Select genomic region:
Overview
1.1
1.2
2.1
2.2
6.1
6.2
6.3
6.4
6.5
6.6
6.7
6.8
6.9
6.10
6.11
6.12
6.13
6.14
6.15
6.16
6.17
6.18
6.19
6.20
6.21
6.22
6.23
6.24
6.25
6.26
6.27
6.28
6.29

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

NZ_WHZR01000002.1 (Streptomyces sp. OM5714)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | arylpolyene,T1PKS,NRPS | 133,478 | 193,464 | Low | amipurimycin | PKS
Region 1.2 | hglE-KS,T1PKS | 338,010 | 391,337 |  |

NZ_WHZR01000003.1 (Streptomyces sp. OM5714)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | other | 22,756 | 63,172 | Low | nenestatin | PKS
Region 2.2 | butyrolactone,T2PKS,phenazine | 74,041 | 126,837 |  |

NZ_WHZR01000001.1 (Streptomyces sp. OM5714)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 6.1 | NRP-metallophore,NRPS | 109,595 | 168,007 | High | coelichelin | NRPS:Type I
Region 6.2 | terpene-precursor | 223,588 | 244,661 |  |
Region 6.3 | RiPP-like | 420,880 | 431,095 | Low | informatipeptin | ribosomal:RiPP:Lanthipeptide
Region 6.4 | terpene | 773,291 | 800,040 | High | hopene | terpene
Region 6.5 | lanthipeptide-class-iii | 864,996 | 887,692 | High | SAL-2242 | ribosomal:RiPP:Lanthipeptide
Region 6.6 | transAT-PKS,NRPS,NRPS-like | 1,041,144 | 1,153,660 | High | inthomycin B | PKS
Region 6.7 | butyrolactone,RiPP-like | 1,340,905 | 1,365,445 | Low | methylenomycin A | other:other
Region 6.8 | hydrogen-cyanide | 1,375,354 | 1,388,292 |  |
Region 6.9 | NI-siderophore | 1,407,571 | 1,438,785 |  |
Region 6.10 | betalactone | 1,520,283 | 1,548,047 |  |
Region 6.11 | terpene | 1,613,342 | 1,635,564 | High | geosmin | terpene:Sesquiterpene
Region 6.12 | RiPP-like | 1,646,617 | 1,658,002 |  |
Region 6.13 | terpene,NRPS-like,T1PKS,prodigiosin | 1,950,056 | 2,020,937 | High | undecylprodigiosin | NRPS:Type I+PKS
Region 6.14 | NI-siderophore | 2,078,914 | 2,108,746 |  |
Region 6.15 | T2PKS,triceptide | 2,590,494 | 2,678,375 | Medium | nybomycin | other:other
Region 6.16 | terpene-precursor | 2,679,807 | 2,700,967 | Low | echoside A/echoside B/echoside C/echoside D/echoside E | NRPS:Type I
Region 6.17 | terpene | 2,708,476 | 2,729,561 | High | albaflavenone | terpene
Region 6.18 | RRE-containing | 2,833,871 | 2,854,929 |  |
Region 6.19 | RRE-containing | 2,876,355 | 2,897,548 |  |
Region 6.20 | NRPS | 3,676,355 | 3,761,612 | High | sarpeptin A/sarpeptin B | NRPS:Type I
Region 6.21 | NI-siderophore | 5,233,483 | 5,263,261 | High | desferrioxamin B/desferrioxamine E | other:other
Region 6.22 | melanin | 5,341,497 | 5,352,129 | Medium | melanin | other:other
Region 6.23 | ectoine | 6,308,121 | 6,318,519 | High | ectoine | other:other
Region 6.24 | RiPP-like | 6,892,135 | 6,904,054 |
Region 6.25 | T3PKS | 6,996,422 | 7,037,606 | High | flaviolin/1,3,6,8-tetrahydroxynaphthalene | PKS
Region 6.26 | T3PKS | 7,322,828 | 7,364,012 | High | germicidin | other:other
Region 6.27 | terpene | 7,566,174 | 7,590,219 | Medium | carotenoid | terpene
Region 6.28 | indole | 7,652,566 | 7,673,693 | High | 5-dimethylallylindole-3-acetonitrile | other:other
Region 6.29 | terpene | 7,848,171 | 7,869,388 | High | 2-methylisoborneol | terpene

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | arylpolyene,T1PKS,NRPS | 133,478 | 193,464 | Low | amipurimycin | PKS
Region 1.2 | hglE-KS,T1PKS | 338,010 | 391,337 |  |
Region 2.1 | other | 22,756 | 63,172 | Low | nenestatin | PKS
Region 2.2 | butyrolactone,T2PKS,phenazine | 74,041 | 126,837 |  |
Region 6.1 | NRP-metallophore,NRPS | 109,595 | 168,007 | High | coelichelin | NRPS:Type I
Region 6.2 | terpene-precursor | 223,588 | 244,661 |  |
Region 6.3 | RiPP-like | 420,880 | 431,095 | Low | informatipeptin | ribosomal:RiPP:Lanthipeptide
Region 6.4 | terpene | 773,291 | 800,040 | High | hopene | terpene
Region 6.5 | lanthipeptide-class-iii | 864,996 | 887,692 | High | SAL-2242 | ribosomal:RiPP:Lanthipeptide
Region 6.6 | transAT-PKS,NRPS,NRPS-like | 1,041,144 | 1,153,660 | High | inthomycin B | PKS
Region 6.7 | butyrolactone,RiPP-like | 1,340,905 | 1,365,445 | Low | methylenomycin A | other:other
Region 6.8 | hydrogen-cyanide | 1,375,354 | 1,388,292 |  |
Region 6.9 | NI-siderophore | 1,407,571 | 1,438,785 |  |
Region 6.10 | betalactone | 1,520,283 | 1,548,047 |  |
Region 6.11 | terpene | 1,613,342 | 1,635,564 | High | geosmin | terpene:Sesquiterpene
Region 6.12 | RiPP-like | 1,646,617 | 1,658,002 |  |
Region 6.13 | terpene,NRPS-like,T1PKS,prodigiosin | 1,950,056 | 2,020,937 | High | undecylprodigiosin | NRPS:Type I+PKS
Region 6.14 | NI-siderophore | 2,078,914 | 2,108,746 |  |
Region 6.15 | T2PKS,triceptide | 2,590,494 | 2,678,375 | Medium | nybomycin | other:other
Region 6.16 | terpene-precursor | 2,679,807 | 2,700,967 | Low | echoside A/echoside B/echoside C/echoside D/echoside E | NRPS:Type I
Region 6.17 | terpene | 2,708,476 | 2,729,561 | High | albaflavenone | terpene
Region 6.18 | RRE-containing | 2,833,871 | 2,854,929 |  |
Region 6.19 | RRE-containing | 2,876,355 | 2,897,548 |  |
Region 6.20 | NRPS | 3,676,355 | 3,761,612 | High | sarpeptin A/sarpeptin B | NRPS:Type I
Region 6.21 | NI-siderophore | 5,233,483 | 5,263,261 | High | desferrioxamin B/desferrioxamine E | other:other
Region 6.22 | melanin | 5,341,497 | 5,352,129 | Medium | melanin | other:other
Region 6.23 | ectoine | 6,308,121 | 6,318,519 | High | ectoine | other:other
Region 6.24 | RiPP-like | 6,892,135 | 6,904,054 |
Region 6.25 | T3PKS | 6,996,422 | 7,037,606 | High | flaviolin/1,3,6,8-tetrahydroxynaphthalene | PKS
Region 6.26 | T3PKS | 7,322,828 | 7,364,012 | High | germicidin | other:other
Region 6.27 | terpene | 7,566,174 | 7,590,219 | Medium | carotenoid | terpene
Region 6.28 | indole | 7,652,566 | 7,673,693 | High | 5-dimethylallylindole-3-acetonitrile | other:other
Region 6.29 | terpene | 7,848,171 | 7,869,388 | High | 2-methylisoborneol | terpene

No secondary metabolite regions were found in these records:
  NZ_WHZR01000004.1 (Streptomyces sp. OM5714)
  NZ_WHZR01000005.1 (Streptomyces sp. OM5714)
  NZ_WHZR01000006.1 (Streptomyces sp. OM5714)

Compact view
NZ_WHZR01000002.1 - Region 1 - NRPS,T1PKS,arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 133,478 - 193,464 nt. (total: 59,987 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
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
STPH1_RS36150: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

STPH1_RS36175: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

STPH1_RS36290: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: aminotransferase
STPH1_RS36170: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

STPH1_RS36220: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: hydrolase
STPH1_RS36140: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Ligases: ligase synthase
STPH1_RS36185: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

STPH1_RS36190: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

STPH1_RS36195: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

STPH1_RS36205: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

STPH1_RS36230: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

STPH1_RS36240: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

STPH1_RS36250: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

STPH1_RS36255: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transport
STPH1_RS36325: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | arylpolyene | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  |  | 1.27 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  |  |  | 1.16 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  |  | 1.15 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  |  | 1.14 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  |  | 1.13 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 1.09 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  |  |  | 1.08 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  |  |  | 1.06 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  |  |  | 1.06 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  |  |  | 1.01 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.67 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (26):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.16 out of 25.88
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.13 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.00 out of 23.43
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.03 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.61 out of 30.97
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 out of 26.12
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.04 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.16 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.09 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.84 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.19 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.94 out of 20.01
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.68 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.60 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.52 out of 39.62
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.52 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.46 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.52 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.78 out of 29.65
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.60 out of 26.85
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 133477 - 193464:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (Cys) + (X) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 133477 - 174614:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (Cys) + (X) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 137265 - 193464:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (Cys) + (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).
STPH1_RS36190: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (19..426): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQSFDVIYQEPFVLTSGEVNQWGTTETHVATWY
  Nearest Stachelhaus code(s):
    Pro DVQFVSQVMK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

STPH1_RS36195: X
AMP-binding (48..383): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNALYGLVAQAAALTVGGDYLTYGLSEAGPRVTT
  Nearest Stachelhaus code(s):
    Suc ALQSTGTPRK (91% 8Å match)
  Stachelhaus code match:
    80% (moderate)

STPH1_RS36240: X
AMP-binding (481..875): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VWGAFDTSVLDPDLISGGDLNEYGPTETTVTATA
  Nearest Stachelhaus code(s):
    Lys DTCDIGTVIK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

STPH1_RS36250: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (467..863): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNSMMSGDISLGGATEGSIWSVF
  Nearest Stachelhaus code(s):
    Cys DLYNMSLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

STPH1_RS36255: mal
PKS_AT (500..795): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 98.6
  inactive: 63.3
  Methylmalonyl-CoA: 54.1
  Methoxymalonyl-CoA: 52.9
  Propionyl-CoA: 35.8
  Ethylmalonyl-CoA: 26.3
  CHC-CoA: 24.1
  2-Methylbutyryl-CoA: 15.9
  Acetyl-CoA: 15.4
  Benzoyl-CoA: 14.6
  trans-1,2-CPDA: 13.6
  fatty_acid: 11.5
  Isobutyryl-CoA: 7.4
  3-Methylbutyryl-CoA: 6.9

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein

NZ_WHZR01000002.1 - Region 2 - T1PKS,hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 338,010 - 391,337 nt. (total: 53,328 nt) Show pHMM detection rules used
hglE-KS: (hglE or hglD)
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
STPH1_RS36910: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS36960: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acylase
STPH1_RS36900: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
STPH1_RS37010: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

STPH1_RS37015: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: synthase
STPH1_RS36905: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

STPH1_RS36915: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
STPH1_RS36890: 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 | hglE-KS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  |  | 0.63 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000869.5 |  |  | 0.60 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001164.3 |  |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.55 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000863.3 |  |  | 0.53 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0000861.5 |  |  | 0.52 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0002648.2 |  |  | 0.52 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.65 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000869.5 |  | 0.63 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000863.3 |  | 0.60 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0000861.5 |  | 0.60 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0002648.2 |  | 0.59 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL

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: 16.82 out of 18.46
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
Additional weak hits (14):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.52 out of 20.97
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.14 out of 29.51
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.70 out of 26.12
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.53 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.96 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.50 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.45 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.02 out of 29.65
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.12 out of 28.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.80 out of 24.78
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.53 out of 32.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.12 out of 26.85
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 4, location 338009 - 391337:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).
STPH1_RS36905: pk
PKS_AT (1057..1375): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

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

STPH1_RS36915: mal
PKS_AT (577..874): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 62.5%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 86.5
  Methoxymalonyl-CoA: 50.3
  inactive: 46.0
  CHC-CoA: 41.0
  Methylmalonyl-CoA: 38.2
  Propionyl-CoA: 25.1
  2-Methylbutyryl-CoA: 16.8
  Isobutyryl-CoA: 16.7
  fatty_acid: 16.6
  trans-1,2-CPDA: 14.9
  Ethylmalonyl-CoA: 12.5
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_WHZR01000003.1 - Region 1 - other
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: 22,756 - 63,172 nt. (total: 40,417 nt) Show pHMM detection rules used
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
STPH1_RS38160: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

STPH1_RS38165: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: glycosyltransferase methyltransferase
STPH1_RS38005: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

STPH1_RS38155: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: amidase dehalogenase
STPH1_RS38090: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

STPH1_RS38140: amidase

smcogs
  SMCOG1105: amidase

Lyases: cyclase dehydratase lyase
STPH1_RS38020: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

STPH1_RS38130: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

STPH1_RS38170: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

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 | other | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000193.3 |  | 0.50 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0001336.5 |  | 0.48 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000214.5 |  | 0.48 | PKS | cosmomycin B | Streptomyces olindensis
BGC0001817.5 |  | 0.48 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0000236.5 |  | 0.48 | PKS | kinamycin | Streptomyces murayamaensis
BGC0000898.5 |  | 0.47 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0000899.4 |  | 0.47 | saccharide | desosamine | Streptomyces narbonensis
BGC0000678.5 |  | 0.46 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000253.4 |  | 0.46 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000278.3 |  | 0.46 | PKS | urdamycin | Streptomyces fradiae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000193.3 |  | 0.50 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0001336.5 |  | 0.48 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000214.5 |  | 0.48 | PKS | cosmomycin B | Streptomyces olindensis
BGC0001817.5 |  | 0.48 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0000236.5 |  | 0.48 | PKS | kinamycin | Streptomyces murayamaensis
BGC0000898.5 |  | 0.47 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0000899.4 |  | 0.47 | saccharide | desosamine | Streptomyces narbonensis
BGC0000678.5 |  | 0.46 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000253.4 |  | 0.46 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000278.3 |  | 0.46 | PKS | urdamycin | Streptomyces fradiae

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.07 out of 30.12
Confidence: medium
Additional weak hits (10):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.44 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.59 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.93 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.22 out of 36.54
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.03 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.49 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.44 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_WHZR01000003.1 - Region 2 - T2PKS,butyrolactone,phenazine
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: 74,041 - 126,837 nt. (total: 52,797 nt) Show pHMM detection rules used
Region on contig edge.
butyrolactone: AfsA
T2PKS: (t2ks and t2clf)
phenazine: phzB

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
STPH1_RS38270: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: methyltransferase transferase
STPH1_RS38245: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

STPH1_RS38380: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Hydrolases: back translocase dehalogenase esterase
STPH1_RS38465: thioesterase

smcogs
  SMCOG1004: thioesterase

STPH1_RS38475: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

STPH1_RS38490: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Ligases: ligase synthase
STPH1_RS38455: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

STPH1_RS38460: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

STPH1_RS38470: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | butyrolactone | T2PKS | phenazine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000849.4 |  |  |  | 0.54 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000231.5 |  |  |  | 0.49 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000848.5 |  |  |  | 0.49 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001513.3 |  |  |  | 0.48 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000272.3 |  |  |  | 0.46 | PKS | spore pigment | Streptomyces collinus
BGC0000850.5 |  |  |  | 0.44 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000221.5 |  |  |  | 0.43 | PKS | erdacin | uncultured soil bacterium V167
BGC0000197.5 |  |  |  | 0.43 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0001366.5 |  |  |  | 0.42 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2
BGC0000204.5 |  |  |  | 0.42 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.70 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.63 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000231.5 |  | 0.59 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001641.4 |  | 0.58 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000272.3 |  | 0.58 | PKS | spore pigment | Streptomyces collinus
BGC0000234.5 |  | 0.56 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001240.4 |  | 0.55 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0002000.4 |  | 0.53 | PKS | setomimycin | Streptomyces aurantiacus JA 4570

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 26.85
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.06 out of 28.19
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (27):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.42 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.18 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.81 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.92 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.45 out of 27.78
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.81 out of 39.62
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.57 out of 36.54
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.19 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.16 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.94 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.16 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.88 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.52 out of 28.19
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.39 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.13 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.71 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.91 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.55 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.96 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.50 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.88 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.57 out of 36.53
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.82 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  80053 to 126837
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:
  8|9 (Score: 649.0; E-value: 5.4e-198)
Product class(es):
  angucycline
  anthracycline
  aureolic acid
  tetracenomycin
  tetracycline
Product molecular weight(s):
  acetyl-CoA_8: 395 Da
  acetyl-CoA_9: 437 Da

STPH1_RS38270
  OXY (Score: 348.4; E-value: 1.7e-106)
STPH1_RS38455
  CLF 8|9 (Score: 649.0; E-value: 5.4e-198)
STPH1_RS38460
  KS (Score: 758.1; E-value: 5.3e-231)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
RutR | Regulator of the pyrimidine and purine metabolism
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_WHZR01000001.1 - Region 1 - 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: 109,595 - 168,007 nt. (total: 58,413 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: oxygenase
STPH1_RS00670: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: formyltransferase kinase
STPH1_RS00675: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

STPH1_RS00715: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Hydrolases: esterase phosphatase
STPH1_RS00575: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

STPH1_RS00625: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

Ligases: ligase
STPH1_RS00640: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000325.5 |  |  | 0.95 | NRPS | coelichelin | Streptomyces coelicolor A3(2)
BGC0001240.4 |  |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001166.5 |  |  | 0.57 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000357.5 |  |  | 0.57 | 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
BGC0000307.4 |  |  | 0.57 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001825.4 |  |  | 0.55 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  |  | 0.55 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  | 0.55 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002476.2 |  |  | 0.42 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0002494.3 |  |  | 0.39 | NRPS | vibriobactin | Vibrio cholerae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000325.5 |  | 0.77 | NRPS | coelichelin | Streptomyces coelicolor A3(2)
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001166.5 |  | 0.62 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000357.5 |  | 0.62 | 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
BGC0000307.4 |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001825.4 |  | 0.61 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.61 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.61 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002476.2 |  | 0.54 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0002494.3 |  | 0.52 | 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:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 35.53 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.30 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 36.53
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.61 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.68 out of 30.12
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.66 out of 30.12
Confidence: medium
Additional weak hits (14):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 25.75
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.79 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.26 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.63 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.89 out of 21.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.02 out of 27.04
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.39 out of 36.53
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 39.62
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.57 out of 36.53
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.74 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.81 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 109594 - 168007:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
STPH1_RS00640: Fo-OH-Orn - Thr - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (144..542): Fo-OH-Orn
nrpys: Fo-OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWQAFDISVNELYLWCGGEYHGYGPAETTIGVSH
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DINYWGGIGK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1637..2050): Thr
nrpys: Thr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LRTHFDFAVWEGNQVFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3089..3491): OH-Orn
nrpys: OH-Orn

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

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

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator

NZ_WHZR01000001.1 - Region 2 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 223,588 - 244,661 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
Hydrolases: deacetylase
STPH1_RS01050: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Ligases: synthetase
STPH1_RS01030: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001456.3 |  | 0.36 | terpene | isorenieratene | Streptomyces argillaceus
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001824.4 |  | 0.36 | NRPS | xefoampeptides A-G | Xenorhabdus beddingii
BGC0001910.4 |  | 0.36 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000906.3 |  | 0.30 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000905.5 |  | 0.29 | other (other) | heme D1 | Heliobacillus mobilis
BGC0001078.5 |  | 0.29 | PKS, terpene | furaquinocin B | Streptomyces sp. KO-3988
BGC0000679.5 |  | 0.29 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0000652.5 |  | 0.28 | terpene | napyradiomycin | Streptomyces sp. CNQ525

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001456.3 |  | 0.36 | terpene | isorenieratene | Streptomyces argillaceus
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001824.4 |  | 0.36 | NRPS | xefoampeptides A-G | Xenorhabdus beddingii
BGC0001910.4 |  | 0.36 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000906.3 |  | 0.30 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000905.5 |  | 0.29 | other (other) | heme D1 | Heliobacillus mobilis
BGC0001078.5 |  | 0.29 | PKS, terpene | furaquinocin B | Streptomyces sp. KO-3988
BGC0000679.5 |  | 0.29 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0000652.5 |  | 0.28 | terpene | napyradiomycin | Streptomyces sp. CNQ525

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:
STPH1_RS01030: PT_FPPS_like
Domain 1 (49 - 333): 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.
No hits above weak threshold.
Weak hits (2):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.47 out of 27.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.37 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_WHZR01000001.1 - Region 3 - 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: 420,880 - 431,095 nt. (total: 10,216 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000518.3 |  | 0.49 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0001555.4 |  | 0.47 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.46 | ribosomal | microcin N | Escherichia coli
BGC0000588.5 |  | 0.46 | ribosomal | microcin L | Escherichia coli
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002698.2 |  | 0.42 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0000484.5 |  | 0.40 | ribosomal | glycocin F | Lactobacillus plantarum
BGC0000589.5 |  | 0.38 | ribosomal | microcin M | Escherichia coli Nissle 1917
BGC0000617.5 |  | 0.38 | ribosomal | coagulin | Bacillus coagulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000518.3 |  | 0.49 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0001555.4 |  | 0.47 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.46 | ribosomal | microcin N | Escherichia coli
BGC0000588.5 |  | 0.46 | ribosomal | microcin L | Escherichia coli
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002698.2 |  | 0.42 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0000484.5 |  | 0.40 | ribosomal | glycocin F | Lactobacillus plantarum
BGC0000589.5 |  | 0.38 | ribosomal | microcin M | Escherichia coli Nissle 1917
BGC0000617.5 |  | 0.38 | ribosomal | coagulin | Bacillus coagulans

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.26 out of 28.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.54 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_WHZR01000001.1 - Region 4 - 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: 773,291 - 800,040 nt. (total: 26,750 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
STPH1_RS03655: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

STPH1_RS03690: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase
STPH1_RS03620: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

STPH1_RS03695: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Ligases: synthase synthetase
STPH1_RS03625: 1-deoxy-D-xylulose-5-phosphate synthase

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

STPH1_RS03650: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.91 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.52 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.91 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.52 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica

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

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

Genes with terpene domains:
STPH1_RS03645: T2TS
Domain 1 (28 - 662): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

STPH1_RS03650: PT_FPPS_like
Domain 1 (60 - 352): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

STPH1_RS03660: PT_phytoene_like
Domain 1 (7 - 299): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

STPH1_RS03665: PT_phytoene_like
Domain 1 (19 - 279): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
Additional weak hits (19):
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.46 out of 29.51
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.08 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.93 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.85 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.47 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.43 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.00 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.68 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.27 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.49 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.49 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.38 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.89 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.89 out of 28.14
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.55 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.85 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.72 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MexT | Global virulence regulator

NZ_WHZR01000001.1 - Region 5 - 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: 864,996 - 887,692 nt. (total: 22,697 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
Transferases: PPTase
STPH1_RS04030: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

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
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.83 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000496.5 |  | 0.64 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000553.3 |  | 0.57 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000501.3 |  | 0.57 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.57 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000518.3 |  | 0.51 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000546.3 |  | 0.51 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0002700.2 |  | 0.48 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002698.2 |  | 0.46 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.83 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000496.5 |  | 0.64 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000553.3 |  | 0.57 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000501.3 |  | 0.57 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.57 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000518.3 |  | 0.51 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000546.3 |  | 0.51 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0002700.2 |  | 0.48 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002698.2 |  | 0.46 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566

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 STPH1_RS04010

STPH1_RS04005
Leader:
MNLFDLQSMETPKEEAMGDVE
Core:
TGSRASLLLCGDSSLSITTCN
Core with dehydrations:
DhbGDhaRADhaLLLCysGDDhaDhaLDhaIDhbDhbCysN

#### antiSMASH-DB 4.0 matches for STPH1_RS04005

100.0%
NZ_BBOK01000011.1 and 23 others:
NZ_BEWD01000001.1 Lanthipeptides: Sru02f_RS01660_lanthipeptide NZ_BMSL01000016.1 Lanthipeptides: IE215_RS23330_lanthipeptide NZ_BMUC01000023.1 Lanthipeptides: IE172_RS32210_lanthipeptide NZ_BMVQ01000005.1 Lanthipeptides: IE283_RS17035_lanthipeptide NZ_BMWI01000025.1 Lanthipeptides: IE253_RS33945_lanthipeptide NZ_CP012382.1 Lanthipeptides: SAM23877_RS30085_lanthipeptide NZ_CP012949.1 Lanthipeptides: SAM40697_RS29010_lanthipeptide NZ_CP042324.1 Lanthipeptides: FQ762_RS34495_lanthipeptide NZ_CP043959.1 Lanthipeptides: F3L20_RS19105_lanthipeptide NZ_CP045547.1 Lanthipeptides: GEV49_RS05730_lanthipeptide NZ_CP054939.1 Lanthipeptides: HUT14_RS29815_lanthipeptide NZ_CP094918.1 Lanthipeptides: MTR79_RS16715_lanthipeptide NZ_GG657756.1 Lanthipeptides: SSPG_RS05020_lanthipeptide NZ_JAAIFS010000001.1 Lanthipeptides: GUR47_RS02255_lanthipeptide NZ_KZ195574.1 Lanthipeptides: B9W62_RS05695_lanthipeptide NZ_LT629768.1 Lanthipeptides: BLU60_RS34110_lanthipeptide NZ_MQUH01000025.1 Lanthipeptides: BSZ07_RS33280_lanthipeptide NZ_RAII01000001.1 Lanthipeptides: EBH12_RS10360_lanthipeptide NZ_RSEG01000006.1 Lanthipeptides: EIA57_RS12710_lanthipeptide NZ_SOAV01000001.1 Lanthipeptides: EV562_RS04520_lanthipeptide NZ_VIUV01000020.1 Lanthipeptides: FB570_RS34060_lanthipeptide NZ_WHZR01000001.1 Lanthipeptides: STPH1_RS04005_lanthipeptide NZ_WXVT01000001.1 Lanthipeptides: STPH2_RS03995_lanthipeptide
Lanthipeptides: APK71_RS25550_lanthipeptide
1
TGSRASLLLCGDSSLSITTCN
21
TGSRASLLLCGDSSLSITTCN
1
TGSRASLLLCGDSSLSITTCN
21
95.2%
NC_018750.1 and 67 others:
NC_018750.1 Lanthipeptides: SVEN_RS32110_lanthipeptide NZ_BBNO01000003.1 Lanthipeptides: TU31_RS37940_lanthipeptide NZ_BMTO01000007.1 Lanthipeptides: IE136_RS15615_lanthipeptide NZ_BMUN01000001.1 Lanthipeptides: IE238_RS00740_lanthipeptide NZ_CP009754.1 Lanthipeptides: NI25_RS05015_lanthipeptide NZ_CP015866.1 Lanthipeptides: Spa2297_RS27800_lanthipeptide NZ_CP017157.1 Lanthipeptides: SL103_RS15895_lanthipeptide NZ_CP019457.1 Lanthipeptides: BXT88_RS03410_lanthipeptide NZ_CP019724.1 Lanthipeptides: B1H29_RS35355_lanthipeptide NZ_CP019779.1 Lanthipeptides: STRMOE7_RS03775_lanthipeptide NZ_CP023691.1 Lanthipeptides: CP981_RS03050_lanthipeptide NZ_CP023700.1 Lanthipeptides: CP969_RS04700_lanthipeptide NZ_CP027299.1 Lanthipeptides: C1N79_RS34970_lanthipeptide NZ_CP029042.1 Lanthipeptides: DDE74_RS03525_lanthipeptide NZ_CP029195.1 Lanthipeptides: DEJ45_RS04995_lanthipeptide NZ_CP029195.1 Lanthipeptides: DEJ45_RS04995_lanthipeptide NZ_CP029196.1 Lanthipeptides: DEJ44_RS30395_lanthipeptide NZ_CP029196.1 Lanthipeptides: DEJ44_RS30395_lanthipeptide NZ_CP029541.1 Lanthipeptides: DKG71_RS05245_lanthipeptide NZ_CP034353.1 Lanthipeptides: D1J63_RS04900_lanthipeptide NZ_CP039123.1 Lanthipeptides: E5N77_RS35250_lanthipeptide NZ_CP043317.1 Lanthipeptides: FYC74_RS09720_lanthipeptide NZ_CP046905.1 Lanthipeptides: GPZ77_RS32930_lanthipeptide NZ_CP047140.1 Lanthipeptides: GLX30_RS11420_lanthipeptide NZ_CP050976.1 Lanthipeptides: HEP86_RS04470_lanthipeptide NZ_CP054920.1 Lanthipeptides: HUT15_RS04615_lanthipeptide NZ_CP060825.1 Lanthipeptides: IAG43_RS32355_lanthipeptide NZ_CP074111.1 Lanthipeptides: KE639_RS31630_lanthipeptide NZ_CP084681.1 Lanthipeptides: KI385_RS00885_lanthipeptide NZ_CP085300.1 Lanthipeptides: LJA35_RS05220_lanthipeptide NZ_CP086217.1 Lanthipeptides: LJ741_RS03435_lanthipeptide NZ_CP094676.1 Lanthipeptides: L6J92_RS09690_lanthipeptide NZ_CP098437.1 Lanthipeptides: NCG97_RS34740_lanthipeptide NZ_CP099468.1 Lanthipeptides: NFX46_RS16770_lanthipeptide NZ_CP101137.1 Lanthipeptides: M6G08_RS24535_lanthipeptide NZ_CP102609.1 Lanthipeptides: NUT86_RS03980_lanthipeptide NZ_CP104697.1 Lanthipeptides: N6Q81_RS33560_lanthipeptide NZ_CP114202.1 Lanthipeptides: STRLI_RS35870_lanthipeptide NZ_CP114203.1 Lanthipeptides: STRNI_RS37360_lanthipeptide NZ_CP114205.1 Lanthipeptides: STRTU_RS33380_lanthipeptide NZ_JACHJE010000006.1 Lanthipeptides: FHS32_RS15850_lanthipeptide NZ_JACSCH020000032.1 Lanthipeptides: E0F75_RS38565_lanthipeptide NZ_JACSCH020000032.1 Lanthipeptides: E0F75_RS38565_lanthipeptide NZ_JACSCH020000032.1 Lanthipeptides: E0F75_RS38565_lanthipeptide NZ_JACWAA010000001.1 Lanthipeptides: ICA23_RS00800_lanthipeptide NZ_JAFEJA010000002.1 Lanthipeptides: JE024_RS34830_lanthipeptide NZ_JAGPYC010000033.1 Lanthipeptides: KBZ00_RS31440_lanthipeptide NZ_JAHLXF010000022.1 Lanthipeptides: KQY13_RS30555_lanthipeptide NZ_JAIHBQ010000001.1 Lanthipeptides: K4902_RS04515_lanthipeptide NZ_JAJJMU010000026.1 Lanthipeptides: LOC25_RS31275_lanthipeptide NZ_JAJNOJ010000002.1 Lanthipeptides: MBT42_RS06255_lanthipeptide NZ_JAJNOJ010000002.1 Lanthipeptides: MBT42_RS06255_lanthipeptide NZ_JAMGSL010000004.1 Lanthipeptides: M5362_RS09920_lanthipeptide NZ_JAMGSL010000004.1 Lanthipeptides: M5362_RS09920_lanthipeptide NZ_JAPKNL010000004.1 Lanthipeptides: OSI21_RS07750_lanthipeptide NZ_JH993790.1 Lanthipeptides: STRVIR_RS0131905_lanthipeptide NZ_KN039948.1 Lanthipeptides: FM21_RS29525_lanthipeptide NZ_LIPF01000004.1 Lanthipeptides: AMK11_RS16660_lanthipeptide NZ_LIVV01000002.1 Lanthipeptides: AMK27_RS08700_lanthipeptide NZ_LIVV01000002.1 Lanthipeptides: AMK27_RS08700_lanthipeptide NZ_LIVX01000004.1 Lanthipeptides: AMK29_RS15650_lanthipeptide NZ_LIWB01000010.1 Lanthipeptides: AMK33_RS24360_lanthipeptide NZ_MPOH02000012.1 Lanthipeptides: BM536_RS17150_lanthipeptide NZ_NNBP01000011.1 Lanthipeptides: CG747_RS19290_lanthipeptide NZ_NNBP01000011.1 Lanthipeptides: CG747_RS19290_lanthipeptide NZ_RAIF01000032.1 Lanthipeptides: EBH09_RS35480_lanthipeptide NZ_SOPG01000008.1 Lanthipeptides: E0I08_RS17090_lanthipeptide
Lanthipeptides: SVEN_RS32110_lanthipeptide
1
TGSRASLLLCGDSSLSITTCN
21
TGSRASLLLCGDSSLS+TTCN
1
TGSRASLLLCGDSSLSVTTCN
21
95.2%
NZ_GG657758.1 and 1 other:
NZ_JACHEM010000005.1 Lanthipeptides: HNQ79_RS11445_lanthipeptide
Lanthipeptides: SSRG_RS03855_lanthipeptide
1
TGSRASLLLCGDSSLSITTCN
21
+GSRASLLLCGDSSLSITTCN
1
SGSRASLLLCGDSSLSITTCN
21
with 71 more sequence matches
Only the first 10 are displayed here.
90.5%
NZ_BMSV01000002.1 and 18 others:
NZ_BMTP01000009.1 Lanthipeptides: IE109_RS18470_lanthipeptide NZ_CP007699.2 Lanthipeptides: T261_RS39185_lanthipeptide NZ_CP020042.1 Lanthipeptides: B4U46_RS32710_lanthipeptide NZ_CP023202.1 Lanthipeptides: SXIN_RS23100_lanthipeptide NZ_CP023692.1 Lanthipeptides: CP980_RS04735_lanthipeptide NZ_CP028158.1 Lanthipeptides: C6361_RS04660_lanthipeptide NZ_CP028159.1 Lanthipeptides: C6W10_RS01185_lanthipeptide NZ_CP034279.1 Lanthipeptides: EIZ62_RS28660_lanthipeptide NZ_CP102332.1 Lanthipeptides: NRO40_RS01140_lanthipeptide NZ_FNHI01000003.1 Lanthipeptides: BLT82_RS06465_lanthipeptide NZ_JADMLH010000003.1 Lanthipeptides: IT780_RS09875_lanthipeptide NZ_JAGGOI010000031.1 Lanthipeptides: J7E87_RS22160_lanthipeptide NZ_JAGPXX010000007.1 Lanthipeptides: KBZ10_RS10785_lanthipeptide NZ_JAPNLM010000003.1 Lanthipeptides: OTB16_RS07305_lanthipeptide NZ_LIVQ01000005.1 Lanthipeptides: AMK16_RS35205_lanthipeptide NZ_LIVQ01000005.1 Lanthipeptides: AMK16_RS35205_lanthipeptide NZ_LIYH01000004.1 Lanthipeptides: AMK26_RS17765_lanthipeptide NZ_NBCN01000003.1 Lanthipeptides: BKD26_RS06570_lanthipeptide
Lanthipeptides: IE106_RS06150_lanthipeptide
2
GSRASLLLCGDSSLSITTCN
21
GSRASLLLCGDSSLS+TTCN
1
GSRASLLLCGDSSLSVTTCN
20
90.5%
NZ_BMTU01000009.1 and 1 other:
NZ_JACHJI010000005.1 Lanthipeptides: FHS37_RS15430_lanthipeptide
Lanthipeptides: IE118_RS22890_lanthipeptide
1
TGSRASLLLCGDSSLSITTCN
21
+GSRASLLLCGDSSLS+TTCN
1
SGSRASLLLCGDSSLSVTTCN
21
90.5%
NZ_BNCA01000002.1 and 1 other:
NZ_CP049782.1 Lanthipeptides: G7Z12_RS34445_lanthipeptide
Lanthipeptides: IE314_RS02760_lanthipeptide
1
TGSRASLLLCGDSSLSITTCN
21
TGSRASLLLCGDSSLS++TCN
1
TGSRASLLLCGDSSLSVSTCN
21
85.7%
NZ_CP036455.1:
Lanthipeptides: EKD16_RS17975_lanthipeptide
2
GSRASLLLCGDSSLSITTCN
21
GS ASLLLCGDSSLS+TTCN
2
GSEASLLLCGDSSLSLTTCN
21
85.7%
NZ_CP048835.1:
Lanthipeptides: C8250_RS00390_lanthipeptide
2
GSRASLLLCGDSSLSITTCN
21
GSRASLLLCG+SSLS+TTCN
2
GSRASLLLCGNSSLSVTTCN
21
85.7%
NZ_QGGR01000008.1:
Lanthipeptides: BC793_RS19230_lanthipeptide
2
GSRASLLLCGDSSLSITTCN
21
GS+ASLLLCGDSSLS+TTCN
2
GSQASLLLCGDSSLSVTTCN
21
83.3%
NZ_BMVE01000003.1 and 22 others:
NZ_BMVL01000005.1 Lanthipeptides: IE257_RS16230_lanthipeptide NZ_CM002280.1 Lanthipeptides: M877_RS44575_lanthipeptide NZ_CP011664.1 Lanthipeptides: M444_RS30240_lanthipeptide NZ_CP018047.1 Lanthipeptides: BBN63_RS03065_lanthipeptide NZ_CP020039.1 Lanthipeptides: B4U39_RS34445_lanthipeptide NZ_CP020555.1 Lanthipeptides: B6R96_RS03515_lanthipeptide NZ_CP023701.1 Lanthipeptides: CP968_RS29065_lanthipeptide NZ_CP029189.1 Lanthipeptides: DEJ51_RS31910_lanthipeptide NZ_CP030286.1 Lanthipeptides: DRB89_RS16930_lanthipeptide NZ_CP033581.1 Lanthipeptides: EES41_RS31595_lanthipeptide NZ_CP034350.1 Lanthipeptides: D1J60_RS32970_lanthipeptide NZ_CP043638.1 Lanthipeptides: F1D59_RS34930_lanthipeptide NZ_CP048397.1 Lanthipeptides: SSPS47_RS31455_lanthipeptide NZ_CP115936.1 Lanthipeptides: PET44_RS28650_lanthipeptide NZ_CP116355.1 Lanthipeptides: KPP03845_RS32700_lanthipeptide NZ_JAFLQY010000003.1 Lanthipeptides: J0X20_RS29030_lanthipeptide NZ_JAINUL010000001.1 Lanthipeptides: K7B10_RS06210_lanthipeptide NZ_JANAVF010000017.1 Lanthipeptides: NLX94_RS31205_lanthipeptide NZ_LIVP01000027.1 Lanthipeptides: AMK15_RS28680_lanthipeptide NZ_LWLD01000038.1 Lanthipeptides: A6A28_RS28600_lanthipeptide NZ_ML123038.1 Lanthipeptides: EES37_RS30340_lanthipeptide NZ_NNBM01000002.1 Lanthipeptides: CG724_RS07855_lanthipeptide
Lanthipeptides: IE248_RS10435_lanthipeptide
2
GSRASLLLCGDSSLSITTCN
21
GSRASLLLCGDSSLSITTCN
5
GSRASLLLCGDSSLSITTCN
24
81.0%
NZ_CP024087.1 and 1 other:
NZ_JAAALO010000001.1 Lanthipeptides: GVV04_RS02250_lanthipeptide
Lanthipeptides: CSH63_RS05810_lanthipeptide
5
ASLLLCGDSSLSITTCN
21
ASLLLCGDSSLSITTCN
1
ASLLLCGDSSLSITTCN
17
81.0%
NZ_CP077658.1:
Lanthipeptides: KQY30_RS33045_lanthipeptide
2
GSRASLLLCGDSSLSITTCN
21
SRASLLLCGDSSLS+ TCN
1
ASRASLLLCGDSSLSVVTCN
20
81.0%
NZ_CP092183.1:
Lanthipeptides: COUCH_RS09775_lanthipeptide
4
RASLLLCGDSSLSITTCN
21
RASLLLCGDSSLS+TTCN
1
RASLLLCGDSSLSVTTCN
18

#### MIBiG 4.0 matches for STPH1_RS04005

54.5%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
1
TGSRASLLLCGDSSLSITTCN
21
TGS+ SLL+C SSLS+ C
1
TGSQVSLLVCEYSSLSVVLCT
21

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 26.03 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 30.11
Confidence: medium
Additional weak hits (13):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.39 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.29 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.66 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.40 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.07 out of 30.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.70 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.69 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.80 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.84 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.10 out of 29.65
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38
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.

STPH1_RS04005 - Class III
  Cleavage pHMM score: 32.20
  RODEO score: 0
  Monoisotopic mass: 1954.0 Da
  Molecular weight: 1955.2 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1973.2 Da N = 1
    1991.2 Da N = 2
    2009.2 Da N = 3
    2027.3 Da N = 4
    2045.3 Da N = 5
    2063.3 Da N = 6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
OsdR | Development and stress management regulator

NZ_WHZR01000001.1 - Region 6 - NRPS,NRPS-like,transAT-PKS
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: 1,041,144 - 1,153,660 nt. (total: 112,517 nt) Show pHMM detection rules used
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer oxidoreductase
STPH1_RS04655: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

STPH1_RS04660: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS04730: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS04740: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS04795: flavodoxin

smcogs
  SMCOG1134: flavodoxin

STPH1_RS39815: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acylase formyltransferase methyltransferase
STPH1_RS04665: methyltransferase

smcogs
  SMCOG1089: methyltransferase

STPH1_RS04690: methyltransferase

smcogs
  SMCOG1089: methyltransferase

STPH1_RS04705: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

STPH1_RS04725: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

STPH1_RS04750: methyltransferase

smcogs
  SMCOG1089: methyltransferase

STPH1_RS04760: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Lyases: dehydratase
STPH1_RS04770: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
STPH1_RS04650: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

STPH1_RS04715: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

STPH1_RS04755: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

STPH1_RS04765: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: permease
STPH1_RS04830: 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 | transAT-PKS | NRPS | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002451.2 |  |  |  |  | 1.58 | PKS | inthomycin B | Streptomyces sp.
BGC0001261.3 |  |  |  |  | 1.35 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  |  |  |  | 1.30 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002135.2 |  |  |  |  | 1.30 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  |  |  |  | 1.28 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  | 1.27 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  |  |  |  | 1.26 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  |  |  |  | 1.21 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001166.5 |  |  |  |  | 1.20 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001758.4 |  |  |  |  | 1.19 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002451.2 |  | 0.92 | PKS | inthomycin B | Streptomyces sp.
BGC0000342.4 |  | 0.74 | NRPS | enniatin | Fusarium equiseti
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002164.2 |  | 0.68 | NRPS | peramine | Epichloe festucae
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001250.4 |  | 0.67 | NRPS | epichloenin A | Epichloe festucae

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:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.17 out of 30.11
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
Additional weak hits (15):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.60 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.84 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.04 out of 18.57
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.55 out of 29.72
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.50 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.43 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.46 out of 36.54
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.42 out of 35.63
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.33 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.69 out of 29.65
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.21 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.37 out of 18.57
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 6, location 1041143 - 1153660:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (ohmal - mal) + (Ser - NMe-X) + (ccmal - Me-ccmal) + (Gly) + (Me-ohmal - Gly - ccmal - ccmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
STPH1_RS04650: X
AMP-binding (23..477): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    ETVLFGRMVE--LA---------GPFEKAVDVAV
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

STPH1_RS04705: mal - mal
PKS_AT (22..311): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 38.7
  Isobutyryl-CoA: 19.4
  Methylmalonyl-CoA: 16.3
  Propionyl-CoA: 14.4
  Benzoyl-CoA: 14.4
  Methoxymalonyl-CoA: 14.2
  inactive: 12.7
  2-Methylbutyryl-CoA: 7.5
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (363..640): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 66.7%
  2-Methylbutyryl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 112.6
  inactive: 50.8
  Methoxymalonyl-CoA: 48.2
  Methylmalonyl-CoA: 47.6
  2-Methylbutyryl-CoA: 36.7
  Propionyl-CoA: 35.2
  fatty_acid: 25.9
  Isobutyryl-CoA: 22.1
  CHC-CoA: 15.8
  Benzoyl-CoA: 12.7
  Ethylmalonyl-CoA: 10.7
  Acetyl-CoA: 10.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

STPH1_RS39815: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (2243..2630): Gly
nrpys: Gly

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

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

STPH1_RS04725: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (565..947): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FTMTFDIAGLELQALCGGEFNMYGPTETTIWSTV
  Nearest Stachelhaus code(s):
    Gly DILQLGMIWK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

STPH1_RS04750: Ser - X
Search NORINE for peptide: strict or relaxed
AMP-binding (513..923): 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:
    RWMTFDVSVWEWHFFCSGEHNLYGPTEAAVDVSH
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (100% 8Å match)
    Ala or Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1610..1988): X
nrpys: Gly, Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    WWKTFDVSVPEWHFETAGEHNLYGPTEGGPITAC
  Nearest Stachelhaus code(s):
    Ala DVPDEALVEK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_WHZR01000001.1 - Region 7 - RiPP-like,butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,340,905 - 1,365,445 nt. (total: 24,541 nt) Show pHMM detection rules used
butyrolactone: AfsA
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
STPH1_RS05635: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

STPH1_RS05650: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

STPH1_RS05665: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS05705: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

STPH1_RS05720: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

STPH1_RS05740: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase
STPH1_RS05715: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Isomerases: racemase
STPH1_RS05645: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: synthase
STPH1_RS05695: 3-oxoacyl-(acyl carrier protein) synthase III

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

STPH1_RS05710: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs
  SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase 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 | butyrolactone | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000848.5 |  |  | 0.92 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  |  | 0.92 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  |  | 0.55 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  |  | 0.34 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002584.2 |  |  | 0.30 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002496.3 |  |  | 0.30 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000234.5 |  |  | 0.29 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001810.3 |  |  | 0.29 | PKS | trehangelin | Polymorphospora rubra
BGC0002554.2 |  |  | 0.29 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
BGC0001850.4 |  |  | 0.29 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.76 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.61 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002506.3 |  | 0.47 | PKS | homopiloquinone, piloquinone | Streptomyces sp. FXJ8.102
BGC0002578.2 |  | 0.46 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001810.3 |  | 0.46 | PKS | trehangelin | Polymorphospora rubra
BGC0001850.4 |  | 0.46 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0002496.3 |  | 0.45 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0002584.2 |  | 0.45 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000922.5 |  | 0.45 | PKS | 2-heptyl-3-hydroxy-4-quinolone, 2,4-Quinolinediol, 2-heptylquinolin-4(1H)-one | Pseudomonas aeruginosa PAO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.36 out of 29.65
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.71 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_WHZR01000001.1 - Region 8 - 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: 1,375,354 - 1,388,292 nt. (total: 12,939 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### 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: oxidoreductase reductase
STPH1_RS05820: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

STPH1_RS05830: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent 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 | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002097.3 |  | 0.19 | NRPS, PKS, saccharide | kosinostatin | Micromonospora sp. 28ISP2-46

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002097.3 |  | 0.19 | NRPS, PKS, saccharide | kosinostatin | Micromonospora sp. 28ISP2-46

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:
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
Additional weak hits (7):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.91 out of 30.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 25.75
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.56 out of 30.22
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.16 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.58 out of 23.43
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
HypR | L-hydroxyproline utilization repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_WHZR01000001.1 - Region 9 - 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: 1,407,571 - 1,438,785 nt. (total: 31,215 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: acetyltransferase aminotransferase
STPH1_RS05980: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

STPH1_RS06055: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Isomerases: mutase
STPH1_RS06060: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.46 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000295.5 |  | 0.45 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0000902.4 |  | 0.43 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0002584.2 |  | 0.41 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002471.3 |  | 0.41 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0002387.2 |  | 0.39 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0000285.5 |  | 0.38 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0002448.2 |  | 0.37 | NRPS | Q6402A | Streptomyces violaceusniger
BGC0000947.5 |  | 0.36 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0002545.3 |  | 0.36 | PKS | sungeidine C, sungeidine B, sungeidine D, sungeidine H, sungeidine A, sungeidine E, sungeidine F, sungeidine G | Micromonospora sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.46 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000295.5 |  | 0.45 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0000902.4 |  | 0.43 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0002584.2 |  | 0.41 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002471.3 |  | 0.41 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0002387.2 |  | 0.39 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0000285.5 |  | 0.38 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0002448.2 |  | 0.37 | NRPS | Q6402A | Streptomyces violaceusniger
BGC0000947.5 |  | 0.36 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0002545.3 |  | 0.36 | PKS | sungeidine C, sungeidine B, sungeidine D, sungeidine H, sungeidine A, sungeidine E, sungeidine F, sungeidine G | Micromonospora 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.
No hits above weak threshold.
Weak hits (8):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.55 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.33 out of 27.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.19 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.06 out of 24.78
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.01 out of 23.43
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.15 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.96 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.52 out of 26.06
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_WHZR01000001.1 - Region 10 - betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,520,283 - 1,548,047 nt. (total: 27,765 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
STPH1_RS06560: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

STPH1_RS06565: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

STPH1_RS06570: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

STPH1_RS06580: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS06590: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Hydrolases: hydrolase
STPH1_RS06545: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
STPH1_RS06520: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

STPH1_RS06550: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.60 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001240.4 |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000357.5 |  | 0.59 | 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
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001261.3 |  | 0.59 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  | 0.59 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.60 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001240.4 |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000357.5 |  | 0.59 | 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
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001261.3 |  | 0.59 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  | 0.59 | NRPS | HC-toxin | Alternaria jesenskae

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: 18.75 out of 23.79
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.37 out of 23.43
Confidence: medium
Additional weak hits (10):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.76 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.54 out of 30.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.14 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.69 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.28 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.07 out of 23.43
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.10 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.00 out of 24.78
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
IolR | Regulator of the inositol catabolism

NZ_WHZR01000001.1 - Region 11 - 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: 1,613,342 - 1,635,564 nt. (total: 22,223 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
Hydrolases: glucanase peptidase
STPH1_RS06920: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

STPH1_RS06930: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: cyclase lyase
STPH1_RS06905: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

STPH1_RS06945: 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 |  | 0.90 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000849.4 |  | 0.46 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0001197.5 |  | 0.45 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002508.2 |  | 0.44 | other (other) | 8-azaguanine | Streptomyces pathocidini
BGC0001483.4 |  | 0.43 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000850.5 |  | 0.41 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001910.4 |  | 0.40 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001285.5 |  | 0.39 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001911.3 |  | 0.39 | terpene | raimonol | Streptomyces anulatus
BGC0000937.5 |  | 0.37 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.90 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000849.4 |  | 0.46 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0001197.5 |  | 0.45 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002508.2 |  | 0.44 | other (other) | 8-azaguanine | Streptomyces pathocidini
BGC0001483.4 |  | 0.43 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000850.5 |  | 0.41 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001910.4 |  | 0.40 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001285.5 |  | 0.39 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001911.3 |  | 0.39 | terpene | raimonol | Streptomyces anulatus
BGC0000937.5 |  | 0.37 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372

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

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:
STPH1_RS06945: T1TS + T1TS
Domain 1 (1 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (327 - 695): 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 (3):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.21 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
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
--- | ---

NZ_WHZR01000001.1 - 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: 1,646,617 - 1,658,002 nt. (total: 11,386 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
STPH1_RS07100: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: deacetylase
STPH1_RS07055: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

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
--- | --- | --- | --- | --- | ---
BGC0000306.5 |  | 0.34 | NRPS | arylomycin | Streptomyces filamentosus NRRL 11379
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002303.3 |  | 0.33 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0000351.5 |  | 0.33 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155
BGC0002663.2 |  | 0.32 | ribosomal | amyloliquecidin GF610 | Bacillus amyloliquefaciens UMAF6639
BGC0002553.2 |  | 0.32 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0002387.2 |  | 0.32 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001928.2 |  | 0.31 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000565.5 |  | 0.31 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0002679.2 |  | 0.30 | NRPS | chromobactin | Chromobacterium violaceum ATCC 12472

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000306.5 |  | 0.34 | NRPS | arylomycin | Streptomyces filamentosus NRRL 11379
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002303.3 |  | 0.33 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0000351.5 |  | 0.33 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155
BGC0002663.2 |  | 0.32 | ribosomal | amyloliquecidin GF610 | Bacillus amyloliquefaciens UMAF6639
BGC0002553.2 |  | 0.32 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0002387.2 |  | 0.32 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001928.2 |  | 0.31 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000565.5 |  | 0.31 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0002679.2 |  | 0.30 | NRPS | chromobactin | Chromobacterium violaceum ATCC 12472

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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 27.49 out of 30.12
Confidence: strong
Additional weak hits (5):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.16 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.84 out of 21.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.43 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.82 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.14 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_WHZR01000001.1 - Region 13 - NRPS-like,T1PKS,prodigiosin,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: 1,950,056 - 2,020,937 nt. (total: 70,882 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
NRPS-like: cds((PP-binding or NAD_binding_4) 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))
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
Terpene
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
STPH1_RS08245: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS08275: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

STPH1_RS08290: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

STPH1_RS08305: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS08310: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

STPH1_RS08460: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: PPTase acyltransferase methyltransferase
STPH1_RS08295: methyltransferase

smcogs
  SMCOG1089: methyltransferase

STPH1_RS08355: acyltransferase

smcogs
  SMCOG1141: acyltransferase

STPH1_RS08375: methyltransferase

smcogs
  SMCOG1089: methyltransferase

STPH1_RS08440: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase
STPH1_RS08380: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
STPH1_RS08385: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase synthetase
STPH1_RS08270: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

STPH1_RS08390: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

STPH1_RS08395: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

STPH1_RS08400: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

STPH1_RS08405: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

STPH1_RS08415: 3-oxoacyl-(acyl carrier protein) synthase III

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

STPH1_RS08425: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

STPH1_RS39455: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: permease
STPH1_RS08350: 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 | terpene | NRPS-like | T1PKS | prodigiosin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001063.5 |  |  |  |  | 1.64 | NRPS, PKS | undecylprodigiosin | Streptomyces coelicolor A3(2)
BGC0000091.5 |  |  |  |  | 1.22 | PKS | marineosin A, marineosin B | Streptomyces sp. CNQ-617
BGC0002090.3 |  |  |  |  | 1.14 | NRPS, PKS | undecylprodigiosin, metacycloprodigiosin | Streptomyces griseoaurantiacus
BGC0001164.3 |  |  |  |  | 1.12 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  |  | 1.11 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001273.3 |  |  |  |  | 0.92 | PKS | asperlactone | Aspergillus ochraceus
BGC0001825.4 |  |  |  |  | 0.91 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001276.3 |  |  |  |  | 0.91 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  |  |  |  | 0.91 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  |  | 0.91 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.82 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001063.5 |  | 0.81 | NRPS, PKS | undecylprodigiosin | Streptomyces coelicolor A3(2)
BGC0000649.3 |  | 0.78 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.74 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000091.5 |  | 0.73 | PKS | marineosin A, marineosin B | Streptomyces sp. CNQ-617
BGC0001164.3 |  | 0.71 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.71 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002090.3 |  | 0.71 | NRPS, PKS | undecylprodigiosin, metacycloprodigiosin | Streptomyces griseoaurantiacus
BGC0000633.3 |  | 0.71 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.70 | terpene | isorenieratene | Streptomyces collinus Tu 365

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
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
STPH1_RS08270: PT_FPPS_like
Domain 1 (58 - 353): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

STPH1_RS08280: PT_phytoene_like
Domain 1 (16 - 304): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

STPH1_RS08300: Lycopene_cycl
Domain 1 (10 - 383): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

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 (7):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.87 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.90 out of 31.73
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.88 out of 19.26
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.64 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.26 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
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 13, location 1950055 - 2020937:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 15, location 1969267 - 2020937:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - 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).
STPH1_RS08395: fatty_acid - mal
CAL_domain (51..499): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 36.6
  NH2: 16.1
  AHBA: 14.0
  shikimic_acid: 9.5
  Acetyl-CoA: 0.2

PKS_AT (1321..1625): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 152.8
  Methoxymalonyl-CoA: 84.3
  inactive: 84.1
  Methylmalonyl-CoA: 74.9
  Ethylmalonyl-CoA: 47.9
  Propionyl-CoA: 34.5
  2-Methylbutyryl-CoA: 23.6
  Isobutyryl-CoA: 22.7
  trans-1,2-CPDA: 19.1
  Acetyl-CoA: 16.9
  Benzoyl-CoA: 15.9
  3-Methylbutyryl-CoA: 14.5
  CHC-CoA: 13.7
  fatty_acid: 10.6

STPH1_RS08400: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (16..427): Pro
nrpys: Pro

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

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

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

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_WHZR01000001.1 - Region 14 - 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: 2,078,914 - 2,108,746 nt. (total: 29,833 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
STPH1_RS08790: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
STPH1_RS08835: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
STPH1_RS08785: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002633.2 |  | 0.48 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002683.2 |  | 0.47 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002470.2 |  | 0.46 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000853.3 |  | 0.45 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.45 | other (ectoine) | ectoine | Streptomyces sp.
BGC0002692.2 |  | 0.44 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000919.5 |  | 0.43 | other (other) | phaseolotoxin | Pseudomonas syringae
BGC0000942.4 |  | 0.41 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.40 | other (other) | ochrobactin | Ochrobactrum anthropi

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002633.2 |  | 0.48 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002683.2 |  | 0.47 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002470.2 |  | 0.46 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000853.3 |  | 0.45 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.45 | other (ectoine) | ectoine | Streptomyces sp.
BGC0002692.2 |  | 0.44 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000919.5 |  | 0.43 | other (other) | phaseolotoxin | Pseudomonas syringae
BGC0000942.4 |  | 0.41 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.40 | other (other) | ochrobactin | Ochrobactrum anthropi

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 25.90 out of 27.18
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 26.06 out of 27.18
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.23 out of 23.43
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
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.70 out of 20.97
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.14 out of 27.18
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
Additional weak hits (9):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.71 out of 39.62
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.25 out of 30.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.34 out of 35.63
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.22 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
BldD | Development and antibiotic global regulator
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_WHZR01000001.1 - Region 15 - T2PKS,triceptide
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: 2,590,494 - 2,678,375 nt. (total: 87,882 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)
triceptide: ((cds(PF04055 and (TIGR04085 or SPASM)) and triceptide_precursor) or triceptide_rSAM)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
STPH1_RS11090: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS11105: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

STPH1_RS11145: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: methyltransferase
STPH1_RS11025: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Hydrolases: hydrolase
STPH1_RS11095: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: cyclase
STPH1_RS11175: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

STPH1_RS11180: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

Isomerases: isomerase
STPH1_RS11100: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
STPH1_RS11045: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

STPH1_RS11055: 3-oxoacyl-(acyl carrier protein) synthase III

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

STPH1_RS11160: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

STPH1_RS11165: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | T2PKS | triceptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000272.3 |  |  | 0.43 | PKS | spore pigment | Streptomyces collinus
BGC0001965.4 |  |  | 0.38 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus
BGC0000271.5 |  |  | 0.37 | PKS | spore pigment | Streptomyces avermitilis
BGC0000215.5 |  |  | 0.36 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  |  | 0.30 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  |  | 0.28 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002493.3 |  |  | 0.26 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001273.3 |  |  | 0.26 | PKS | asperlactone | Aspergillus ochraceus
BGC0002474.2 |  |  | 0.25 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0001513.3 |  |  | 0.24 | PKS | anthrabenzoxocinone | Actinobacteria bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000272.3 |  | 0.74 | PKS | spore pigment | Streptomyces collinus
BGC0001965.4 |  | 0.70 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus
BGC0000271.5 |  | 0.70 | PKS | spore pigment | Streptomyces avermitilis
BGC0000215.5 |  | 0.69 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.64 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.61 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002493.3 |  | 0.60 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001273.3 |  | 0.59 | PKS | asperlactone | Aspergillus ochraceus
BGC0001444.5 |  | 0.59 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0002474.2 |  | 0.58 | NRPS | agrobactin | Agrobacterium tumefaciens

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.85 out of 30.22
Confidence: medium
Additional weak hits (14):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.55 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.66 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.24 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.39 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.91 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.16 out of 21.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.07 out of 30.22
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.64 out of 32.93
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.45 out of 27.18
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.29 out of 24.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.67 out of 22.40
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 20.87 out of 32.93
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.21 out of 26.85
Confidence: weak
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
Type II PKS
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).
STPH1_RS11045: X
AMP-binding (17..423): X
nrpys: (unknown)

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

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

Link to PARAS substrate predictor
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  2590493 to 2663036
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

STPH1_RS11040
  OXY (Score: 61.3; E-value: 2e-19)
STPH1_RS11090
  KR (Score: 174.2; E-value: 9.1e-54)
STPH1_RS11145
  OXY (Score: 271.4; E-value: 3.8e-83)
STPH1_RS11155
  CYC C5-C18 (Score: 218.5; E-value: 5.1e-68)
STPH1_RS11160
  KS (Score: 709.5; E-value: 2.8e-216)
STPH1_RS11165
  CLF (Score: 553.6; E-value: 5.6e-169)
STPH1_RS11170
  ACP (Score: 72.4; E-value: 5.5e-23)
STPH1_RS11175
  CYC C9-C14 (Score: 250.1; E-value: 1.4e-77)
STPH1_RS11180
  CYC C4-C21/C2-C23|C2-C19 (Score: 153.1; E-value: 5e-48)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ClgR | Caseinolytic protease gene regulator
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_WHZR01000001.1 - Region 16 - 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: 2,679,807 - 2,700,967 nt. (total: 21,161 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
STPH1_RS11400: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: methyltransferase
STPH1_RS11425: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
STPH1_RS11460: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000948.5 |  | 0.45 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000563.4 |  | 0.42 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000340.5 |  | 0.41 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0000678.5 |  | 0.39 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000664.5 |  | 0.38 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000948.5 |  | 0.45 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000563.4 |  | 0.42 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000340.5 |  | 0.41 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0000678.5 |  | 0.39 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000664.5 |  | 0.38 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350

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:
STPH1_RS11460: PT_FPPS_like
Domain 1 (94 - 384): 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.09 out of 23.43
Confidence: medium
Additional weak hits (10):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 30.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.43 out of 29.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.31 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.74 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.64 out of 29.65
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.47 out of 32.38
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.89 out of 23.43
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
CRP | Cyclic AMP receptor protein
ToxT | Regulator of MSHA biosynthesis

NZ_WHZR01000001.1 - Region 17 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,708,476 - 2,729,561 nt. (total: 21,086 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
STPH1_RS11585: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Hydrolases: deformylase
STPH1_RS11595: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Lyases: cyclase
STPH1_RS11590: 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
--- | --- | --- | --- | --- | ---
BGC0000660.5 |  | 0.93 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001911.3 |  | 0.41 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.40 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002339.3 |  | 0.38 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0000650.3 |  | 0.36 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000678.5 |  | 0.36 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002012.4 |  | 0.34 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772
BGC0001315.3 |  | 0.34 | terpene | cucurbitacin C | Cucumis sativus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000660.5 |  | 0.93 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001911.3 |  | 0.41 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.40 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002339.3 |  | 0.38 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0000650.3 |  | 0.36 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000678.5 |  | 0.36 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002012.4 |  | 0.34 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772
BGC0001315.3 |  | 0.34 | terpene | cucurbitacin C | Cucumis sativus

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:
STPH1_RS11590: T1TS
Domain 1 (11 - 339): Type 1 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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.16 out of 27.04
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 25.12 out of 27.18
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.21 out of 27.18
Confidence: medium
Additional weak hits (2):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.19 out of 30.22
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
--- | ---
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
NrdR | Represses ribonucleotide reductase encoding genes

NZ_WHZR01000001.1 - Region 18 - RRE-containing
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: 2,833,871 - 2,854,929 nt. (total: 21,059 nt) Show pHMM detection rules used
RRE-containing: 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
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 | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002656.2 |  | 0.42 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.42 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002698.2 |  | 0.41 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001639.3 |  | 0.41 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0000496.5 |  | 0.40 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002115.3 |  | 0.40 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0000585.5 |  | 0.39 | ribosomal | microcin C7 | Escherichia coli
BGC0001294.5 |  | 0.39 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002447.3 |  | 0.39 | ribosomal | cerecyclin | Bacillus cereus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002656.2 |  | 0.42 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.42 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002698.2 |  | 0.41 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001639.3 |  | 0.41 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0000496.5 |  | 0.40 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002115.3 |  | 0.40 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0000585.5 |  | 0.39 | ribosomal | microcin C7 | Escherichia coli
BGC0001294.5 |  | 0.39 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002447.3 |  | 0.39 | ribosomal | cerecyclin | Bacillus cereus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.61 out of 26.85
Confidence: medium
Additional weak hits (4):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.93 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.14 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.60 out of 27.78
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (2833870...2854929)
STPH1_RS12180
  RRE type: Pantocin_Microcin_RRE
  Location: 1 - 85
  Score: 42.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
RutR | Regulator of the pyrimidine and purine metabolism

NZ_WHZR01000001.1 - Region 19 - RRE-containing
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: 2,876,355 - 2,897,548 nt. (total: 21,194 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
STPH1_RS12325: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
STPH1_RS12340: methyltransferase

smcogs
  SMCOG1089: methyltransferase

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 | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000585.5 |  | 0.47 | ribosomal | microcin C7 | Escherichia coli
BGC0002317.2 |  | 0.44 | ribosomal | herbicolin O, mcceh252, pantocin A | Pantoea agglomerans
BGC0000812.3 |  | 0.39 | other (other) | huperzine A | Shiraia sp. slf14
BGC0001485.4 |  | 0.37 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000197.5 |  | 0.32 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0000916.5 |  | 0.32 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0000631.5 |  | 0.32 | terpene | Botrydial, 8,9-epibotrydial, 1-epibotrydial, Dihydrobotrydial, 10-Oxo-dihydrobotrydial, 10-dehydroxy dihydrobotrydialone, 10-epi-dihydrobotrydial, Botryendial, Botryenalol, Botrydienal, Norbotrydialone acetate, 10-Oxodihydrobotry-1(9),4(5)-diendial, 10-Oxodehydrodihydrobotrydial, Dehydrobotrydienol, 11-Hydroxydehydrobotrydienol, 12-hydroxydehydrobotrydienol, Secobotrytriendiol, Secobotrytriene-10,12,15-triol, Secobotrydiene-3,10,15-triol, Secobotrydiene-3,4,10,15-tetraol, 4β-Acetoxytetrahydrobotryslactone | Botrytis cinerea B05.10
BGC0000252.5 |  | 0.31 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0001510.5 |  | 0.31 | other (other) | anisomycin | Streptomyces hygrospinosus
BGC0002504.2 |  | 0.31 | PKS | nocardiopsistin A, nocardiopsistin B, nocardiopsistin C | Nocardiopsis sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000585.5 |  | 0.47 | ribosomal | microcin C7 | Escherichia coli
BGC0002317.2 |  | 0.44 | ribosomal | herbicolin O, mcceh252, pantocin A | Pantoea agglomerans
BGC0000812.3 |  | 0.39 | other (other) | huperzine A | Shiraia sp. slf14
BGC0001485.4 |  | 0.37 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000197.5 |  | 0.32 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0000916.5 |  | 0.32 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0000631.5 |  | 0.32 | terpene | Botrydial, 8,9-epibotrydial, 1-epibotrydial, Dihydrobotrydial, 10-Oxo-dihydrobotrydial, 10-dehydroxy dihydrobotrydialone, 10-epi-dihydrobotrydial, Botryendial, Botryenalol, Botrydienal, Norbotrydialone acetate, 10-Oxodihydrobotry-1(9),4(5)-diendial, 10-Oxodehydrodihydrobotrydial, Dehydrobotrydienol, 11-Hydroxydehydrobotrydienol, 12-hydroxydehydrobotrydienol, Secobotrytriendiol, Secobotrytriene-10,12,15-triol, Secobotrydiene-3,10,15-triol, Secobotrydiene-3,4,10,15-tetraol, 4β-Acetoxytetrahydrobotryslactone | Botrytis cinerea B05.10
BGC0000252.5 |  | 0.31 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0001510.5 |  | 0.31 | other (other) | anisomycin | Streptomyces hygrospinosus
BGC0002504.2 |  | 0.31 | PKS | nocardiopsistin A, nocardiopsistin B, nocardiopsistin C | Nocardiopsis 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.
No hits above weak threshold.
Weak hits (8):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.49 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.32 out of 36.54
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.53 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.25 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.22 out of 27.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.00 out of 32.93
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.92 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.53 out of 35.63
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (2876354...2897548)
STPH1_RS12355
  RRE type: Pantocin_Microcin_RRE
  Location: 5 - 101
  Score: 89.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_WHZR01000001.1 - Region 20 - 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: 3,676,355 - 3,761,612 nt. (total: 85,258 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
STPH1_RS16085: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

STPH1_RS16090: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

STPH1_RS16115: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

STPH1_RS16120: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

STPH1_RS16155: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Hydrolases: esterase
STPH1_RS16130: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase
STPH1_RS16125: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

STPH1_RS16170: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

STPH1_RS16175: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

STPH1_RS16180: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001984.3 |  | 0.79 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.74 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001984.3 |  | 0.79 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.74 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.31 out of 23.79
Confidence: medium
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 25.13 out of 30.22
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.17 out of 23.43
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.25 out of 29.38
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.40 out of 26.12
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.95 out of 39.62
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.04 out of 24.78
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.05 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 24, location 3676354 - 3761612:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - Asp - Tyr - Thr - D-Leu) + (Asp - Gly - Pro - Gly) + (Gly - Ala - NMe-Gly)

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).
STPH1_RS16125: NH2
CAL_domain (42..485): NH2
minowa: NH2

Prediction, score:
  NH2: 111.3
  fatty_acid: 31.7
  AHBA: 6.2
  Acetyl-CoA: 4.5
  shikimic_acid: 0.0

STPH1_RS16170: Gly - Ala - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (477..854): Gly
nrpys: Gly

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

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

AMP-binding (1520..1920): Ala
nrpys: Ala

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

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

AMP-binding (2587..2990): Gly
nrpys: Gly

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

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

STPH1_RS16175: Asp - Gly - Pro - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (481..860): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRASFDLTVTGTKGVLGGEINAYGPTEATVNCLE
  Nearest Stachelhaus code(s):
    Asp DLTKVGAVNK (100% 8Å match)
    Asp DLTKVGAVNK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1524..1915): Gly
nrpys: Gly

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

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

AMP-binding (2576..2981): Pro
nrpys: Pro

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

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

AMP-binding (3650..4024): Gly
nrpys: Gly

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

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

STPH1_RS16180: Gly - Asp - Tyr - Thr - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (476..862): Gly
nrpys: Gly

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

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

AMP-binding (2217..2597): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRATFDLTITCTKGVLGGEVNAYGPTEATVNVME
  Nearest Stachelhaus code(s):
    Asp DLTKVGAVNK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3784..4168): Tyr
nrpys: 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:
    Polar aromatic ring (Tyr, bOH-Tyr)
  Single AA prediction:
    tyr (Tyr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASVSEVTLAVAGEINAYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Tyr DASTAAAVCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4834..5246): Thr
nrpys: Thr

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

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

AMP-binding (5928..6324): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSWDASILEVFLATGGDVNAYGPTEVTVMALS
  Nearest Stachelhaus code(s):
    Leu DALFAGAVMK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
ClgR | Caseinolytic protease gene regulator
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_WHZR01000001.1 - Region 21 - 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: 5,233,483 - 5,263,261 nt. (total: 29,779 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
STPH1_RS23270: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

STPH1_RS23290: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

STPH1_RS23315: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: carboxylase transferase
STPH1_RS23300: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

STPH1_RS23305: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Lyases: decarboxylase
STPH1_RS23275: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: synthase
STPH1_RS23295: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000940.5 |  | 0.90 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.85 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000941.3 |  | 0.83 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.82 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002690.2 |  | 0.63 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002464.3 |  | 0.63 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002073.3 |  | 0.62 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0000244.4 |  | 0.60 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000940.5 |  | 0.90 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.85 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000941.3 |  | 0.83 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.82 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002690.2 |  | 0.63 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002464.3 |  | 0.63 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002073.3 |  | 0.62 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0000244.4 |  | 0.60 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.36 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.26 out of 23.43
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.94 out of 36.53
Confidence: medium
Additional weak hits (5):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.25 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.16 out of 27.78
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.05 out of 33.73
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_WHZR01000001.1 - Region 22 - melanin
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: 5,341,497 - 5,352,129 nt. (total: 10,633 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
STPH1_RS23710: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Transferases: glycosyltransferase
STPH1_RS23665: 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 | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.87 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.80 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.68 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.47 | other (other) | melanin | Streptomyces avermitilis
BGC0000662.5 |  | 0.42 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.42 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.36 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001624.3 |  | 0.35 | other (other) | iso-A82775C | Pestalotiopsis fici
BGC0001592.5 |  | 0.35 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.87 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.80 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.68 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.47 | other (other) | melanin | Streptomyces avermitilis
BGC0000662.5 |  | 0.42 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.42 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.36 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001624.3 |  | 0.35 | other (other) | iso-A82775C | Pestalotiopsis fici
BGC0001592.5 |  | 0.35 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis

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:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.29 out of 27.55
Confidence: medium
Additional weak hits (6):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.82 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.68 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.93 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.26 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.23 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.51 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
GnfM | Regulator of nitrogen-fixation genes

NZ_WHZR01000001.1 - Region 23 - 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: 6,308,121 - 6,318,519 nt. (total: 10,399 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
STPH1_RS28055: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

STPH1_RS28070: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

STPH1_RS28080: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

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
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.85 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.84 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.59 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.85 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.84 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.59 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.08 out of 26.85
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (6):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.04 out of 26.12
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.79 out of 30.97
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.04 out of 26.12
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.15 out of 35.63
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.27 out of 30.12
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
RutR | Regulator of the pyrimidine and purine metabolism

NZ_WHZR01000001.1 - Region 24 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,892,135 - 6,904,054 nt. (total: 11,920 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
STPH1_RS30775: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

STPH1_RS30785: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: hydratase
STPH1_RS30780: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

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
--- | --- | --- | --- | --- | ---
BGC0001157.6 |  | 0.42 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000468.5 |  | 0.42 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0000470.6 |  | 0.42 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000469.6 |  | 0.42 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001485.4 |  | 0.41 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001928.2 |  | 0.40 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000812.3 |  | 0.40 | other (other) | huperzine A | Shiraia sp. slf14
BGC0000509.4 |  | 0.39 | ribosomal | epilancin 15x | Staphylococcus epidermidis
BGC0002138.2 |  | 0.38 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670
BGC0000507.5 |  | 0.37 | ribosomal | epicidin | Staphylococcus epidermidis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001157.6 |  | 0.42 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000468.5 |  | 0.42 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0000470.6 |  | 0.42 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000469.6 |  | 0.42 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001485.4 |  | 0.41 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001928.2 |  | 0.40 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000812.3 |  | 0.40 | other (other) | huperzine A | Shiraia sp. slf14
BGC0000509.4 |  | 0.39 | ribosomal | epilancin 15x | Staphylococcus epidermidis
BGC0002138.2 |  | 0.38 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670
BGC0000507.5 |  | 0.37 | ribosomal | epicidin | Staphylococcus epidermidis

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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.90 out of 30.12
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
Additional weak hits (4):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.85 out of 30.22
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.13 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.49 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_WHZR01000001.1 - Region 25 - 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: 6,996,422 - 7,037,606 nt. (total: 41,185 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS 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 reductase
STPH1_RS31350: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

STPH1_RS31360: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

STPH1_RS31375: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

STPH1_RS31390: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

STPH1_RS31400: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

STPH1_RS31405: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

STPH1_RS31410: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: aminotransferase
STPH1_RS31285: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: deformylase
STPH1_RS31340: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Ligases: synthase
STPH1_RS31365: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase 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 | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002127.3 |  | 0.92 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.75 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.64 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001310.5 |  | 0.63 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001336.5 |  | 0.50 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001948.3 |  | 0.49 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000280.5 |  | 0.48 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.47 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0001078.5 |  | 0.47 | PKS, terpene | furaquinocin B | Streptomyces sp. KO-3988
BGC0000706.3 |  | 0.45 | saccharide | kanamycin | Streptomyces kanamyceticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002127.3 |  | 0.92 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.75 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.64 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001310.5 |  | 0.63 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001336.5 |  | 0.50 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001948.3 |  | 0.49 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000280.5 |  | 0.48 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.47 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0001078.5 |  | 0.47 | PKS, terpene | furaquinocin B | Streptomyces sp. KO-3988
BGC0000706.3 |  | 0.45 | saccharide | kanamycin | Streptomyces kanamyceticus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.37 out of 20.47
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.43 out of 23.79
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.19 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.56 out of 30.11
Confidence: medium
Additional weak hits (9):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.65 out of 23.43
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.35 out of 27.55
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.03 out of 27.04
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.66 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.63 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.03 out of 29.38
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.33 out of 32.93
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 30.11
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
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_WHZR01000001.1 - Region 26 - 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: 7,322,828 - 7,364,012 nt. (total: 41,185 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS 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
STPH1_RS32695: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS32700: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS32750: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

STPH1_RS32780: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

STPH1_RS32805: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS32815: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

STPH1_RS32830: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase
STPH1_RS32810: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: dehalogenase
STPH1_RS32755: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: synthase
STPH1_RS32740: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

STPH1_RS32775: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.87 | other (other) | germicidin | Streptomyces argillaceus
BGC0000866.5 |  | 0.52 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.48 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001917.4 |  | 0.47 | PKS | 5aTHQ-9i, 5aTHQ-9n, 5aTHQ-10a, STAMs-9i, STAMs-9n | Streptomyces nigrescens
BGC0000131.5 |  | 0.47 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001177.4 |  | 0.45 | PKS | mensacaricin | Streptomyces bottropensis
BGC0000265.5 |  | 0.44 | PKS | rhodomycin | Streptomyces purpurascens
BGC0002514.3 |  | 0.44 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0001928.2 |  | 0.43 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.87 | other (other) | germicidin | Streptomyces argillaceus
BGC0000866.5 |  | 0.52 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.48 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001917.4 |  | 0.47 | PKS | 5aTHQ-9i, 5aTHQ-9n, 5aTHQ-10a, STAMs-9i, STAMs-9n | Streptomyces nigrescens
BGC0000131.5 |  | 0.47 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001177.4 |  | 0.45 | PKS | mensacaricin | Streptomyces bottropensis
BGC0000265.5 |  | 0.44 | PKS | rhodomycin | Streptomyces purpurascens
BGC0002514.3 |  | 0.44 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0001928.2 |  | 0.43 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37

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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.79 out of 25.75
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (7):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.07 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.01 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.67 out of 30.22
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.91 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.36 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.41 out of 28.19
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
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
MatP | Cell cycle regulator
MexT | Global virulence regulator

NZ_WHZR01000001.1 - Region 27 - 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: 7,566,174 - 7,590,219 nt. (total: 24,046 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
STPH1_RS33830: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

STPH1_RS33835: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

STPH1_RS33855: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
STPH1_RS33845: methyltransferase

smcogs
  SMCOG1089: methyltransferase

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
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.72 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.67 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.65 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.64 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.64 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000645.3 |  | 0.49 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.47 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium
BGC0000249.5 |  | 0.47 | PKS | nogalamycin | Streptomyces nogalater
BGC0000640.3 |  | 0.46 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.72 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.67 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.65 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.64 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.64 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000645.3 |  | 0.49 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.47 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium
BGC0000249.5 |  | 0.47 | PKS | nogalamycin | Streptomyces nogalater
BGC0000640.3 |  | 0.46 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

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

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
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
STPH1_RS33850: Lycopene_cycl
Domain 1 (6 - 386): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

STPH1_RS33860: PT_phytoene_like
Domain 1 (16 - 314): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.13 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 30.11
Confidence: medium
Additional weak hits (6):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.32 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.07 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.52 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.91 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor

NZ_WHZR01000001.1 - Region 28 - indole
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,652,566 - 7,673,693 nt. (total: 21,128 nt) Show pHMM detection rules used
indole: (indsynth or dmat or indole_PTase)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
STPH1_RS34270: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Ligases: ligase
STPH1_RS34285: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | indole | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002128.3 |  | 0.86 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001483.4 |  | 0.49 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001294.5 |  | 0.47 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0001840.2 |  | 0.42 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325
BGC0001910.4 |  | 0.41 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.40 | terpene | raimonol | Streptomyces anulatus
BGC0002701.2 |  | 0.39 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0001887.3 |  | 0.38 | ribosomal | huazacin | Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0002805.2 |  | 0.37 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001592.5 |  | 0.37 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002128.3 |  | 0.86 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001483.4 |  | 0.49 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001294.5 |  | 0.47 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0001840.2 |  | 0.42 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325
BGC0001910.4 |  | 0.41 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.40 | terpene | raimonol | Streptomyces anulatus
BGC0002701.2 |  | 0.39 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0001887.3 |  | 0.38 | ribosomal | huazacin | Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0002805.2 |  | 0.37 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001592.5 |  | 0.37 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis

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: 17.11 out of 19.52
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.25 out of 30.22
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.52 out of 29.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 26.85
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.77 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.74 out of 27.04
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production

NZ_WHZR01000001.1 - Region 29 - 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: 7,848,171 - 7,869,388 nt. (total: 21,218 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: methyltransferase
STPH1_RS35130: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase
STPH1_RS35135: 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
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.85 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.79 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  | 0.64 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001895.4 |  | 0.36 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0001321.3 |  | 0.32 | terpene | monoterpenes-diterpenes | Solanum habrochaites
BGC0002387.2 |  | 0.30 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001322.3 |  | 0.29 | terpene | lycosantalonol, β-phellandrene | Solanum lycopersicum
BGC0000518.3 |  | 0.29 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002666.2 |  | 0.27 | NRPS, other (other) | Legonmycin A, Legonmycin B, Legonindolizine A, Legonindolizine B | Streptomyces sp. MA37
BGC0001377.5 |  | 0.26 | PKS | uncialamycin | Streptomyces uncialis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.85 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.79 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  | 0.64 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001895.4 |  | 0.36 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0001321.3 |  | 0.32 | terpene | monoterpenes-diterpenes | Solanum habrochaites
BGC0002387.2 |  | 0.30 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001322.3 |  | 0.29 | terpene | lycosantalonol, β-phellandrene | Solanum lycopersicum
BGC0000518.3 |  | 0.29 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002666.2 |  | 0.27 | NRPS, other (other) | Legonmycin A, Legonmycin B, Legonindolizine A, Legonindolizine B | Streptomyces sp. MA37
BGC0001377.5 |  | 0.26 | PKS | uncialamycin | Streptomyces uncialis

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
--- | --- | --- | --- | --- | ---
monoterpene |  | 2-methylisoborneol | C11 | C1-C6 | OH
monoterpene |  | 2-methylenebornane | C11 | C1-C6 | none

Genes with terpene domains:
STPH1_RS35135: T1TS
Domain 1 (4 - 399): Type 1 terpene synthase
Subtype: 2-Methylisoborneol synthase type

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 23.86 out of 27.55
Confidence: medium
Additional weak hits (4):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.10 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.50 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.77 out of 36.54
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.30 out of 30.22
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
2-MeGPP | 2-methylgeranyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
GnfM | Regulator of nitrogen-fixation genes