Select genomic region:
Overview
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### Identified secondary metabolite regions using strictness 'relaxed'

NC_013947.1 (Stackebrandtia nassauensis DSM 44728)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | T3PKS,NRPS,T1PKS | 127,865 | 226,181 | Low | loseolamycin A1/loseolamycin A2 | PKS
Region 2 | lanthipeptide-class-iii | 545,473 | 568,034 | Medium | catenulipeptin | ribosomal:RiPP:Lanthipeptide
Region 3 | lanthipeptide-class-iv | 619,322 | 641,415 |  |
Region 4 | terpene-precursor | 796,978 | 818,018 |  |
Region 5 | terpene | 1,190,588 | 1,212,897 | High | geosmin | terpene:Sesquiterpene
Region 6 | prodigiosin | 1,220,758 | 1,250,320 |
Region 7 | terpene | 2,099,818 | 2,129,308 |  |
Region 8 | redox-cofactor | 2,309,711 | 2,331,850 | Low | lankacidin C | NRPS:Type I+PKS
Region 9 | lanthipeptide-class-ii | 3,678,950 | 3,702,159 |
Region 10 | terpene | 3,744,170 | 3,764,955 |  |
Region 11 | lanthipeptide-class-i | 3,817,203 | 3,841,317 |
Region 12 | RiPP-like | 3,862,489 | 3,872,842 |
Region 13 | NI-siderophore | 3,963,971 | 3,995,332 |  |
Region 14 | NRPS,T1PKS | 4,302,622 | 4,350,615 |  |
Region 15 | hydrogen-cyanide,T1PKS | 4,372,230 | 4,443,056 |  |
Region 16 | lassopeptide | 4,526,579 | 4,549,108 |
Region 17 | NRP-metallophore,NRPS | 4,794,873 | 4,844,603 | Medium | griseobactin | NRPS:Type I
Region 18 | terpene-precursor | 5,327,596 | 5,348,669 |
Region 19 | lanthipeptide-class-i | 5,738,774 | 5,762,888 |
Region 20 | phosphonate | 6,013,721 | 6,031,783 | Low | phosphonoglycans | saccharide
Region 21 | ectoine | 6,176,106 | 6,186,525 | High | ectoine | other:other

NC_013947.1 - Region 1 - NRPS,T1PKS,T3PKS
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: 127,865 - 226,181 nt. (total: 98,317 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
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
SNAS_RS00730: Hydroxylation

MITE
  MITE0000081Hydroxylation (identity: 63.90%)
smcogs
  SMCOG1006: acyl-CoA dehydrogenase

SNAS_RS00795: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

SNAS_RS00830: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

SNAS_RS01055: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: carboxylase glycosyltransferase methyltransferase
SNAS_RS00615: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

SNAS_RS00735: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SNAS_RS00770: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SNAS_RS00900: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

SNAS_RS00965: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase hydrolase
SNAS_RS00755: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

SNAS_RS00935: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

SNAS_RS00955: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: lyase
SNAS_RS00975: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
SNAS_RS00620: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

SNAS_RS00725: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

SNAS_RS00945: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SNAS_RS00960: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SNAS_RS32180: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
SNAS_RS00865: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

SNAS_RS01020: 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 | T3PKS | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000342.4 |  |  |  | 0.85 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  |  |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0000465.4 |  |  |  | 0.73 | NRPS | xenortide A, xenortide B, xenortide C, xenortide D | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  |  |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  |  |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  |  |  | 0.71 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002135.2 |  |  |  | 0.70 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.74 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0000465.4 |  | 0.69 | NRPS | xenortide A, xenortide B, xenortide C, xenortide D | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001077.4 |  | 0.69 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

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: 16.24 out of 19.26
Confidence: medium
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 27.32 out of 32.93
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52
Confidence: strong
Additional weak hits (27):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.08 out of 18.57
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.82 out of 27.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.70 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.15 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.23 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.54 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.04 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.59 out of 36.54
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.13 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.01 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.64 out of 29.65
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.20 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.64 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.06 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.57 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.35 out of 28.19
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 24.53 out of 32.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.13 out of 35.63
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.03 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.43 out of 24.78
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.72 out of 32.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.79 out of 35.63
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.95 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 1, location 127864 - 226181:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (NMe-Ser) + (Gly) + (Leu - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 167114 - 222991:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (NMe-Ser) + (Gly) + (Leu - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 183016 - 226181:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (NMe-Ser) + (Gly) + (Leu - 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).
SNAS_RS00945: Leu - X
Search NORINE for peptide: strict or relaxed
AMP-binding (15..400): 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:
    leu (Leu)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHAFDASVWESFLLTGGDVNNYGPTECTVVATS
  Nearest Stachelhaus code(s):
    Leu DAWFLGNVVK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1052..1437): X
nrpys: Asp, Asn, Glu, Gln, Aad

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:
    LAYSFDPAVRELGAFCGGELHGYGPTETTVSVCF
  Nearest Stachelhaus code(s):
    Arg DPWGFGLVDK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

SNAS_RS00960: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (457..845): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    QAFTFDPVFIEVQALTGGEHNVYGPTETTVWATS
  Nearest Stachelhaus code(s):
    Gly DILQLGVVWK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

SNAS_RS00965: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (494..893): 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:
    RWMTFDVSVWEWHFFTSGDDNLYGPTECAIDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLIDK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

SNAS_RS32180: mal
PKS_AT (595..876): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 70.8%
  inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 54.6
  Methoxymalonyl-CoA: 32.1
  Methylmalonyl-CoA: 24.2
  inactive: 21.5
  fatty_acid: 12.5
  CHC-CoA: 9.2
  Isobutyryl-CoA: 4.1
  trans-1,2-CPDA: 0.0
  Propionyl-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
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
RicR | Copper-responsive regulator

NC_013947.1 - Region 2 - lanthipeptide-class-iii
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: 545,473 - 568,034 nt. (total: 22,562 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_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
Lanthipeptides
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
SNAS_RS02620: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

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 | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.67 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.65 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000501.3 |  | 0.61 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000553.3 |  | 0.54 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0001226.4 |  | 0.53 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000563.4 |  | 0.53 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000518.3 |  | 0.52 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.67 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.65 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000501.3 |  | 0.61 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000553.3 |  | 0.54 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0001226.4 |  | 0.53 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000563.4 |  | 0.53 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000518.3 |  | 0.52 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai

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 SNAS_RS02645

SNAS_RS34700
Leader:
MALLDLQGLESPADLSATR
Core:
G G S S G S G H S C P S N L S A T L C G G T S G L S V L I C H
Core with dehydrations:
G G Dha Dha G Dha G H Dha Cys P Dha N L Dha A Dhb L Cys G G Dhb Dha G L Dha V L I Cys H

#### antiSMASH-DB 4.0 matches for SNAS_RS34700

100.0%
NC_013947.1:
Lanthipeptides: SNAS_RS34700_lanthipeptide
1
G G S S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
G G S S G S G H S C P S N L S A T L C G G T S G L S V L I C H
1
G G S S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
90.3%
NZ_FNGF01000002.1:
Lanthipeptides: BLS99_RS06065_lanthipeptide
1
G G S S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
G G S S S G H S C P S N L S A T L C G G T S G L S+L+C H
1
G G S S A S G H S C P S N L S A T L C G G T S G L S I L L C H
31
87.1%
NZ_FWXV01000003.1:
Lanthipeptides: B9C43_RS55710_lanthipeptide
2
G S S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
G S S S G H S C P S N L S T L C G G T S G L S+L I C H
1
G S S N S G H S C P S N L S V T L C G G T S G L S L L I C H
30
with 60 more sequence matches
Only the first 10 are displayed here.
87.1%
NZ_JAAATY010000001.1:
Lanthipeptides: GC106_RS02675_lanthipeptide
2
G S S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
G S S S G H S C P S N L S T L C G G T S G L S+L I C H
1
G S S N S G H S C P S N L S L T L C G G T S G L S L L I C H
30
83.9%
NZ_RSEB01000004.1 and 1 other:
NZ_WIAO01000001.1 Lanthipeptides: GFD30_RS00960_lanthipeptide
Lanthipeptides: EIW28_RS16895_lanthipeptide
4
S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
S S G H S C P S N L S A T L C G G T S G L S V L+C H
1
S A S G H S C P S N L S A T L C G G T S G L S V L L C H
28
80.6%
NZ_BNAU01000004.1:
Lanthipeptides: IE290_RS20710_lanthipeptide
4
S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
S S G S C P S N L S T L C G G T S G L S V L I C H
1
S A S G K S C P S N L S V T L C G G T S G L S V L I C H
28
80.6%
NZ_CDME01000008.1:
Lanthipeptides: BN1199_RS56280_lanthipeptide
2
G S S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
G S S S G H S C P S N L S T L C G+S G L S+L I C H
1
G S S N S G H S C P S N L S L T L C D G S S G L S L L I C H
30
80.6%
NZ_CP012752.1:
Lanthipeptides: AOZ06_RS57330_lanthipeptide
2
G S S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
G S S S G H S C P S N L S T L C G S G L S+L I C H
1
G S S N S G H S C P S N L S L T L C N G G S G L S L L I C H
30
80.6%
NZ_KB903814.1:
Lanthipeptides: A3G1_RS40055_lanthipeptide
4
S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
S S G H S C P S N L S T L C G G+S G L S V L I C H
1
S T S G H S C P S N L S V T L C G G S S G L S V L I C H
28
80.6%
NZ_SGWQ01000004.1:
Lanthipeptides: EV193_RS13500_lanthipeptide
4
S G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
S S G H S C P S N L S T L C G G T S G L S+L I C H
1
S A S G H S C P S N L S V T L C G G T S G L S L L I C H
28
77.4%
NZ_CP091196.1:
Lanthipeptides: L1857_RS00175_lanthipeptide
5
G S G H S C P S N L S A T L C G G T S G L S V L I C H
31
S G S C P S N L S T L C G G T S G L S V L I C H
1
A S G K S C P S N L S V T L C G G T S G L S V L I C H
27
77.4%
NZ_JAGFNP010000002.1:
Lanthipeptides: J5V16_RS05050_lanthipeptide
6
S G H S C P S N L S A T L C G G T S G L S V L I C H
31
S G H S C P S N L S A T L C G G T S L S V L+C H
1
S G H S C P S N L S A T L C G G T S S L S V L L C H
26
74.2%
NZ_FNAD01000001.1:
Lanthipeptides: BLQ63_RS02575_lanthipeptide
6
S G H S C P S N L S A T L C G G T S G L S V L I C H
31
S G H S C P S N L S A L C G G T S G L S+L+C H
2
S G H S C P S N L S A A L C G G T S G L S I L L C H
27

#### MIBiG 4.0 matches for SNAS_RS34700

25.8%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
12
S N L S A T L C G G T S G L S V L I C
30
S +S +C +S L S V++C
3
S Q V S L L V C E Y S S-L S V V L C
20

#### 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.
No hits above weak threshold.
Weak hits (3):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.84 out of 20.01
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.57 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.41 out of 27.78
Confidence: weak
Lanthipeptides
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.

SNAS_RS34700 - Class III
  Cleavage pHMM score: 4.50
  RODEO score: 0
  Monoisotopic mass: 2665.3 Da
  Molecular weight: 2666.9 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2684.9 Da N = 1
    2703.0 Da N = 2
    2721.0 Da N = 3
    2739.0 Da N = 4
    2757.0 Da N = 5
    2775.0 Da N = 6
    2793.1 Da N = 7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NC_013947.1 - Region 3 - lanthipeptide-class-iv
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: 619,322 - 641,415 nt. (total: 22,094 nt) Show pHMM detection rules used
lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

#### 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
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
SNAS_RS02965: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

SNAS_RS02985: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

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 | lanthipeptide-class-iv | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002337.2 |  | 0.58 | ribosomal | class IV lanthipeptide, SflA | Streptomyces sp. NRRL S-1022
BGC0000563.4 |  | 0.51 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000496.5 |  | 0.48 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000504.5 |  | 0.44 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000553.3 |  | 0.43 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0001788.3 |  | 0.40 | ribosomal | suicin 65 | Streptococcus suis
BGC0002260.3 |  | 0.40 | terpene | trichobrasilenol, xylarenic acid B, brasilane A, brasilane F, brasilane E, brasilane D | Annulohypoxylon truncatum
BGC0000285.5 |  | 0.40 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001294.5 |  | 0.40 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002110.3 |  | 0.39 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002337.2 |  | 0.58 | ribosomal | class IV lanthipeptide, SflA | Streptomyces sp. NRRL S-1022
BGC0000563.4 |  | 0.51 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000496.5 |  | 0.48 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000504.5 |  | 0.44 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000553.3 |  | 0.43 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0001788.3 |  | 0.40 | ribosomal | suicin 65 | Streptococcus suis
BGC0002260.3 |  | 0.40 | terpene | trichobrasilenol, xylarenic acid B, brasilane A, brasilane F, brasilane E, brasilane D | Annulohypoxylon truncatum
BGC0000285.5 |  | 0.40 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001294.5 |  | 0.40 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002110.3 |  | 0.39 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908

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.
Lanthipeptides - No core peptides 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 (1):
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98
Confidence: weak
Lanthipeptides
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.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NC_013947.1 - Region 4 - 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: 796,978 - 818,018 nt. (total: 21,041 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: dehydrogenase
SNAS_RS03800: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: dehydratase
SNAS_RS03745: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthetase
SNAS_RS33695: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Translocases: transporter
SNAS_RS03735: 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 | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000706.3 |  | 0.39 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000678.5 |  | 0.39 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001778.5 |  | 0.39 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000664.5 |  | 0.37 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000666.5 |  | 0.37 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0000665.5 |  | 0.36 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000871.4 |  | 0.36 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000706.3 |  | 0.39 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000678.5 |  | 0.39 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001778.5 |  | 0.39 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000664.5 |  | 0.37 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000666.5 |  | 0.37 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0000665.5 |  | 0.36 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000871.4 |  | 0.36 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622

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:
SNAS_RS33695: PT_FPPS_like
Domain 1 (55 - 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:
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.46 out of 27.18
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 out of 25.31
Confidence: medium
Additional weak hits (4):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.44 out of 27.78
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.90 out of 20.01
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.97 out of 31.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.07 out of 30.22
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
NrdR | Represses ribonucleotide reductase encoding genes

NC_013947.1 - Region 5 - 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: 1,190,588 - 1,212,897 nt. (total: 22,310 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: acyltransferase
SNAS_RS05545: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Hydrolases: glucanase
SNAS_RS05585: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

Lyases: cyclase
SNAS_RS05575: 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 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002285.2 |  | 0.46 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001659.3 |  | 0.42 | terpene | mangicol A | Fusarium equiseti
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0001743.3 |  | 0.39 | ribosomal | plantaricyclin | Lactobacillus plantarum
BGC0000522.3 |  | 0.38 | ribosomal | lacticin Z | Lactococcus lactis
BGC0000497.3 |  | 0.37 | ribosomal | BHT-Aα, BHT-Aβ | Streptococcus ratti
BGC0000552.3 |  | 0.37 | ribosomal | SmbA, SmbB | Streptococcus mutans
BGC0000543.5 |  | 0.36 | ribosomal | pep5 | Staphylococcus epidermidis
BGC0002144.3 |  | 0.36 | ribosomal | phazolicin | Rhizobium sp. Pop5

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002285.2 |  | 0.46 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001659.3 |  | 0.42 | terpene | mangicol A | Fusarium equiseti
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0001743.3 |  | 0.39 | ribosomal | plantaricyclin | Lactobacillus plantarum
BGC0000522.3 |  | 0.38 | ribosomal | lacticin Z | Lactococcus lactis
BGC0000497.3 |  | 0.37 | ribosomal | BHT-Aα, BHT-Aβ | Streptococcus ratti
BGC0000552.3 |  | 0.37 | ribosomal | SmbA, SmbB | Streptococcus mutans
BGC0000543.5 |  | 0.36 | ribosomal | pep5 | Staphylococcus epidermidis
BGC0002144.3 |  | 0.36 | ribosomal | phazolicin | Rhizobium sp. Pop5

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:
SNAS_RS05575: T1TS + T1TS
Domain 1 (4 - 332): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (337 - 699): 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.
No hits above weak threshold.
Weak hits (4):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.57 out of 32.74
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.75 out of 30.98
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.04 out of 23.43
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
--- | ---

NC_013947.1 - Region 6 - prodigiosin
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: 1,220,758 - 1,250,320 nt. (total: 29,563 nt) Show pHMM detection rules used
prodigiosin: (PPDK_N and AMP-binding and PP-binding and PKS_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 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
Transferases: acyltransferase halogenase kinase
SNAS_RS05655: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

SNAS_RS05660: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

SNAS_RS05690: halogenase

smcogs
  SMCOG1119: halogenase

SNAS_RS05760: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Ligases: ligase synthase
SNAS_RS05695: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SNAS_RS05700: 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 | prodigiosin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001244.3 |  | 0.61 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002174.2 |  | 0.60 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001273.3 |  | 0.60 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000357.5 |  | 0.60 | 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
BGC0001240.4 |  | 0.59 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001284.4 |  | 0.58 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0000037.4 |  | 0.57 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0002154.2 |  | 0.57 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001244.3 |  | 0.61 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002174.2 |  | 0.60 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001273.3 |  | 0.60 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000357.5 |  | 0.60 | 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
BGC0001240.4 |  | 0.59 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001284.4 |  | 0.58 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0000037.4 |  | 0.57 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0002154.2 |  | 0.57 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.75 out of 23.05
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.35 out of 26.85
Confidence: medium
Additional weak hits (15):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.93 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.73 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.80 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.75 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.06 out of 20.01
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.69 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.76 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.07 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.45 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.07 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.77 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.56 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.24 out of 35.63
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).
SNAS_RS05695: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (10..401): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YQIFFDGSVHDVFSLFGGEEVLYGPTELTIASTA
  Nearest Stachelhaus code(s):
    Gly DLHFLCLIAK (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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
RutR | Regulator of the pyrimidine and purine metabolism

NC_013947.1 - Region 7 - 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: 2,099,818 - 2,129,308 nt. (total: 29,491 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
SNAS_RS09780: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acetyltransferase methyltransferase
SNAS_RS09800: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

SNAS_RS09825: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase
SNAS_RS09830: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase synthetase
SNAS_RS09820: pseudouridine synthase

smcogs
  SMCOG1279: pseudouridine synthase

SNAS_RS09850: 1-deoxy-D-xylulose-5-phosphate synthase

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

SNAS_RS09860: 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
--- | --- | --- | --- | --- | ---
BGC0000657.5 |  | 0.63 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000659.3 |  | 0.63 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000658.3 |  | 0.61 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001361.3 |  | 0.54 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.54 | terpene | sodorifen | Serratia plymuthica
BGC0002162.3 |  | 0.53 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000677.5 |  | 0.47 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000665.5 |  | 0.47 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002309.2 |  | 0.46 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000666.5 |  | 0.45 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000657.5 |  | 0.63 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000659.3 |  | 0.63 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000658.3 |  | 0.61 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001361.3 |  | 0.54 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.54 | terpene | sodorifen | Serratia plymuthica
BGC0002162.3 |  | 0.53 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000677.5 |  | 0.47 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000665.5 |  | 0.47 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002309.2 |  | 0.46 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000666.5 |  | 0.45 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999

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:
SNAS_RS09830: T1TS
Domain 1 (6 - 362): Type 1 terpene synthase
Subtype: 2-Methylisoborneol synthase type

Reactions:
  2-MeGPP → 2-methylisoborneol
  2-MeGPP → 2-methylenebornane

SNAS_RS09860: PT_FPPS_like
Domain 1 (56 - 365): 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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52
Confidence: medium
Additional weak hits (13):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.71 out of 25.88
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.21 out of 20.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.88 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.92 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.05 out of 30.97
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 23.65 out of 32.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.41 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.79 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.02 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.08 out of 32.93
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: 16.84 out of 28.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.20 out of 24.78
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
2-MeGPP | 2-methylgeranyl diphosphate
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
HPP | Hexaprenyl diphosphate
IPP | Isopentenyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NC_013947.1 - Region 8 - 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: 2,309,711 - 2,331,850 nt. (total: 22,140 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
Transferases: glycosyltransferase
SNAS_RS10690: 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
--- | --- | --- | --- | --- | ---
BGC0000601.4 |  | 0.45 | ribosomal | sporulation killing factor | Bacillus subtilis subsp. subtilis str. 168
BGC0001948.3 |  | 0.42 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0002508.2 |  | 0.41 | other (other) | 8-azaguanine | Streptomyces pathocidini
BGC0001100.5 |  | 0.36 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0000706.3 |  | 0.34 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0002471.3 |  | 0.34 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0001440.5 |  | 0.34 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0001778.5 |  | 0.32 | other (other) | showdomycin | Streptomyces showdoensis
BGC0001366.5 |  | 0.32 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2
BGC0002591.2 |  | 0.31 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000601.4 |  | 0.45 | ribosomal | sporulation killing factor | Bacillus subtilis subsp. subtilis str. 168
BGC0001948.3 |  | 0.42 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0002508.2 |  | 0.41 | other (other) | 8-azaguanine | Streptomyces pathocidini
BGC0001100.5 |  | 0.36 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0000706.3 |  | 0.34 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0002471.3 |  | 0.34 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0001440.5 |  | 0.34 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0001778.5 |  | 0.32 | other (other) | showdomycin | Streptomyces showdoensis
BGC0001366.5 |  | 0.32 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2
BGC0002591.2 |  | 0.31 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.

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: 18.44 out of 23.79
Confidence: medium
Additional weak hits (1):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.53 out of 27.55
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (2309710...2331850)
SNAS_RS36195
  RRE type: PqqD_RRE
  Location: 2 - 86
  Score: 77.2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism

NC_013947.1 - Region 9 - lanthipeptide-class-ii
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: 3,678,950 - 3,702,159 nt. (total: 23,210 nt) Show pHMM detection rules used
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
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: oxidase
SNAS_RS17200: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Lyases: cyclase
SNAS_RS17190: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C 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 | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000503.5 |  | 0.47 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000504.5 |  | 0.46 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000500.5 |  | 0.45 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002698.2 |  | 0.44 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001210.5 |  | 0.43 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000516.4 |  | 0.43 | ribosomal | geobacillin II | Geobacillus thermodenitrificans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000503.5 |  | 0.47 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000504.5 |  | 0.46 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000500.5 |  | 0.45 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002698.2 |  | 0.44 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001210.5 |  | 0.43 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000516.4 |  | 0.43 | ribosomal | geobacillin II | Geobacillus thermodenitrificans

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.

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 SNAS_RS17190

SNAS_RS17185
Leader:
MSTATITRAWTDVEFRAGLSTEELELVEHPAG
Core:
D L D A E L R E L Y I H E A T A Q S T N C T K W T G S P N C C C
Core with dehydrations:
D L D A E L R E L Y I H E A Dhb A Q Dha Dhb N Cys Dhb K W Dhb G Dha P N Cys Cys Cys

#### antiSMASH-DB 4.0 matches for SNAS_RS17185

100.0%
NC_013947.1:
Lanthipeptides: SNAS_RS17185_lanthipeptide
1
D L D A E L R E L Y I H E A T A Q S T N C T K W T G S P N C C C
32
D L D A E L R E L Y I H E A T A Q S T N C T K W T G S P N C C C
1
D L D A E L R E L Y I H E A T A Q S T N C T K W T G S P N C C C
32
21.9%
NZ_CP059557.1:
Lassopeptides: H2Q94_RS14010_lassopeptide
11
I H E A T A Q S T N C T K W
24
E A A Q +N C+ W
6
F F E A P A Q H S N C S N W
19
10.7%
NZ_CP016076.1:
Lanthipeptides: allorf_2109745_2109951_lanthipeptide
15
T A Q S T N C T K W T G S
27
T Q+ +C T ++G S
3
T G Q N P D C T G F S G S
15

#### 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
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 (1):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
Lanthipeptides
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.

SNAS_RS17185 - Class II
  Cleavage pHMM score: -2.60
  RODEO score: 0
  Monoisotopic mass: 3463.5 Da
  Molecular weight: 3465.8 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3483.8 Da N = 1
    3501.8 Da N = 2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
VqsM | Regulator of quorum-sensing signalling systems

NC_013947.1 - Region 10 - 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: 3,744,170 - 3,764,955 nt. (total: 20,786 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
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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001972.4 |  | 0.35 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis
BGC0002429.3 |  | 0.23 | PKS, terpene | higginsianin B, higginsianin A, higginsianin C, 13-epi-higginsianin C, higginsianin D, higginsianin E | Colletotrichum higginsianum IMI 349063
BGC0000059.5 |  | 0.22 | PKS | filipin | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002032.4 |  | 0.21 | PKS | pentamycin | Streptomyces sp. S816
BGC0000138.5 |  | 0.20 | PKS | rimocidin | Streptomyces diastaticus
BGC0000709.5 |  | 0.20 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000069.5 |  | 0.20 | PKS | gephyronic acid | Archangium violaceum Cb vi76
BGC0002506.3 |  | 0.19 | PKS | homopiloquinone, piloquinone | Streptomyces sp. FXJ8.102
BGC0001283.3 |  | 0.19 | PKS | Bisenarsan | Streptomyces lividans 1326

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001972.4 |  | 0.35 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis
BGC0002429.3 |  | 0.23 | PKS, terpene | higginsianin B, higginsianin A, higginsianin C, 13-epi-higginsianin C, higginsianin D, higginsianin E | Colletotrichum higginsianum IMI 349063
BGC0000059.5 |  | 0.22 | PKS | filipin | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002032.4 |  | 0.21 | PKS | pentamycin | Streptomyces sp. S816
BGC0000138.5 |  | 0.20 | PKS | rimocidin | Streptomyces diastaticus
BGC0000709.5 |  | 0.20 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000069.5 |  | 0.20 | PKS | gephyronic acid | Archangium violaceum Cb vi76
BGC0002506.3 |  | 0.19 | PKS | homopiloquinone, piloquinone | Streptomyces sp. FXJ8.102
BGC0001283.3 |  | 0.19 | PKS | Bisenarsan | Streptomyces lividans 1326

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:
No product predictions
Genes with terpene domains:
SNAS_RS17490: TS_Pyr4
Domain 1 (4 - 169): Pyr4 type 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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.75 out of 23.05
Confidence: medium
Additional weak hits (6):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.84 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.35 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.12 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.51 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.69 out of 29.65
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production

NC_013947.1 - Region 11 - 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: 3,817,203 - 3,841,317 nt. (total: 24,115 nt) Show pHMM detection rules used
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
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: cyclase dehydratase
SNAS_RS17755: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

SNAS_RS17760: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C 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 | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.50 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001289.5 |  | 0.45 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000560.5 |  | 0.43 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000506.4 |  | 0.40 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000559.4 |  | 0.39 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000529.5 |  | 0.34 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0002637.3 |  | 0.19 | NRPS | rimomycin A, rimomycin B, rimomycin C | Streptomyces sp. WAC 06783

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.50 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001289.5 |  | 0.45 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000560.5 |  | 0.43 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000506.4 |  | 0.40 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000559.4 |  | 0.39 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000529.5 |  | 0.34 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0002637.3 |  | 0.19 | NRPS | rimomycin A, rimomycin B, rimomycin C | Streptomyces sp. WAC 06783

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.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides 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):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.50 out of 25.88
Confidence: weak
Lanthipeptides
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.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (3817202...3841317)
SNAS_RS17755
  RRE type: Lanthipeptide_LanB_RRE
  Location: 139 - 228
  Score: 44.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NC_013947.1 - Region 12 - 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: 3,862,489 - 3,872,842 nt. (total: 10,354 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
Hydrolases: hydrolase
SNAS_RS17925: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase 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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001294.5 |  | 0.40 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002316.2 |  | 0.37 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000528.5 |  | 0.37 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002346.3 |  | 0.34 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000503.5 |  | 0.32 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000502.5 |  | 0.32 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001561.4 |  | 0.29 | NRPS | curacomycin | Streptomyces curacoi
BGC0001920.4 |  | 0.28 | ribosomal | siamycin I | Streptomyces sp.
BGC0002015.4 |  | 0.28 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001674.5 |  | 0.28 | ribosomal | MS-271 | Streptomyces mirabilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001294.5 |  | 0.40 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002316.2 |  | 0.37 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000528.5 |  | 0.37 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002346.3 |  | 0.34 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000503.5 |  | 0.32 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000502.5 |  | 0.32 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001561.4 |  | 0.29 | NRPS | curacomycin | Streptomyces curacoi
BGC0001920.4 |  | 0.28 | ribosomal | siamycin I | Streptomyces sp.
BGC0002015.4 |  | 0.28 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001674.5 |  | 0.28 | ribosomal | MS-271 | Streptomyces mirabilis

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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05
Confidence: strong
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production

NC_013947.1 - Region 13 - 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: 3,963,971 - 3,995,332 nt. (total: 31,362 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
Transferases: acyltransferase
SNAS_RS18350: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Lyases: decarboxylase
SNAS_RS18415: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Isomerases: isomerase
SNAS_RS18420: isochorismate synthase

smcogs
  SMCOG1018: isochorismate 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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.52 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0001478.5 |  | 0.51 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002527.2 |  | 0.50 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001408.5 |  | 0.49 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0001499.5 |  | 0.48 | other (other) | aerobactin | Pantoea ananatis
BGC0000944.5 |  | 0.48 | other (non-nrp siderophore) | staphyloferrin A | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002681.3 |  | 0.46 | other (other) | rhizoferrin | Francisella tularensis subsp. tularensis SCHU S4
BGC0000947.5 |  | 0.44 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000943.5 |  | 0.42 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002471.3 |  | 0.41 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.52 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0001478.5 |  | 0.51 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002527.2 |  | 0.50 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001408.5 |  | 0.49 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0001499.5 |  | 0.48 | other (other) | aerobactin | Pantoea ananatis
BGC0000944.5 |  | 0.48 | other (non-nrp siderophore) | staphyloferrin A | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002681.3 |  | 0.46 | other (other) | rhizoferrin | Francisella tularensis subsp. tularensis SCHU S4
BGC0000947.5 |  | 0.44 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000943.5 |  | 0.42 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002471.3 |  | 0.41 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE

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 (5):
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.36 out of 36.53
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.60 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.81 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.28 out of 36.54
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.93 out of 29.25
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NC_013947.1 - Region 14 - 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: 4,302,622 - 4,350,615 nt. (total: 47,994 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 oxidoreductase
SNAS_RS20020: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

SNAS_RS20055: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

SNAS_RS20075: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Transferases: kinase
SNAS_RS20050: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

SNAS_RS20070: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Hydrolases: esterase
SNAS_RS20015: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
SNAS_RS20000: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

SNAS_RS20005: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  | 0.84 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000342.4 |  |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001825.4 |  |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.67 | 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:
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.53 out of 30.25
Confidence: medium
Additional weak hits (7):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.30 out of 31.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.96 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.16 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.43 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.06 out of 21.55
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.35 out of 27.18
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 17, location 4302621 - 4350615:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X) + (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).
SNAS_RS20000: X - X
AMP-binding (20..416): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    IWHMFDAFVTEPALHTGGDVNCYGPSETTVDATA
  Nearest Stachelhaus code(s):
    Gln DAVQMGCVDK (62% 8Å match)
    Arg DADDSGCVDK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1089..1472): X
nrpys: (unknown)

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:
    LWHAFDVSIGEPDLLTGGDLNAYGPTEATVTATS
  Nearest Stachelhaus code(s):
    Arg DVGDIGAVTK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

SNAS_RS20005: mal
PKS_AT (517..812): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 134.2
  Methoxymalonyl-CoA: 66.3
  Methylmalonyl-CoA: 57.5
  inactive: 47.5
  Propionyl-CoA: 41.1
  Ethylmalonyl-CoA: 35.8
  2-Methylbutyryl-CoA: 28.4
  Isobutyryl-CoA: 23.7
  CHC-CoA: 21.0
  Benzoyl-CoA: 19.6
  Acetyl-CoA: 17.4
  trans-1,2-CPDA: 11.6
  fatty_acid: 11.6
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
ColR | Phenol-responsive regulator

NC_013947.1 - Region 15 - T1PKS,hydrogen-cyanide
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: 4,372,230 - 4,443,056 nt. (total: 70,827 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)
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 reductase
SNAS_RS20255: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

SNAS_RS20265: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

SNAS_RS20285: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

SNAS_RS20410: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase kinase methyltransferase
SNAS_RS20365: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

SNAS_RS20405: methyltransferase

smcogs
  SMCOG1089: methyltransferase

SNAS_RS20445: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: phosphatase
SNAS_RS20295: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

Ligases: synthase
SNAS_RS20385: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SNAS_RS20390: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

SNAS_RS20395: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

SNAS_RS36315: 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 | hydrogen-cyanide | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.43 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.43 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.43 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  |  | 0.37 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001276.3 |  |  | 0.31 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  |  | 0.30 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.30 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001257.3 |  |  | 0.30 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002191.2 |  |  | 0.30 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002154.2 |  |  | 0.30 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.69 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
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
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
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

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: 18.25 out of 18.46
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.81 out of 29.51
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
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 25.90 out of 35.63
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 24.71 out of 29.65
Confidence: medium
Additional weak hits (8):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.31 out of 21.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.56 out of 28.14
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.70 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.38 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 18, location 4372229 - 4443056:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-ccmal) + (Me-redmal) + (mal) + (Me-mal)
Non-colinear ordering:
  SNAS_RS36315 + SNAS_RS20395 + SNAS_RS20390 + SNAS_RS20385

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 20, location 4382572 - 4443056:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-ccmal) + (Me-redmal) + (mal) + (Me-mal)
Non-colinear ordering:
  SNAS_RS36315 + SNAS_RS20395 + SNAS_RS20390 + SNAS_RS20385

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).
SNAS_RS36315: mmal - mmal
PKS_AT (99..395): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 75.0%
  Ethylmalonyl-CoA: 66.7%
  Methoxymalonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 169.6
  Ethylmalonyl-CoA: 158.2
  Methoxymalonyl-CoA: 135.1
  2-Methylbutyryl-CoA: 115.5
  Propionyl-CoA: 113.8
  trans-1,2-CPDA: 107.5
  Malonyl-CoA: 91.4
  CHC-CoA: 83.7
  Benzoyl-CoA: 61.5
  Isobutyryl-CoA: 54.9
  fatty_acid: 35.5
  3-Methylbutyryl-CoA: 31.4
  Acetyl-CoA: 31.3
  inactive: 22.7

PKS_AT (1085..1376): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 173.9
  Ethylmalonyl-CoA: 159.8
  Methoxymalonyl-CoA: 134.3
  2-Methylbutyryl-CoA: 93.6
  CHC-CoA: 89.0
  trans-1,2-CPDA: 86.5
  Malonyl-CoA: 79.7
  Propionyl-CoA: 75.4
  Isobutyryl-CoA: 72.8
  Benzoyl-CoA: 40.7
  3-Methylbutyryl-CoA: 30.7
  Acetyl-CoA: 30.0
  fatty_acid: 28.3
  inactive: 26.7

SNAS_RS20385: mmal
PKS_AT (565..860): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Malonyl-CoA: 79.2%
  Methoxymalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 179.8
  Ethylmalonyl-CoA: 151.9
  Methoxymalonyl-CoA: 150.3
  2-Methylbutyryl-CoA: 129.6
  trans-1,2-CPDA: 107.6
  Malonyl-CoA: 95.4
  Propionyl-CoA: 94.3
  Isobutyryl-CoA: 92.0
  CHC-CoA: 72.4
  3-Methylbutyryl-CoA: 54.8
  Benzoyl-CoA: 49.8
  Acetyl-CoA: 42.3
  fatty_acid: 26.7
  inactive: 25.7

SNAS_RS20390: mal
PKS_AT (565..845): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 220.7
  inactive: 122.9
  Methoxymalonyl-CoA: 64.2
  Methylmalonyl-CoA: 56.9
  Propionyl-CoA: 35.5
  fatty_acid: 22.7
  Isobutyryl-CoA: 22.6
  Acetyl-CoA: 21.7
  Ethylmalonyl-CoA: 19.3
  2-Methylbutyryl-CoA: 15.6
  CHC-CoA: 11.2
  Benzoyl-CoA: 10.2
  3-Methylbutyryl-CoA: 3.9
  trans-1,2-CPDA: 0.0

SNAS_RS20395: mmal
PKS_AT (566..858): 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: 196.7
  Ethylmalonyl-CoA: 182.3
  Methoxymalonyl-CoA: 150.1
  2-Methylbutyryl-CoA: 112.6
  Malonyl-CoA: 101.9
  trans-1,2-CPDA: 99.4
  CHC-CoA: 93.2
  Propionyl-CoA: 90.4
  Isobutyryl-CoA: 77.5
  Benzoyl-CoA: 53.3
  Acetyl-CoA: 51.4
  3-Methylbutyryl-CoA: 46.4
  fatty_acid: 42.3
  inactive: 28.2

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
CRP | Cyclic AMP receptor protein
DosR | Hypoxia stress response regulator
LexA variant 1 | Repressor of DNA damage response
NrtR | NAD synthesis repressor
RpoN | Regulator of nitrogen assimilation and virulence

NC_013947.1 - Region 16 - lassopeptide
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: 4,526,579 - 4,549,108 nt. (total: 22,530 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### 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
Lasso peptides
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
Hydrolases: hydrolase
SNAS_RS20935: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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 | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001307.3 |  | 0.56 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0001548.4 |  | 0.54 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001655.3 |  | 0.53 | ribosomal | LP2006 | Nocardiopsis alba DSM 43377
BGC0001496.3 |  | 0.49 | ribosomal | actinokineosin | Actinokineospora spheciospongiae
BGC0001645.3 |  | 0.49 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001889.2 |  | 0.46 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0002015.4 |  | 0.46 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000579.4 |  | 0.41 | ribosomal | SSV-2083 | Streptomyces sviceus ATCC 29083
BGC0001920.4 |  | 0.40 | ribosomal | siamycin I | Streptomyces sp.
BGC0001674.5 |  | 0.40 | ribosomal | MS-271 | Streptomyces mirabilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001307.3 |  | 0.56 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0001548.4 |  | 0.54 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001655.3 |  | 0.53 | ribosomal | LP2006 | Nocardiopsis alba DSM 43377
BGC0001496.3 |  | 0.49 | ribosomal | actinokineosin | Actinokineospora spheciospongiae
BGC0001645.3 |  | 0.49 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001889.2 |  | 0.46 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0002015.4 |  | 0.46 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000579.4 |  | 0.41 | ribosomal | SSV-2083 | Streptomyces sviceus ATCC 29083
BGC0001920.4 |  | 0.40 | ribosomal | siamycin I | Streptomyces sp.
BGC0001674.5 |  | 0.40 | ribosomal | MS-271 | Streptomyces mirabilis

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.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lassopeptide(s) for SNAS_RS20930

SNAS_RS20930
Leader:
MRPVLAPGTCYTDLPDGGAALVTPTGGDVVHLDAVAAAFVKALSEHERDTAVTVLAEHFDVSTTTI
Full core:
A A D L D D F T A T L V D Y G V M T G G A S
Putative macrolactam:

#### antiSMASH-DB 4.0 matches for SNAS_RS20930

100.0%
NC_013947.1:
Lassopeptides: SNAS_RS20930_lassopeptide
1
A A D L D D F T A T L V D Y G V M T G G A S
22
A A D L D D F T A T L V D Y G V M T G G A S
1
A A D L D D F T A T L V D Y G V M T G G A S
22

#### MIBiG 4.0 matches for SNAS_RS20930

9.8%
BGC0002120.3 (NQE92413.1):
Lanthipeptide: nocathioamide A
5
D D F T A T L V D Y G V M T G G A S
22
D D F ++D + +S
16
D D F D L N I I D S S M F D D E S S
33

#### Lassopeptide(s) for SNAS_RS37230

SNAS_RS37230
Leader:
MNTKKTPARRTRYARPTVTLLGDAVKLTN
Full core:
G G Q Y N D T H D S R Q Y Y Y
Putative macrolactam:
G G Q Y N D T H D

#### antiSMASH-DB 4.0 matches for SNAS_RS37230

100.0%
NC_013947.1:
Lassopeptides: allorf_4539121_4539270_lassopeptide
1
G G Q Y N D T H D S R Q Y Y Y
15
G G Q Y N D T H D S R Q Y Y Y
1
G G Q Y N D T H D S R Q Y Y Y
15
46.7%
NC_015951.1:
Lassopeptides: STRVI_RS44745_lassopeptide
1
G G Q Y N D T H D S R Q Y
13
G Q Y D+ D Q Y
1
G T Q Y Q D S A D D T Q Y
13
46.7%
NZ_JACEIQ010000003.1:
Lassopeptides: H1191_RS05090_lassopeptide
1
G G Q Y N D T H D S R Q Y Y Y
15
G + D T D ++Y Y Y
1
G D E E R D T A D L K E Y Y Y
15
with 3 more sequence matches
40.0%
NZ_JALMDK010000025.1:
Lassopeptides: MZC64_RS46020_lassopeptide
1
G G Q Y N D T H D S R Q Y Y Y
15
G ++D T + R Y Y+
1
G S A F D D T M E K R S Y Y F
15
40.0%
NZ_KB913024.1:
Lassopeptides: ACTMO_RS22770_lassopeptide
1
G G Q Y N D T H D S R Q Y Y Y
15
G ++D T D +++Y Y
1
G T S F D D T A D R K R W Y Y
15
33.3%
NZ_CP014168.1:
Lassopeptides: J0A91_RS18750_lassopeptide
1
G G Q Y N D T H D S R Q Y
13
G ++D T D R Q
3
G A P F S D T G D G R Q L
15

#### 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.
No hits above weak threshold.
Weak hits (4):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.61 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
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.57 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.42 out of 29.25
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

SNAS_RS20930 - Class II
  Cleavage pHMM score: -7.70
  RODEO score: 19
  Monoisotopic mass: 2171.0 Da
  Molecular weight: 2172.3 Da
  Number of bridges: 0
SNAS_RS37230 - Class II
  Cleavage pHMM score: 3.20
  RODEO score: 21
  Monoisotopic mass: 1847.7 Da
  Molecular weight: 1848.8 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (4526578...4549108)
SNAS_RS20930
  RRE type: Stand_Alone_Lasso_RRE
  Location: 10 - 83
  Score: 28.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NC_013947.1 - Region 17 - 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: 4,794,873 - 4,844,603 nt. (total: 49,731 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 oxidoreductase
SNAS_RS22235: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

SNAS_RS22285: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: formyltransferase
SNAS_RS22220: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: hydrolase
SNAS_RS22205: HAD-superfamily hydrolase, subfamily IA, variant

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

SNAS_RS22300: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: dehydratase
SNAS_RS22255: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: isomerase
SNAS_RS22290: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
SNAS_RS22295: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

SNAS_RS22335: 1-deoxy-D-xylulose-5-phosphate synthase

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

SNAS_RS33115: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease
SNAS_RS22350: 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 | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000343.5 |  |  | 0.78 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0002492.3 |  |  | 0.58 | NRPS | myxochelin B, myxochelin A | Myxococcus xanthus DK 1622
BGC0001135.5 |  |  | 0.58 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001185.5 |  |  | 0.56 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0002324.3 |  |  | 0.54 | NRPS, PKS | myxochelin B, myxochelin N, myxochelin O, myxochelin P, myxochelin Q, myxochelin A | Archangium violaceum
BGC0002276.2 |  |  | 0.54 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001345.5 |  |  | 0.53 | NRPS | myxochelin A, myxochelin B | Stigmatella aurantiaca Sg a15
BGC0002474.2 |  |  | 0.52 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0000401.5 |  |  | 0.49 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0002494.3 |  |  | 0.47 | NRPS | vibriobactin | Vibrio cholerae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000343.5 |  | 0.71 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0002492.3 |  | 0.63 | NRPS | myxochelin B, myxochelin A | Myxococcus xanthus DK 1622
BGC0001135.5 |  | 0.62 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001185.5 |  | 0.62 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0002324.3 |  | 0.61 | NRPS, PKS | myxochelin B, myxochelin N, myxochelin O, myxochelin P, myxochelin Q, myxochelin A | Archangium violaceum
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001345.5 |  | 0.60 | NRPS | myxochelin A, myxochelin B | Stigmatella aurantiaca Sg a15
BGC0002474.2 |  | 0.60 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0000401.5 |  | 0.58 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0002494.3 |  | 0.57 | NRPS | vibriobactin | Vibrio cholerae

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: 20.58 out of 23.05
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
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.55 out of 19.26
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.07 out of 36.53
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
Additional weak hits (8):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.94 out of 19.26
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
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.17 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.41 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.38 out of 36.53
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.61 out of 35.63
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.65 out of 23.43
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 22, location 4794872 - 4844603:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Lys)

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).
SNAS_RS22295: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (31..422): 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:
    SVALFPLSSPGGAVQVGGAQQVFGMAEGLVCYTR
  Nearest Stachelhaus code(s):
    diOH-Bz or Sal PLPAQGVVNK (88% 8Å match)
    diOH-Bz PLPAQGVVNK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

SNAS_RS33115: Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (416..825): Lys
nrpys: Lys

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:
    FSAAFDAHVEEVDLIIGGEINSYGPTEATVVCLA
  Nearest Stachelhaus code(s):
    Lys DAEDIGSVVK (74% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NC_013947.1 - Region 18 - 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: 5,327,596 - 5,348,669 nt. (total: 21,074 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
Ligases: ligase synthetase
SNAS_RS24855: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

SNAS_RS24895: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine 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-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.43 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002111.3 |  | 0.42 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0001485.4 |  | 0.42 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000486.4 |  | 0.40 | ribosomal | butyrivibriocin AR10 | Butyrivibrio fibrisolvens
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001456.3 |  | 0.39 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000664.5 |  | 0.39 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.43 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002111.3 |  | 0.42 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0001485.4 |  | 0.42 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000486.4 |  | 0.40 | ribosomal | butyrivibriocin AR10 | Butyrivibrio fibrisolvens
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001456.3 |  | 0.39 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000664.5 |  | 0.39 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus

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:
SNAS_RS24855: PT_FPPS_like
Domain 1 (45 - 351): 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:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.33 out of 36.53
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (7):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.56 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.57 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.02 out of 21.55
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
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.83 out of 24.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.57 out of 36.53
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.10 out of 25.88
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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
DmdR1 | Iron(II)-dependent repressor

NC_013947.1 - Region 19 - 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: 5,738,774 - 5,762,888 nt. (total: 24,115 nt) Show pHMM detection rules used
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
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: methyltransferase
SNAS_RS26770: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase dehydratase
SNAS_RS26775: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

SNAS_RS33385: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C 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 | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001289.5 |  | 0.48 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000560.5 |  | 0.45 | ribosomal | subtilomycin | Bacillus subtilis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000514.5 |  | 0.39 | ribosomal | gallidermin | Staphylococcus gallinarum
BGC0002120.3 |  | 0.36 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000796.3 |  | 0.27 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0001435.4 |  | 0.25 | NRPS, PKS | ikarugamycin | Streptomyces sp. ZJ306
BGC0000700.5 |  | 0.24 | saccharide | istamycin | Streptomyces tenjimariensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001289.5 |  | 0.48 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000560.5 |  | 0.45 | ribosomal | subtilomycin | Bacillus subtilis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000514.5 |  | 0.39 | ribosomal | gallidermin | Staphylococcus gallinarum
BGC0002120.3 |  | 0.36 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000796.3 |  | 0.27 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0001435.4 |  | 0.25 | NRPS, PKS | ikarugamycin | Streptomyces sp. ZJ306
BGC0000700.5 |  | 0.24 | saccharide | istamycin | Streptomyces tenjimariensis

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.

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 SNAS_RS26775

SNAS_RS34480
Leader:
MKPTLEATTDIEAFEDLFKLDVRIEAEGPSLSRCNPT
Core:
N D G C S N S C T S V G C S A N C
Core with dehydrations:
N D G Cys Dha N Dha Cys Dhb Dha V G Cys Dha A N Cys

#### antiSMASH-DB 4.0 matches for SNAS_RS34480

100.0%
NC_013947.1:
Lanthipeptides: SNAS_RS34480_lanthipeptide
1
N D G C S N S C T S V G C S A N C
17
N D G C S N S C T S V G C S A N C
1
N D G C S N S C T S V G C S A N C
17
65.0%
NC_013947.1:
Lanthipeptides: SNAS_RS34155_lanthipeptide
1
N D G C S N S C T S V G C S
14
N D G C S N S C T S V G C
6
N D G C S N S C T S V G C P
19
58.3%
NZ_CP043661.1:
Lanthipeptides: F1D05_RS10920_lanthipeptide
1
N D G C S N S C T S V G C S A N C
17
N D G C S S C S V G C S A C
3
N D G C S A S C P S V G C S A T C
19
with 26 more sequence matches
Only the first 10 are displayed here.
42.9%
NZ_JACHJO010000003.1:
Lanthipeptides: FHS13_RS04620_lanthipeptide
1
N D G C S N S C T S V G C S A N C
17
N D G C +C S C S +C
2
N D G C G K T C Q S A-C S P S C
17
41.2%
NZ_SPFR01000005.1:
Lanthipeptides: FGQ83_RS17540_lanthipeptide
1
N D G C S N S C T S V G C S
14
G C S C T + C S
3
T K G C S Q F C T I I C C S
16
39.1%
NZ_CP047146.1 and 3 others:
NZ_CP047146.1 Lanthipeptides: GR130_RS38445_lanthipeptide NZ_CP048875.1 Lanthipeptides: G3260_RS00640_lanthipeptide NZ_CP048875.1 Lanthipeptides: G3260_RS00640_lanthipeptide
Lanthipeptides: GR130_RS38445_lanthipeptide
1
N D G C S N S C T S V G C S A N C
17
+D G C +C S C S A C
7
D D G C G Q T C E S-A C S A T C
22
39.1%
NZ_JABBWZ010000004.1 and 4 others:
NZ_JABBWZ010000004.1 Lanthipeptides: HHX40_RS10860_lanthipeptide NZ_JABBWZ010000004.1 Lanthipeptides: HHX40_RS10860_lanthipeptide NZ_VYTZ01000008.1 Lanthipeptides: F5972_RS22705_lanthipeptide NZ_VYTZ01000008.1 Lanthipeptides: F5972_RS22705_lanthipeptide
Lanthipeptides: HHX40_RS10860_lanthipeptide
1
N D G C S N S C T S V G C S A N C
17
+D G C S C S C A C
7
D D G C G T S C Q S-A C P A T C
22
39.1%
NZ_JACHGT010000013.1 and 1 other:
NZ_JACHGT010000013.1 Lanthipeptides: HNR73_RS27205_lanthipeptide
Lanthipeptides: HNR73_RS27205_lanthipeptide
1
N D G C S N S C T S V G C S A N C
17
N D G C +C S C S C
7
N D G C G Q T C Q S-A C S T T C
22
34.8%
NC_013131.1:
Lanthipeptides: allorf_05058087_05058206_lanthipeptide
1
N D G C S N S C T S V G C S A N C
17
N G C + T S V A+C
1
N S G C R H R I T S V E S R A S C
17
34.8%
NZ_CP054916.1 and 1 other:
NZ_CP054916.1 Lanthipeptides: HUT19_RS32830_lanthipeptide
Lanthipeptides: HUT19_RS32830_lanthipeptide
1
N D G C S N S C T S V G C S A N C
17
+D G C +C S C S C
7
D D G C G Q T C Q S-A C S T T C
22
34.8%
NZ_JAFIQY010000070.1 and 1 other:
NZ_JAFIQY010000070.1 Lanthipeptides: JXZ78_RS39125_lanthipeptide
Lanthipeptides: JXZ78_RS39125_lanthipeptide
1
N D G C S N S C T S V G C S A N C
17
+D G C +C S C S C
7
D D G C G Q T C E S-A C S T T C
22
33.3%
NZ_BMRB01000002.1 and 1 other:
NZ_CP031087.1 Lanthipeptides: Actkin_RS21245_lanthipeptide
Lanthipeptides: IEY98_RS16230_lanthipeptide
1
N D G C S N S C T S V G C S A N C
17
N D G C ++C S C+A+C
7
N D G C G H T C D S A-C A A S C
22
30.4%
NZ_BMSK01000006.1:
Lanthipeptides: IE251_RS13810_lanthipeptide
1
N D G C S N S C T S V G C S
14
G C S C T V C+
4
T Q G C S G L C T I V I C A
17

#### 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:
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 26.27 out of 27.18
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.13 out of 18.57
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 (3):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.01 out of 29.65
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.06 out of 29.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.99 out of 33.14
Confidence: weak
Lanthipeptides
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.

SNAS_RS34480 - Class I
  Cleavage pHMM score: -5.10
  RODEO score: 19
  Monoisotopic mass: 1530.5 Da
  Molecular weight: 1531.6 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1549.6 Da N = 1

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (5738773...5762888)
SNAS_RS26775
  RRE type: Lanthipeptide_LanB_RRE
  Location: 138 - 227
  Score: 43.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NrdR | Represses ribonucleotide reductase encoding genes
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NC_013947.1 - Region 20 - phosphonate
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: 6,013,721 - 6,031,783 nt. (total: 18,063 nt) Show pHMM detection rules used
phosphonate: (phosphonates and minimum(1, [2-Hacid_dh_C, Aldedh, Aminotran_1_2, Aminotran_5, AurF, CTP_transf_like, DUF4992, Fe-ADH, HMGL-like, Metallophos_2, NTP_transf_3, NTP_transf_5, PALP, PEP_mutase, TPP_enzyme_C, TPP_enzyme_N, phosphonates]) and not (phosphonatesHydrolase or phosphonatesMeIsocitrateLyase))

#### 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: oxidase
SNAS_RS28020: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

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 | phosphonate | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000807.3 |  | 0.74 | saccharide | phosphonoglycans | Stackebrandtia nassauensis DSM 44728
BGC0000938.5 |  | 0.47 | other (aminocoumarin) | fosfomycin | Streptomyces fradiae
BGC0001739.3 |  | 0.41 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0002670.2 |  | 0.40 | other (other) | fosfonochlorin | Fusarium oxysporum f. sp. lycopersici 4287
BGC0000616.4 |  | 0.39 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000806.5 |  | 0.39 | saccharide | phosphonoglycans | Glycomyces sp. NRRL B-16210
BGC0000897.5 |  | 0.39 | other (other) | dehydrophos | Streptomyces luridus
BGC0002747.3 |  | 0.38 | ribosomal | lentinulin A | Lentinula edodes
BGC0001684.3 |  | 0.37 | other (other) | N-acyloxyacyl glutamine | Klebsiella variicola
BGC0001655.3 |  | 0.36 | ribosomal | LP2006 | Nocardiopsis alba DSM 43377

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000807.3 |  | 0.74 | saccharide | phosphonoglycans | Stackebrandtia nassauensis DSM 44728
BGC0000938.5 |  | 0.47 | other (aminocoumarin) | fosfomycin | Streptomyces fradiae
BGC0001739.3 |  | 0.41 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0002670.2 |  | 0.40 | other (other) | fosfonochlorin | Fusarium oxysporum f. sp. lycopersici 4287
BGC0000616.4 |  | 0.39 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000806.5 |  | 0.39 | saccharide | phosphonoglycans | Glycomyces sp. NRRL B-16210
BGC0000897.5 |  | 0.39 | other (other) | dehydrophos | Streptomyces luridus
BGC0002747.3 |  | 0.38 | ribosomal | lentinulin A | Lentinula edodes
BGC0001684.3 |  | 0.37 | other (other) | N-acyloxyacyl glutamine | Klebsiella variicola
BGC0001655.3 |  | 0.36 | ribosomal | LP2006 | Nocardiopsis alba DSM 43377

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: 18.92 out of 20.47
Confidence: medium
Additional weak hits (5):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.18 out of 21.55
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.94 out of 24.78
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.89 out of 23.43
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.50 out of 36.54
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.50 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NC_013947.1 - Region 21 - 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: 6,176,106 - 6,186,525 nt. (total: 10,420 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
Transferases: aminotransferase
SNAS_RS28765: 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 |  | 0.81 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.81 | other (other) | ectoine | Streptomyces anulatus
BGC0000855.3 |  | 0.72 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.72 | other (other) | ectoine | Methylophaga thalassica
BGC0000859.3 |  | 0.72 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.67 | other (other) | ectoine | Methylobacter marinus
BGC0000857.3 |  | 0.64 | other (other) | ectoine | Methylophaga alcalica
BGC0000854.3 |  | 0.63 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000860.3 |  | 0.50 | other (other) | ectoine | Methylarcula marina

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.81 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.81 | other (other) | ectoine | Streptomyces anulatus
BGC0000855.3 |  | 0.72 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.72 | other (other) | ectoine | Methylophaga thalassica
BGC0000859.3 |  | 0.72 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.67 | other (other) | ectoine | Methylobacter marinus
BGC0000857.3 |  | 0.64 | other (other) | ectoine | Methylophaga alcalica
BGC0000854.3 |  | 0.63 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000860.3 |  | 0.50 | other (other) | ectoine | Methylarcula marina

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 (4):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.94 out of 33.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.97 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.58 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.10 out of 29.38
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---