: 24.6
  Benzoyl-CoA: 22.8
  Acetyl-CoA: 22.5
  2-Methylbutyryl-CoA: 14.8
  fatty_acid: 14.3
  CHC-CoA: 14.1
  trans-1,2-CPDA: 13.7
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2121..2422): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 243.6
  inactive: 118.5
  Methoxymalonyl-CoA: 75.9
  Methylmalonyl-CoA: 66.8
  Propionyl-CoA: 36.6
  Isobutyryl-CoA: 31.6
  Ethylmalonyl-CoA: 25.2
  Acetyl-CoA: 24.2
  Benzoyl-CoA: 19.4
  fatty_acid: 16.2
  trans-1,2-CPDA: 13.4
  2-Methylbutyryl-CoA: 12.1
  CHC-CoA: 9.5
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3675..3981): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 242.5
  inactive: 125.0
  Methoxymalonyl-CoA: 78.5
  Methylmalonyl-CoA: 67.4
  Propionyl-CoA: 40.8
  Isobutyryl-CoA: 30.3
  Ethylmalonyl-CoA: 25.8
  Acetyl-CoA: 20.5
  trans-1,2-CPDA: 19.3
  Benzoyl-CoA: 17.8
  fatty_acid: 15.7
  2-Methylbutyryl-CoA: 12.7
  CHC-CoA: 10.4
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5034..5332): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 232.7
  Methylmalonyl-CoA: 229.8
  Methoxymalonyl-CoA: 185.5
  2-Methylbutyryl-CoA: 153.9
  trans-1,2-CPDA: 133.2
  CHC-CoA: 115.8
  Malonyl-CoA: 115.2
  Propionyl-CoA: 113.7
  Isobutyryl-CoA: 89.3
  Benzoyl-CoA: 63.7
  3-Methylbutyryl-CoA: 48.7
  inactive: 44.3
  Acetyl-CoA: 41.0
  fatty_acid: 28.2

PKS_AT (6608..6910): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 241.1
  inactive: 120.3
  Methoxymalonyl-CoA: 77.1
  Methylmalonyl-CoA: 67.9
  Propionyl-CoA: 33.1
  Isobutyryl-CoA: 30.6
  Acetyl-CoA: 25.2
  Benzoyl-CoA: 18.7
  Ethylmalonyl-CoA: 18.6
  fatty_acid: 16.7
  trans-1,2-CPDA: 13.0
  2-Methylbutyryl-CoA: 12.0
  CHC-CoA: 7.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS06000: mal - mal - mal
PKS_AT (573..875): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 250.8
  inactive: 123.9
  Methoxymalonyl-CoA: 77.0
  Methylmalonyl-CoA: 67.8
  Propionyl-CoA: 38.3
  Isobutyryl-CoA: 32.8
  Ethylmalonyl-CoA: 27.5
  Acetyl-CoA: 23.6
  Benzoyl-CoA: 19.5
  fatty_acid: 15.2
  2-Methylbutyryl-CoA: 14.8
  trans-1,2-CPDA: 14.1
  CHC-CoA: 7.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2125..2426): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 243.8
  inactive: 120.2
  Methoxymalonyl-CoA: 72.6
  Methylmalonyl-CoA: 62.8
  Propionyl-CoA: 36.6
  Isobutyryl-CoA: 33.6
  Acetyl-CoA: 23.7
  Ethylmalonyl-CoA: 22.4
  Benzoyl-CoA: 18.2
  2-Methylbutyryl-CoA: 16.2
  fatty_acid: 13.1
  trans-1,2-CPDA: 10.6
  CHC-CoA: 9.6
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3682..3985): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 228.8
  inactive: 120.5
  Methoxymalonyl-CoA: 71.1
  Methylmalonyl-CoA: 59.9
  Propionyl-CoA: 36.0
  Isobutyryl-CoA: 34.0
  Benzoyl-CoA: 31.4
  Ethylmalonyl-CoA: 23.2
  Acetyl-CoA: 19.5
  2-Methylbutyryl-CoA: 18.4
  fatty_acid: 14.4
  trans-1,2-CPDA: 8.2
  CHC-CoA: 8.2
  3-Methylbutyryl-CoA: 0.0

CFP59_RS06005: mmal - mal
PKS_AT (565..863): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 229.5
  Ethylmalonyl-CoA: 229.0
  Methoxymalonyl-CoA: 185.6
  2-Methylbutyryl-CoA: 152.2
  trans-1,2-CPDA: 130.9
  Malonyl-CoA: 112.7
  Propionyl-CoA: 111.1
  CHC-CoA: 105.9
  Isobutyryl-CoA: 86.1
  Benzoyl-CoA: 63.5
  Acetyl-CoA: 42.5
  3-Methylbutyryl-CoA: 41.6
  inactive: 37.8
  fatty_acid: 30.9

PKS_AT (2296..2597): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 242.1
  inactive: 120.1
  Methoxymalonyl-CoA: 75.1
  Methylmalonyl-CoA: 66.2
  Propionyl-CoA: 36.4
  Isobutyryl-CoA: 36.0
  Acetyl-CoA: 26.3
  Ethylmalonyl-CoA: 21.0
  Benzoyl-CoA: 19.8
  2-Methylbutyryl-CoA: 15.0
  fatty_acid: 12.2
  trans-1,2-CPDA: 11.0
  CHC-CoA: 5.8
  3-Methylbutyryl-CoA: 0.0

CFP59_RS06010: mmal - pk - mal
PKS_AT (573..871): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 230.8
  Ethylmalonyl-CoA: 230.2
  Methoxymalonyl-CoA: 188.7
  2-Methylbutyryl-CoA: 155.9
  trans-1,2-CPDA: 135.3
  Malonyl-CoA: 115.5
  Propionyl-CoA: 114.0
  CHC-CoA: 108.1
  Isobutyryl-CoA: 85.6
  Benzoyl-CoA: 68.1
  Acetyl-CoA: 43.8
  3-Methylbutyryl-CoA: 41.4
  fatty_acid: 34.9
  inactive: 33.5

PKS_AT (2303..2601): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 236.0
  Methylmalonyl-CoA: 231.8
  Methoxymalonyl-CoA: 189.1
  2-Methylbutyryl-CoA: 153.1
  trans-1,2-CPDA: 137.1
  Malonyl-CoA: 117.8
  Propionyl-CoA: 113.3
  CHC-CoA: 109.1
  Isobutyryl-CoA: 89.0
  Benzoyl-CoA: 65.7
  3-Methylbutyryl-CoA: 48.2
  inactive: 44.2
  Acetyl-CoA: 40.3
  fatty_acid: 31.7

PKS_AT (3863..4166): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 226.5
  inactive: 118.2
  Methoxymalonyl-CoA: 76.3
  Methylmalonyl-CoA: 66.2
  Propionyl-CoA: 37.7
  Isobutyryl-CoA: 36.6
  Acetyl-CoA: 28.8
  Ethylmalonyl-CoA: 24.0
  2-Methylbutyryl-CoA: 19.8
  Benzoyl-CoA: 17.0
  fatty_acid: 14.4
  CHC-CoA: 7.6
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism
NrdR | Represses ribonucleotide reductase encoding genes
ToxT | Regulator of MSHA biosynthesis

NZ_CP025018.1 - Region 11 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,774,909 - 1,948,524 nt. (total: 173,616 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CFP59_RS07090: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

CFP59_RS07105: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS07190: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CFP59_RS07195: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CFP59_RS07255: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS07280: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

CFP59_RS07290: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acylase aminotransferase kinase methyltransferase
CFP59_RS07070: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CFP59_RS07145: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CFP59_RS07230: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

CFP59_RS07310: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

CFP59_RS51805: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase esterase
CFP59_RS07110: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

CFP59_RS07245: thioesterase

smcogs
  SMCOG1004: thioesterase

Isomerases: isomerase
CFP59_RS07315: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
CFP59_RS07040: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS07075: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS07095: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS07120: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS07125: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS07130: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS07135: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS07140: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS07295: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS51800: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000114.5 |  |  | 0.85 | PKS | nigericin | Streptomyces violaceusniger
BGC0001276.3 |  |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001273.3 |  |  | 0.62 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.61 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002191.2 |  |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001254.3 |  |  | 0.56 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  |  | 0.56 | PKS | FR901512 | fungal sp. No.14919

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000114.5 |  | 0.92 | PKS | nigericin | Streptomyces violaceusniger
BGC0001276.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002038.2 |  | 0.66 | PKS | nigericin | Streptomyces sp. DASNCL29
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
Additional weak hits (21):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.55 out of 26.06
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.29 out of 27.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.27 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.24 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.15 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.40 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.36 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.79 out of 23.43
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.91 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.74 out of 27.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.77 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.95 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.90 out of 29.65
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.55 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.08 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.08 out of 26.06
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.95 out of 26.85
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 21, location 1774908 - 1948524:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-mal) + (Me-redmal) + (ccmal - Me-redmal) + (Me-ccmal - redmal) + (Me-ccmal - Me-redmal) + (Me-ohmal) + (ohmal - ohmal - ohmal) + (Me-redmal) + (Me-ccmal) + (Me-redmal)
Non-colinear ordering:
  CFP59_RS07140 + CFP59_RS07135 + CFP59_RS07130 + CFP59_RS07125 + CFP59_RS07120 + CFP59_RS51805 + CFP59_RS51800 + CFP59_RS07070 + CFP59_RS07075 + CFP59_RS07290

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 22, location 1774908 - 1906864:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-mal) + (Me-redmal) + (ccmal - Me-redmal) + (Me-ccmal - redmal) + (Me-ccmal - Me-redmal) + (Me-ohmal) + (ohmal - ohmal - ohmal) + (Me-redmal) + (Me-ccmal)
Non-colinear ordering:
  CFP59_RS07140 + CFP59_RS07135 + CFP59_RS07130 + CFP59_RS07125 + CFP59_RS07120 + CFP59_RS51805 + CFP59_RS51800 + CFP59_RS07070 + CFP59_RS07075

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 23, location 1902083 - 1948524:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS07040: X
AMP-binding (27..439): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FYQAWAYGYFAGAASAAGERDHYGSTELGMVVAH
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CFP59_RS51800: mal - mal - mal
PKS_AT (583..882): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 164.7
  inactive: 78.9
  Methoxymalonyl-CoA: 64.9
  Methylmalonyl-CoA: 56.6
  fatty_acid: 34.0
  Propionyl-CoA: 28.8
  Isobutyryl-CoA: 27.9
  Ethylmalonyl-CoA: 23.0
  2-Methylbutyryl-CoA: 20.0
  Acetyl-CoA: 19.5
  trans-1,2-CPDA: 13.3
  Benzoyl-CoA: 12.5
  CHC-CoA: 9.7
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2151..2450): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 171.1
  inactive: 82.1
  Methoxymalonyl-CoA: 66.8
  Methylmalonyl-CoA: 58.8
  fatty_acid: 35.7
  Propionyl-CoA: 28.7
  Isobutyryl-CoA: 28.6
  Ethylmalonyl-CoA: 24.5
  2-Methylbutyryl-CoA: 21.9
  Acetyl-CoA: 17.7
  Benzoyl-CoA: 12.2
  trans-1,2-CPDA: 11.7
  CHC-CoA: 10.5
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3702..3995): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 166.0
  inactive: 83.2
  Methoxymalonyl-CoA: 67.2
  Methylmalonyl-CoA: 54.7
  fatty_acid: 28.8
  Propionyl-CoA: 28.0
  Isobutyryl-CoA: 25.1
  Ethylmalonyl-CoA: 20.0
  2-Methylbutyryl-CoA: 18.6
  Acetyl-CoA: 18.3
  trans-1,2-CPDA: 13.0
  Benzoyl-CoA: 10.8
  CHC-CoA: 10.4
  3-Methylbutyryl-CoA: 0.0

CFP59_RS07070: mmal
PKS_AT (576..876): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 204.8
  Ethylmalonyl-CoA: 192.5
  Methoxymalonyl-CoA: 171.2
  2-Methylbutyryl-CoA: 143.8
  trans-1,2-CPDA: 122.4
  Propionyl-CoA: 119.9
  Malonyl-CoA: 96.7
  CHC-CoA: 92.7
  Isobutyryl-CoA: 72.9
  fatty_acid: 50.6
  Benzoyl-CoA: 50.5
  Acetyl-CoA: 43.5
  3-Methylbutyryl-CoA: 35.2
  inactive: 16.6

CFP59_RS07075: mmal
PKS_AT (575..875): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.2
  Ethylmalonyl-CoA: 197.5
  Methoxymalonyl-CoA: 170.5
  2-Methylbutyryl-CoA: 147.2
  trans-1,2-CPDA: 124.8
  Propionyl-CoA: 120.7
  Malonyl-CoA: 101.2
  CHC-CoA: 94.9
  Isobutyryl-CoA: 71.1
  fatty_acid: 49.6
  Benzoyl-CoA: 46.4
  Acetyl-CoA: 45.4
  3-Methylbutyryl-CoA: 39.9
  inactive: 17.3

CFP59_RS51805: mmal
PKS_AT (587..887): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 207.3
  Ethylmalonyl-CoA: 206.5
  Methoxymalonyl-CoA: 175.5
  2-Methylbutyryl-CoA: 130.6
  trans-1,2-CPDA: 129.2
  Propionyl-CoA: 110.4
  Malonyl-CoA: 107.8
  CHC-CoA: 93.2
  Isobutyryl-CoA: 64.9
  Benzoyl-CoA: 43.9
  Acetyl-CoA: 41.8
  fatty_acid: 38.6
  inactive: 23.1
  3-Methylbutyryl-CoA: 20.2

CFP59_RS07120: mmal - mmal
PKS_AT (567..870): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 214.1
  Ethylmalonyl-CoA: 207.6
  Methoxymalonyl-CoA: 176.0
  trans-1,2-CPDA: 149.0
  2-Methylbutyryl-CoA: 137.8
  Propionyl-CoA: 116.6
  CHC-CoA: 107.6
  Malonyl-CoA: 107.4
  Isobutyryl-CoA: 78.4
  Benzoyl-CoA: 67.8
  fatty_acid: 52.3
  Acetyl-CoA: 46.2
  3-Methylbutyryl-CoA: 35.7
  inactive: 25.7

PKS_AT (2379..2682): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 208.5
  Ethylmalonyl-CoA: 206.1
  Methoxymalonyl-CoA: 174.0
  trans-1,2-CPDA: 139.2
  2-Methylbutyryl-CoA: 128.3
  Propionyl-CoA: 107.2
  Malonyl-CoA: 104.2
  CHC-CoA: 96.5
  Isobutyryl-CoA: 73.6
  Benzoyl-CoA: 58.6
  Acetyl-CoA: 43.3
  fatty_acid: 39.1
  3-Methylbutyryl-CoA: 26.7
  inactive: 22.0

CFP59_RS07125: mmal - mal
PKS_AT (567..867): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 211.6
  Ethylmalonyl-CoA: 209.0
  Methoxymalonyl-CoA: 174.8
  2-Methylbutyryl-CoA: 134.7
  trans-1,2-CPDA: 133.8
  Propionyl-CoA: 113.1
  CHC-CoA: 108.9
  Malonyl-CoA: 108.7
  Isobutyryl-CoA: 75.3
  Benzoyl-CoA: 70.6
  Acetyl-CoA: 49.6
  fatty_acid: 48.2
  3-Methylbutyryl-CoA: 37.3
  inactive: 21.2

PKS_AT (2364..2652): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 177.2
  inactive: 92.6
  Methylmalonyl-CoA: 61.6
  Methoxymalonyl-CoA: 58.2
  fatty_acid: 37.4
  Isobutyryl-CoA: 36.5
  Propionyl-CoA: 33.7
  2-Methylbutyryl-CoA: 26.7
  Ethylmalonyl-CoA: 22.7
  Acetyl-CoA: 22.7
  trans-1,2-CPDA: 13.8
  CHC-CoA: 13.4
  Benzoyl-CoA: 7.9
  3-Methylbutyryl-CoA: 0.0

CFP59_RS07130: mal - mmal
PKS_AT (596..895): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 222.3
  inactive: 117.0
  Methoxymalonyl-CoA: 56.0
  Methylmalonyl-CoA: 45.5
  Propionyl-CoA: 30.1
  Isobutyryl-CoA: 27.9
  Acetyl-CoA: 23.2
  Benzoyl-CoA: 17.3
  Ethylmalonyl-CoA: 11.4
  2-Methylbutyryl-CoA: 9.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2412..2715): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 215.3
  Ethylmalonyl-CoA: 211.2
  Methoxymalonyl-CoA: 179.3
  trans-1,2-CPDA: 148.4
  2-Methylbutyryl-CoA: 142.4
  Propionyl-CoA: 125.0
  Malonyl-CoA: 111.5
  CHC-CoA: 100.5
  Isobutyryl-CoA: 72.7
  Benzoyl-CoA: 61.3
  Acetyl-CoA: 58.8
  fatty_acid: 53.7
  3-Methylbutyryl-CoA: 31.8
  inactive: 24.8

CFP59_RS07135: mmal
PKS_AT (564..864): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 212.3
  Ethylmalonyl-CoA: 211.6
  Methoxymalonyl-CoA: 176.4
  trans-1,2-CPDA: 141.1
  2-Methylbutyryl-CoA: 126.6
  Propionyl-CoA: 114.3
  Malonyl-CoA: 107.7
  CHC-CoA: 105.6
  Isobutyryl-CoA: 75.9
  Benzoyl-CoA: 74.7
  Acetyl-CoA: 50.3
  fatty_acid: 49.2
  3-Methylbutyryl-CoA: 36.4
  inactive: 26.7

CFP59_RS07140: mal - mmal
PKS_AT (541..848): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 210.2
  inactive: 95.8
  Methoxymalonyl-CoA: 74.1
  Methylmalonyl-CoA: 63.8
  Isobutyryl-CoA: 42.6
  Ethylmalonyl-CoA: 30.4
  Acetyl-CoA: 29.1
  Propionyl-CoA: 27.3
  Benzoyl-CoA: 27.1
  CHC-CoA: 18.9
  fatty_acid: 14.3
  3-Methylbutyryl-CoA: 12.7
  2-Methylbutyryl-CoA: 10.2
  trans-1,2-CPDA: 0.2

PKS_AT (1577..1880): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 200.2
  Ethylmalonyl-CoA: 194.9
  Methoxymalonyl-CoA: 168.6
  trans-1,2-CPDA: 129.4
  2-Methylbutyryl-CoA: 126.6
  Propionyl-CoA: 116.3
  Malonyl-CoA: 105.8
  CHC-CoA: 91.7
  Isobutyryl-CoA: 71.4
  Benzoyl-CoA: 48.0
  fatty_acid: 43.2
  Acetyl-CoA: 38.6
  inactive: 24.2
  3-Methylbutyryl-CoA: 20.0

CFP59_RS07290: mmal
PKS_AT (572..867): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Malonyl-CoA: 75.0%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 146.1
  Ethylmalonyl-CoA: 131.4
  Methoxymalonyl-CoA: 124.3
  Malonyl-CoA: 98.0
  2-Methylbutyryl-CoA: 87.5
  Isobutyryl-CoA: 86.8
  Propionyl-CoA: 85.0
  trans-1,2-CPDA: 81.2
  Acetyl-CoA: 63.3
  CHC-CoA: 48.1
  fatty_acid: 38.0
  3-Methylbutyryl-CoA: 36.0
  inactive: 31.9
  Benzoyl-CoA: 18.6

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production

NZ_CP025018.1 - Region 12 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,039,904 - 2,119,811 nt. (total: 79,908 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
CFP59_RS07785: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CFP59_RS07805: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CFP59_RS07815: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

CFP59_RS07875: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS07920: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: acylase glycosyltransferase transferase transketolase
CFP59_RS07780: transketolase

smcogs
  SMCOG1204: transketolase

CFP59_RS07850: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CFP59_RS07870: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CFP59_RS07910: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: esterase
CFP59_RS07855: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
CFP59_RS07775: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

CFP59_RS07820: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

CFP59_RS07905: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
CFP59_RS07860: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS07865: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS50015: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002291.3 |  | 0.99 | PKS | efomycin K, efomycin L | Streptomyces sp. M56
BGC0000053.5 |  | 0.84 | PKS | elaiophylin | Unknown. Unclassified.
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.64 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000058.5 |  | 0.63 | PKS | FD-891 | Streptomyces graminofaciens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002291.3 |  | 0.99 | PKS | efomycin K, efomycin L | Streptomyces sp. M56
BGC0000053.5 |  | 0.84 | PKS | elaiophylin | Unknown. Unclassified.
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.64 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000058.5 |  | 0.63 | PKS | FD-891 | Streptomyces graminofaciens

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.67 out of 19.26
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.71 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (21):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.86 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.88 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.04 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.05 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.26 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.22 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.77 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.29 out of 18.57
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.35 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.01 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.08 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.75 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.79 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.74 out of 27.78
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.28 out of 29.51
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.61 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.89 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.95 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.89 out of 32.93
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.06 out of 27.18
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 24, location 2039903 - 2119811:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - ccemal - ohmal) + (Me-ohmal) + (pk) + (pk - ccmal) + (ccmal)
Non-colinear ordering:
  CFP59_RS50015 + CFP59_RS07875 + CFP59_RS07870 + CFP59_RS07865 + CFP59_RS07860

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS07860: mal
PKS_AT (566..859): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 189.1
  inactive: 93.0
  Methoxymalonyl-CoA: 59.2
  Methylmalonyl-CoA: 45.3
  Propionyl-CoA: 31.2
  Ethylmalonyl-CoA: 24.2
  Acetyl-CoA: 23.0
  Benzoyl-CoA: 21.5
  Isobutyryl-CoA: 20.7
  CHC-CoA: 14.2
  2-Methylbutyryl-CoA: 11.9
  fatty_acid: 8.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS07865: pk - mal
PKS_AT (572..864): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 228.1
  Methylmalonyl-CoA: 224.3
  Methoxymalonyl-CoA: 182.8
  2-Methylbutyryl-CoA: 159.8
  trans-1,2-CPDA: 133.3
  Propionyl-CoA: 118.0
  CHC-CoA: 105.4
  Malonyl-CoA: 100.3
  Isobutyryl-CoA: 70.2
  Benzoyl-CoA: 54.9
  3-Methylbutyryl-CoA: 52.7
  Acetyl-CoA: 40.7
  fatty_acid: 35.5
  inactive: 23.8

PKS_AT (2103..2404): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 215.4
  inactive: 115.9
  Methoxymalonyl-CoA: 58.3
  Methylmalonyl-CoA: 39.9
  Propionyl-CoA: 28.6
  Benzoyl-CoA: 19.5
  Acetyl-CoA: 19.4
  Ethylmalonyl-CoA: 12.4
  Isobutyryl-CoA: 10.6
  2-Methylbutyryl-CoA: 10.1
  fatty_acid: 9.6
  CHC-CoA: 5.4
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS07870: pk
PKS_AT (568..859): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 224.0
  Methylmalonyl-CoA: 221.0
  Methoxymalonyl-CoA: 178.0
  2-Methylbutyryl-CoA: 156.6
  trans-1,2-CPDA: 130.0
  Propionyl-CoA: 111.9
  CHC-CoA: 110.2
  Malonyl-CoA: 94.4
  Isobutyryl-CoA: 77.3
  3-Methylbutyryl-CoA: 58.9
  Benzoyl-CoA: 58.8
  Acetyl-CoA: 40.5
  fatty_acid: 36.8
  inactive: 22.3

CFP59_RS07875: mmal
PKS_AT (601..895): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.9
  Ethylmalonyl-CoA: 205.5
  Methoxymalonyl-CoA: 171.5
  2-Methylbutyryl-CoA: 150.9
  trans-1,2-CPDA: 125.4
  Propionyl-CoA: 115.7
  CHC-CoA: 114.3
  Malonyl-CoA: 96.2
  Isobutyryl-CoA: 82.0
  3-Methylbutyryl-CoA: 64.8
  Benzoyl-CoA: 61.2
  Acetyl-CoA: 50.7
  fatty_acid: 44.3
  inactive: 28.7

CFP59_RS50015: mal - emal - mal
PKS_AT (536..826): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 207.0
  inactive: 117.5
  Methoxymalonyl-CoA: 57.5
  Methylmalonyl-CoA: 42.3
  Isobutyryl-CoA: 25.9
  Benzoyl-CoA: 25.3
  Propionyl-CoA: 20.3
  Acetyl-CoA: 17.6
  Ethylmalonyl-CoA: 15.7
  fatty_acid: 14.8
  CHC-CoA: 9.1
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (1544..1842): emal
ATSignature: Ethylmalonyl-CoA

Top 3 matches:
  Ethylmalonyl-CoA: 95.8%
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 216.2
  Methylmalonyl-CoA: 195.9
  Methoxymalonyl-CoA: 177.9
  trans-1,2-CPDA: 143.2
  2-Methylbutyryl-CoA: 139.7
  CHC-CoA: 115.8
  Malonyl-CoA: 111.9
  Propionyl-CoA: 106.2
  Isobutyryl-CoA: 75.8
  Benzoyl-CoA: 73.4
  3-Methylbutyryl-CoA: 46.7
  Acetyl-CoA: 45.5
  fatty_acid: 42.9
  inactive: 18.9

PKS_AT (3366..3656): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 212.0
  inactive: 118.5
  Methoxymalonyl-CoA: 58.0
  Methylmalonyl-CoA: 43.3
  Benzoyl-CoA: 26.3
  Acetyl-CoA: 22.4
  Isobutyryl-CoA: 22.0
  Propionyl-CoA: 21.1
  fatty_acid: 18.8
  Ethylmalonyl-CoA: 12.0
  CHC-CoA: 7.4
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 13 - redox-cofactor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,155,093 - 2,177,184 nt. (total: 22,092 nt) Show pHMM detection rules used
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CFP59_RS08135: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase
CFP59_RS08130: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000518.3 |  | 0.41 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002316.2 |  | 0.40 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001221.5 |  | 0.40 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0000515.4 |  | 0.39 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0002535.2 |  | 0.39 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002346.3 |  | 0.39 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000506.4 |  | 0.39 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000511.5 |  | 0.39 | ribosomal | ericin S | Bacillus subtilis
BGC0001789.3 |  | 0.39 | ribosomal | suicin 90-1330 | Streptococcus suis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000518.3 |  | 0.41 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002316.2 |  | 0.40 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001221.5 |  | 0.40 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0000515.4 |  | 0.39 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0002535.2 |  | 0.39 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002346.3 |  | 0.39 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000506.4 |  | 0.39 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000511.5 |  | 0.39 | ribosomal | ericin S | Bacillus subtilis
BGC0001789.3 |  | 0.39 | ribosomal | suicin 90-1330 | Streptococcus suis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.03 out of 36.53
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.80 out of 29.51
Confidence: medium
Additional weak hits (5):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.39 out of 20.97
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.63 out of 26.12
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.36 out of 27.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.49 out of 30.22
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (2155092...2177184)
CFP59_RS08145
  RRE type: PqqD_RRE
  Location: 13 - 93
  Score: 66.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor
DosR | Hypoxia stress response regulator

NZ_CP025018.1 - Region 14 - hserlactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,287,395 - 2,308,153 nt. (total: 20,759 nt) Show pHMM detection rules used
hserlactone: Autoind_synth

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CFP59_RS08735: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Transferases: acyltransferase methyltransferase
CFP59_RS08685: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CFP59_RS08710: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Hydrolases: deformylase
CFP59_RS08700: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Ligases: ligase
CFP59_RS08715: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | hserlactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002128.3 |  | 0.47 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001682.3 |  | 0.45 | other (other) | N-acyl lysine, N-acyl ornithine | Pseudomonas aeruginosa LESB58
BGC0001765.3 |  | 0.36 | saccharide | salecan | Agrobacterium tumefaciens
BGC0002545.3 |  | 0.36 | PKS | sungeidine C, sungeidine B, sungeidine D, sungeidine H, sungeidine A, sungeidine E, sungeidine F, sungeidine G | Micromonospora sp.
BGC0002362.3 |  | 0.35 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0001380.3 |  | 0.35 | saccharide | salecan | Agrobacterium sp. ZX09
BGC0000896.5 |  | 0.34 | other (other) | cycloserine | Streptomyces lavendulae subsp. lavendulae
BGC0001377.5 |  | 0.33 | PKS | uncialamycin | Streptomyces uncialis
BGC0000692.5 |  | 0.32 | saccharide | apramycin | Streptoalloteichus hindustanus
BGC0001292.5 |  | 0.31 | other (other) | A33853 | Streptomyces sp. NRRL 12068

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002128.3 |  | 0.47 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001682.3 |  | 0.45 | other (other) | N-acyl lysine, N-acyl ornithine | Pseudomonas aeruginosa LESB58
BGC0001765.3 |  | 0.36 | saccharide | salecan | Agrobacterium tumefaciens
BGC0002545.3 |  | 0.36 | PKS | sungeidine C, sungeidine B, sungeidine D, sungeidine H, sungeidine A, sungeidine E, sungeidine F, sungeidine G | Micromonospora sp.
BGC0002362.3 |  | 0.35 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0001380.3 |  | 0.35 | saccharide | salecan | Agrobacterium sp. ZX09
BGC0000896.5 |  | 0.34 | other (other) | cycloserine | Streptomyces lavendulae subsp. lavendulae
BGC0001377.5 |  | 0.33 | PKS | uncialamycin | Streptomyces uncialis
BGC0000692.5 |  | 0.32 | saccharide | apramycin | Streptoalloteichus hindustanus
BGC0001292.5 |  | 0.31 | other (other) | A33853 | Streptomyces sp. NRRL 12068

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.15 out of 27.04
Confidence: medium
Additional weak hits (2):
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.85 out of 27.04
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.69 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
DasR | N-acetylglucosamine dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 15 - butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,319,042 - 2,329,977 nt. (total: 10,936 nt) Show pHMM detection rules used
butyrolactone: AfsA

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
CFP59_RS08825: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS08835: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: hydrolase
CFP59_RS08810: HAD-superfamily hydrolase, subfamily IA, variant

smcogs
  SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.76 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.75 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.57 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.44 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001659.3 |  | 0.37 | terpene | mangicol A | Fusarium equiseti
BGC0000914.5 |  | 0.35 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0001909.3 |  | 0.34 | PKS | strobilurin A | Strobilurus tenacellus
BGC0000723.5 |  | 0.33 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus
BGC0002571.2 |  | 0.33 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0000843.5 |  | 0.32 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.76 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.75 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.57 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.44 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001659.3 |  | 0.37 | terpene | mangicol A | Fusarium equiseti
BGC0000914.5 |  | 0.35 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0001909.3 |  | 0.34 | PKS | strobilurin A | Strobilurus tenacellus
BGC0000723.5 |  | 0.33 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus
BGC0002571.2 |  | 0.33 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0000843.5 |  | 0.32 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (9):
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.67 out of 22.40
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.82 out of 39.62
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.60 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.90 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.73 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.63 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.18 out of 18.57
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.49 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP025018.1 - Region 16 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,503,248 - 2,551,386 nt. (total: 48,139 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CFP59_RS09785: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CFP59_RS09825: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: dehydratase
CFP59_RS09790: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Translocases: transport
CFP59_RS09805: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002138.2 |  | 0.44 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670
BGC0002155.3 |  | 0.43 | PKS | nectriapyrone C, nectriapyrone D, nectriapyrone | Pyricularia oryzae 70-15
BGC0002515.2 |  | 0.43 | PKS | solanapyrone A | Ascochyta rabiei
BGC0001858.2 |  | 0.40 | PKS | alternapyrone B, alternapyrone C, alternapyrone D, alternapyrone E, alternapyrone F | Parastagonospora nodorum SN15
BGC0000979.3 |  | 0.40 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E9
BGC0000980.3 |  | 0.40 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 22D11
BGC0001161.5 |  | 0.40 | PKS | 1-heptadecene | Moorea bouillonii PNG

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002138.2 |  | 0.44 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670
BGC0002155.3 |  | 0.43 | PKS | nectriapyrone C, nectriapyrone D, nectriapyrone | Pyricularia oryzae 70-15
BGC0002515.2 |  | 0.43 | PKS | solanapyrone A | Ascochyta rabiei
BGC0001858.2 |  | 0.40 | PKS | alternapyrone B, alternapyrone C, alternapyrone D, alternapyrone E, alternapyrone F | Parastagonospora nodorum SN15
BGC0000979.3 |  | 0.40 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E9
BGC0000980.3 |  | 0.40 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 22D11
BGC0001161.5 |  | 0.40 | PKS | 1-heptadecene | Moorea bouillonii PNG

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.

No significant matches found.

Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.61 out of 20.97
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.93 out of 26.33
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
Additional weak hits (11):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.06 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.25 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.30 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.82 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.60 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.08 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.16 out of 35.63
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.82 out of 25.88
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.44 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 28, location 2503247 - 2551386:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-pk)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS09785: pk
PKS_AT (668..972): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  Methylmalonyl-CoA: 66.7%
  Propionyl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 114.6
  Methoxymalonyl-CoA: 105.5
  Malonyl-CoA: 90.2
  Ethylmalonyl-CoA: 80.2
  Propionyl-CoA: 73.6
  2-Methylbutyryl-CoA: 68.7
  Isobutyryl-CoA: 66.3
  fatty_acid: 45.7
  CHC-CoA: 43.8
  Benzoyl-CoA: 36.0
  Acetyl-CoA: 23.0
  trans-1,2-CPDA: 19.1
  inactive: 19.1
  3-Methylbutyryl-CoA: 17.9

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A

NZ_CP025018.1 - Region 17 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,889,388 - 2,915,841 nt. (total: 26,454 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CFP59_RS11495: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS11525: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase
CFP59_RS11440: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

CFP59_RS11530: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Ligases: synthase synthetase
CFP59_RS11445: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs
  SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

CFP59_RS11470: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.74 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.51 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0001361.3 |  | 0.48 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.48 | terpene | sodorifen | Serratia plymuthica
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000651.5 |  | 0.48 | terpene | KS-505a | Streptomyces argenteolus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.74 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.51 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0001361.3 |  | 0.48 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.48 | terpene | sodorifen | Serratia plymuthica
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000651.5 |  | 0.48 | terpene | KS-505a | Streptomyces argenteolus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
triterpene | hopanoid |  | C30 | hopanoid skeleton | unknown
triterpene | polypodane |  | C30 | polypodane skeleton | unknown

Genes with terpene domains:
CFP59_RS11465: T2TS
Domain 1 (12 - 639): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

CFP59_RS11470: PT_FPPS_like
Domain 1 (69 - 355): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

CFP59_RS11480: PT_phytoene_like
Domain 1 (13 - 308): Prenyltransferase; Phytoene synthase like
Subtype: unknown

Reactions:
  FPP → squalene
  FPP → PSPP
  FPP → diapophytoene
  GGPP → phytoene
  PSPP → hydroxysqualene

CFP59_RS11485: PT_phytoene_like
Domain 1 (6 - 265): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72
Confidence: medium
Additional weak hits (5):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.78 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.89 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.82 out of 36.54
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.74 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
HPP | Hexaprenyl diphosphate
IPP | Isopentenyl diphosphate
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C

NZ_CP025018.1 - Region 18 - T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,111,295 - 3,183,810 nt. (total: 72,516 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidase oxidoreductase oxygenase
CFP59_RS12380: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

CFP59_RS12515: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CFP59_RS12600: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CFP59_RS12605: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

Transferases: PPTase acetyltransferase aminotransferase methyltransferase
CFP59_RS12565: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CFP59_RS12580: aminotransferase

smcogs
  SMCOG1019: aminotransferase

CFP59_RS12645: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CFP59_RS12665: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

CFP59_RS12670: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: deacetylase hydrolase
CFP59_RS12490: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CFP59_RS12680: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Lyases: cyclase
CFP59_RS12545: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

CFP59_RS12550: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

Ligases: synthase
CFP59_RS12530: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS12535: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000271.5 |  | 0.76 | PKS | spore pigment | Streptomyces avermitilis
BGC0000272.3 |  | 0.73 | PKS | spore pigment | Streptomyces collinus
BGC0000215.5 |  | 0.72 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.61 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001513.3 |  | 0.58 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000275.4 |  | 0.57 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002000.4 |  | 0.55 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001895.4 |  | 0.54 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000271.5 |  | 0.76 | PKS | spore pigment | Streptomyces avermitilis
BGC0000272.3 |  | 0.73 | PKS | spore pigment | Streptomyces collinus
BGC0000215.5 |  | 0.72 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.61 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001513.3 |  | 0.58 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000275.4 |  | 0.57 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002000.4 |  | 0.55 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001895.4 |  | 0.54 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.10 out of 23.43
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.87 out of 27.04
Confidence: medium
Additional weak hits (7):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.43 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.48 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.41 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.66 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.79 out of 29.65
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  3111294 to 3183810
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

CFP59_RS12485
  OXY (Score: 34.1; E-value: 3.7e-11)
CFP59_RS12515
  OXY (Score: 263.3; E-value: 1.1e-80)
CFP59_RS12525
  CYC C5-C18 (Score: 214.7; E-value: 8e-67)
CFP59_RS12530
  KS (Score: 707.0; E-value: 1.6e-215)
CFP59_RS12535
  CLF (Score: 542.8; E-value: 1.1e-165)
CFP59_RS12540
  ACP (Score: 63.0; E-value: 4.6e-20)
CFP59_RS12545
  CYC C9-C14 (Score: 246.6; E-value: 1.7e-76)
CFP59_RS12550
  CYC C4-C21/C2-C23|C2-C19 (Score: 148.6; E-value: 1.2e-46)
CFP59_RS12565
  MET C6|C8 (Score: 497.5; E-value: 3.4e-152)
CFP59_RS12645
  MET (Score: 28.8; E-value: 1.5e-09)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
DasR | N-acetylglucosamine dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 19 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,294,877 - 3,357,541 nt. (total: 62,665 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidase oxidoreductase oxygenase
CFP59_RS13215: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

CFP59_RS13225: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CFP59_RS13325: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: back translocase
CFP59_RS13375: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Ligases: synthase
CFP59_RS50815: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  | 0.58 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0000024.5 |  | 0.55 | PKS | aureothin | Streptomyces thioluteus
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000041.3 |  | 0.54 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002228.3 |  | 0.52 | NRPS | CIML B, CIML A, CIML D, CIML C | Colletotrichum incanum
BGC0000844.5 |  | 0.51 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001665.3 |  | 0.50 | PKS | methylated alkyl-resorcinol, methylated acyl-phloroglucinol | Mycobacterium marinum M

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  | 0.58 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0000024.5 |  | 0.55 | PKS | aureothin | Streptomyces thioluteus
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000041.3 |  | 0.54 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002228.3 |  | 0.52 | NRPS | CIML B, CIML A, CIML D, CIML C | Colletotrichum incanum
BGC0000844.5 |  | 0.51 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001665.3 |  | 0.50 | PKS | methylated alkyl-resorcinol, methylated acyl-phloroglucinol | Mycobacterium marinum M

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.79 out of 23.79
Confidence: medium
Additional weak hits (12):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.22 out of 29.51
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.54 out of 27.55
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.14 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.09 out of 36.54
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.56 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.18 out of 24.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.29 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 31, location 3294876 - 3357541:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-mal - Me-ccmal) + (Me-redmal - Me-mal)
Non-colinear ordering:
  CFP59_RS50815 + CFP59_RS50820

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS50815: mmal - mmal - mmal
PKS_AT (581..862): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 191.7
  Ethylmalonyl-CoA: 182.4
  Methoxymalonyl-CoA: 160.3
  2-Methylbutyryl-CoA: 115.6
  trans-1,2-CPDA: 112.6
  Malonyl-CoA: 112.1
  Propionyl-CoA: 99.7
  CHC-CoA: 96.3
  Isobutyryl-CoA: 71.3
  Acetyl-CoA: 49.6
  Benzoyl-CoA: 44.5
  inactive: 33.5
  3-Methylbutyryl-CoA: 30.2
  fatty_acid: 22.6

PKS_AT (1585..1882): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 211.1
  Ethylmalonyl-CoA: 193.4
  Methoxymalonyl-CoA: 169.5
  2-Methylbutyryl-CoA: 131.1
  trans-1,2-CPDA: 120.2
  CHC-CoA: 108.5
  Propionyl-CoA: 104.5
  Malonyl-CoA: 100.6
  Isobutyryl-CoA: 84.0
  Benzoyl-CoA: 66.0
  Acetyl-CoA: 54.7
  3-Methylbutyryl-CoA: 44.4
  inactive: 35.6
  fatty_acid: 33.5

PKS_AT (2602..2888): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 216.4
  Ethylmalonyl-CoA: 202.7
  Methoxymalonyl-CoA: 176.6
  2-Methylbutyryl-CoA: 143.5
  trans-1,2-CPDA: 122.5
  Malonyl-CoA: 117.6
  CHC-CoA: 115.1
  Propionyl-CoA: 112.9
  Isobutyryl-CoA: 89.7
  Benzoyl-CoA: 63.7
  Acetyl-CoA: 63.3
  3-Methylbutyryl-CoA: 47.0
  inactive: 45.4
  fatty_acid: 36.5

CFP59_RS50820: mmal - mmal
PKS_AT (566..851): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.2
  Ethylmalonyl-CoA: 192.4
  Methoxymalonyl-CoA: 166.7
  2-Methylbutyryl-CoA: 130.5
  trans-1,2-CPDA: 113.5
  Malonyl-CoA: 112.6
  CHC-CoA: 107.0
  Propionyl-CoA: 103.8
  Isobutyryl-CoA: 73.2
  Acetyl-CoA: 59.5
  Benzoyl-CoA: 53.7
  inactive: 34.9
  3-Methylbutyryl-CoA: 29.8
  fatty_acid: 19.0

PKS_AT (2647..2951): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 218.8
  Ethylmalonyl-CoA: 210.2
  Methoxymalonyl-CoA: 183.1
  2-Methylbutyryl-CoA: 125.9
  trans-1,2-CPDA: 124.9
  Malonyl-CoA: 122.6
  Propionyl-CoA: 101.7
  Isobutyryl-CoA: 95.7
  CHC-CoA: 94.0
  Benzoyl-CoA: 75.5
  Acetyl-CoA: 69.4
  3-Methylbutyryl-CoA: 59.3
  inactive: 50.9
  fatty_acid: 30.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism

NZ_CP025018.1 - Region 20 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,421,522 - 3,433,093 nt. (total: 11,572 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
No tailoring functions detected.
Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002387.2 |  | 0.28 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001377.5 |  | 0.25 | PKS | uncialamycin | Streptomyces uncialis
BGC0000874.5 |  | 0.25 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0002788.2 |  | 0.24 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000495.5 |  | 0.24 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0002713.2 |  | 0.24 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0001060.5 |  | 0.22 | PKS | dynemicin A | Micromonospora chersina
BGC0001984.3 |  | 0.21 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0001514.5 |  | 0.20 | other (other) | aristeromycin | Streptomyces citricolor
BGC0000241.5 |  | 0.19 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002387.2 |  | 0.28 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001377.5 |  | 0.25 | PKS | uncialamycin | Streptomyces uncialis
BGC0000874.5 |  | 0.25 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0002788.2 |  | 0.24 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000495.5 |  | 0.24 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0002713.2 |  | 0.24 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0001060.5 |  | 0.22 | PKS | dynemicin A | Micromonospora chersina
BGC0001984.3 |  | 0.21 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0001514.5 |  | 0.20 | other (other) | aristeromycin | Streptomyces citricolor
BGC0000241.5 |  | 0.19 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.04 out of 23.43
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.93 out of 26.85
Confidence: medium
Additional weak hits (4):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.88 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.81 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.60 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.73 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP025018.1 - Region 21 - NRPS,aminocoumarin,arylpolyene,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,520,150 - 3,601,467 nt. (total: 81,318 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
aminocoumarin: (novK or novJ or novI or novH or SpcDK_cou)
arylpolyene: (APE_KS1 or APE_KS2)
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CFP59_RS14155: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

CFP59_RS14185: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS14220: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS14325: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS14335: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acyltransferase glycosyltransferase methyltransferase transferase
CFP59_RS14115: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

CFP59_RS14120: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CFP59_RS14180: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CFP59_RS14200: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

CFP59_RS14340: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CFP59_RS14350: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase
CFP59_RS14275: thioesterase

smcogs
  SMCOG1004: thioesterase

Isomerases: isomerase
CFP59_RS14310: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase synthetase
CFP59_RS14130: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs
  SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CFP59_RS14135: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS14160: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS14190: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CFP59_RS14205: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS14240: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS14255: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS14260: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS14265: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS14330: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

CFP59_RS14360: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs
  SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | aminocoumarin | arylpolyene | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  |  |  | 1.20 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001529.5 |  |  |  |  | 1.16 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0001128.4 |  |  |  |  | 1.16 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  |  |  | 1.15 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  |  |  | 1.14 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  |  |  |  | 1.13 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  |  | 1.11 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  |  | 1.11 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  |  |  | 1.08 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  |  |  |  | 1.08 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001529.5 |  | 0.80 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0001132.4 |  | 0.78 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  | 0.76 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.75 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001249.5 |  | 0.75 | NRPS | dimethylcoprogen | Alternaria alternata

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
CFP59_RS14330: PT_FPPS_like
Domain 1 (58 - 344): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.37 out of 30.12
Confidence: medium
Additional weak hits (15):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.62 out of 32.74
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.07 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.56 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.01 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.46 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.92 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.53 out of 23.43
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.46 out of 26.06
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.53 out of 32.93
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.40 out of 20.01
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.01 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.78 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.65 out of 39.62
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.12 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.66 out of 30.25
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 33, location 3520149 - 3601467:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - D-Leu) + (Ser - D-Asp) + (Ala - Ser) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 34, location 3520149 - 3586043:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - D-Leu) + (Ser - D-Asp) + (Ala - Ser) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 35, location 3552957 - 3594091:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - D-Leu) + (Ser - D-Asp)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS14135: NH2
CAL_domain (44..486): NH2
minowa: NH2

Prediction, score:
  NH2: 110.9
  Acetyl-CoA: 38.1
  fatty_acid: 10.9
  shikimic_acid: 0.0
  AHBA: 0.0

CFP59_RS14190: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (464..873): Thr
nrpys: Thr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LATHFDFSVWEGNQVFGGEVNMYGITETTVHVSY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

CFP59_RS14200: Ala - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (464..864): Ala
nrpys: Ala

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    ala (Ala)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWATFDVSVFEGSALLCGEANVYGPTEATVYATA
  Nearest Stachelhaus code(s):
    Ala DVFSLAVVYK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1521..1932): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFLCSGEHNLYGPTEASVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

CFP59_RS14205: Ser - Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (463..869): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFLCSGEHNLYGPTEASVDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1529..1932): Asp
nrpys: Asp

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    asp,asn (Asp, Asn)
  Single AA prediction:
    asp (Asp)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWTSFDLSVTATKALLGGELNVYGPTEGTVNVAE
  Nearest Stachelhaus code(s):
    Asp DLTKLGVVNK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

CFP59_RS14210: Thr - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (13..422): Thr
nrpys: Thr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSTHFDFSVWEGNQVFGGEVNMYGITETTVHVSY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1081..1479): Leu
nrpys: Leu

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FTEAFDAAVLEMLIIVGGEVNAYGPTESTVAATT
  Nearest Stachelhaus code(s):
    Leu DALLIGAVAK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
HPP | Hexaprenyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
OsdR | Development and stress management regulator

NZ_CP025018.1 - Region 22 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,669,966 - 3,700,128 nt. (total: 30,163 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CFP59_RS14685: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
CFP59_RS14720: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
CFP59_RS14670: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002633.2 |  | 0.50 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0002683.2 |  | 0.49 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000858.3 |  | 0.48 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium kenyense
BGC0002470.2 |  | 0.48 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000856.3 |  | 0.48 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.48 | other (other) | ectoine | Methylophaga alcalica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002633.2 |  | 0.50 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0002683.2 |  | 0.49 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000858.3 |  | 0.48 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium kenyense
BGC0002470.2 |  | 0.48 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000856.3 |  | 0.48 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.48 | other (other) | ectoine | Methylophaga alcalica

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.07 out of 26.85
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05
Confidence: strong
Additional weak hits (13):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.22 out of 27.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.19 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.51 out of 27.18
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.32 out of 27.18
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.84 out of 26.85
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 30.11
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
LexA variant 2 | Repressor of DNA damage response
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP025018.1 - Region 23 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,287,332 - 4,330,178 nt. (total: 42,847 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
CFP59_RS17285: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS17305: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

CFP59_RS17340: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: methyltransferase
CFP59_RS17365: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: dehydratase
CFP59_RS17315: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
CFP59_RS17320: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000340.5 |  | 0.95 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0002277.2 |  | 0.65 | NRPS | atromentin | Suillus grevillei
BGC0002274.2 |  | 0.65 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002193.2 |  | 0.64 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001295.5 |  | 0.47 | other (other) | cremeomycin | Streptomyces cremeus
BGC0001844.4 |  | 0.46 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0001873.3 |  | 0.46 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0002404.2 |  | 0.46 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000197.5 |  | 0.45 | PKS, saccharide | aranciamycin | Streptomyces echinatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000340.5 |  | 0.95 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0002277.2 |  | 0.65 | NRPS | atromentin | Suillus grevillei
BGC0002274.2 |  | 0.65 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002193.2 |  | 0.64 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001295.5 |  | 0.47 | other (other) | cremeomycin | Streptomyces cremeus
BGC0001844.4 |  | 0.46 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0001873.3 |  | 0.46 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0002404.2 |  | 0.46 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000197.5 |  | 0.45 | PKS, saccharide | aranciamycin | Streptomyces echinatus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.50 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.07 out of 30.12
Confidence: medium
Additional weak hits (8):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.89 out of 33.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.62 out of 20.97
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.17 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.78 out of 30.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.82 out of 27.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.81 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.12 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 38, location 4287331 - 4330178:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS17320: X
AMP-binding (44..450): X
nrpys: Ppa

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    SGKIHVAALLELFTVSGGEWPAFGMTETCAGSIY
  Nearest Stachelhaus code(s):
    Ppa VALFVGAAGK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
OsdR | Development and stress management regulator
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 24 - thioamitides
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,632,899 - 4,655,465 nt. (total: 22,567 nt) Show pHMM detection rules used
thioamitides: ((YcaO or TIGR03604) and TfuA)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
No tailoring functions detected.
Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | thioamitides | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001849.4 |  | 0.53 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0002560.3 |  | 0.39 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0000483.5 |  | 0.33 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000625.5 |  | 0.33 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0000473.4 |  | 0.33 | ribosomal | aerucyclamide A, aerucyclamide B, aerucyclamide C, aerucyclamide D | Microcystis aeruginosa NIES-298
BGC0002120.3 |  | 0.33 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000474.4 |  | 0.32 | ribosomal | microcyclamide | Microcystis aeruginosa PCC 7806
BGC0001696.5 |  | 0.32 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0001802.5 |  | 0.32 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0002669.2 |  | 0.32 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001849.4 |  | 0.53 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0002560.3 |  | 0.39 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0000483.5 |  | 0.33 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000625.5 |  | 0.33 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0000473.4 |  | 0.33 | ribosomal | aerucyclamide A, aerucyclamide B, aerucyclamide C, aerucyclamide D | Microcystis aeruginosa NIES-298
BGC0002120.3 |  | 0.33 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000474.4 |  | 0.32 | ribosomal | microcyclamide | Microcystis aeruginosa PCC 7806
BGC0001696.5 |  | 0.32 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0001802.5 |  | 0.32 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0002669.2 |  | 0.32 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.40 out of 27.04
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.23 out of 23.79
Confidence: medium
Additional weak hits (2):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.36 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 25 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,861,531 - 4,890,692 nt. (total: 29,162 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CFP59_RS19910: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

CFP59_RS19930: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Hydrolases: hydrolase
CFP59_RS19975: HAD-superfamily hydrolase, subfamily IA, variant

smcogs
  SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

Lyases: decarboxylase
CFP59_RS19905: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002305.2 |  | 0.83 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.82 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  | 0.74 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.74 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.63 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002690.2 |  | 0.60 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002620.2 |  | 0.54 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002469.2 |  | 0.53 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002305.2 |  | 0.83 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.82 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  | 0.74 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.74 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.63 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002690.2 |  | 0.60 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002620.2 |  | 0.54 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002469.2 |  | 0.53 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 36.53
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (5):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.55 out of 21.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.44 out of 21.55
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.56 out of 29.51
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.04 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
DmdR1 | Iron(II)-dependent repressor

NZ_CP025018.1 - Region 26 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,951,394 - 5,973,679 nt. (total: 22,286 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
CFP59_RS24835: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS24870: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Hydrolases: amidase
CFP59_RS24865: amidase

smcogs
  SMCOG1105: amidase

Lyases: cyclase
CFP59_RS24860: Terpene synthase/cyclase metal-binding domain protein

smcogs
  SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001224.5 |  | 0.46 | other (other) | reductasporine | uncultured bacterium
BGC0001336.5 |  | 0.45 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000851.5 |  | 0.44 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001223.5 |  | 0.41 | other (other) | hydroxysporine | uncultured bacterium
BGC0002669.2 |  | 0.39 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001224.5 |  | 0.46 | other (other) | reductasporine | uncultured bacterium
BGC0001336.5 |  | 0.45 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000851.5 |  | 0.44 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001223.5 |  | 0.41 | other (other) | hydroxysporine | uncultured bacterium
BGC0002669.2 |  | 0.39 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene |  | germacradienol | C15 | C1-C10 | OH
sesquiterpene |  | geosmin | C12 | C1-C10 | OH

Genes with terpene domains:
CFP59_RS24860: T1TS + T1TS
Domain 1 (3 - 289): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (339 - 702): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.15 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (6):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.50 out of 26.85
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.21 out of 23.43
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.24 out of 27.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.47 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.93 out of 27.78
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 27 - indole
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,562,376 - 6,583,524 nt. (total: 21,149 nt) Show pHMM detection rules used
indole: (indsynth or dmat or indole_PTase)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CFP59_RS27530: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS27555: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Isomerases: racemase
CFP59_RS27570: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | indole | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001483.4 |  | 0.57 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0001294.5 |  | 0.56 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002643.2 |  | 0.46 | other (other) | aetokthonotoxin | Aetokthonos hydrillicola Thurmond2011
BGC0000844.5 |  | 0.46 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001911.3 |  | 0.45 | terpene | raimonol | Streptomyces anulatus
BGC0002128.3 |  | 0.45 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001910.4 |  | 0.44 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001483.4 |  | 0.57 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0001294.5 |  | 0.56 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002643.2 |  | 0.46 | other (other) | aetokthonotoxin | Aetokthonos hydrillicola Thurmond2011
BGC0000844.5 |  | 0.46 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001911.3 |  | 0.45 | terpene | raimonol | Streptomyces anulatus
BGC0002128.3 |  | 0.45 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001910.4 |  | 0.44 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 25.31
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
Additional weak hits (3):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.60 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.04 out of 25.88
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor

NZ_CP025018.1 - Region 28 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,786,863 - 6,830,873 nt. (total: 44,011 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CFP59_RS28440: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

CFP59_RS28550: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Hydrolases: deacetylase hydrolase
CFP59_RS28445: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

CFP59_RS28465: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase
CFP59_RS28455: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
CFP59_RS28410: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.44 out of 27.04
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.29 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.69 out of 30.11
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.73 out of 23.79
Confidence: medium
Additional weak hits (18):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.38 out of 27.78
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.53 out of 32.93
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.91 out of 19.26
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.05 out of 25.88
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.71 out of 29.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.18 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.82 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.31 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.75 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.16 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.23 out of 20.01
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.81 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 43, location 6786862 - 6830873:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS28455: X
AMP-binding (471..874): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    CWMTFDASVCEWQFSSGGENNLYGPTETTIQIAH
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIQK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 29 - HR-T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,880,819 - 6,931,023 nt. (total: 50,205 nt) Show pHMM detection rules used
HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-synt))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
CFP59_RS28900: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CFP59_RS28905: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CFP59_RS28955: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS29000: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS29080: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Transferases: PPTase acylase carboxylase
CFP59_RS28980: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CFP59_RS29015: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

CFP59_RS29025: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: amidase dehalogenase hydrolase
CFP59_RS29010: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CFP59_RS29020: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CFP59_RS29030: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

CFP59_RS29075: amidase

smcogs
  SMCOG1105: amidase

Ligases: synthase
CFP59_RS28925: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS28930: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS28945: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS28975: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | HR-T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000234.5 |  | 0.54 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001987.2 |  | 0.52 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000867.3 |  | 0.51 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002510.2 |  | 0.50 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0000218.5 |  | 0.49 | PKS | doxorubicin | Streptomyces peucetius
BGC0002477.3 |  | 0.49 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0001177.4 |  | 0.49 | PKS | mensacaricin | Streptomyces bottropensis
BGC0000225.5 |  | 0.48 | PKS | frenolicin B | Streptomyces roseofulvus
BGC0002369.2 |  | 0.48 | PKS | maduralactomycin A, maduralactomycin B, actinospirol A, actinospirol B | Actinomadura rubteroloni

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000234.5 |  | 0.54 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001987.2 |  | 0.52 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000867.3 |  | 0.51 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002510.2 |  | 0.50 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0000218.5 |  | 0.49 | PKS | doxorubicin | Streptomyces peucetius
BGC0002477.3 |  | 0.49 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0001177.4 |  | 0.49 | PKS | mensacaricin | Streptomyces bottropensis
BGC0000225.5 |  | 0.48 | PKS | frenolicin B | Streptomyces roseofulvus
BGC0002369.2 |  | 0.48 | PKS | maduralactomycin A, maduralactomycin B, actinospirol A, actinospirol B | Actinomadura rubteroloni

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.68 out of 27.04
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (14):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.79 out of 25.88
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.68 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.77 out of 32.74
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.05 out of 30.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.81 out of 27.04
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.20 out of 24.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.07 out of 33.14
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS28980: mal
PKS_AT (20..306): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 58.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 103.0
  Methylmalonyl-CoA: 45.8
  Methoxymalonyl-CoA: 43.5
  Propionyl-CoA: 36.3
  inactive: 35.0
  Ethylmalonyl-CoA: 18.9
  CHC-CoA: 18.0
  2-Methylbutyryl-CoA: 13.7
  trans-1,2-CPDA: 10.4
  Acetyl-CoA: 9.4
  fatty_acid: 6.4
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  Isobutyryl-CoA: -2.4

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
DasR | N-acetylglucosamine dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 30 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,937,785 - 6,950,181 nt. (total: 12,397 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CFP59_RS29150: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CFP59_RS29160: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002584.2 |  | 0.43 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002115.3 |  | 0.41 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0000483.5 |  | 0.41 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000477.3 |  | 0.40 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0000565.5 |  | 0.40 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0002485.2 |  | 0.38 | other (other), ribosomal | muscoride A, muscoride B | Desmonostoc sp. PCC 7906
BGC0002551.2 |  | 0.38 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398
BGC0000583.5 |  | 0.38 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000193.3 |  | 0.38 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0000471.4 |  | 0.37 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002584.2 |  | 0.43 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002115.3 |  | 0.41 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0000483.5 |  | 0.41 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000477.3 |  | 0.40 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0000565.5 |  | 0.40 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0002485.2 |  | 0.38 | other (other), ribosomal | muscoride A, muscoride B | Desmonostoc sp. PCC 7906
BGC0002551.2 |  | 0.38 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398
BGC0000583.5 |  | 0.38 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000193.3 |  | 0.38 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0000471.4 |  | 0.37 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.07 out of 23.43
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.62 out of 23.79
Confidence: medium
Additional weak hits (5):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.81 out of 23.43
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.87 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.94 out of 35.63
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.88 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.49 out of 28.19
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RiPP-like protocluster (6937784...6950181)
CFP59_RS29135
  RRE type: Goadsporin_CD_RRE
  Location: 3 - 106
  Score: 63.6
  RRE type: NHLP_CD_RRE
  Location: 3 - 103
  Score: 53.6
  RRE type: Cyanobactin_D_RRE
  Location: 3 - 88
  Score: 44.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
BldD | Development and antibiotic global regulator
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 31 - T1PKS,lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,086,447 - 7,271,689 nt. (total: 185,243 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase
CFP59_RS29795: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

CFP59_RS29800: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CFP59_RS29890: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS29970: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase acylase kinase
CFP59_RS29780: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

CFP59_RS29855: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

CFP59_RS29880: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CFP59_RS29990: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase esterase
CFP59_RS29815: thioesterase

smcogs
  SMCOG1004: thioesterase

CFP59_RS29980: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

CFP59_RS30005: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase dehydratase
CFP59_RS29945: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

CFP59_RS29950: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

Ligases: synthase
CFP59_RS29850: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS29860: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS29865: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS29870: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS29875: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS29885: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002498.3 |  |  | 0.57 | other (other) | desulfoclethramycin, clethramycin | Streptomyces sp.
BGC0002357.3 |  |  | 0.48 | PKS, other (other) | neomediomycin B | Streptomyces sp. RK95-74
BGC0002356.3 |  |  | 0.44 | PKS, other (other) | mediomycin A | Streptomyces blastmyceticus
BGC0001662.4 |  |  | 0.44 | PKS | mediomycin A | Kitasatospora mediocidica
BGC0002355.2 |  |  | 0.44 | PKS, other (other) | tetrafibricin | Streptomyces neyagawaensis
BGC0001273.3 |  |  | 0.42 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.42 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.41 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002072.3 |  |  | 0.38 | PKS | linearmycin A, linearmycin B, linearmycin C, linearmycin C | Streptomyces sp. Mg1
BGC0000542.3 |  |  | 0.38 | ribosomal | paenicidin B | Paenibacillus terrae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002498.3 |  | 0.76 | other (other) | desulfoclethramycin, clethramycin | Streptomyces sp.
BGC0002355.2 |  | 0.74 | PKS, other (other) | tetrafibricin | Streptomyces neyagawaensis
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002357.3 |  | 0.72 | PKS, other (other) | neomediomycin B | Streptomyces sp. RK95-74
BGC0002356.3 |  | 0.68 | PKS, other (other) | mediomycin A | Streptomyces blastmyceticus
BGC0001662.4 |  | 0.68 | PKS | mediomycin A | Kitasatospora mediocidica
BGC0000041.3 |  | 0.66 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002072.3 |  | 0.64 | PKS | linearmycin A, linearmycin B, linearmycin C, linearmycin C | Streptomyces sp. Mg1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lanthipeptide(s) for CFP59_RS29945

CFP59_RS29940
Leader:
MSAQQTSPMPKAGTSYAADATSDFDLNIEVLADALVVPG
Core:
L L N D T G D G C T A T C Q S A C S N S T C G
Core with dehydrations:
L L N D Dhb G D G Cys Dhb A Dhb Cys Q Dha A Cys Dha N Dha Dhb Cys G

#### antiSMASH-DB 4.0 matches for CFP59_RS29940

100.0%
NZ_BBUZ01000023.1 and 5 others:
NZ_BBUZ01000023.1 Lanthipeptides: ASC60_RS09240_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide
Lanthipeptides: ASC60_RS09240_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C G
23
L L N D T G D G C T A T C Q S A C S N S T C G
1
L L N D T G D G C T A T C Q S A C S N S T C G
23
91.3%
NZ_BBYG01000008.1 and 3 others:
NZ_BBYG01000008.1 Lanthipeptides: AOQ37_RS04295_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide
Lanthipeptides: AOQ37_RS04295_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C G
23
L N D T G D G C T+T C Q S A C S N S T C G
1
L N D T G D G C T S T C Q S A C S N S T C G
22
87.0%
NZ_CP104318.1 and 1 other:
NZ_CP104318.1 Lanthipeptides: NW605_RS33555_lanthipeptide
Lanthipeptides: NW605_RS33555_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C
22
L N D T G D G C T A T C+S A C S N S T C
1
L N D T G D G C T A T C E S A C S N S T C
21
with 193 more sequence matches
Only the first 10 are displayed here.
84.0%
NZ_CP045096.1 and 1 other:
NZ_CP045096.1 Lanthipeptides: F9278_RS23695_lanthipeptide
Lanthipeptides: F9278_RS23695_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N D T G D G C A T C Q S A C S N S T C
1
L L N D T G D G C G A T C Q S A C S N S T C
22
82.6%
NZ_CP086322.1 and 1 other:
NZ_CP086322.1 Lanthipeptides: K9S39_RS30905_lanthipeptide
Lanthipeptides: K9S39_RS30905_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C G
23
L N D T G D G C T C+S A C S N S T C G
1
L N D T G D G C G Q T C E S A C S N S T C G
22
82.6%
NZ_KQ257877.1 and 1 other:
NZ_KQ257877.1 Lanthipeptides: IQ64_RS44800_lanthipeptide
Lanthipeptides: IQ64_RS44800_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C
22
L N D T G D G C T C Q S A C S N S T C
1
L N D T G D G C G Q T C Q S A C S N S T C
21
79.2%
NZ_VEHK01000015.1 and 1 other:
NZ_VEHK01000015.1 Lanthipeptides: FS984_RS32600_lanthipeptide
Lanthipeptides: FS984_RS32600_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C
22
L N D T D G C T+T C Q S A C S N S T C
1
L N D T S D G C T S T C Q S A C S N S T C
21
76.9%
NZ_CP029188.1 and 3 others:
NZ_CP029188.1 Lanthipeptides: DDW44_RS30840_lanthipeptide NZ_CP031264.1 Lanthipeptides: C7M71_RS17720_lanthipeptide NZ_CP031264.1 Lanthipeptides: C7M71_RS17720_lanthipeptide
Lanthipeptides: DDW44_RS30840_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N D T G D G C +T C Q S A C S N S T C
2
L L N D T G D G C G S T C Q S A C S N S T C
23
76.0%
NZ_FOLM01000004.1 and 1 other:
NZ_FOLM01000004.1 Lanthipeptides: BM242_RS10130_lanthipeptide
Lanthipeptides: BM242_RS10130_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N D T D C T+T C Q S A C S N S T C
1
L L N D T D D N C T S T C Q S A C S N S T C
22
75.0%
NZ_CP084541.1 and 1 other:
NZ_CP084541.1 Lanthipeptides: LC193_RS13810_lanthipeptide
Lanthipeptides: LC193_RS13810_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N D T G D G C T+T C Q S A C S N S T C
4
L L N D T G D G C T S T C Q S A C S N S T C
25
75.0%
NZ_LJFZ01000009.1 and 2 others:
NZ_LJFZ01000009.1 Lanthipeptides: UK94_RS32440_lanthipeptide NZ_LJFZ01000009.1 Lanthipeptides: UK94_RS32440_lanthipeptide
Lanthipeptides: UK94_RS32440_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N T D C T+T C Q S A C S N S T C
1
L L N S T S D N C T S T C Q S A C S N S T C
22
73.1%
NZ_AP024135.1 and 3 others:
NZ_AP024135.1 Lanthipeptides: K6K39_RS04810_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide
Lanthipeptides: K6K39_RS04810_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N D T G D G C +T C Q S A C+N S T C
2
L L N D T G D G C G S T C Q S A C A N S T C
23
70.8%
NZ_BMSX01000001.1 and 10 others:
NZ_BMSX01000001.1 Lanthipeptides: IE263_RS00615_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide
Lanthipeptides: IE263_RS00615_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C
22
L N D T D C T+T C Q S A C+N S T C
1
L N D T S D N C T S T C Q S A C T N S T C
21

#### Lanthipeptide(s) for CFP59_RS29955

CFP59_RS29940
Leader:
MSAQQTSPMPKAGTSYAADATSDFDLNIEVLADALVVPG
Core:
L L N D T G D G C T A T C Q S A C S N S T C G
Core with dehydrations:
L L N D Dhb G D G Cys Dhb A Dhb Cys Q Dha A Cys Dha N Dha Dhb Cys G

#### antiSMASH-DB 4.0 matches for CFP59_RS29940

100.0%
NZ_BBUZ01000023.1 and 5 others:
NZ_BBUZ01000023.1 Lanthipeptides: ASC60_RS09240_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide
Lanthipeptides: ASC60_RS09240_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C G
23
L L N D T G D G C T A T C Q S A C S N S T C G
1
L L N D T G D G C T A T C Q S A C S N S T C G
23
91.3%
NZ_BBYG01000008.1 and 3 others:
NZ_BBYG01000008.1 Lanthipeptides: AOQ37_RS04295_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide
Lanthipeptides: AOQ37_RS04295_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C G
23
L N D T G D G C T+T C Q S A C S N S T C G
1
L N D T G D G C T S T C Q S A C S N S T C G
22
87.0%
NZ_CP104318.1 and 1 other:
NZ_CP104318.1 Lanthipeptides: NW605_RS33555_lanthipeptide
Lanthipeptides: NW605_RS33555_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C
22
L N D T G D G C T A T C+S A C S N S T C
1
L N D T G D G C T A T C E S A C S N S T C
21
with 193 more sequence matches
Only the first 10 are displayed here.
84.0%
NZ_CP045096.1 and 1 other:
NZ_CP045096.1 Lanthipeptides: F9278_RS23695_lanthipeptide
Lanthipeptides: F9278_RS23695_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N D T G D G C A T C Q S A C S N S T C
1
L L N D T G D G C G A T C Q S A C S N S T C
22
82.6%
NZ_CP086322.1 and 1 other:
NZ_CP086322.1 Lanthipeptides: K9S39_RS30905_lanthipeptide
Lanthipeptides: K9S39_RS30905_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C G
23
L N D T G D G C T C+S A C S N S T C G
1
L N D T G D G C G Q T C E S A C S N S T C G
22
82.6%
NZ_KQ257877.1 and 1 other:
NZ_KQ257877.1 Lanthipeptides: IQ64_RS44800_lanthipeptide
Lanthipeptides: IQ64_RS44800_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C
22
L N D T G D G C T C Q S A C S N S T C
1
L N D T G D G C G Q T C Q S A C S N S T C
21
79.2%
NZ_VEHK01000015.1 and 1 other:
NZ_VEHK01000015.1 Lanthipeptides: FS984_RS32600_lanthipeptide
Lanthipeptides: FS984_RS32600_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C
22
L N D T D G C T+T C Q S A C S N S T C
1
L N D T S D G C T S T C Q S A C S N S T C
21
76.9%
NZ_CP029188.1 and 3 others:
NZ_CP029188.1 Lanthipeptides: DDW44_RS30840_lanthipeptide NZ_CP031264.1 Lanthipeptides: C7M71_RS17720_lanthipeptide NZ_CP031264.1 Lanthipeptides: C7M71_RS17720_lanthipeptide
Lanthipeptides: DDW44_RS30840_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N D T G D G C +T C Q S A C S N S T C
2
L L N D T G D G C G S T C Q S A C S N S T C
23
76.0%
NZ_FOLM01000004.1 and 1 other:
NZ_FOLM01000004.1 Lanthipeptides: BM242_RS10130_lanthipeptide
Lanthipeptides: BM242_RS10130_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N D T D C T+T C Q S A C S N S T C
1
L L N D T D D N C T S T C Q S A C S N S T C
22
75.0%
NZ_CP084541.1 and 1 other:
NZ_CP084541.1 Lanthipeptides: LC193_RS13810_lanthipeptide
Lanthipeptides: LC193_RS13810_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N D T G D G C T+T C Q S A C S N S T C
4
L L N D T G D G C T S T C Q S A C S N S T C
25
75.0%
NZ_LJFZ01000009.1 and 2 others:
NZ_LJFZ01000009.1 Lanthipeptides: UK94_RS32440_lanthipeptide NZ_LJFZ01000009.1 Lanthipeptides: UK94_RS32440_lanthipeptide
Lanthipeptides: UK94_RS32440_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N T D C T+T C Q S A C S N S T C
1
L L N S T S D N C T S T C Q S A C S N S T C
22
73.1%
NZ_AP024135.1 and 3 others:
NZ_AP024135.1 Lanthipeptides: K6K39_RS04810_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide
Lanthipeptides: K6K39_RS04810_lanthipeptide
1
L L N D T G D G C T A T C Q S A C S N S T C
22
L L N D T G D G C +T C Q S A C+N S T C
2
L L N D T G D G C G S T C Q S A C A N S T C
23
70.8%
NZ_BMSX01000001.1 and 10 others:
NZ_BMSX01000001.1 Lanthipeptides: IE263_RS00615_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide
Lanthipeptides: IE263_RS00615_lanthipeptide
2
L N D T G D G C T A T C Q S A C S N S T C
22
L N D T D C T+T C Q S A C+N S T C
1
L N D T S D N C T S T C Q S A C T N S T C
21

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.52 out of 23.79
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 23.52 out of 26.33
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.47 out of 27.04
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 25.31
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.17 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
Additional weak hits (16):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.64 out of 21.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.87 out of 39.62
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.80 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.38 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.88 out of 27.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.37 out of 25.88
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.42 out of 36.54
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.76 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.69 out of 26.85
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.20 out of 20.97
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.31 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.27 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

CFP59_RS29940 - Class I
  Cleavage pHMM score: -5.50
  RODEO score: 21
  Monoisotopic mass: 2094.8 Da
  Molecular weight: 2096.2 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2114.2 Da N = 1
    2132.3 Da N = 2
    2150.3 Da N = 3
CFP59_RS29940 - Class I
  Cleavage pHMM score: -5.50
  RODEO score: 21
  Monoisotopic mass: 2094.8 Da
  Molecular weight: 2096.2 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2114.2 Da N = 1
    2132.3 Da N = 2
    2150.3 Da N = 3

Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 46, location 7086446 - 7271689:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ohmal - ohmal - ccmal - ohmal - ohmal) + (ccmal - ohmal) + (ccmal - ohmal - ccmal - ohmal - ccmal) + (Me-ohmal) + (ohmal - ccmal - ccmal) + (ccmal - ccmal - ccmal - ccmal) + (Me-ohmal - Me-ohmal) + (ccmal - redmal - ccmal) + (ccmal - Me-ccmal)
Non-colinear ordering:
  CFP59_RS29850 + CFP59_RS29855 + CFP59_RS29860 + CFP59_RS29865 + CFP59_RS29870 + CFP59_RS29875 + CFP59_RS29880 + CFP59_RS29885 + CFP59_RS29890

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 47, location 7086446 - 7269467:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ohmal - ohmal - ccmal - ohmal - ohmal) + (ccmal - ohmal) + (ccmal - ohmal - ccmal - ohmal - ccmal) + (Me-ohmal) + (ohmal - ccmal - ccmal) + (ccmal - ccmal - ccmal - ccmal) + (Me-ohmal - Me-ohmal) + (ccmal - redmal - ccmal) + (ccmal - Me-ccmal)
Non-colinear ordering:
  CFP59_RS29850 + CFP59_RS29855 + CFP59_RS29860 + CFP59_RS29865 + CFP59_RS29870 + CFP59_RS29875 + CFP59_RS29880 + CFP59_RS29885 + CFP59_RS29890

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS29850: mal - mal - mal - mal - mal
PKS_AT (674..972): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 229.9
  inactive: 123.4
  Methoxymalonyl-CoA: 77.5
  Methylmalonyl-CoA: 75.1
  Isobutyryl-CoA: 48.9
  Propionyl-CoA: 39.2
  Acetyl-CoA: 35.2
  Ethylmalonyl-CoA: 27.1
  2-Methylbutyryl-CoA: 23.2
  Benzoyl-CoA: 20.1
  CHC-CoA: 14.7
  trans-1,2-CPDA: 10.2
  fatty_acid: 8.3
  3-Methylbutyryl-CoA: 5.9

PKS_AT (2223..2513): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 238.8
  inactive: 127.2
  Methylmalonyl-CoA: 64.6
  Methoxymalonyl-CoA: 63.9
  Propionyl-CoA: 43.1
  Acetyl-CoA: 25.3
  Isobutyryl-CoA: 25.1
  2-Methylbutyryl-CoA: 21.9
  trans-1,2-CPDA: 20.8
  Benzoyl-CoA: 20.8
  Ethylmalonyl-CoA: 18.1
  CHC-CoA: 11.6
  fatty_acid: 8.6
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3751..4042): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 236.4
  inactive: 121.5
  Methoxymalonyl-CoA: 67.6
  Methylmalonyl-CoA: 66.3
  Propionyl-CoA: 42.9
  Benzoyl-CoA: 25.7
  Acetyl-CoA: 24.2
  Isobutyryl-CoA: 24.1
  Ethylmalonyl-CoA: 23.3
  2-Methylbutyryl-CoA: 18.7
  CHC-CoA: 17.8
  trans-1,2-CPDA: 16.5
  fatty_acid: 9.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5578..5869): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 240.9
  inactive: 121.4
  Methoxymalonyl-CoA: 71.8
  Methylmalonyl-CoA: 68.5
  Propionyl-CoA: 45.2
  Isobutyryl-CoA: 40.3
  Ethylmalonyl-CoA: 33.7
  Benzoyl-CoA: 27.0
  2-Methylbutyryl-CoA: 24.2
  Acetyl-CoA: 19.9
  CHC-CoA: 17.7
  trans-1,2-CPDA: 15.4
  fatty_acid: 12.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (7120..7415): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 75.0%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 227.2
  inactive: 119.9
  Methoxymalonyl-CoA: 75.8
  Methylmalonyl-CoA: 75.5
  Isobutyryl-CoA: 50.5
  Propionyl-CoA: 42.2
  Ethylmalonyl-CoA: 34.1
  Acetyl-CoA: 22.6
  Benzoyl-CoA: 21.8
  2-Methylbutyryl-CoA: 19.6
  3-Methylbutyryl-CoA: 15.2
  trans-1,2-CPDA: 13.9
  CHC-CoA: 13.8
  fatty_acid: 0.0

CFP59_RS29855: mal - mal
PKS_AT (576..867): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 236.5
  inactive: 118.4
  Methoxymalonyl-CoA: 69.4
  Methylmalonyl-CoA: 67.5
  Propionyl-CoA: 43.9
  Isobutyryl-CoA: 40.4
  Benzoyl-CoA: 26.3
  Acetyl-CoA: 24.1
  2-Methylbutyryl-CoA: 22.7
  trans-1,2-CPDA: 16.0
  CHC-CoA: 13.5
  fatty_acid: 11.1
  3-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -3.9

PKS_AT (2366..2658): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 242.4
  inactive: 121.0
  Methoxymalonyl-CoA: 70.1
  Methylmalonyl-CoA: 65.3
  Propionyl-CoA: 41.2
  Isobutyryl-CoA: 25.7
  Benzoyl-CoA: 23.7
  Acetyl-CoA: 20.0
  Ethylmalonyl-CoA: 19.5
  2-Methylbutyryl-CoA: 18.6
  CHC-CoA: 13.2
  trans-1,2-CPDA: 11.8
  fatty_acid: 9.3
  3-Methylbutyryl-CoA: 0.0

CFP59_RS29860: mal - mal - mal - mal - mal
PKS_AT (567..858): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 240.6
  inactive: 128.7
  Methoxymalonyl-CoA: 72.0
  Methylmalonyl-CoA: 71.6
  Propionyl-CoA: 46.7
  Ethylmalonyl-CoA: 32.1
  Isobutyryl-CoA: 30.5
  Benzoyl-CoA: 27.9
  2-Methylbutyryl-CoA: 27.8
  Acetyl-CoA: 24.6
  trans-1,2-CPDA: 18.1
  CHC-CoA: 17.3
  fatty_acid: 10.4
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2395..2686): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 241.7
  inactive: 123.7
  Methoxymalonyl-CoA: 72.4
  Methylmalonyl-CoA: 70.6
  Propionyl-CoA: 48.2
  Isobutyryl-CoA: 30.7
  2-Methylbutyryl-CoA: 29.7
  Acetyl-CoA: 29.1
  Ethylmalonyl-CoA: 26.0
  Benzoyl-CoA: 22.6
  trans-1,2-CPDA: 17.3
  CHC-CoA: 15.5
  fatty_acid: 11.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3873..4166): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 239.5
  inactive: 121.3
  Methoxymalonyl-CoA: 72.2
  Methylmalonyl-CoA: 68.8
  Propionyl-CoA: 48.1
  Isobutyryl-CoA: 35.0
  Ethylmalonyl-CoA: 31.8
  2-Methylbutyryl-CoA: 28.4
  Benzoyl-CoA: 26.8
  Acetyl-CoA: 23.0
  trans-1,2-CPDA: 17.8
  CHC-CoA: 17.0
  fatty_acid: 13.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5731..6022): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 240.7
  inactive: 127.1
  Methoxymalonyl-CoA: 72.6
  Methylmalonyl-CoA: 72.4
  Propionyl-CoA: 49.7
  Isobutyryl-CoA: 34.6
  2-Methylbutyryl-CoA: 33.4
  Acetyl-CoA: 29.0
  Benzoyl-CoA: 26.7
  Ethylmalonyl-CoA: 25.9
  trans-1,2-CPDA: 16.9
  CHC-CoA: 15.2
  fatty_acid: 11.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (7279..7571): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 238.1
  inactive: 121.4
  Methoxymalonyl-CoA: 69.7
  Methylmalonyl-CoA: 67.4
  Propionyl-CoA: 42.6
  Isobutyryl-CoA: 26.7
  Benzoyl-CoA: 26.7
  Acetyl-CoA: 26.7
  Ethylmalonyl-CoA: 24.2
  2-Methylbutyryl-CoA: 20.8
  trans-1,2-CPDA: 17.5
  CHC-CoA: 14.5
  fatty_acid: 11.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS29865: mmal
PKS_AT (567..866): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 224.0
  Ethylmalonyl-CoA: 220.0
  Methoxymalonyl-CoA: 177.0
  2-Methylbutyryl-CoA: 137.7
  trans-1,2-CPDA: 127.4
  CHC-CoA: 99.7
  Propionyl-CoA: 98.8
  Malonyl-CoA: 94.2
  Isobutyryl-CoA: 81.7
  Benzoyl-CoA: 70.0
  3-Methylbutyryl-CoA: 55.8
  Acetyl-CoA: 41.1
  fatty_acid: 33.8
  inactive: 30.1

CFP59_RS29870: mal - mal - mal
PKS_AT (572..866): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 244.6
  inactive: 118.3
  Methoxymalonyl-CoA: 70.4
  Methylmalonyl-CoA: 61.1
  Propionyl-CoA: 36.2
  Isobutyryl-CoA: 29.2
  Benzoyl-CoA: 21.1
  2-Methylbutyryl-CoA: 20.6
  Ethylmalonyl-CoA: 20.3
  Acetyl-CoA: 17.5
  CHC-CoA: 10.4
  trans-1,2-CPDA: 7.1
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2134..2426): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 236.3
  inactive: 120.9
  Methoxymalonyl-CoA: 67.3
  Methylmalonyl-CoA: 62.5
  Propionyl-CoA: 40.4
  Isobutyryl-CoA: 29.1
  Benzoyl-CoA: 26.7
  Acetyl-CoA: 20.2
  Ethylmalonyl-CoA: 15.2
  2-Methylbutyryl-CoA: 14.9
  trans-1,2-CPDA: 11.9
  CHC-CoA: 11.5
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3890..4193): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 222.0
  inactive: 109.0
  Methoxymalonyl-CoA: 65.5
  Methylmalonyl-CoA: 62.3
  Propionyl-CoA: 40.5
  Isobutyryl-CoA: 29.5
  Ethylmalonyl-CoA: 23.7
  2-Methylbutyryl-CoA: 23.7
  Acetyl-CoA: 21.0
  Benzoyl-CoA: 18.8
  trans-1,2-CPDA: 16.0
  CHC-CoA: 12.9
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS29875: mal - mal - mal - mal
PKS_AT (575..866): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 242.0
  inactive: 127.2
  Methoxymalonyl-CoA: 74.7
  Methylmalonyl-CoA: 70.5
  Propionyl-CoA: 45.0
  Isobutyryl-CoA: 43.9
  Benzoyl-CoA: 33.5
  Ethylmalonyl-CoA: 31.5
  Acetyl-CoA: 25.2
  2-Methylbutyryl-CoA: 24.9
  trans-1,2-CPDA: 20.9
  CHC-CoA: 19.6
  fatty_acid: 14.7
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2427..2716): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 235.0
  inactive: 129.5
  Methylmalonyl-CoA: 68.6
  Methoxymalonyl-CoA: 68.4
  Propionyl-CoA: 48.6
  Benzoyl-CoA: 29.8
  Ethylmalonyl-CoA: 29.1
  Isobutyryl-CoA: 28.2
  2-Methylbutyryl-CoA: 23.3
  Acetyl-CoA: 21.3
  trans-1,2-CPDA: 20.9
  CHC-CoA: 19.2
  fatty_acid: 10.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4231..4522): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 244.1
  inactive: 121.0
  Methoxymalonyl-CoA: 73.4
  Methylmalonyl-CoA: 68.4
  Propionyl-CoA: 43.7
  Isobutyryl-CoA: 32.4
  Ethylmalonyl-CoA: 27.2
  2-Methylbutyryl-CoA: 25.2
  Benzoyl-CoA: 23.4
  Acetyl-CoA: 20.2
  CHC-CoA: 12.6
  trans-1,2-CPDA: 12.4
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (6043..6331): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 235.7
  inactive: 125.4
  Methoxymalonyl-CoA: 68.4
  Methylmalonyl-CoA: 67.2
  Propionyl-CoA: 45.7
  Isobutyryl-CoA: 32.0
  Benzoyl-CoA: 30.0
  Acetyl-CoA: 27.0
  2-Methylbutyryl-CoA: 23.1
  Ethylmalonyl-CoA: 22.3
  trans-1,2-CPDA: 20.5
  CHC-CoA: 16.2
  fatty_acid: 11.3
  3-Methylbutyryl-CoA: 0.0

CFP59_RS29880: mmal - mmal
PKS_AT (570..869): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 223.6
  Ethylmalonyl-CoA: 220.5
  Methoxymalonyl-CoA: 174.5
  2-Methylbutyryl-CoA: 138.6
  trans-1,2-CPDA: 126.6
  CHC-CoA: 100.8
  Propionyl-CoA: 100.5
  Malonyl-CoA: 100.2
  Isobutyryl-CoA: 73.3
  Benzoyl-CoA: 59.4
  3-Methylbutyryl-CoA: 46.6
  fatty_acid: 41.1
  Acetyl-CoA: 40.3
  inactive: 24.7

PKS_AT (2117..2416): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 222.7
  Ethylmalonyl-CoA: 212.4
  Methoxymalonyl-CoA: 176.2
  2-Methylbutyryl-CoA: 144.1
  trans-1,2-CPDA: 127.9
  Propionyl-CoA: 102.1
  Malonyl-CoA: 97.7
  CHC-CoA: 96.3
  Isobutyryl-CoA: 90.7
  Benzoyl-CoA: 71.8
  3-Methylbutyryl-CoA: 63.9
  Acetyl-CoA: 49.4
  fatty_acid: 40.0
  inactive: 34.7

CFP59_RS29885: mal - mal - mal
PKS_AT (580..870): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 235.8
  inactive: 125.5
  Methoxymalonyl-CoA: 77.2
  Methylmalonyl-CoA: 67.0
  Isobutyryl-CoA: 43.6
  Propionyl-CoA: 39.0
  Ethylmalonyl-CoA: 33.9
  Benzoyl-CoA: 29.7
  2-Methylbutyryl-CoA: 24.8
  Acetyl-CoA: 22.8
  CHC-CoA: 18.6
  trans-1,2-CPDA: 15.2
  fatty_acid: 13.3
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2340..2633): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 241.4
  inactive: 135.5
  Methylmalonyl-CoA: 68.6
  Methoxymalonyl-CoA: 67.9
  Propionyl-CoA: 44.9
  Isobutyryl-CoA: 38.1
  2-Methylbutyryl-CoA: 27.2
  Ethylmalonyl-CoA: 24.6
  Acetyl-CoA: 23.8
  Benzoyl-CoA: 23.5
  CHC-CoA: 15.5
  trans-1,2-CPDA: 14.4
  fatty_acid: 10.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4420..4708): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 234.2
  inactive: 125.0
  Methoxymalonyl-CoA: 73.2
  Methylmalonyl-CoA: 70.3
  Propionyl-CoA: 42.9
  Ethylmalonyl-CoA: 33.5
  Benzoyl-CoA: 27.9
  Acetyl-CoA: 27.5
  Isobutyryl-CoA: 25.6
  2-Methylbutyryl-CoA: 24.6
  CHC-CoA: 18.2
  trans-1,2-CPDA: 16.7
  fatty_acid: 13.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS29890: mal - mmal
PKS_AT (591..884): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 230.6
  inactive: 117.9
  Methoxymalonyl-CoA: 69.2
  Methylmalonyl-CoA: 64.0
  Propionyl-CoA: 39.9
  Ethylmalonyl-CoA: 27.5
  Isobutyryl-CoA: 26.8
  Acetyl-CoA: 25.4
  trans-1,2-CPDA: 22.5
  Benzoyl-CoA: 21.8
  2-Methylbutyryl-CoA: 19.3
  CHC-CoA: 16.8
  fatty_acid: 11.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2389..2688): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 222.5
  Ethylmalonyl-CoA: 215.8
  Methoxymalonyl-CoA: 174.6
  2-Methylbutyryl-CoA: 142.3
  trans-1,2-CPDA: 134.3
  Propionyl-CoA: 101.7
  Malonyl-CoA: 98.3
  CHC-CoA: 97.4
  Isobutyryl-CoA: 84.7
  Benzoyl-CoA: 68.0
  3-Methylbutyryl-CoA: 57.0
  Acetyl-CoA: 46.2
  fatty_acid: 42.1
  inactive: 29.9

CFP59_RS29990: pk
PKS_AT (11..282): pk
ATSignature: (unknown)
No matches above 50%
minowa: CHC-CoA

Prediction, score:
  CHC-CoA: 14.1
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Malonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (7246508...7271689)
CFP59_RS29945
  RRE type: Lanthipeptide_LanB_RRE
  Location: 153 - 241
  Score: 56.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CatR | H2O2-responsive repressor
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 32 - ectoine
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,288,587 - 8,298,991 nt. (total: 10,405 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CFP59_RS34430: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: aminotransferase
CFP59_RS34435: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

CFP59_RS34450: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.86 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.86 | other (other) | ectoine | Streptomyces anulatus
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.86 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.86 | other (other) | ectoine | Streptomyces anulatus
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.52 out of 19.26
Confidence: medium
Additional weak hits (4):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 out of 26.12
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.40 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.61 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein

NZ_CP025018.1 - Region 33 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,455,701 - 8,487,532 nt. (total: 31,832 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CFP59_RS35300: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: methyltransferase transferase
CFP59_RS35220: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

CFP59_RS35305: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: decarboxylase
CFP59_RS35240: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: synthase
CFP59_RS35265: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001408.5 |  | 0.63 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002527.2 |  | 0.60 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000946.5 |  | 0.59 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0000947.5 |  | 0.50 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0002692.2 |  | 0.50 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000844.5 |  | 0.48 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002127.3 |  | 0.48 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002031.3 |  | 0.47 | other (other) | kitasetaline | Kitasatospora setae KM-6054

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001408.5 |  | 0.63 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002527.2 |  | 0.60 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000946.5 |  | 0.59 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0000947.5 |  | 0.50 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0002692.2 |  | 0.50 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000844.5 |  | 0.48 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002127.3 |  | 0.48 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002031.3 |  | 0.47 | other (other) | kitasetaline | Kitasatospora setae KM-6054

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.62 out of 20.97
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 26.17 out of 29.65
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.90 out of 36.53
Confidence: medium
Additional weak hits (12):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.96 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.03 out of 28.14
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.34 out of 21.55
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.84 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.66 out of 30.22
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.73 out of 24.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.26 out of 35.63
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.88 out of 23.43
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.97 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.59 out of 28.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
DmdR1 | Iron(II)-dependent repressor
LexA variant 1 | Repressor of DNA damage response

NZ_CP025018.1 - Region 34 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,522,312 - 8,551,458 nt. (total: 29,147 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CFP59_RS35505: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Lyases: lyase
CFP59_RS35480: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Isomerases: isomerase
CFP59_RS35535: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase synthetase
CFP59_RS35495: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS35515: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs
  SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

CFP59_RS35520: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Translocases: transport
CFP59_RS35475: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002458.3 |  | 0.65 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000665.5 |  | 0.52 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002591.2 |  | 0.50 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000668.5 |  | 0.49 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830
BGC0000666.5 |  | 0.49 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0000663.5 |  | 0.48 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0001594.3 |  | 0.48 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0000937.5 |  | 0.47 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002458.3 |  | 0.65 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000665.5 |  | 0.52 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002591.2 |  | 0.50 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000668.5 |  | 0.49 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830
BGC0000666.5 |  | 0.49 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0000663.5 |  | 0.48 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0001594.3 |  | 0.48 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0000937.5 |  | 0.47 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
CFP59_RS35490: TS_Pyr4
Domain 1 (4 - 213): Pyr4 type terpene synthase
Subtype: unknown
CFP59_RS35520: PT_FPPS_like
Domain 1 (61 - 349): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
Additional weak hits (2):
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.54 out of 23.43
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
HPP | Hexaprenyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein

NZ_CP025018.1 - Region 35 - 2dos,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,762,999 - 8,846,225 nt. (total: 83,227 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
2dos: ((DOIS or DHQ_synthase or ValA or salQ) and DegT_DnrJ_EryC1 and (LipV or ADSI-DH or cds(ADH_N and ADH_zinc_N)))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase reductase
CFP59_RS36475: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CFP59_RS36490: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

CFP59_RS36515: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CFP59_RS36590: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

CFP59_RS36610: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CFP59_RS36625: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CFP59_RS49800: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
CFP59_RS36585: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: hydrolase
CFP59_RS36595: HAD-superfamily hydrolase, subfamily IA, variant

smcogs
  SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

Lyases: dehydratase
CFP59_RS36655: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
CFP59_RS36535: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS36540: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS36560: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS36565: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS36575: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

CFP59_RS36605: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS36630: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS36635: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs
  SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

Translocases: permease
CFP59_RS36500: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | NRPS-like | 2dos | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  |  | 1.30 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  | 1.28 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  | 1.28 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  |  |  | 1.26 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  |  |  | 1.02 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  | 1.01 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000041.3 |  |  |  | 1.00 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000018.5 |  |  |  | 0.92 | PKS | angolamycin | Streptomyces eurythermus
BGC0002191.2 |  |  |  | 0.90 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001254.3 |  |  |  | 0.89 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000018.5 |  | 0.70 | PKS | angolamycin | Streptomyces eurythermus
BGC0001164.3 |  | 0.70 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.70 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000041.3 |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001254.3 |  | 0.64 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001163.3 |  | 0.64 | PKS | 1-heptadecene | Moorea producens 3L

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (13):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.00 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.69 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.90 out of 21.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.73 out of 25.75
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.56 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.14 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.27 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.92 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.86 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.71 out of 27.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.09 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 52, location 8762998 - 8846225:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Me-ccmal - mal - pk) + (Me-redmal) + (Me-redmal) + (Me-ccmal) + (pk)
Non-colinear ordering:
  CFP59_RS36535 + CFP59_RS36540 + CFP59_RS49800 + CFP59_RS36560 + CFP59_RS36565

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS36535: AHBA - mmal - mal - pk
CAL_domain (33..448): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 419.1
  shikimic_acid: 241.6
  Acetyl-CoA: 10.5
  fatty_acid: 0.0
  NH2: 0.0

PKS_AT (1568..1867): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Malonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 191.0
  Ethylmalonyl-CoA: 181.9
  Methoxymalonyl-CoA: 153.8
  2-Methylbutyryl-CoA: 110.4
  trans-1,2-CPDA: 109.1
  Propionyl-CoA: 101.3
  Isobutyryl-CoA: 99.5
  CHC-CoA: 92.3
  Malonyl-CoA: 79.9
  Benzoyl-CoA: 58.1
  fatty_acid: 49.2
  Acetyl-CoA: 37.5
  3-Methylbutyryl-CoA: 34.8
  inactive: 21.0

PKS_AT (3264..3558): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 79.2%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 193.5
  inactive: 78.5
  Methoxymalonyl-CoA: 69.0
  Methylmalonyl-CoA: 53.7
  Isobutyryl-CoA: 37.5
  Propionyl-CoA: 33.9
  Ethylmalonyl-CoA: 27.8
  trans-1,2-CPDA: 18.0
  Acetyl-CoA: 16.3
  CHC-CoA: 12.3
  Benzoyl-CoA: 12.3
  2-Methylbutyryl-CoA: 12.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4574..4875): pk
ATSignature: Ethylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Ethylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 87.5%
  Methylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 189.6
  Ethylmalonyl-CoA: 184.7
  Methoxymalonyl-CoA: 149.9
  2-Methylbutyryl-CoA: 128.5
  CHC-CoA: 106.8
  trans-1,2-CPDA: 103.4
  Malonyl-CoA: 102.2
  Propionyl-CoA: 98.2
  Isobutyryl-CoA: 95.9
  Acetyl-CoA: 51.0
  Benzoyl-CoA: 49.3
  fatty_acid: 48.1
  3-Methylbutyryl-CoA: 23.4
  inactive: 22.6

CFP59_RS36540: mmal
PKS_AT (570..869): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Malonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 183.3
  Ethylmalonyl-CoA: 174.7
  Methoxymalonyl-CoA: 148.8
  trans-1,2-CPDA: 110.6
  2-Methylbutyryl-CoA: 93.2
  Propionyl-CoA: 91.5
  Isobutyryl-CoA: 87.7
  CHC-CoA: 81.6
  Malonyl-CoA: 78.3
  Benzoyl-CoA: 56.1
  Acetyl-CoA: 32.6
  fatty_acid: 30.9
  3-Methylbutyryl-CoA: 21.4
  inactive: 17.4

CFP59_RS49800: mmal
PKS_AT (566..859): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 83.3%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 170.4
  Ethylmalonyl-CoA: 160.4
  Methoxymalonyl-CoA: 147.2
  trans-1,2-CPDA: 97.6
  Isobutyryl-CoA: 96.2
  2-Methylbutyryl-CoA: 95.0
  Propionyl-CoA: 84.3
  CHC-CoA: 78.3
  Malonyl-CoA: 74.5
  Benzoyl-CoA: 51.6
  fatty_acid: 44.0
  3-Methylbutyryl-CoA: 31.0
  Acetyl-CoA: 22.8
  inactive: 16.9

CFP59_RS36560: mmal
PKS_AT (570..868): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.8
  Ethylmalonyl-CoA: 198.4
  Methoxymalonyl-CoA: 167.4
  2-Methylbutyryl-CoA: 124.9
  trans-1,2-CPDA: 121.7
  Propionyl-CoA: 107.7
  CHC-CoA: 87.9
  Malonyl-CoA: 83.1
  Isobutyryl-CoA: 77.4
  Benzoyl-CoA: 66.0
  fatty_acid: 34.7
  Acetyl-CoA: 29.6
  3-Methylbutyryl-CoA: 25.6
  inactive: 21.9

CFP59_RS36565: pk
PKS_AT (572..871): pk
ATSignature: Ethylmalonyl-CoA

Top 3 matches:
  Ethylmalonyl-CoA: 83.3%
  Methylmalonyl-CoA: 79.2%
  Methoxymalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 184.2
  Ethylmalonyl-CoA: 178.2
  Methoxymalonyl-CoA: 157.3
  trans-1,2-CPDA: 129.9
  2-Methylbutyryl-CoA: 115.3
  Malonyl-CoA: 99.3
  CHC-CoA: 97.3
  Propionyl-CoA: 95.3
  Isobutyryl-CoA: 87.3
  Benzoyl-CoA: 61.6
  fatty_acid: 50.1
  3-Methylbutyryl-CoA: 44.5
  Acetyl-CoA: 40.0
  inactive: 28.6

CFP59_RS36605: X
AMP-binding (47..462): X
nrpys: Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAIL---ITVSSTAFSEGARATYGMTELSIGTWT
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CFP59_RS36630: Acetyl-CoA
CAL_domain (45..497): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 49.1
  fatty_acid: 15.3
  AHBA: 2.7
  NH2: 2.2
  shikimic_acid: -4.9

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CelR | Cellobiose uptake repressor
ToxT | Regulator of MSHA biosynthesis

NZ_CP025018.1 - Region 36 - NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,881,451 - 8,958,135 nt. (total: 76,685 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CFP59_RS36865: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS36890: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CFP59_RS36920: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CFP59_RS37030: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CFP59_RS37040: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CFP59_RS37080: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase
CFP59_RS36945: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase phosphatase
CFP59_RS37045: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

CFP59_RS37090: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: synthase
CFP59_RS36940: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS36950: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS49160: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.86 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  | 0.85 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000067.5 |  |  | 0.60 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0002191.2 |  |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001160.5 |  |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  |  | 0.57 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  |  | 0.56 | PKS | FR901512 | fungal sp. No.14919
BGC0001257.3 |  |  | 0.56 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000067.5 |  | 0.64 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000041.3 |  | 0.63 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001258.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (16):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.52 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.31 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.82 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.91 out of 21.84
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.37 out of 31.73
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.32 out of 20.01
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.73 out of 18.57
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.62 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.38 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.83 out of 20.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.85 out of 31.73
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 53, location 8881450 - 8958135:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - pk - redmal) + (pk) + (Me-ccmal - pk) + (ccmal)
Non-colinear ordering:
  CFP59_RS49160 + CFP59_RS36950 + CFP59_RS36945 + CFP59_RS36940

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS36940: mal
PKS_AT (552..835): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 169.4
  inactive: 81.7
  Methoxymalonyl-CoA: 66.0
  Methylmalonyl-CoA: 54.0
  Ethylmalonyl-CoA: 29.6
  Propionyl-CoA: 28.2
  Isobutyryl-CoA: 13.9
  2-Methylbutyryl-CoA: 13.5
  CHC-CoA: 12.4
  Benzoyl-CoA: 12.1
  trans-1,2-CPDA: 8.5
  fatty_acid: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS36945: mmal - pk
PKS_AT (550..839): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Malonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 196.7
  Ethylmalonyl-CoA: 187.9
  Methoxymalonyl-CoA: 156.6
  2-Methylbutyryl-CoA: 129.3
  trans-1,2-CPDA: 101.6
  Propionyl-CoA: 93.8
  CHC-CoA: 90.2
  Malonyl-CoA: 84.7
  Isobutyryl-CoA: 71.6
  Benzoyl-CoA: 62.2
  Acetyl-CoA: 53.5
  fatty_acid: 37.0
  3-Methylbutyryl-CoA: 31.5
  inactive: 22.2

PKS_AT (2211..2505): pk
ATSignature: Methoxymalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%
  Methylmalonyl-CoA: 87.5%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 177.8
  Methylmalonyl-CoA: 169.6
  Methoxymalonyl-CoA: 154.0
  trans-1,2-CPDA: 110.4
  2-Methylbutyryl-CoA: 103.8
  Propionyl-CoA: 88.5
  CHC-CoA: 86.6
  Malonyl-CoA: 80.9
  Benzoyl-CoA: 45.8
  Isobutyryl-CoA: 36.3
  Acetyl-CoA: 30.6
  fatty_acid: 16.0
  3-Methylbutyryl-CoA: 14.8
  inactive: 13.2

CFP59_RS36950: pk
PKS_AT (569..863): pk
ATSignature: Methoxymalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%
  Methylmalonyl-CoA: 87.5%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 173.4
  Methylmalonyl-CoA: 168.9
  Methoxymalonyl-CoA: 153.6
  trans-1,2-CPDA: 108.3
  2-Methylbutyryl-CoA: 106.1
  Propionyl-CoA: 88.6
  CHC-CoA: 85.0
  Malonyl-CoA: 77.2
  Benzoyl-CoA: 45.5
  Isobutyryl-CoA: 34.2
  Acetyl-CoA: 30.5
  fatty_acid: 13.8
  3-Methylbutyryl-CoA: 13.7
  inactive: 13.0

CFP59_RS49160: AHBA - pk - mal
CAL_domain (34..440): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 380.8
  shikimic_acid: 254.5
  NH2: 10.6
  fatty_acid: 0.0
  Acetyl-CoA: -4.1

PKS_AT (1511..1805): pk
ATSignature: Methoxymalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%
  Methylmalonyl-CoA: 87.5%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 180.0
  Methylmalonyl-CoA: 169.5
  Methoxymalonyl-CoA: 157.9
  trans-1,2-CPDA: 112.2
  2-Methylbutyryl-CoA: 106.4
  Propionyl-CoA: 91.3
  CHC-CoA: 85.9
  Malonyl-CoA: 81.9
  Benzoyl-CoA: 50.8
  Isobutyryl-CoA: 35.2
  Acetyl-CoA: 29.3
  inactive: 15.0
  3-Methylbutyryl-CoA: 14.2
  fatty_acid: 10.7

PKS_AT (3176..3459): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 169.4
  inactive: 81.7
  Methoxymalonyl-CoA: 66.0
  Methylmalonyl-CoA: 54.0
  Ethylmalonyl-CoA: 29.6
  Propionyl-CoA: 28.2
  Isobutyryl-CoA: 13.9
  2-Methylbutyryl-CoA: 13.5
  CHC-CoA: 12.4
  Benzoyl-CoA: 12.1
  trans-1,2-CPDA: 8.5
  fatty_acid: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP025018.1 - Region 37 - PKS-like,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,032,523 - 9,076,634 nt. (total: 44,112 nt) Show pHMM detection rules used
PKS-like: (t2pks2 or ksIII)
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CFP59_RS37525: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

CFP59_RS37585: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase methyltransferase
CFP59_RS37540: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CFP59_RS37555: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
CFP59_RS37480: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Lyases: cyclase dehydratase
CFP59_RS37560: Terpene synthase/cyclase metal-binding domain protein

smcogs
  SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

CFP59_RS37570: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
CFP59_RS37530: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs
  SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CFP59_RS37535: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | PKS-like | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000658.3 |  |  | 1.21 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  |  | 1.03 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000065.5 |  |  | 0.39 | PKS | rustmicin | Streptomyces galbus
BGC0000275.4 |  |  | 0.25 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0002045.3 |  |  | 0.23 | PKS | persiamycin A | Streptomonospora sp. PA3
BGC0002514.3 |  |  | 0.23 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0002504.2 |  |  | 0.23 | PKS | nocardiopsistin A, nocardiopsistin B, nocardiopsistin C | Nocardiopsis sp.
BGC0001782.3 |  |  | 0.23 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0002443.3 |  |  | 0.23 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.84 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.79 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000065.5 |  | 0.58 | PKS | rustmicin | Streptomyces galbus
BGC0000657.5 |  | 0.55 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000675.5 |  | 0.50 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.49 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001475.4 |  | 0.49 | terpene | aspterric acid | Aspergillus terreus NIH2624
BGC0002173.2 |  | 0.47 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000798.3 |  | 0.46 | saccharide | dhurrin | Sorghum bicolor
BGC0000886.4 |  | 0.46 | other (other) | allylmalonyl-CoA | Streptomyces tsukubensis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
monoterpene |  | 2-methylisoborneol | C11 | C1-C6 | OH
monoterpene |  | 2-methylenebornane | C11 | C1-C6 | none

Genes with terpene domains:
CFP59_RS37560: T1TS
Domain 1 (9 - 431): Type 1 terpene synthase
Subtype: 2-Methylisoborneol synthase type

Reactions:
  2-MeGPP → 2-methylisoborneol
  2-MeGPP → 2-methylenebornane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.11 out of 23.05
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
Additional weak hits (19):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.12 out of 27.55
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.14 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.90 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.65 out of 23.43
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.95 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.00 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.93 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.52 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.29 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.44 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.45 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.76 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.26 out of 20.01
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 54, location 9032522 - 9076634:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mxmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 55, location 9032522 - 9073551:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mxmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS37540: mxmal
PKS_AT (20..290): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 20.9
  Malonyl-CoA: 19.3
  Methylmalonyl-CoA: 18.2
  2-Methylbutyryl-CoA: 10.0
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
2-MeGPP | 2-methylgeranyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production

NZ_CP025018.1 - Region 38 - NRPS-like,T1PKS,betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,392,965 - 9,489,931 nt. (total: 96,967 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
betalactone: (HMGL-like and AMP-binding)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CFP59_RS39025: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS39050: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CFP59_RS39060: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CFP59_RS39080: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CFP59_RS39275: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase methyltransferase
CFP59_RS39095: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CFP59_RS39135: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Hydrolases: hydrolase phosphatase
CFP59_RS39015: HAD-superfamily hydrolase, subfamily IA, variant

smcogs
  SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

CFP59_RS39065: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Lyases: dehydratase hydratase lyase
CFP59_RS39110: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

CFP59_RS39205: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

CFP59_RS39210: L-carnitine dehydratase/bile acid-inducible

smcogs
  SMCOG1189: L-carnitine dehydratase/bile acid-inducible

CFP59_RS39215: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Isomerases: racemase
CFP59_RS39125: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase synthase
CFP59_RS39035: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

CFP59_RS39090: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS39100: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS39120: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

CFP59_RS39200: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS39220: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | NRPS-like | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000068.5 |  |  |  | 1.01 | PKS | geldanamycin | Streptomyces hygroscopicus
BGC0000067.5 |  |  |  | 0.99 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001275.3 |  |  |  | 0.83 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  |  |  | 0.75 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002191.2 |  |  |  | 0.59 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001276.3 |  |  |  | 0.59 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000066.5 |  |  |  | 0.58 | PKS | geldanamycin | Streptomyces hygroscopicus
BGC0001160.5 |  |  |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  |  |  | 0.55 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  |  |  | 0.53 | NRPS, PKS | fusarin C | Fusarium fujikuroi

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000068.5 |  | 0.94 | PKS | geldanamycin | Streptomyces hygroscopicus
BGC0000067.5 |  | 0.88 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000066.5 |  | 0.73 | PKS | geldanamycin | Streptomyces hygroscopicus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.70 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000074.5 |  | 0.66 | PKS | herbimycin A | Streptomyces hygroscopicus
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.48 out of 23.79
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.29 out of 23.79
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 26.33 out of 29.51
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.63 out of 28.19
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.52 out of 24.78
Confidence: medium
Additional weak hits (20):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.32 out of 39.62
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.96 out of 32.93
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.03 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.49 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.36 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.11 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.96 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.15 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.24 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.12 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.10 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.49 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.88 out of 30.97
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.92 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.19 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.01 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 57, location 9392964 - 9489931:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Me-redmal - redmxmal - Me-ohmal) + (Me-ccmal - ohmxmal) + (redmal - Me-ccmal)
Non-colinear ordering:
  CFP59_RS39100 + CFP59_RS39095 + CFP59_RS39090

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 58, location 9392964 - 9475446:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Me-redmal - redmxmal - Me-ohmal) + (Me-ccmal - ohmxmal) + (redmal - Me-ccmal)
Non-colinear ordering:
  CFP59_RS39100 + CFP59_RS39095 + CFP59_RS39090

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS39090: mal - mmal
PKS_AT (583..889): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 225.2
  inactive: 123.7
  Methoxymalonyl-CoA: 64.6
  Methylmalonyl-CoA: 51.9
  Isobutyryl-CoA: 30.1
  Propionyl-CoA: 28.2
  Benzoyl-CoA: 25.5
  Acetyl-CoA: 18.4
  CHC-CoA: 8.9
  2-Methylbutyryl-CoA: 8.9
  Ethylmalonyl-CoA: 8.0
  trans-1,2-CPDA: 7.9
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2652..2949): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Malonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 208.7
  Ethylmalonyl-CoA: 185.7
  Methoxymalonyl-CoA: 174.3
  2-Methylbutyryl-CoA: 124.8
  Propionyl-CoA: 111.5
  Malonyl-CoA: 99.5
  trans-1,2-CPDA: 98.7
  CHC-CoA: 79.4
  Isobutyryl-CoA: 70.9
  Benzoyl-CoA: 55.5
  Acetyl-CoA: 41.8
  3-Methylbutyryl-CoA: 37.0
  fatty_acid: 26.1
  inactive: 25.5

CFP59_RS39095: mmal - mxmal
PKS_AT (573..872): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Malonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 212.1
  Ethylmalonyl-CoA: 193.8
  Methoxymalonyl-CoA: 175.8
  2-Methylbutyryl-CoA: 128.9
  Propionyl-CoA: 112.4
  Malonyl-CoA: 100.8
  trans-1,2-CPDA: 96.8
  CHC-CoA: 75.9
  Isobutyryl-CoA: 71.8
  Benzoyl-CoA: 57.2
  Acetyl-CoA: 39.9
  3-Methylbutyryl-CoA: 38.6
  fatty_acid: 27.1
  inactive: 22.3

PKS_AT (2335..2635): mxmal
ATSignature: Methoxymalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 100.0%
  Ethylmalonyl-CoA: 91.7%
  Methylmalonyl-CoA: 91.7%

minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 186.6
  Methylmalonyl-CoA: 183.0
  Ethylmalonyl-CoA: 173.8
  2-Methylbutyryl-CoA: 120.0
  trans-1,2-CPDA: 93.3
  Malonyl-CoA: 88.6
  Propionyl-CoA: 86.3
  CHC-CoA: 73.4
  Isobutyryl-CoA: 58.1
  Benzoyl-CoA: 49.9
  Acetyl-CoA: 30.6
  3-Methylbutyryl-CoA: 25.8
  inactive: 25.5
  fatty_acid: 8.0

CFP59_RS39100: AHBA - mmal - mxmal - mmal
CAL_domain (34..442): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 532.3
  shikimic_acid: 272.5
  Acetyl-CoA: 13.2
  fatty_acid: 0.0
  NH2: 0.0

PKS_AT (1668..1965): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Malonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.3
  Ethylmalonyl-CoA: 181.6
  Methoxymalonyl-CoA: 167.9
  2-Methylbutyryl-CoA: 124.4
  Propionyl-CoA: 110.2
  Malonyl-CoA: 101.0
  trans-1,2-CPDA: 96.0
  CHC-CoA: 76.5
  Isobutyryl-CoA: 69.6
  Benzoyl-CoA: 56.5
  Acetyl-CoA: 37.7
  3-Methylbutyryl-CoA: 36.8
  inactive: 24.2
  fatty_acid: 23.4

PKS_AT (3732..4032): mxmal
ATSignature: Methoxymalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 100.0%
  Ethylmalonyl-CoA: 91.7%
  Methylmalonyl-CoA: 91.7%

minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 185.5
  Methylmalonyl-CoA: 182.7
  Ethylmalonyl-CoA: 173.2
  2-Methylbutyryl-CoA: 120.6
  trans-1,2-CPDA: 92.0
  Malonyl-CoA: 89.9
  Propionyl-CoA: 85.2
  CHC-CoA: 74.2
  Isobutyryl-CoA: 60.4
  Benzoyl-CoA: 51.2
  Acetyl-CoA: 32.1
  inactive: 26.6
  3-Methylbutyryl-CoA: 26.2
  fatty_acid: 7.5

PKS_AT (5787..6084): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Malonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 207.5
  Ethylmalonyl-CoA: 185.3
  Methoxymalonyl-CoA: 173.0
  2-Methylbutyryl-CoA: 124.6
  Propionyl-CoA: 111.1
  Malonyl-CoA: 99.6
  trans-1,2-CPDA: 98.6
  CHC-CoA: 77.6
  Isobutyryl-CoA: 70.8
  Benzoyl-CoA: 55.1
  Acetyl-CoA: 41.9
  3-Methylbutyryl-CoA: 36.7
  fatty_acid: 26.2
  inactive: 25.7

CFP59_RS39200: X
AMP-binding (15..430): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    DFSRHAGSTLSASGWV---VAGYGLSEASPNVAQ
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
ZuR variant 1 | Zinc-responsive repressor

NZ_CP025018.1 - Region 39 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,545,856 - 9,567,855 nt. (total: 22,000 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CFP59_RS39545: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS39565: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS39570: Hydroxylation

MITE
  MITE0000062Hydroxylation (identity: 94.30%)
smcogs
  SMCOG1034: cytochrome P450

CFP59_RS39575: Hydroxylation

MITE
  MITE0000061Hydroxylation (identity: 95.10%)
smcogs
  SMCOG1034: cytochrome P450

CFP59_RS39610: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Ligases: synthetase
CFP59_RS39585: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.91 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000660.5 |  | 0.59 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0002391.2 |  | 0.57 | terpene | zealexin B3, zealexin C2 | Zea mays
BGC0002736.2 |  | 0.57 | terpene | preaspterpenacid I | Aspergillus terreus NIH2624
BGC0000675.5 |  | 0.55 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001911.3 |  | 0.52 | terpene | raimonol | Streptomyces anulatus
BGC0001475.4 |  | 0.52 | terpene | aspterric acid | Aspergillus terreus NIH2624
BGC0001910.4 |  | 0.52 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.91 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000660.5 |  | 0.59 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0002391.2 |  | 0.57 | terpene | zealexin B3, zealexin C2 | Zea mays
BGC0002736.2 |  | 0.57 | terpene | preaspterpenacid I | Aspergillus terreus NIH2624
BGC0000675.5 |  | 0.55 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001911.3 |  | 0.52 | terpene | raimonol | Streptomyces anulatus
BGC0001475.4 |  | 0.52 | terpene | aspterric acid | Aspergillus terreus NIH2624
BGC0001910.4 |  | 0.52 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
CFP59_RS39580: T1TS
Domain 1 (94 - 295): Type 1 terpene synthase
Subtype: unknown
CFP59_RS39585: PT_FPPS_like
Domain 1 (52 - 358): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
Additional weak hits (6):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.56 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.48 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.07 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.07 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.75 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.24 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
HPP | Hexaprenyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 40 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,576,395 - 9,597,585 nt. (total: 21,191 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase
CFP59_RS39665: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Lyases: cyclase hydratase
CFP59_RS39675: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

CFP59_RS39705: Terpene synthase/cyclase metal-binding domain protein

smcogs
  SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: ligase
CFP59_RS39670: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS39700: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001746.3 |  | 0.79 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0000683.3 |  | 0.76 | terpene | avermitilol | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002708.2 |  | 0.75 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002274.2 |  | 0.55 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001758.4 |  | 0.55 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.55 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.55 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.55 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001746.3 |  | 0.79 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0000683.3 |  | 0.76 | terpene | avermitilol | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002708.2 |  | 0.75 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002274.2 |  | 0.55 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0001758.4 |  | 0.55 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.55 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.55 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.55 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene |  |  | C15 | C1-C11 | none

Genes with terpene domains:
CFP59_RS39705: T1TS
Domain 1 (1 - 341): Type 1 terpene synthase
Subtype: Isoafricanol synthase type

Reactions:
  FPP → sesquiterpene_C1-C11

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.19 out of 20.47
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
Additional weak hits (3):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.50 out of 25.75
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.39 out of 32.74
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.00 out of 27.04
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 41 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,795,135 - 9,912,586 nt. (total: 117,452 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CFP59_RS40695: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CFP59_RS40880: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS51380: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Hydrolases: glucosidase
CFP59_RS40720: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Lyases: dehydratase
CFP59_RS40955: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: racemase
CFP59_RS40700: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase synthase
CFP59_RS40710: argininosuccinate synthase

smcogs
  SMCOG1291: argininosuccinate synthase

CFP59_RS40750: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS49195: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS51375: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
CFP59_RS40735: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001012.3 |  |  | 0.82 | NRPS, PKS | meridamycin | Streptomyces violaceusniger
BGC0000342.4 |  |  | 0.74 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002285.2 |  |  | 0.69 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001135.5 |  |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000307.4 |  |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.62 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  | 0.62 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001012.3 |  | 0.86 | NRPS, PKS | meridamycin | Streptomyces violaceusniger
BGC0000041.3 |  | 0.71 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001011.5 |  | 0.69 | NRPS, PKS | meridamycin | Streptomyces sp. NRRL 30748
BGC0002285.2 |  | 0.68 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000067.5 |  | 0.66 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 19.46 out of 20.01
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.87 out of 23.79
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (10):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.98 out of 30.22
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.21 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.54 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.64 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.48 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.70 out of 28.14
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.89 out of 20.01
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.94 out of 33.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.10 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 62, location 9795134 - 9912586:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpr) + (mal - pk - Me-ccmal - ohmal) + (pk - pk - Me-redmal - pk) + (ohmal - ohmal - pk - ohmal - ohmal - pk - ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 63, location 9795134 - 9839907:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpr) + (mal - pk - Me-ccmal - ohmal) + (pk - pk - Me-redmal - pk)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 64, location 9799960 - 9912586:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpr) + (mal - pk - Me-ccmal - ohmal) + (pk - pk - Me-redmal - pk) + (ohmal - ohmal - pk - ohmal - ohmal - pk - ccmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS40750: Hpr
Search NORINE for peptide: strict or relaxed
AMP-binding (487..928): Hpr
nrpys: Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pro (Pro)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQAFDISLQESFVSQAGEHNHYGPSEAHVVTSY
  Nearest Stachelhaus code(s):
    Hpr DIQFSAHVVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

CFP59_RS49195: mal - pk - mmal - mal
PKS_AT (550..848): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 188.1
  inactive: 92.3
  Methoxymalonyl-CoA: 66.7
  Methylmalonyl-CoA: 50.5
  Acetyl-CoA: 27.5
  Propionyl-CoA: 22.9
  Isobutyryl-CoA: 22.9
  Ethylmalonyl-CoA: 19.3
  fatty_acid: 15.7
  Benzoyl-CoA: 12.6
  2-Methylbutyryl-CoA: 9.5
  CHC-CoA: 8.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (1569..1856): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 215.8
  Methylmalonyl-CoA: 210.8
  Methoxymalonyl-CoA: 169.4
  2-Methylbutyryl-CoA: 145.5
  trans-1,2-CPDA: 136.7
  CHC-CoA: 124.7
  Propionyl-CoA: 111.0
  Malonyl-CoA: 92.8
  Isobutyryl-CoA: 76.2
  Benzoyl-CoA: 66.1
  Acetyl-CoA: 46.0
  fatty_acid: 43.2
  inactive: 12.9
  3-Methylbutyryl-CoA: 11.7

PKS_AT (3021..3306): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 207.4
  Ethylmalonyl-CoA: 206.8
  Methoxymalonyl-CoA: 166.5
  trans-1,2-CPDA: 139.9
  2-Methylbutyryl-CoA: 133.8
  CHC-CoA: 116.0
  Propionyl-CoA: 113.5
  Malonyl-CoA: 93.5
  Isobutyryl-CoA: 75.5
  Benzoyl-CoA: 67.5
  Acetyl-CoA: 45.0
  fatty_acid: 44.3
  inactive: 29.1
  3-Methylbutyryl-CoA: 8.2

PKS_AT (4702..4975): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.6
  inactive: 111.7
  Methoxymalonyl-CoA: 57.9
  Methylmalonyl-CoA: 46.9
  Propionyl-CoA: 33.1
  Isobutyryl-CoA: 28.7
  Ethylmalonyl-CoA: 22.4
  Benzoyl-CoA: 21.3
  Acetyl-CoA: 16.9
  2-Methylbutyryl-CoA: 13.5
  CHC-CoA: 11.4
  fatty_acid: 11.2
  trans-1,2-CPDA: 9.1
  3-Methylbutyryl-CoA: 0.0

CFP59_RS51375: pk - pk - mmal - pk
PKS_AT (558..856): pk
ATSignature: Methoxymalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%
  Methylmalonyl-CoA: 79.2%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 184.5
  Methylmalonyl-CoA: 177.6
  Methoxymalonyl-CoA: 150.6
  2-Methylbutyryl-CoA: 114.9
  trans-1,2-CPDA: 112.3
  Propionyl-CoA: 94.1
  CHC-CoA: 89.9
  Malonyl-CoA: 77.7
  Isobutyryl-CoA: 60.2
  fatty_acid: 36.8
  Benzoyl-CoA: 35.5
  Acetyl-CoA: 30.3
  inactive: 21.0
  3-Methylbutyryl-CoA: 12.5

PKS_AT (2294..2580): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 221.4
  Methylmalonyl-CoA: 211.9
  Methoxymalonyl-CoA: 173.9
  2-Methylbutyryl-CoA: 154.2
  trans-1,2-CPDA: 139.0
  Propionyl-CoA: 116.9
  CHC-CoA: 113.5
  Malonyl-CoA: 88.9
  Isobutyryl-CoA: 66.2
  Benzoyl-CoA: 59.3
  fatty_acid: 39.8
  Acetyl-CoA: 37.7
  3-Methylbutyryl-CoA: 31.8
  inactive: 22.9

PKS_AT (3853..4141): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 207.8
  Ethylmalonyl-CoA: 207.8
  Methoxymalonyl-CoA: 167.5
  2-Methylbutyryl-CoA: 138.7
  trans-1,2-CPDA: 137.2
  CHC-CoA: 121.1
  Propionyl-CoA: 118.6
  Malonyl-CoA: 92.3
  Isobutyryl-CoA: 74.5
  Benzoyl-CoA: 69.7
  Acetyl-CoA: 51.0
  fatty_acid: 43.7
  inactive: 24.9
  3-Methylbutyryl-CoA: 23.5

PKS_AT (5913..6198): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 206.2
  Methylmalonyl-CoA: 203.7
  Methoxymalonyl-CoA: 163.1
  2-Methylbutyryl-CoA: 135.0
  trans-1,2-CPDA: 130.5
  CHC-CoA: 118.9
  Propionyl-CoA: 110.9
  Malonyl-CoA: 90.7
  Isobutyryl-CoA: 69.7
  Benzoyl-CoA: 69.6
  Acetyl-CoA: 46.3
  fatty_acid: 40.7
  inactive: 23.3
  3-Methylbutyryl-CoA: 12.3

CFP59_RS51380: mal - mal - pk - mal - mal - pk - mal
PKS_AT (555..828): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.4
  inactive: 119.9
  Methoxymalonyl-CoA: 54.9
  Methylmalonyl-CoA: 49.9
  Isobutyryl-CoA: 37.7
  Propionyl-CoA: 34.4
  Ethylmalonyl-CoA: 24.6
  Benzoyl-CoA: 17.3
  Acetyl-CoA: 16.9
  CHC-CoA: 13.6
  fatty_acid: 12.2
  2-Methylbutyryl-CoA: 11.8
  trans-1,2-CPDA: 10.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2008..2281): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 202.3
  inactive: 124.0
  Methoxymalonyl-CoA: 57.4
  Methylmalonyl-CoA: 51.5
  Isobutyryl-CoA: 45.6
  Propionyl-CoA: 40.6
  Benzoyl-CoA: 27.9
  Ethylmalonyl-CoA: 23.1
  Acetyl-CoA: 21.6
  fatty_acid: 17.4
  2-Methylbutyryl-CoA: 16.4
  trans-1,2-CPDA: 9.8
  CHC-CoA: 9.5
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3459..3747): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 210.2
  Methylmalonyl-CoA: 209.4
  Methoxymalonyl-CoA: 168.8
  trans-1,2-CPDA: 143.0
  2-Methylbutyryl-CoA: 132.3
  CHC-CoA: 118.5
  Propionyl-CoA: 115.6
  Malonyl-CoA: 95.4
  Isobutyryl-CoA: 76.9
  Benzoyl-CoA: 68.0
  Acetyl-CoA: 46.4
  fatty_acid: 40.1
  inactive: 30.1
  3-Methylbutyryl-CoA: 9.0

PKS_AT (4998..5271): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 209.9
  inactive: 117.0
  Methoxymalonyl-CoA: 66.4
  Methylmalonyl-CoA: 56.1
  Isobutyryl-CoA: 43.1
  Propionyl-CoA: 42.0
  Ethylmalonyl-CoA: 32.8
  Benzoyl-CoA: 30.1
  Acetyl-CoA: 23.7
  fatty_acid: 18.2
  2-Methylbutyryl-CoA: 17.0
  CHC-CoA: 14.6
  trans-1,2-CPDA: 14.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (6457..6730): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 207.1
  inactive: 116.8
  Methoxymalonyl-CoA: 63.5
  Methylmalonyl-CoA: 51.8
  Propionyl-CoA: 31.3
  Isobutyryl-CoA: 29.5
  Ethylmalonyl-CoA: 25.6
  Benzoyl-CoA: 21.4
  Acetyl-CoA: 20.4
  2-Methylbutyryl-CoA: 12.1
  fatty_acid: 9.9
  CHC-CoA: 9.5
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (8001..8275): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 218.0
  Methylmalonyl-CoA: 208.0
  Methoxymalonyl-CoA: 165.3
  2-Methylbutyryl-CoA: 148.5
  trans-1,2-CPDA: 132.5
  CHC-CoA: 118.0
  Propionyl-CoA: 108.4
  Malonyl-CoA: 86.3
  Isobutyryl-CoA: 67.1
  Benzoyl-CoA: 58.2
  Acetyl-CoA: 46.6
  fatty_acid: 41.7
  inactive: 17.9
  3-Methylbutyryl-CoA: 15.6

PKS_AT (10119..10420): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 199.1
  inactive: 94.0
  Methoxymalonyl-CoA: 65.4
  Methylmalonyl-CoA: 57.2
  Propionyl-CoA: 34.9
  Isobutyryl-CoA: 30.8
  Ethylmalonyl-CoA: 27.0
  Acetyl-CoA: 20.5
  Benzoyl-CoA: 14.5
  2-Methylbutyryl-CoA: 14.2
  fatty_acid: 13.2
  CHC-CoA: 12.0
  trans-1,2-CPDA: 9.8
  3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
ArgR | Regulator of arginine biosynthesis genes
IolR | Regulator of the inositol catabolism

NZ_CP025018.1 - Region 42 - NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,916,695 - 10,000,645 nt. (total: 83,951 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase reductase
CFP59_RS41050: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CFP59_RS41055: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

CFP59_RS41065: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CFP59_RS41075: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS41105: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS41140: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

CFP59_RS41165: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: aminotransferase methyltransferase
CFP59_RS40995: methyltransferase

smcogs
  SMCOG1248: methyltransferase

CFP59_RS41170: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: hydrolase
CFP59_RS41160: HAD-superfamily hydrolase, subfamily IA, variant

smcogs
  SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

Ligases: synthase
CFP59_RS41070: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS41080: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS41085: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS41090: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000075.5 |  |  | 1.17 | PKS | hygrocin A, hygrocin B | Streptomyces sp. LZ35
BGC0001273.3 |  |  | 0.86 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.85 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  |  | 0.83 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  |  | 0.69 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000067.5 |  |  | 0.61 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0002191.2 |  |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  |  | 0.57 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001164.3 |  |  | 0.56 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.56 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000075.5 |  | 0.92 | PKS | hygrocin A, hygrocin B | Streptomyces sp. LZ35
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.67 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000067.5 |  | 0.64 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000113.5 |  | 0.63 | PKS | niddamycin | Streptomyces caelestis
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (11):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.83 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.03 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.10 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.62 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.93 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.06 out of 21.55
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 19.26
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.56 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.43 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 65, location 9916694 - 10000645:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - Me-ccmal - mal - ohmal) + (redemal) + (ccmal) + (Me-redmal) + (Me-mal - ccmal)
Non-colinear ordering:
  CFP59_RS41070 + CFP59_RS41075 + CFP59_RS41080 + CFP59_RS41085 + CFP59_RS41090

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS41070: AHBA - mmal - mal - mal
CAL_domain (34..442): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 405.3
  shikimic_acid: 244.7
  fatty_acid: 0.0
  NH2: 0.0
  Acetyl-CoA: 0.0

PKS_AT (1641..1940): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 206.7
  Ethylmalonyl-CoA: 192.4
  Methoxymalonyl-CoA: 157.2
  2-Methylbutyryl-CoA: 122.5
  trans-1,2-CPDA: 114.9
  Propionyl-CoA: 103.5
  Malonyl-CoA: 91.5
  CHC-CoA: 82.0
  Isobutyryl-CoA: 72.7
  Benzoyl-CoA: 64.0
  Acetyl-CoA: 51.0
  fatty_acid: 33.0
  inactive: 32.2
  3-Methylbutyryl-CoA: 20.1

PKS_AT (3362..3665): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 215.7
  inactive: 134.2
  Methoxymalonyl-CoA: 73.4
  Methylmalonyl-CoA: 49.1
  Propionyl-CoA: 34.9
  Benzoyl-CoA: 24.4
  Isobutyryl-CoA: 21.0
  Acetyl-CoA: 20.0
  Ethylmalonyl-CoA: 18.9
  2-Methylbutyryl-CoA: 13.7
  CHC-CoA: 3.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4405..4703): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.8
  inactive: 108.0
  Methoxymalonyl-CoA: 59.2
  Methylmalonyl-CoA: 51.6
  Propionyl-CoA: 30.3
  Acetyl-CoA: 22.3
  Isobutyryl-CoA: 17.1
  Ethylmalonyl-CoA: 15.7
  fatty_acid: 11.0
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

CFP59_RS41075: emal
PKS_AT (614..911): emal
ATSignature: Ethylmalonyl-CoA

Top 3 matches:
  Ethylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 83.3%
  Methylmalonyl-CoA: 79.2%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 187.5
  Methylmalonyl-CoA: 183.3
  Methoxymalonyl-CoA: 143.7
  2-Methylbutyryl-CoA: 117.4
  Propionyl-CoA: 104.9
  trans-1,2-CPDA: 95.6
  CHC-CoA: 87.9
  Malonyl-CoA: 80.7
  Isobutyryl-CoA: 78.1
  Benzoyl-CoA: 55.0
  Acetyl-CoA: 42.5
  fatty_acid: 36.0
  3-Methylbutyryl-CoA: 35.6
  inactive: 24.8

CFP59_RS41080: mal
PKS_AT (570..865): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 216.7
  inactive: 108.2
  Methoxymalonyl-CoA: 62.7
  Methylmalonyl-CoA: 51.5
  Propionyl-CoA: 28.6
  Isobutyryl-CoA: 25.2
  Acetyl-CoA: 20.6
  Ethylmalonyl-CoA: 18.5
  fatty_acid: 11.8
  CHC-CoA: 6.4
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

CFP59_RS41085: mmal
PKS_AT (571..870): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 200.5
  Ethylmalonyl-CoA: 184.4
  Methoxymalonyl-CoA: 148.0
  2-Methylbutyryl-CoA: 122.5
  trans-1,2-CPDA: 103.0
  Propionyl-CoA: 100.8
  CHC-CoA: 83.2
  Malonyl-CoA: 82.5
  Isobutyryl-CoA: 71.5
  Benzoyl-CoA: 65.0
  Acetyl-CoA: 48.0
  fatty_acid: 42.8
  inactive: 32.1
  3-Methylbutyryl-CoA: 29.0

CFP59_RS41090: mmal - mal
PKS_AT (564..863): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 196.3
  Ethylmalonyl-CoA: 180.5
  Methoxymalonyl-CoA: 144.3
  2-Methylbutyryl-CoA: 110.3
  Propionyl-CoA: 97.5
  trans-1,2-CPDA: 97.1
  Malonyl-CoA: 84.0
  CHC-CoA: 78.7
  Isobutyryl-CoA: 60.8
  Benzoyl-CoA: 59.3
  Acetyl-CoA: 40.3
  fatty_acid: 35.8
  inactive: 29.9
  3-Methylbutyryl-CoA: 17.6

PKS_AT (1584..1882): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.5
  inactive: 108.7
  Methoxymalonyl-CoA: 58.2
  Methylmalonyl-CoA: 50.9
  Propionyl-CoA: 28.3
  Acetyl-CoA: 22.3
  Isobutyryl-CoA: 21.3
  Ethylmalonyl-CoA: 15.5
  fatty_acid: 9.9
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP025018.1 - Region 43 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,029,151 - 10,050,233 nt. (total: 21,083 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase methyltransferase
CFP59_RS41305: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

CFP59_RS41345: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Ligases: synthetase
CFP59_RS41360: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001810.3 |  | 0.37 | PKS | trehangelin | Polymorphospora rubra
BGC0000676.5 |  | 0.37 | terpene | aphidicolin, aphidicolan-16β-ol, 3-deoxyaphidicolin, 17-deoxyaphidicolin | Phoma betae
BGC0001364.3 |  | 0.36 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000688.4 |  | 0.36 | terpene | copalyl diphosphate | Diaporthe amygdali

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001810.3 |  | 0.37 | PKS | trehangelin | Polymorphospora rubra
BGC0000676.5 |  | 0.37 | terpene | aphidicolin, aphidicolan-16β-ol, 3-deoxyaphidicolin, 17-deoxyaphidicolin | Phoma betae
BGC0001364.3 |  | 0.36 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000688.4 |  | 0.36 | terpene | copalyl diphosphate | Diaporthe amygdali

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
CFP59_RS41360: PT_FPPS_like
Domain 1 (64 - 359): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.26 out of 27.04
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.21 out of 23.79
Confidence: medium
Additional weak hits (8):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.61 out of 30.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.32 out of 25.88
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.67 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.08 out of 21.55
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.16 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.97 out of 24.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
HPP | Hexaprenyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP025018.1 - Region 44 - RiPP-like,T1PKS,hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,129,891 - 10,256,044 nt. (total: 126,154 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
hglE-KS: (hglE or hglD)
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CFP59_RS41785: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CFP59_RS41895: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

CFP59_RS41955: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS41970: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: glycosyltransferase methyltransferase
CFP59_RS41890: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CFP59_RS41935: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: hydrolase
CFP59_RS41930: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
CFP59_RS41805: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS41810: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS41815: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

CFP59_RS41855: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS41915: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS41920: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS49855: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS51390: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS51395: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | T1PKS | hglE-KS | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002497.3 |  |  |  | 1.15 | other (other) | hexacosalactone A | Streptomyces sp.
BGC0001276.3 |  |  |  | 0.75 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  |  |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001160.5 |  |  |  | 0.56 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002192.3 |  |  |  | 0.53 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  |  |  | 0.51 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002497.3 |  | 0.92 | other (other) | hexacosalactone A | Streptomyces sp.
BGC0001276.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.75 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.72 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000067.5 |  | 0.66 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001050.5 |  | 0.63 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.44 out of 23.79
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (9):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.49 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.67 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.52 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.85 out of 26.06
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.39 out of 27.18
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.32 out of 25.88
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.99 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 67, location 10129890 - 10256044:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk - ohmal - pk - pk) + (Me-ohmal - ohmal - pk - ohmal) + (pk - ccmal) + (mal) + (Me-mal) + (pk - ccmal - pk)
Non-colinear ordering:
  CFP59_RS51390 + CFP59_RS41855 + CFP59_RS51395 + CFP59_RS41915 + CFP59_RS41920 + CFP59_RS41925 + CFP59_RS49855

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 68, location 10129890 - 10254227:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk - ohmal - pk - pk) + (Me-ohmal - ohmal - pk - ohmal) + (pk - ccmal) + (mal) + (Me-mal) + (pk - ccmal - pk)
Non-colinear ordering:
  CFP59_RS51390 + CFP59_RS41855 + CFP59_RS51395 + CFP59_RS41915 + CFP59_RS41920 + CFP59_RS41925 + CFP59_RS49855

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS41805: X
AMP-binding (9..412): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    NTTLHTFGQTGTMGFSGGSYEGYGLTEASPVVAY
  Nearest Stachelhaus code(s):
    Leu DFLYFGGVVK (29% 8Å match)
  Stachelhaus code match:
    60% (weak)

CFP59_RS41810: X
AMP-binding (15..416): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TLRLHSGSGADLTLSYGGCLQFYGTTETSGISVL
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CFP59_RS41820: pk
PKS_AT (57..164): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

Prediction, score:
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Malonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

CFP59_RS51390: pk - mal - pk - pk
PKS_AT (558..856): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 83.3%
  Ethylmalonyl-CoA: 79.2%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 209.5
  Methylmalonyl-CoA: 208.3
  2-Methylbutyryl-CoA: 183.8
  Methoxymalonyl-CoA: 172.2
  trans-1,2-CPDA: 135.2
  Propionyl-CoA: 128.4
  CHC-CoA: 111.6
  Malonyl-CoA: 95.3
  Isobutyryl-CoA: 93.3
  Benzoyl-CoA: 68.3
  Acetyl-CoA: 51.2
  3-Methylbutyryl-CoA: 40.7
  fatty_acid: 31.8
  inactive: 23.9

PKS_AT (1585..1869): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 233.0
  inactive: 120.2
  Methoxymalonyl-CoA: 57.7
  Methylmalonyl-CoA: 46.1
  Propionyl-CoA: 35.9
  2-Methylbutyryl-CoA: 16.8
  Isobutyryl-CoA: 16.4
  Acetyl-CoA: 11.9
  Benzoyl-CoA: 11.3
  Ethylmalonyl-CoA: 10.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3069..3367): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 234.7
  Methylmalonyl-CoA: 228.1
  Methoxymalonyl-CoA: 185.7
  2-Methylbutyryl-CoA: 171.9
  trans-1,2-CPDA: 140.1
  Propionyl-CoA: 135.4
  CHC-CoA: 112.6
  Malonyl-CoA: 112.3
  Isobutyryl-CoA: 74.9
  Benzoyl-CoA: 68.7
  Acetyl-CoA: 45.0
  fatty_acid: 42.7
  inactive: 26.6
  3-Methylbutyryl-CoA: 22.0

PKS_AT (4403..4697): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 229.1
  Methylmalonyl-CoA: 224.9
  Methoxymalonyl-CoA: 180.2
  2-Methylbutyryl-CoA: 160.8
  trans-1,2-CPDA: 128.6
  Propionyl-CoA: 118.4
  CHC-CoA: 113.9
  Malonyl-CoA: 104.0
  Isobutyryl-CoA: 80.1
  Benzoyl-CoA: 67.0
  Acetyl-CoA: 40.0
  fatty_acid: 38.3
  3-Methylbutyryl-CoA: 32.4
  inactive: 27.4

CFP59_RS41855: mmal - mal - pk - mal
PKS_AT (576..874): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 229.2
  Ethylmalonyl-CoA: 228.4
  Methoxymalonyl-CoA: 184.7
  2-Methylbutyryl-CoA: 180.5
  trans-1,2-CPDA: 134.9
  Propionyl-CoA: 132.2
  CHC-CoA: 114.2
  Malonyl-CoA: 109.8
  Isobutyryl-CoA: 87.9
  Benzoyl-CoA: 69.7
  fatty_acid: 39.3
  Acetyl-CoA: 37.6
  3-Methylbutyryl-CoA: 36.0
  inactive: 28.3

PKS_AT (2153..2444): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 233.6
  inactive: 119.1
  Methoxymalonyl-CoA: 55.5
  Methylmalonyl-CoA: 43.7
  Propionyl-CoA: 31.2
  Isobutyryl-CoA: 19.3
  2-Methylbutyryl-CoA: 14.1
  Acetyl-CoA: 9.6
  Ethylmalonyl-CoA: 9.5
  fatty_acid: 7.1
  Benzoyl-CoA: 6.7
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3711..4009): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 234.8
  Methylmalonyl-CoA: 231.7
  Methoxymalonyl-CoA: 186.1
  2-Methylbutyryl-CoA: 169.5
  trans-1,2-CPDA: 150.4
  Propionyl-CoA: 131.5
  CHC-CoA: 115.7
  Malonyl-CoA: 113.0
  Isobutyryl-CoA: 75.3
  Benzoyl-CoA: 72.0
  Acetyl-CoA: 47.6
  fatty_acid: 41.3
  3-Methylbutyryl-CoA: 27.3
  inactive: 26.2

PKS_AT (5501..5787): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 228.8
  inactive: 121.0
  Methoxymalonyl-CoA: 57.5
  Methylmalonyl-CoA: 45.7
  Propionyl-CoA: 34.4
  2-Methylbutyryl-CoA: 15.9
  Isobutyryl-CoA: 15.3
  Acetyl-CoA: 12.4
  Benzoyl-CoA: 9.3
  Ethylmalonyl-CoA: 7.1
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS51395: pk - mal
PKS_AT (570..868): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 230.8
  Methylmalonyl-CoA: 227.6
  Methoxymalonyl-CoA: 184.6
  2-Methylbutyryl-CoA: 156.5
  trans-1,2-CPDA: 133.1
  Propionyl-CoA: 112.8
  CHC-CoA: 109.5
  Malonyl-CoA: 96.5
  Isobutyryl-CoA: 83.8
  Benzoyl-CoA: 70.1
  Acetyl-CoA: 39.8
  3-Methylbutyryl-CoA: 33.4
  fatty_acid: 28.0
  inactive: 26.2

PKS_AT (2338..2626): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 222.1
  inactive: 116.7
  Methoxymalonyl-CoA: 48.8
  Methylmalonyl-CoA: 38.6
  Propionyl-CoA: 30.7
  Isobutyryl-CoA: 16.2
  Acetyl-CoA: 12.8
  Benzoyl-CoA: 10.4
  2-Methylbutyryl-CoA: 5.8
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS49855: pk - mal - pk
PKS_AT (570..868): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 233.0
  Methylmalonyl-CoA: 228.8
  Methoxymalonyl-CoA: 184.0
  2-Methylbutyryl-CoA: 161.8
  trans-1,2-CPDA: 139.2
  Propionyl-CoA: 120.2
  CHC-CoA: 111.2
  Malonyl-CoA: 100.2
  Isobutyryl-CoA: 83.8
  Benzoyl-CoA: 72.8
  Acetyl-CoA: 40.8
  3-Methylbutyryl-CoA: 37.7
  fatty_acid: 32.8
  inactive: 27.6

PKS_AT (2351..2638): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 230.9
  inactive: 118.2
  Methoxymalonyl-CoA: 59.7
  Methylmalonyl-CoA: 48.5
  Propionyl-CoA: 35.7
  2-Methylbutyryl-CoA: 16.9
  Isobutyryl-CoA: 13.7
  Acetyl-CoA: 11.8
  Benzoyl-CoA: 9.3
  Ethylmalonyl-CoA: 5.2
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4181..4479): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 236.0
  Methylmalonyl-CoA: 229.8
  Methoxymalonyl-CoA: 187.5
  2-Methylbutyryl-CoA: 163.6
  trans-1,2-CPDA: 139.2
  Propionyl-CoA: 125.6
  CHC-CoA: 114.1
  Malonyl-CoA: 107.7
  Isobutyryl-CoA: 77.6
  Benzoyl-CoA: 72.3
  Acetyl-CoA: 47.9
  fatty_acid: 35.8
  3-Methylbutyryl-CoA: 31.3
  inactive: 30.9

CFP59_RS41915: mal
PKS_AT (1274..1566): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 58.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 68.7
  Methoxymalonyl-CoA: 33.1
  Methylmalonyl-CoA: 31.3
  inactive: 24.6
  Propionyl-CoA: 18.5
  CHC-CoA: 10.9
  Isobutyryl-CoA: 7.9
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

CFP59_RS41920: mmal
PKS_AT (629..841): mmal
ATSignature: (unknown)
No matches above 50%
minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 8.5
  Malonyl-CoA: 4.6
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism

NZ_CP025018.1 - Region 45 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,264,496 - 10,343,248 nt. (total: 78,753 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CFP59_RS42075: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

CFP59_RS42090: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS42145: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS42160: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CFP59_RS42175: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

CFP59_RS42205: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: kinase
CFP59_RS42190: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Hydrolases: hydrolase
CFP59_RS42125: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

CFP59_RS42155: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase
CFP59_RS42115: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS42120: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001240.4 |  | 0.70 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001240.4 |  | 0.70 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.98 out of 23.79
Confidence: medium
Additional weak hits (12):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.76 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.93 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.47 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.67 out of 30.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.16 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.87 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.65 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.69 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.48 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 70, location 10264495 - 10343248:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - D-Ala - D-Val - D-Ala - X) + (D-X - Thr - D-Orn - Val - D-Leu)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS42115: X - Thr - Orn - Val - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (518..905): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGHAFDTSLEGLDLMLGGEYNFYGPTECTIDALA
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2024..2442): Thr
nrpys: Thr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LETHFDFSVWEGSQVFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3110..3502): Orn
nrpys: Orn

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDHAFDTSWEGVDVMVGGEYNFYGPTECTVDAVY
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4629..5007): Val
nrpys: Val

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDAATYEVWLWTGGDVDGYGPTETTTFATS
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5666..6044): Leu
nrpys: Leu

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAASFDASVLEVLIIVGGDVNSYGPTEATVVSTW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (79% 8Å match)
    Leu DALLIGAVVK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

CFP59_RS42120: Leu - Ala - Val - Ala - X
Search NORINE for peptide: strict or relaxed
AMP-binding (41..424): Leu
nrpys: Leu

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAASFDASVLESLIIVGAEVNSYGPTEATVVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (76% 8Å match)
    Leu DALLIGAVVK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1089..1489): Ala
nrpys: Ala

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    ala (Ala)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWATFDVSVFECSAVLAGEANLYGPTEATVYATA
  Nearest Stachelhaus code(s):
    Ala DVFSVALVYK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2609..3006): Val
nrpys: Val

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDASTYEVWLWTGGEVDGYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4127..4528): Ala
nrpys: Ala

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    ala (Ala)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWATFDVSVFECSAVLAGEANIYGPTEATVYATA
  Nearest Stachelhaus code(s):
    Ala DVFSVAIVYK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5649..6028): X
nrpys: Leu, 3OH-Leu

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAESFDASVLEMLIIVGGDINAYGPTETTVVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (85% 8Å match)
    Leu DALLIGAVVK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 46 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,366,147 - 10,389,936 nt. (total: 23,790 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CFP59_RS42370: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CFP59_RS42375: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

Transferases: aminotransferase sulfotransferase
CFP59_RS42340: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

CFP59_RS42350: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Ligases: synthetase
CFP59_RS42355: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002007.2 |  | 0.55 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0002584.2 |  | 0.54 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000632.5 |  | 0.54 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001206.5 |  | 0.43 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001896.4 |  | 0.43 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0002019.3 |  | 0.42 | terpene | tiancilactone A, tiancilactone B, tiancilactone C, tiancilactone D, tiancilactone E, tiancilactone F, tiancilactone G, tiancilactone H | Streptomyces sp. CB03234
BGC0000665.5 |  | 0.42 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001529.5 |  | 0.41 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000640.3 |  | 0.41 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002007.2 |  | 0.55 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0002584.2 |  | 0.54 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000632.5 |  | 0.54 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001206.5 |  | 0.43 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001896.4 |  | 0.43 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0002019.3 |  | 0.42 | terpene | tiancilactone A, tiancilactone B, tiancilactone C, tiancilactone D, tiancilactone E, tiancilactone F, tiancilactone G, tiancilactone H | Streptomyces sp. CB03234
BGC0000665.5 |  | 0.42 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001529.5 |  | 0.41 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000640.3 |  | 0.41 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
CFP59_RS42355: PT_FPPS_like
Domain 1 (44 - 336): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

CFP59_RS42365: T2TS
Domain 1 (271 - 551): Type 2 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.13 out of 29.72
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.37 out of 30.12
Confidence: medium
Additional weak hits (5):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.19 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.69 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.56 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.77 out of 26.85
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.93 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
HPP | Hexaprenyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator

NZ_CP025018.1 - Region 47 - NRPS,T1PKS,lanthipeptide-class-ii,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,498,358 - 10,573,363 nt. (total: 75,006 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
Terpene
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CFP59_RS42970: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CFP59_RS42990: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CFP59_RS43005: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

CFP59_RS43075: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

CFP59_RS43170: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CFP59_RS43195: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: carbamoyltransferase methyltransferase
CFP59_RS43055: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

CFP59_RS43085: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: phosphatase
CFP59_RS43115: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Lyases: cyclase
CFP59_RS43150: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: ligase synthase
CFP59_RS43060: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS43090: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CFP59_RS43095: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS43100: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CFP59_RS43105: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS43110: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS43125: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs
  SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | terpene | NRPS | T1PKS | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  |  |  | 0.84 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  |  |  | 0.82 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  |  |  | 0.81 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  |  |  | 0.79 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  |  | 0.79 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  |  |  | 0.76 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  |  |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  |  |  |  | 0.74 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  |  |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  |  |  |  | 0.72 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lanthipeptide(s) for CFP59_RS43150

CFP59_RS43145
Leader:
MNTTVTAWKNAMYREGLAVEPAHPAGA
Core:
V D L S A D L P D E T G T G A A E T L S T Q P F F D C C G
Core with dehydrations:
V D L Dha A D L P D E Dhb G Dhb G A A E Dhb L Dha Dhb Q P F F D Cys Cys G

#### antiSMASH-DB 4.0 matches for CFP59_RS43145

100.0%
NZ_BDFA01000012.1 and 6 others:
NZ_CP019458.1 Lanthipeptides: BV401_RS04085_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS43145_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS43375_lanthipeptide NZ_CP065050.1 Lanthipeptides: I1A49_RS03785_lanthipeptide NZ_JAALLH010000001.1 Lanthipeptides: SMALB_RS03525_lanthipeptide NZ_LJIW01000001.1 Lanthipeptides: SMF913_RS04065_lanthipeptide
Lanthipeptides: BGB88_RS46105_lanthipeptide
1
V D L S A D L P D E T G T G A A E T L S T Q P F F D C C G
29
V D L S A D L P D E T G T G A A E T L S T Q P F F D C C G
1
V D L S A D L P D E T G T G A A E T L S T Q P F F D C C G
29
48.3%
NZ_CP058693.1:
Lanthipeptides: HYQ63_RS37670_lanthipeptide
16
A E T L S T Q P F F D C C G
29
A E T L S T Q P F F D C C G
1
A E T L S T Q P F F D C C G
14
37.9%
NC_016582.1:
Lanthipeptides: SBI_RS52400_lanthipeptide
18
T L S T Q P F F D C C G
29
T L S T Q P F F C C G
2
T L S T Q P F F Q C C G
13
with 5 more sequence matches
37.9%
NZ_CP097290.1 and 1 other:
NZ_LIWB01000016.1 Lanthipeptides: AMK33_RS42540_lanthipeptide
Lanthipeptides: M4V62_RS43190_lanthipeptide
18
T L S T Q P F F D C C G
29
T L S T Q P F F+C C G
1
T L S T Q P F F N C C G
12
37.9%
NZ_NNBP01000002.1:
Lanthipeptides: CG747_RS46875_lanthipeptide
17
E T L S T Q P F F D C C G
29
+T L S T Q P F F+C C G
1
K T L S T Q P F F N C C G
13
31.0%
NZ_CP072827.1:
Lanthipeptides: J7W19_RS04815_lanthipeptide
11
T G T G A A E T L S T Q P F F D C C
28
+G T A +T+S P F+ C C
1
S G T I A I K T M S-A P F W T C C
17
26.5%
NZ_JACSPO010000013.1 and 1 other:
NZ_JACSPO010000013.1 Lanthipeptides: H9624_RS14885_lanthipeptide
Lanthipeptides: H9624_RS14885_lanthipeptide
1
V D L S A D L P D E T G T G A A E T
18
+ +S A L P D T G A T
15
I A I S A A L P D F C P T G A C T T
32
19.0%
NC_019757.1:
Lanthipeptides: allorf_3744133_3744366_lanthipeptide
10
E T G T G A A E T L S T Q
22
E T G T + +T L+T Q
25
E T G T K S R Q T L N T Q
37

#### MIBiG 4.0 matches for CFP59_RS43145

13.7%
BGC0002120.3 (NQE92413.1):
Lanthipeptide: nocathioamide A
9
D E T G T G A A E T L S T Q P F F D C C G
29
D E+ A A T C C
30
D E S S R P A A P A C H T L S S L P C C A
50
allorf_10559447_10559644
Leader:
MHSNLLGPDGRGRGGIGEWKTLCDIAGA
Core:
L I R E C T L P V A S M N A L W N N Y R L S I D W S P A R S G E R G E R R
Core with dehydrations:
L I R E Cys Dhb L P V A Dha M N A L W N N Y R L Dha I D W Dha P A R Dha G E R G E R R

#### antiSMASH-DB 4.0 matches for allorf_10559447_10559644

100.0%
NZ_BDFA01000012.1 and 5 others:
NZ_CP019458.1 Lanthipeptides: allorf_00977807_00978004_lanthipeptide NZ_CP025018.1 Lanthipeptides: allorf_10559447_10559644_lanthipeptide NZ_CP029823.1 Lanthipeptides: allorf_10618326_10618523_lanthipeptide NZ_CP065050.1 Lanthipeptides: allorf_00914907_00915104_lanthipeptide NZ_LJIW01000001.1 Lanthipeptides: allorf_0970850_0971047_lanthipeptide
Lanthipeptides: allorf_122316_122513_lanthipeptide
1
L I R E C T L P V A S M N A L W N N Y R L S I D W S P A R S G E R G E R R
37
L I R E C T L P V A S M N A L W N N Y R L S I D W S P A R S G E R G E R R
1
L I R E C T L P V A S M N A L W N N Y R L S I D W S P A R S G E R G E R R
37
97.3%
NZ_JAALLH010000001.1:
Lanthipeptides: allorf_0868516_0868713_lanthipeptide
1
L I R E C T L P V A S M N A L W N N Y R L S I D W S P A R S G E R G E R R
37
L I R E C T L P V A S M N A L W N N Y R L S D W S P A R S G E R G E R R
1
L I R E C T L P V A S M N A L W N N Y R L S T D W S P A R S G E R G E R R
37
21.6%
NZ_JAENHX010000011.1:
Lanthipeptides: JIN86_RS20375_lanthipeptide
9
V A S M N A L W N N Y R L S I D W S P A R S G
31
+A+ L N N Y ++ W S +G
11
I A N A V G L G N N Y G M A C T W S A E C N G
33
with 2 more sequence matches
18.4%
NC_017327.1 and 1 other:
NZ_CP021217.1 Lanthipeptides: allorf_1158639_1158842_lanthipeptide
Lanthipeptides: allorf_0125265_0125468_lanthipeptide
20
R L S I D W S P A R S G E R G E R
36
R ++ S P++ R G E R
7
R P A V G L S P S K P Q G R G E R
23
16.2%
NZ_RBZW01000021.1:
Lassopeptides: D8Y22_RS07925_lassopeptide
23
I D W S P A R S G E R G E R R
37
+D + +G R G R R
7
V D G N S G T T G N R G H R R
21
allorf_10559500_10559625
Leader:
MENVVRYRGSAHPGM
Core:
H A T G R F H E C A V E Q L P P L Y R L V T C E K W
Core with dehydrations:
H A Dhb G R F H E Cys A V E Q L P P L Y R L V Dhb Cys E K W

#### antiSMASH-DB 4.0 matches for allorf_10559500_10559625

100.0%
NZ_BDFA01000012.1 and 5 others:
NZ_CP025018.1 Lanthipeptides: allorf_10559500_10559625_lanthipeptide NZ_CP029823.1 Lanthipeptides: allorf_10618379_10618504_lanthipeptide NZ_CP065050.1 Lanthipeptides: allorf_00914926_00915051_lanthipeptide NZ_JAALLH010000001.1 Lanthipeptides: allorf_0868535_0868660_lanthipeptide NZ_LJIW01000001.1 Lanthipeptides: allorf_0970869_0970994_lanthipeptide
Lanthipeptides: allorf_122369_122494_lanthipeptide
1
H A T G R F H E C A V E Q L P P L Y R L V T C E K W
26
H A T G R F H E C A V E Q L P P L Y R L V T C E K W
1
H A T G R F H E C A V E Q L P P L Y R L V T C E K W
26
96.2%
NZ_CP019458.1:
Lanthipeptides: allorf_00977826_00977951_lanthipeptide
1
H A T G R F H E C A V E Q L P P L Y R L V T C E K W
26
H A T G R F H E C V E Q L P P L Y R L V T C E K W
1
H A T G R F H E C T V E Q L P P L Y R L V T C E K W
26
20.5%
NZ_KZ819178.1 and 1 other:
NZ_KZ819178.1 Lanthipeptides: allorf_4075416_4075610_lanthipeptide
Lanthipeptides: allorf_4075416_4075610_lanthipeptide
3
T G R F H E C A V E Q L P P L Y R L V T C
23
+G R F H A V P L C
10
S G R F H R P A V R P P S P L L L R P R C
30
with 2 more sequence matches
17.9%
NZ_CP039292.1 and 1 other:
NZ_CP039292.1 Lanthipeptides: allorf_0076338_0076511_lanthipeptide
Lanthipeptides: allorf_0076338_0076511_lanthipeptide
1
H A T G R F H E C A V E Q L P P L Y R
19
+G R +C + P Y+
6
E G S G R V S D C L C K G C G P T Y K
24
16.7%
NZ_KB217478.1:
Lanthipeptides: allorf_3684331_3684489_lanthipeptide
13
Q L P P L Y R L V T C
23
Q+P L Y L+ C
16
Q V P T L Y T L I N C
26
allorf_10559568_10559699
Leader:
MRCGTTTASLSTGHLREVVSA
Core:
E S G G R D S V P V R V N V P M L C G D R P
Core with dehydrations:
E Dha G G R D Dha V P V R V N V P M L Cys G D R P

#### antiSMASH-DB 4.0 matches for allorf_10559568_10559699

100.0%
NZ_BDFA01000012.1 and 6 others:
NZ_CP019458.1 Lanthipeptides: allorf_00977752_00977883_lanthipeptide NZ_CP025018.1 Lanthipeptides: allorf_10559568_10559699_lanthipeptide NZ_CP029823.1 Lanthipeptides: allorf_10618447_10618578_lanthipeptide NZ_CP065050.1 Lanthipeptides: allorf_00914852_00914983_lanthipeptide NZ_JAALLH010000001.1 Lanthipeptides: allorf_0868461_0868592_lanthipeptide NZ_LJIW01000001.1 Lanthipeptides: allorf_0970795_0970926_lanthipeptide
Lanthipeptides: allorf_122437_122568_lanthipeptide
1
E S G G R D S V P V R V N V P M L C G D R P
22
E S G G R D S V P V R V N V P M L C G D R P
1
E S G G R D S V P V R V N V P M L C G D R P
22

#### MIBiG 4.0 matches for allorf_10559568_10559699

18.2%
BGC0000477.3 (ACA04491.1 (core 2)):
Cyanobactin: patellin 2 or patellin 3
13
N V P M L C
18
V P L C
1
T V P T L C
6

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
triterpene |  | squalene | C30 | acyclic | none
triterpene |  | PSPP | C30 | acyclic | PP
triterpene | C30 carotenoid | diapophytoene | C30 | acyclic | none
tetraterpene | C40 carotenoid | phytoene | C40 | acyclic | none
triterpene |  | hydroxysqualene | C30 | acyclic | OH

Genes with terpene domains:
CFP59_RS42980: PT_phytoene_like
Domain 1 (18 - 282): Prenyltransferase; Phytoene synthase like
Subtype: unknown

Reactions:
  FPP → squalene
  FPP → PSPP
  FPP → diapophytoene
  GGPP → phytoene
  PSPP → hydroxysqualene

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47
Confidence: medium
Additional weak hits (15):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.34 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.30 out of 32.74
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.04 out of 19.26
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.20 out of 21.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.60 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.76 out of 31.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.29 out of 20.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.27 out of 31.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.52 out of 24.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.27 out of 25.88
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

CFP59_RS43145 - Class II
  Cleavage pHMM score: -6.00
  RODEO score: 0
  Monoisotopic mass: 2851.3 Da
  Molecular weight: 2853.0 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2871.0 Da N = 1
    2889.1 Da N = 2
    2907.1 Da N = 3
    2925.1 Da N = 4
allorf_10559447_10559644 - Class II
  Cleavage pHMM score: -1.80
  RODEO score: 0
  Monoisotopic mass: 4226.2 Da
  Molecular weight: 4228.8 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4246.8 Da N = 1
    4264.8 Da N = 2
    4282.8 Da N = 3
    4300.8 Da N = 4
allorf_10559500_10559625 - Class II
  Cleavage pHMM score: -5.60
  RODEO score: 0
  Monoisotopic mass: 3046.5 Da
  Molecular weight: 3048.5 Da
  Number of bridges: 2
allorf_10559568_10559699 - Class II
  Cleavage pHMM score: -5.90
  RODEO score: 0
  Monoisotopic mass: 2303.1 Da
  Molecular weight: 2304.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2322.6 Da N = 1

Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 72, location 10498357 - 10573363:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe) + (ohmal) + (Pro) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 74, location 10508110 - 10573027:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe) + (ohmal) + (Pro) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS43060: X
AMP-binding (497..889): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    VGLGFDVSLQQPDVISGGEFNCYGPTECTVNTTV
  Nearest Stachelhaus code(s):
    Cap DPQDIGIVNK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

CFP59_RS43095: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (477..878): Pro
nrpys: Pro

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pro (Pro)

Stachelhaus prediction details:
  Stachelhaus sequence:
    MWEVFDVSAQETYMMTAGEENQYGSSECQVVSSL
  Nearest Stachelhaus code(s):
    Pro DVQFMAQVVK (62% 8Å match)
  Stachelhaus code match:
    90% (moderate)

CFP59_RS43100: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (606..997): Leu
nrpys: Leu

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    VASVFDASVWEMYLITGGDFVAYGPTEGTIVQTW
  Nearest Stachelhaus code(s):
    Leu DAWIIGAIVK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

CFP59_RS43105: mal
PKS_AT (568..859): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 66.7%
  inactive: 58.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 99.0
  inactive: 49.3
  Methylmalonyl-CoA: 43.0
  Methoxymalonyl-CoA: 40.5
  Isobutyryl-CoA: 32.2
  Ethylmalonyl-CoA: 20.3
  Propionyl-CoA: 18.1
  Benzoyl-CoA: 11.7
  fatty_acid: 11.6
  2-Methylbutyryl-CoA: 10.5
  CHC-CoA: 5.6
  trans-1,2-CPDA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CFP59_RS43110: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (481..879): Phe
nrpys: Phe

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    Unpolar aromatic ring (Phe, Trp)
  Single AA prediction:
    phe (Phe)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASVWEMTAVAAGEVNAYGPTETTVAATA
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
PP | Diphosphate
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 48 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,607,706 - 10,650,444 nt. (total: 42,739 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
CFP59_RS43410: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

CFP59_RS43515: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CFP59_RS43540: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: acetyltransferase aminotransferase methyltransferase
CFP59_RS43440: methyltransferase

smcogs
  SMCOG1248: methyltransferase

CFP59_RS43480: aminotransferase

smcogs
  SMCOG1019: aminotransferase

CFP59_RS43495: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase
CFP59_RS43445: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: dehydratase
CFP59_RS43475: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
CFP59_RS43470: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002277.2 |  | 0.65 | NRPS | atromentin | Suillus grevillei
BGC0002274.2 |  | 0.64 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002193.2 |  | 0.64 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.60 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000340.5 |  | 0.53 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0000820.5 |  | 0.49 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0001206.5 |  | 0.47 | other (other) | indolmycin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002277.2 |  | 0.65 | NRPS | atromentin | Suillus grevillei
BGC0002274.2 |  | 0.64 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002193.2 |  | 0.64 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.60 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000340.5 |  | 0.53 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0000820.5 |  | 0.49 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0001206.5 |  | 0.47 | other (other) | indolmycin | Streptomyces griseus subsp. griseus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (5):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.46 out of 20.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.22 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 76, location 10607705 - 10650444:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS43470: X
AMP-binding (29..426): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    glu,gln (Glu, Gln)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    AGKIHIAAIEALFTISGGEVPAFGMTETCAGSVF
  Nearest Stachelhaus code(s):
    Ppa VALFIGAAGK (71% 8Å match)
    4-ohPpa IAAFLGAAGK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 49 - NAPAA
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,937,152 - 10,971,414 nt. (total: 34,263 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase reductase
CFP59_RS45015: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CFP59_RS45045: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: methyltransferase
CFP59_RS44945: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CFP59_RS44985: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: amidase hydrolase
CFP59_RS45000: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

CFP59_RS45025: amidase

smcogs
  SMCOG1105: amidase

Lyases: dehydratase
CFP59_RS44915: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
CFP59_RS52280: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001833.4 |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.59 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001833.4 |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.59 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.63 out of 18.46
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.54 out of 18.46
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
Additional weak hits (6):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.24 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.67 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.13 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.15 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 77, location 10937151 - 10971414:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS52280: X
AMP-binding (60..455): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FVAMFDFSVEEVCCLVSGELNVYGPTEATVTATW
  Nearest Stachelhaus code(s):
    Ile or Val DFLCLGVVIK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP025018.1 - Region 50 - T1PKS,T3PKS,nucleoside
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 11,203,965 - 11,407,643 nt. (total: 203,679 nt) Show pHMM detection rules used
nucleoside: (LipM or LipV or LipU or TunD or pur6 or pur10 or nikJ or nikO or truD)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
CFP59_RS46250: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CFP59_RS46260: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CFP59_RS46340: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS46405: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS46470: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS46500: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CFP59_RS46540: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CFP59_RS46655: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase methyltransferase
CFP59_RS46185: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CFP59_RS46195: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: deacetylase peptidase phosphatase
CFP59_RS46175: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

CFP59_RS46265: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

CFP59_RS46520: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

Lyases: decarboxylase
CFP59_RS46275: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: ligase synthase
CFP59_RS46280: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS46285: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

CFP59_RS46290: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS46310: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS46335: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS46355: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS46465: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CFP59_RS46565: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

CFP59_RS51545: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CFP59_RS52035: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | nucleoside | T1PKS | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001454.5 |  |  |  | 0.64 | other (other) | germicidin | Streptomyces argillaceus
BGC0001276.3 |  |  |  | 0.47 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  |  | 0.47 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  | 0.46 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  | 0.45 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  |  |  | 0.39 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000068.5 |  |  |  | 0.35 | PKS | geldanamycin | Streptomyces hygroscopicus
BGC0001537.5 |  |  |  | 0.35 | PKS | butyrolactol A | Streptomyces sp. NBRC 110030
BGC0000847.4 |  |  |  | 0.33 | other (non-nrp beta-lactam) | thienamycin | Streptomyces cattleya
BGC0000147.5 |  |  |  | 0.33 | PKS | soraphen A | Sorangium cellulosum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.86 | other (other) | germicidin | Streptomyces argillaceus
BGC0001276.3 |  | 0.77 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.71 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000067.5 |  | 0.66 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000018.5 |  | 0.64 | PKS | angolamycin | Streptomyces eurythermus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.00 out of 23.79
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.84 out of 30.12
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.03 out of 26.85
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
Additional weak hits (38):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.18 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.92 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.94 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.18 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.15 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.11 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.78 out of 21.55
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.39 out of 25.88
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.03 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.52 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.84 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.61 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.04 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.63 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.61 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.59 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.18 out of 25.75
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.21 out of 26.85
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.13 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.17 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.32 out of 29.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.92 out of 36.54
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.16 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.62 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.07 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.55 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.98 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.78 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.81 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.72 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.04 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.07 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.56 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 78, location 11203964 - 11407643:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (emal - Me-ohmal - ohmal - ohmal) + (Me-ccmal - Me-ccmal) + (Me-mal - ccmal - pk) + (Me-mal - Me-ohmal - ohmal - Me-mal) + (Me-ohmal - pk - ccmal) + (pk - Me-redmal - Me-ohmal - Me-ccmal) + (pk) + (Me-ccmal - ohmal) + (Me-redmal - ccmal) + (pk)
Non-colinear ordering:
  CFP59_RS52035 + CFP59_RS46465 + CFP59_RS46280 + CFP59_RS46305 + CFP59_RS46310 + CFP59_RS46335 + CFP59_RS46340 + CFP59_RS46355 + CFP59_RS51545 + CFP59_RS46405

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 80, location 11211978 - 11382762:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (emal - Me-ohmal - ohmal - ohmal) + (Me-ccmal - Me-ccmal) + (Me-mal - ccmal - pk) + (Me-mal - Me-ohmal - ohmal - Me-mal) + (Me-ohmal - pk - ccmal) + (pk - Me-redmal - Me-ohmal - Me-ccmal) + (pk) + (Me-ccmal - ohmal) + (Me-redmal - ccmal) + (pk)
Non-colinear ordering:
  CFP59_RS52035 + CFP59_RS46465 + CFP59_RS46280 + CFP59_RS46305 + CFP59_RS46310 + CFP59_RS46335 + CFP59_RS46340 + CFP59_RS46355 + CFP59_RS51545 + CFP59_RS46405

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS46280: mmal - mal - pk
PKS_AT (554..852): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.3
  Ethylmalonyl-CoA: 203.8
  Methoxymalonyl-CoA: 176.5
  2-Methylbutyryl-CoA: 134.8
  trans-1,2-CPDA: 126.3
  Propionyl-CoA: 112.5
  CHC-CoA: 95.7
  Isobutyryl-CoA: 85.6
  Malonyl-CoA: 80.1
  Benzoyl-CoA: 63.7
  Acetyl-CoA: 40.8
  3-Methylbutyryl-CoA: 37.9
  fatty_acid: 28.2
  inactive: 18.5

PKS_AT (1570..1865): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 75.0%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.1
  inactive: 94.6
  Methoxymalonyl-CoA: 70.0
  Methylmalonyl-CoA: 66.3
  Isobutyryl-CoA: 38.8
  Ethylmalonyl-CoA: 37.8
  Propionyl-CoA: 28.8
  CHC-CoA: 24.2
  Benzoyl-CoA: 21.7
  Acetyl-CoA: 20.8
  fatty_acid: 19.2
  trans-1,2-CPDA: 11.8
  2-Methylbutyryl-CoA: 11.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3334..3634): pk
ATSignature: Methoxymalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 91.7%
  Methylmalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 185.7
  Ethylmalonyl-CoA: 184.8
  Methoxymalonyl-CoA: 180.4
  2-Methylbutyryl-CoA: 127.4
  Malonyl-CoA: 99.0
  trans-1,2-CPDA: 91.9
  Propionyl-CoA: 89.7
  Isobutyryl-CoA: 87.9
  CHC-CoA: 75.2
  Benzoyl-CoA: 51.5
  Acetyl-CoA: 50.2
  3-Methylbutyryl-CoA: 44.7
  inactive: 30.4
  fatty_acid: 28.1

CFP59_RS46290: X
AMP-binding (13..422): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    NVAS--SSGSAVTITYVGSLQLYGTTEISGISML
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CFP59_RS46305: mmal - mmal - mal - mmal
PKS_AT (532..810): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 87.5%
  Malonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 198.4
  Ethylmalonyl-CoA: 186.3
  Methoxymalonyl-CoA: 167.6
  2-Methylbutyryl-CoA: 140.4
  Malonyl-CoA: 104.7
  Propionyl-CoA: 97.7
  trans-1,2-CPDA: 91.7
  CHC-CoA: 82.4
  Isobutyryl-CoA: 81.3
  Benzoyl-CoA: 53.0
  Acetyl-CoA: 45.6
  inactive: 34.9
  fatty_acid: 26.5
  3-Methylbutyryl-CoA: 14.6

PKS_AT (1508..1805): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.6
  Ethylmalonyl-CoA: 208.5
  Methoxymalonyl-CoA: 173.6
  2-Methylbutyryl-CoA: 147.8
  Propionyl-CoA: 113.5
  trans-1,2-CPDA: 111.0
  CHC-CoA: 105.4
  Malonyl-CoA: 100.1
  Benzoyl-CoA: 83.3
  Isobutyryl-CoA: 76.8
  Acetyl-CoA: 64.3
  3-Methylbutyryl-CoA: 33.8
  fatty_acid: 33.4
  inactive: 21.4

PKS_AT (3026..3318): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 195.8
  inactive: 76.0
  Methoxymalonyl-CoA: 69.8
  Methylmalonyl-CoA: 60.5
  Isobutyryl-CoA: 31.2
  Propionyl-CoA: 28.4
  Acetyl-CoA: 20.9
  Benzoyl-CoA: 18.9
  Ethylmalonyl-CoA: 17.9
  2-Methylbutyryl-CoA: 16.6
  CHC-CoA: 14.2
  fatty_acid: 11.8
  trans-1,2-CPDA: 8.5
  3-Methylbutyryl-CoA: 6.1

PKS_AT (4490..4785): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 206.3
  Ethylmalonyl-CoA: 188.1
  Methoxymalonyl-CoA: 178.4
  2-Methylbutyryl-CoA: 113.7
  trans-1,2-CPDA: 112.7
  Malonyl-CoA: 107.4
  CHC-CoA: 105.7
  Isobutyryl-CoA: 97.5
  Propionyl-CoA: 94.4
  Benzoyl-CoA: 87.1
  Acetyl-CoA: 59.6
  3-Methylbutyryl-CoA: 48.5
  inactive: 40.3
  fatty_acid: 36.1

CFP59_RS46310: mmal - pk - mal
PKS_AT (560..842): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.1
  Ethylmalonyl-CoA: 205.3
  Methoxymalonyl-CoA: 168.7
  2-Methylbutyryl-CoA: 131.8
  trans-1,2-CPDA: 128.7
  Propionyl-CoA: 102.8
  CHC-CoA: 91.7
  Malonyl-CoA: 90.4
  Isobutyryl-CoA: 52.6
  Benzoyl-CoA: 51.0
  Acetyl-CoA: 32.9
  3-Methylbutyryl-CoA: 27.0
  inactive: 26.6
  fatty_acid: 23.1

PKS_AT (2066..2358): pk
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 83.3%
  Ethylmalonyl-CoA: 79.2%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 181.2
  Methylmalonyl-CoA: 180.0
  Methoxymalonyl-CoA: 167.5
  2-Methylbutyryl-CoA: 136.3
  trans-1,2-CPDA: 104.5
  Propionyl-CoA: 102.5
  CHC-CoA: 82.4
  Malonyl-CoA: 82.1
  Isobutyryl-CoA: 53.1
  Acetyl-CoA: 39.2
  Benzoyl-CoA: 36.5
  3-Methylbutyryl-CoA: 32.2
  inactive: 18.2
  fatty_acid: 16.5

PKS_AT (3523..3820): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 209.5
  inactive: 106.6
  Methoxymalonyl-CoA: 67.0
  Methylmalonyl-CoA: 57.4
  Propionyl-CoA: 33.0
  Ethylmalonyl-CoA: 25.2
  Isobutyryl-CoA: 23.4
  Acetyl-CoA: 23.0
  2-Methylbutyryl-CoA: 21.1
  CHC-CoA: 12.7
  Benzoyl-CoA: 11.7
  fatty_acid: 9.4
  trans-1,2-CPDA: 9.1
  3-Methylbutyryl-CoA: 0.0

CFP59_RS46335: pk - mmal - mmal - mmal
PKS_AT (574..855): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 219.5
  Methylmalonyl-CoA: 218.3
  Methoxymalonyl-CoA: 182.7
  2-Methylbutyryl-CoA: 145.4
  trans-1,2-CPDA: 128.6
  Malonyl-CoA: 106.8
  CHC-CoA: 105.4
  Propionyl-CoA: 103.1
  Isobutyryl-CoA: 79.3
  Benzoyl-CoA: 65.1
  Acetyl-CoA: 37.2
  fatty_acid: 26.7
  3-Methylbutyryl-CoA: 24.6
  inactive: 24.0

PKS_AT (2230..2513): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.8
  Ethylmalonyl-CoA: 204.9
  Methoxymalonyl-CoA: 168.5
  2-Methylbutyryl-CoA: 143.7
  trans-1,2-CPDA: 124.4
  Propionyl-CoA: 108.6
  Malonyl-CoA: 92.1
  CHC-CoA: 91.4
  Isobutyryl-CoA: 65.9
  Benzoyl-CoA: 61.1
  Acetyl-CoA: 37.8
  3-Methylbutyryl-CoA: 32.2
  fatty_acid: 27.7
  inactive: 20.7

PKS_AT (4195..4483): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 211.4
  Ethylmalonyl-CoA: 207.9
  Methoxymalonyl-CoA: 167.0
  2-Methylbutyryl-CoA: 132.0
  trans-1,2-CPDA: 129.3
  Propionyl-CoA: 103.2
  CHC-CoA: 92.9
  Malonyl-CoA: 85.3
  Isobutyryl-CoA: 64.9
  Benzoyl-CoA: 55.3
  Acetyl-CoA: 35.3
  3-Methylbutyryl-CoA: 28.3
  inactive: 25.4
  fatty_acid: 20.7

PKS_AT (5646..5928): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 216.6
  Ethylmalonyl-CoA: 213.6
  Methoxymalonyl-CoA: 175.1
  trans-1,2-CPDA: 139.2
  2-Methylbutyryl-CoA: 133.9
  Propionyl-CoA: 106.4
  CHC-CoA: 97.3
  Malonyl-CoA: 90.6
  Isobutyryl-CoA: 65.2
  Benzoyl-CoA: 53.4
  Acetyl-CoA: 34.3
  fatty_acid: 29.1
  inactive: 26.2
  3-Methylbutyryl-CoA: 25.8

CFP59_RS46340: pk
PKS_AT (565..845): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 221.6
  Methylmalonyl-CoA: 216.8
  Methoxymalonyl-CoA: 179.4
  2-Methylbutyryl-CoA: 144.3
  trans-1,2-CPDA: 139.9
  Propionyl-CoA: 114.9
  CHC-CoA: 110.3
  Malonyl-CoA: 102.2
  Isobutyryl-CoA: 78.6
  Benzoyl-CoA: 60.5
  Acetyl-CoA: 43.8
  inactive: 26.9
  3-Methylbutyryl-CoA: 26.8
  fatty_acid: 24.8

CFP59_RS46345: pk
PKS_AT (26..248): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

Prediction, score:
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Malonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

CFP59_RS46355: mmal - mal
PKS_AT (557..837): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.6
  Ethylmalonyl-CoA: 200.9
  Methoxymalonyl-CoA: 170.3
  2-Methylbutyryl-CoA: 137.1
  trans-1,2-CPDA: 133.5
  Propionyl-CoA: 107.8
  Malonyl-CoA: 93.7
  CHC-CoA: 81.5
  Isobutyryl-CoA: 56.5
  Benzoyl-CoA: 48.1
  3-Methylbutyryl-CoA: 42.6
  Acetyl-CoA: 41.8
  inactive: 33.7
  fatty_acid: 16.3

PKS_AT (2238..2498): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 163.9
  inactive: 72.9
  Methoxymalonyl-CoA: 63.1
  Methylmalonyl-CoA: 45.3
  Isobutyryl-CoA: 23.9
  Acetyl-CoA: 23.5
  fatty_acid: 20.2
  Propionyl-CoA: 19.5
  CHC-CoA: 16.2
  Benzoyl-CoA: 15.5
  Ethylmalonyl-CoA: 13.9
  2-Methylbutyryl-CoA: 7.8
  trans-1,2-CPDA: 6.7
  3-Methylbutyryl-CoA: 0.0

CFP59_RS51545: mmal - mal
PKS_AT (571..857): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.8
  Ethylmalonyl-CoA: 198.1
  Methoxymalonyl-CoA: 176.8
  2-Methylbutyryl-CoA: 144.6
  trans-1,2-CPDA: 122.2
  CHC-CoA: 112.7
  Propionyl-CoA: 112.4
  Malonyl-CoA: 89.0
  Isobutyryl-CoA: 75.6
  Benzoyl-CoA: 56.9
  Acetyl-CoA: 29.9
  inactive: 24.0
  3-Methylbutyryl-CoA: 23.1
  fatty_acid: 22.4

PKS_AT (2556..2821): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 175.9
  inactive: 83.7
  Methoxymalonyl-CoA: 78.5
  Methylmalonyl-CoA: 59.9
  CHC-CoA: 22.6
  Ethylmalonyl-CoA: 22.2
  Isobutyryl-CoA: 18.6
  Benzoyl-CoA: 16.8
  trans-1,2-CPDA: 16.4
  fatty_acid: 16.2
  Acetyl-CoA: 16.0
  Propionyl-CoA: 15.8
  2-Methylbutyryl-CoA: 10.4
  3-Methylbutyryl-CoA: 0.0

CFP59_RS46405: pk
PKS_AT (557..852): pk
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 185.3
  Methylmalonyl-CoA: 181.2
  Methoxymalonyl-CoA: 157.2
  2-Methylbutyryl-CoA: 114.8
  trans-1,2-CPDA: 95.3
  Propionyl-CoA: 91.5
  CHC-CoA: 86.9
  Malonyl-CoA: 77.7
  Isobutyryl-CoA: 70.5
  3-Methylbutyryl-CoA: 52.3
  Acetyl-CoA: 49.7
  Benzoyl-CoA: 45.4
  inactive: 24.6
  fatty_acid: 11.6

CFP59_RS52035: emal - mmal - mal - mal
PKS_AT (97..394): emal
ATSignature: Isobutyryl-CoA

Top 3 matches:
  Isobutyryl-CoA: 83.3%
  2-Methylbutyryl-CoA: 79.2%
  Malonyl-CoA: 75.0%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 157.8
  Methylmalonyl-CoA: 156.8
  2-Methylbutyryl-CoA: 156.4
  Methoxymalonyl-CoA: 124.7
  Propionyl-CoA: 116.0
  CHC-CoA: 96.6
  trans-1,2-CPDA: 90.2
  Malonyl-CoA: 70.5
  Isobutyryl-CoA: 66.6
  3-Methylbutyryl-CoA: 37.3
  Benzoyl-CoA: 34.0
  Acetyl-CoA: 27.7
  inactive: 25.5
  fatty_acid: 19.5

PKS_AT (1097..1395): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.6
  Ethylmalonyl-CoA: 194.6
  Methoxymalonyl-CoA: 166.7
  2-Methylbutyryl-CoA: 141.6
  trans-1,2-CPDA: 117.9
  CHC-CoA: 108.1
  Malonyl-CoA: 99.9
  Propionyl-CoA: 99.6
  Isobutyryl-CoA: 74.6
  Benzoyl-CoA: 69.1
  Acetyl-CoA: 47.7
  3-Methylbutyryl-CoA: 40.0
  inactive: 35.4
  fatty_acid: 25.0

PKS_AT (2622..2912): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 197.7
  inactive: 90.9
  Methoxymalonyl-CoA: 69.5
  Methylmalonyl-CoA: 59.1
  Isobutyryl-CoA: 36.6
  Ethylmalonyl-CoA: 23.0
  Acetyl-CoA: 18.5
  Benzoyl-CoA: 17.7
  Propionyl-CoA: 17.3
  fatty_acid: 15.6
  CHC-CoA: 14.2
  2-Methylbutyryl-CoA: 8.8
  trans-1,2-CPDA: 7.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4085..4357): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 70.8%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 164.8
  inactive: 81.7
  Methoxymalonyl-CoA: 78.9
  Methylmalonyl-CoA: 68.4
  Propionyl-CoA: 38.3
  Ethylmalonyl-CoA: 33.4
  CHC-CoA: 30.9
  fatty_acid: 28.8
  Isobutyryl-CoA: 27.5
  Acetyl-CoA: 21.3
  2-Methylbutyryl-CoA: 21.3
  trans-1,2-CPDA: 19.9
  Benzoyl-CoA: 19.0
  3-Methylbutyryl-CoA: 16.1

CFP59_RS46465: mmal - mmal
PKS_AT (555..837): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 212.1
  Ethylmalonyl-CoA: 208.4
  Methoxymalonyl-CoA: 176.8
  2-Methylbutyryl-CoA: 146.4
  trans-1,2-CPDA: 126.6
  Propionyl-CoA: 111.2
  Malonyl-CoA: 97.9
  CHC-CoA: 89.4
  Isobutyryl-CoA: 62.5
  Benzoyl-CoA: 50.2
  3-Methylbutyryl-CoA: 31.6
  inactive: 29.9
  Acetyl-CoA: 27.9
  fatty_acid: 17.9

PKS_AT (2241..2530): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 201.0
  Ethylmalonyl-CoA: 186.7
  Methoxymalonyl-CoA: 170.7
  2-Methylbutyryl-CoA: 146.0
  trans-1,2-CPDA: 121.4
  Propionyl-CoA: 108.4
  CHC-CoA: 99.4
  Malonyl-CoA: 93.5
  Isobutyryl-CoA: 66.4
  Benzoyl-CoA: 59.9
  3-Methylbutyryl-CoA: 40.2
  Acetyl-CoA: 39.4
  fatty_acid: 24.9
  inactive: 21.4

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
OsdR | Development and stress management regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP025018.1 - Region 51 - NRP-metallophore,NRPS,betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
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Location: 11,421,156 - 11,497,318 nt. (total: 76,163 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
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Automatically zoom to filtered/selected features

Identifier | Product | Length | Function | Sequence | NCBI Blast | Filter details
--- | --- | --- | --- | --- | --- | ---
|  | NT | AA |  | NT | AA |  |

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CFP59_RS46850: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CFP59_RS46855: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CFP59_RS46975: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: aminotransferase sulfhydrylase
CFP59_RS46820: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

CFP59_RS47135: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase
CFP59_RS46980: thioesterase

smcogs
  SMCOG1004: thioesterase

Isomerases: isomerase
CFP59_RS47000: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
CFP59_RS46865: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS46950: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CFP59_RS46955: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CFP59_RS46960: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CFP59_RS47010: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

CFP59_RS47020: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

CFP59_RS47045: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

CFP59_RS47070: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | betalactone | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000324.5 |  |  |  | 1.24 | NRPS | coelibactin | Streptomyces coelicolor A3(2)
BGC0001641.4 |  |  |  | 0.82 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001250.4 |  |  |  | 0.80 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  |  | 0.80 | NRPS | epichloenin A | Epichloe festucae
BGC0002276.2 |  |  |  | 0.69 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001164.3 |  |  |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001833.4 |  |  |  | 0.61 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  | 0.60 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000324.5 |  | 0.83 | NRPS | coelibactin | Streptomyces coelicolor A3(2)
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000357.5 |  | 0.63 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001133.4 |  | 0.63 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 25.86 out of 28.19
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.01 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.67 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.21 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.85 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.69 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.49 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.73 out of 28.19
Confidence: medium
Additional weak hits (35):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.80 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.69 out of 33.14
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.32 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.26 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.99 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.46 out of 23.43
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.03 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.49 out of 27.78
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.89 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.46 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.71 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.21 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.05 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.76 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.90 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.96 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.73 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.03 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.39 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.87 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.64 out of 20.97
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.13 out of 24.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.51 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.00 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.32 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.06 out of 23.43
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.93 out of 24.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.56 out of 35.63
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.29 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 82, location 11421155 - 11497318:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - Cys) + (Me-Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 84, location 11433913 - 11497318:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - Cys) + (Me-Cys)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CFP59_RS46865: X
AMP-binding (33..428): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    MAYAHAAGLA-PSGWYATGSQIYGQTESAGIGTV
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CFP59_RS46950: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (31..448): diOH-Bz
nrpys: diOH-Bz

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
  Small clusters prediction:
    Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
  Single AA prediction:
    dhb (diOH-Bz)

Stachelhaus prediction details:
  Stachelhaus sequence:
    NASLFTLSCPGGSLQVGGAQQVFGMAEGLINLTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPSQGVVNK (82% 8Å match)
    diOH-Bz or Sal TLPAQGVIAK (79% 8Å match)
  Stachelhaus code match:
    80% (moderate)

CFP59_RS46955: Thr - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (567..962): Thr
nrpys: Thr

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    arg (Arg)
  Single AA prediction:
    arg (Arg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAMSFDLATWDTQCLLGGDVALGGMTEAAVHSTV
  Nearest Stachelhaus code(s):
    Thr DLWQLGLVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1620..2023): Cys
nrpys: Cys

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNTLISGDVALGGATEAAIWSNT
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

CFP59_RS46960: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (545..942): Cys
nrpys: Cys

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDVAFDLSVYDGNSLISGDISLGGATEGSIWSIA
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ZuR variant 1 | Zinc-responsive repressor