Select genomic region:
Overview
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1.41
1.42
1.43
1.44
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1.46
1.47
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1.49

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

NZ_CP011509.1 (Archangium gephyra)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | terpene | 433,370 | 454,284 |  |
Region 2 | terpene | 574,413 | 595,447 |
Region 3 | RiPP-like | 627,277 | 638,113 |
Region 4 | indole | 688,567 | 709,640 |
Region 5 | RiPP-like | 1,049,061 | 1,059,960 |
Region 6 | NRPS | 1,963,108 | 2,010,893 | High | 1-heptadecene | PKS:Type I
Region 7 | terpene | 2,100,494 | 2,122,029 |
Region 8 | terpene,T3PKS,NRPS-like | 2,192,195 | 2,269,012 | High | carotenoid | terpene
Region 9 | RiPP-like | 2,608,399 | 2,623,774 |
Region 10 | RiPP-like,terpene | 2,729,915 | 2,759,377 | High | geosmin | terpene:Sesquiterpene
Region 11 | NRPS-like,T1PKS,NRPS | 2,938,641 | 2,992,273 | Low | crocacin | NRPS:Type I+PKS
Region 12 | T1PKS | 3,029,565 | 3,074,862 |
Region 13 | terpene | 3,583,681 | 3,605,564 |
Region 14 | microviridin | 3,624,566 | 3,644,760 | Low | microviridin K | ribosomal:RiPP
Region 15 | NRPS-like | 3,684,431 | 3,728,837 | High | VEPE/AEPE/TG-1 | other:nucleoside
Region 16 | NRPS | 3,831,232 | 3,886,645 |
Region 17 | terpene,lanthipeptide-class-ii | 4,020,820 | 4,055,797 | Medium | 2-hydroxysorangiadenosine | terpene
Region 18 | terpene,proteusin | 4,443,765 | 4,478,787 |
Region 19 | RiPP-like | 4,701,952 | 4,712,794 |
Region 20 | RiPP-like | 4,767,513 | 4,778,355 |
Region 21 | NRPS,T1PKS | 4,938,532 | 5,062,262 | Low | nostopeptolide A2 | NRPS:Type I+PKS
Region 22 | terpene | 5,122,567 | 5,159,619 |
Region 23 | terpene-precursor | 5,318,262 | 5,339,152 |
Region 24 | NRP-metallophore,NRPS,T1PKS | 5,423,898 | 5,570,224 | Medium | myxochelin B/myxochelin N/myxochelin O/myxochelin P/myxochelin Q/myxochelin A | NRPS:Type I+PKS
Region 25 | azole-containing-RiPP | 6,040,054 | 6,065,091 |
Region 26 | oligosaccharide | 6,096,866 | 6,139,943 | Low | myxalamid/myxalamid A/myxalamid C/myxalamid D | NRPS:Type I+PKS
Region 27 | NRPS | 6,173,716 | 6,233,063 |
Region 28 | RiPP-like | 6,283,311 | 6,294,168 |
Region 29 | terpene | 6,323,536 | 6,344,627 |
Region 30 | terpene,NRPS,T1PKS | 6,376,546 | 6,492,237 |  |
Region 31 | terpene-precursor | 6,502,735 | 6,523,739 |
Region 32 | phenazine,NRPS,T1PKS,microviridin | 6,533,679 | 6,580,989 | Low | myxochromide D | NRPS:Type I+PKS:Iterative type I
Region 33 | RRE-containing,terpene-precursor | 6,669,690 | 6,710,332 |
Region 34 | NRPS,T1PKS | 7,320,981 | 7,397,535 | Low | melithiazol A | NRPS:Type I+PKS:Type I
Region 35 | RiPP-like | 7,604,383 | 7,616,032 |
Region 36 | lanthipeptide-class-ii | 8,166,194 | 8,189,421 |
Region 37 | lanthipeptide-class-i | 8,274,361 | 8,298,826 |
Region 38 | T1PKS | 8,416,505 | 8,476,008 | Low | stigmatellin | NRPS:Type I+PKS:Type I
Region 39 | terpene | 8,585,532 | 8,607,100 |
Region 40 | hserlactone | 9,122,031 | 9,142,663 |
Region 41 | lanthipeptide-class-v,thioamitides | 9,290,987 | 9,333,228 |
Region 42 | thioamitides | 9,383,722 | 9,406,072 |
Region 43 | T1PKS,NRPS | 10,228,405 | 10,279,069 | Low | myxothiazol | NRPS:Type I+PKS:Type I
Region 44 | NRPS | 10,561,540 | 10,609,297 | Low | amipurimycin | PKS
Region 45 | RRE-containing | 10,689,840 | 10,710,151 |  |
Region 46 | terpene | 10,875,544 | 10,897,769 | High | geosmin | terpene:Sesquiterpene
Region 47 | T3PKS | 11,561,755 | 11,619,860 | Low | alkylpyrone-407/alkylpyrone-393 | PKS
Region 48 | terpene,triceptide | 12,003,229 | 12,032,766 |
Region 49 | terpene | 12,173,873 | 12,194,847 |

NZ_CP011509.1 - Region 1 - 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: 433,370 - 454,284 nt. (total: 20,915 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: peptidase
AA314_RS01955: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

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
--- | --- | --- | --- | --- | ---
BGC0002218.2 |  | 0.38 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0000990.3 |  | 0.28 | NRPS, PKS | epothilone | Sorangium cellulosum
BGC0001571.3 |  | 0.25 | terpene | demethoxyviridin | Nodulisporium sp.
BGC0000448.5 |  | 0.22 | NRPS | tomaymycin | Streptomyces achromogenes
BGC0001652.5 |  | 0.21 | NRPS | limazepine C, limazepine D, limazepine E, limazepine F, limazepine A | Streptomyces sp. ICBB 8177
BGC0000907.5 |  | 0.21 | other (other) | lincomycin | Streptomyces lincolnensis
BGC0000374.5 |  | 0.20 | NRPS | hormaomycin, hormaomycin A1, hormaomycin A2, hormaomycin A3, hormaomycin A4, hormaomycin A5, hormaomycin A6 | Streptomyces griseoflavus
BGC0000203.3 |  | 0.20 | PKS | BE-7585A | Amycolatopsis orientalis subsp. vinearia
BGC0000428.5 |  | 0.20 | NRPS | sibiromycin | Streptosporangium sibiricum
BGC0000409.5 |  | 0.19 | NRPS | porothramycin A | Streptomyces albus subsp. albus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002218.2 |  | 0.38 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0000990.3 |  | 0.28 | NRPS, PKS | epothilone | Sorangium cellulosum
BGC0001571.3 |  | 0.25 | terpene | demethoxyviridin | Nodulisporium sp.
BGC0000448.5 |  | 0.22 | NRPS | tomaymycin | Streptomyces achromogenes
BGC0001652.5 |  | 0.21 | NRPS | limazepine C, limazepine D, limazepine E, limazepine F, limazepine A | Streptomyces sp. ICBB 8177
BGC0000907.5 |  | 0.21 | other (other) | lincomycin | Streptomyces lincolnensis
BGC0000374.5 |  | 0.20 | NRPS | hormaomycin, hormaomycin A1, hormaomycin A2, hormaomycin A3, hormaomycin A4, hormaomycin A5, hormaomycin A6 | Streptomyces griseoflavus
BGC0000203.3 |  | 0.20 | PKS | BE-7585A | Amycolatopsis orientalis subsp. vinearia
BGC0000428.5 |  | 0.20 | NRPS | sibiromycin | Streptosporangium sibiricum
BGC0000409.5 |  | 0.19 | NRPS | porothramycin A | Streptomyces albus subsp. albus

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene |  |  | C15 | C1-C6 | none
diterpene |  |  | C20 | C1-C6 | none
diterpene |  |  | C20 | C1-C7 + C6-C10 | none
sesterterpene |  |  | C25 | C1-C7 + C6-C10 | none

Genes with terpene domains:
AA314_RS01925: TS_UbiA
Domain 1 (8 - 303): UbiA type terpene synthase

Reactions:
  FPP → sesquiterpene_C1-C6
  GGPP → diterpene_C1-C6
  GGPP → diterpene_C1-C7/C6-C10
  GFPP → sesterterpene_C1-C7/C6-C10

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:
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 26.42 out of 30.22
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.94 out of 23.79
Confidence: medium
Additional weak hits (4):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.44 out of 32.74
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.67 out of 30.97
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.36 out of 39.62
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.52 out of 26.85
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ClgR | Caseinolytic protease gene regulator
IolR | Regulator of the inositol catabolism

NZ_CP011509.1 - Region 2 - 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: 574,413 - 595,447 nt. (total: 21,035 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
AA314_RS02585: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001839.3 |  | 0.52 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000640.3 |  | 0.41 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000639.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0001456.3 |  | 0.36 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000638.3 |  | 0.36 | terpene | carotenoid | Pantoea ananatis
BGC0000664.5 |  | 0.35 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001483.4 |  | 0.32 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000663.5 |  | 0.29 | terpene | hopene | Streptomyces coelicolor A3(2)

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001839.3 |  | 0.52 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000640.3 |  | 0.41 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000639.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0001456.3 |  | 0.36 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000638.3 |  | 0.36 | terpene | carotenoid | Pantoea ananatis
BGC0000664.5 |  | 0.35 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001483.4 |  | 0.32 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000663.5 |  | 0.29 | terpene | hopene | Streptomyces coelicolor A3(2)

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
triterpene |  | squalene | C30 | acyclic | none
triterpene | C30 carotenoid | diapophytoene | C30 | acyclic | none
triterpene |  | PSPP | C30 | acyclic | PP
tetraterpene | C40 carotenoid | phytoene | C40 | acyclic | none
triterpene |  | hydroxysqualene | C30 | acyclic | OH

Genes with terpene domains:
AA314_RS02580: PT_phytoene_like
Domain 1 (17 - 294): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.66 out of 23.79
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.52 out of 27.18
Confidence: medium
Additional weak hits (9):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.56 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.60 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.91 out of 29.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 30.25
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.70 out of 27.18
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP011509.1 - 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: 627,277 - 638,113 nt. (total: 10,837 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
AA314_RS02710: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

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
--- | --- | --- | --- | --- | ---
BGC0000723.5 |  | 0.26 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus
BGC0001285.5 |  | 0.26 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0000722.5 |  | 0.25 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. jinggangensis
BGC0001215.5 |  | 0.22 | NRPS | conglobatin | Streptomyces conglobatus
BGC0002025.4 |  | 0.22 | NRPS, PKS | thaxteramide C | Jahnella sp. MSr9139
BGC0002788.2 |  | 0.22 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000464.5 |  | 0.22 | NRPS | xenoamicin A, xenoamicin B | Xenorhabdus doucetiae
BGC0001567.4 |  | 0.21 | NRPS | cysteoamide | Streptomyces lincolnensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000723.5 |  | 0.26 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus
BGC0001285.5 |  | 0.26 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0000722.5 |  | 0.25 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. jinggangensis
BGC0001215.5 |  | 0.22 | NRPS | conglobatin | Streptomyces conglobatus
BGC0002025.4 |  | 0.22 | NRPS, PKS | thaxteramide C | Jahnella sp. MSr9139
BGC0002788.2 |  | 0.22 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000464.5 |  | 0.22 | NRPS | xenoamicin A, xenoamicin B | Xenorhabdus doucetiae
BGC0001567.4 |  | 0.21 | NRPS | cysteoamide | Streptomyces lincolnensis

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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
Additional weak hits (2):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.28 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
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

NZ_CP011509.1 - Region 4 - 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: 688,567 - 709,640 nt. (total: 21,074 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
Transferases: glycosyltransferase
AA314_RS02985: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

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
--- | --- | --- | --- | --- | ---
BGC0002573.2 |  | 0.42 | other (other) | phosphoramidon | Streptomyces mozunensis
BGC0002294.3 |  | 0.30 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0002425.3 |  | 0.29 | ribosomal | stlassin | Streptomyces sp.
BGC0002805.2 |  | 0.28 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0000651.5 |  | 0.26 | terpene | KS-505a | Streptomyces argenteolus
BGC0001966.3 |  | 0.25 | NRPS, PKS | BII-rafflesfungin | Phoma sp.
BGC0000227.5 |  | 0.25 | PKS | granaticin | Streptomyces violaceoruber
BGC0002460.3 |  | 0.25 | other (other) | loonamycin A, loonamycin B, loonamycin C | Nocardiopsis flavescens
BGC0001430.4 |  | 0.25 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca Sg a15
BGC0000017.5 |  | 0.24 | PKS, other (other) | anatoxin-a, homoanatoxin-a | [Oscillatoria] sp. PCC 6506

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002573.2 |  | 0.42 | other (other) | phosphoramidon | Streptomyces mozunensis
BGC0002294.3 |  | 0.30 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0002425.3 |  | 0.29 | ribosomal | stlassin | Streptomyces sp.
BGC0002805.2 |  | 0.28 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0000651.5 |  | 0.26 | terpene | KS-505a | Streptomyces argenteolus
BGC0001966.3 |  | 0.25 | NRPS, PKS | BII-rafflesfungin | Phoma sp.
BGC0000227.5 |  | 0.25 | PKS | granaticin | Streptomyces violaceoruber
BGC0002460.3 |  | 0.25 | other (other) | loonamycin A, loonamycin B, loonamycin C | Nocardiopsis flavescens
BGC0001430.4 |  | 0.25 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca Sg a15
BGC0000017.5 |  | 0.24 | PKS, other (other) | anatoxin-a, homoanatoxin-a | [Oscillatoria] sp. PCC 6506

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (12):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.85 out of 27.78
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.85 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.85 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.85 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.85 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.85 out of 23.43
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.67 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.41 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP011509.1 - Region 5 - 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: 1,049,061 - 1,059,960 nt. (total: 10,900 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.

No matches found.

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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.07 out of 25.31
Confidence: medium
Additional weak hits (8):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.61 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.77 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.28 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.82 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.19 out of 21.55
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.72 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.26 out of 29.38
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 out of 30.98
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CatR | H2O2-responsive repressor

NZ_CP011509.1 - Region 6 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,963,108 - 2,010,893 nt. (total: 47,786 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: oxygenase
AA314_RS08130: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Ligases: ligase
AA314_RS08125: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AA314_RS08135: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000357.5 |  | 0.67 | 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
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.66 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  | 0.66 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001251.4 |  | 0.66 | NRPS | epichloenin A | Epichloe festucae
BGC0000307.4 |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  | 0.66 | NRPS | epichloenin A | Epichloe festucae
BGC0000342.4 |  | 0.65 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000357.5 |  | 0.67 | 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
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.66 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  | 0.66 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001251.4 |  | 0.66 | NRPS | epichloenin A | Epichloe festucae
BGC0000307.4 |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  | 0.66 | NRPS | epichloenin A | Epichloe festucae
BGC0000342.4 |  | 0.65 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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:
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.94 out of 29.51
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 28.31 out of 30.12
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
Additional weak hits (9):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.79 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.63 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.39 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.73 out of 35.63
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.49 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.07 out of 29.25
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.70 out of 27.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.07 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 6, location 1963107 - 2010893:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AA314_RS08125: X
AMP-binding (450..848): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTLGFDTSVKQVDTLVGGEVNMYGPTECTVNATT
  Nearest Stachelhaus code(s):
    Asp DMKDLGMVDK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AA314_RS08135: NH2
CAL_domain (42..479): NH2
minowa: NH2

Prediction, score:
  NH2: 187.7
  Acetyl-CoA: 59.1
  fatty_acid: 23.1
  AHBA: 18.8
  shikimic_acid: 8.9

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
DosR | Hypoxia stress response regulator
OsdR | Development and stress management regulator

NZ_CP011509.1 - Region 7 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,100,494 - 2,122,029 nt. (total: 21,536 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: aminotransferase
AA314_RS08645: aminotransferase

smcogs
  SMCOG1019: aminotransferase

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
--- | --- | --- | --- | --- | ---
BGC0001198.3 |  | 0.56 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0002148.2 |  | 0.30 | other (other) | guanitoxin | Sphaerospermopsis torques-reginae ITEP-024
BGC0000632.5 |  | 0.30 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001044.4 |  | 0.22 | NRPS | sirodesmin PL | Leptosphaeria maculans
BGC0000611.5 |  | 0.21 | ribosomal | siomycin A | Streptomyces sioyaensis
BGC0000614.5 |  | 0.20 | ribosomal | thiostrepton | Streptomyces laurentii
BGC0000432.6 |  | 0.20 | NRPS | streptothricin F, streptothricin E, streptothricin D, streptothricin C | Streptomyces rochei NBRC 12908
BGC0000316.5 |  | 0.20 | NRPS | capreomycin IA, capreomycin IB, capreomycin IIA, capreomycin IIB | Saccharothrix mutabilis subsp. capreolus
BGC0000982.5 |  | 0.20 | NRPS, PKS | cystothiazole A | Cystobacter fuscus
BGC0001379.5 |  | 0.20 | NRPS | BD-12 | Streptomyces luteocolor

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001198.3 |  | 0.56 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0002148.2 |  | 0.30 | other (other) | guanitoxin | Sphaerospermopsis torques-reginae ITEP-024
BGC0000632.5 |  | 0.30 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001044.4 |  | 0.22 | NRPS | sirodesmin PL | Leptosphaeria maculans
BGC0000611.5 |  | 0.21 | ribosomal | siomycin A | Streptomyces sioyaensis
BGC0000614.5 |  | 0.20 | ribosomal | thiostrepton | Streptomyces laurentii
BGC0000432.6 |  | 0.20 | NRPS | streptothricin F, streptothricin E, streptothricin D, streptothricin C | Streptomyces rochei NBRC 12908
BGC0000316.5 |  | 0.20 | NRPS | capreomycin IA, capreomycin IB, capreomycin IIA, capreomycin IIB | Saccharothrix mutabilis subsp. capreolus
BGC0000982.5 |  | 0.20 | NRPS, PKS | cystothiazole A | Cystobacter fuscus
BGC0001379.5 |  | 0.20 | NRPS | BD-12 | Streptomyces luteocolor

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

No significant matches found.

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
No domains found
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
Additional weak hits (4):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.55 out of 30.22
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.64 out of 29.65
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.88 out of 28.19
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
--- | ---
CRP | Cyclic AMP receptor protein
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP011509.1 - Region 8 - NRPS-like,T3PKS,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: 2,192,195 - 2,269,012 nt. (total: 76,818 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)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
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
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 oxidase reductase
AA314_RS09055: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

AA314_RS09065: hydroxymethylglutaryl-CoA reductase

smcogs
  SMCOG1187: hydroxymethylglutaryl-CoA reductase

AA314_RS09070: Halogenation

MITE
  MITE0000024Halogenation (identity: 65.50%)
smcogs
  SMCOG1222: dehydrogenase

AA314_RS09130: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

AA314_RS09240: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: aminotransferase dehydrogenase
AA314_RS09070: Halogenation

MITE
  MITE0000024Halogenation (identity: 65.50%)
smcogs
  SMCOG1222: dehydrogenase

AA314_RS09140: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: esterase
AA314_RS09235: putative esterase

smcogs
  SMCOG1104: putative esterase

Lyases: dehydratase
AA314_RS09040: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase synthetase
AA314_RS09050: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

AA314_RS09180: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

AA314_RS09270: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AA314_RS49935: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | terpene | T3PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000648.3 |  |  |  | 0.83 | terpene | carotenoid | Myxococcus xanthus
BGC0002286.3 |  |  |  | 0.53 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001160.5 |  |  |  | 0.53 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  | 0.53 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000647.3 |  |  |  | 0.46 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000189.4 |  |  |  | 0.44 | PKS | 3-(2'-hydroxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-hydroxy-3'-oxo-4'-methylhexyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylhexyl)-indole | Xenorhabdus bovienii SS-2004
BGC0001831.3 |  |  |  | 0.36 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000286.3 |  |  |  | 0.36 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0000679.5 |  |  |  | 0.32 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0001163.3 |  |  |  | 0.31 | PKS | 1-heptadecene | Moorea producens 3L

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000648.3 |  | 0.82 | terpene | carotenoid | Myxococcus xanthus
BGC0000647.3 |  | 0.76 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.64 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000664.5 |  | 0.58 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000640.3 |  | 0.57 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0001456.3 |  | 0.57 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000638.3 |  | 0.56 | terpene | carotenoid | Pantoea ananatis

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:
AA314_RS09050: PT_FPPS_like
Domain 1 (57 - 358): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

AA314_RS09060: PT_phytoene_like
Domain 1 (21 - 312): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

AA314_RS09085: Lycopene_cycl
Domain 1 (1 - 91): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

AA314_RS09090: Lycopene_cycl
Domain 1 (6 - 99): 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.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.00 out of 20.47
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 25.31
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (11):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.23 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.94 out of 21.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.68 out of 39.62
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.73 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.89 out of 27.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.93 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.32 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.67 out of 27.04
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.20 out of 26.06
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.98 out of 36.53
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.63 out of 32.93
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 8, location 2192194 - 2269012:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 2208887 - 2250078:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 11, location 2224539 - 2269012:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2)

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).
AA314_RS49935: NH2
CAL_domain (46..494): NH2
minowa: NH2

Prediction, score:
  NH2: 25.5
  fatty_acid: 17.8
  AHBA: 16.4
  shikimic_acid: 0.0
  Acetyl-CoA: -3.7

AA314_RS09270: X
AMP-binding (34..446): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

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

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
--- | ---
CatR | H2O2-responsive repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP011509.1 - Region 9 - 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: 2,608,399 - 2,623,774 nt. (total: 15,376 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
--- | --- | --- | --- | --- | ---
BGC0000473.4 |  | 0.44 | ribosomal | aerucyclamide A, aerucyclamide B, aerucyclamide C, aerucyclamide D | Microcystis aeruginosa NIES-298
BGC0000474.4 |  | 0.44 | ribosomal | microcyclamide | Microcystis aeruginosa PCC 7806
BGC0000483.5 |  | 0.43 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0002551.2 |  | 0.42 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398
BGC0002485.2 |  | 0.42 | other (other), ribosomal | muscoride A, muscoride B | Desmonostoc sp. PCC 7906
BGC0000471.4 |  | 0.42 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112
BGC0000480.5 |  | 0.42 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000475.5 |  | 0.42 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0000565.5 |  | 0.39 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000477.3 |  | 0.39 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000473.4 |  | 0.44 | ribosomal | aerucyclamide A, aerucyclamide B, aerucyclamide C, aerucyclamide D | Microcystis aeruginosa NIES-298
BGC0000474.4 |  | 0.44 | ribosomal | microcyclamide | Microcystis aeruginosa PCC 7806
BGC0000483.5 |  | 0.43 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0002551.2 |  | 0.42 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398
BGC0002485.2 |  | 0.42 | other (other), ribosomal | muscoride A, muscoride B | Desmonostoc sp. PCC 7906
BGC0000471.4 |  | 0.42 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112
BGC0000480.5 |  | 0.42 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000475.5 |  | 0.42 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0000565.5 |  | 0.39 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000477.3 |  | 0.39 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A

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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.39 out of 25.31
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47
Confidence: medium
Additional weak hits (6):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.13 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.16 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.63 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.71 out of 27.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RiPP-like protocluster (2608398...2623774)
AA314_RS10745
  RRE type: NHLP_CD_RRE
  Location: 6 - 99
  Score: 66.4
  RRE type: Cyanobactin_D_RRE
  Location: 5 - 83
  Score: 51.6
  RRE type: Goadsporin_CD_RRE
  Location: 6 - 102
  Score: 47.8

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP011509.1 - Region 10 - RiPP-like,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,729,915 - 2,759,377 nt. (total: 29,463 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))
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: hydrolase
AA314_RS11195: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: cyclase
AA314_RS11170: 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 | RiPP-like | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001181.4 |  |  | 0.54 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000657.5 |  |  | 0.24 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001485.4 |  |  | 0.10 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000468.5 |  |  | 0.06 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  |  | 0.06 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000470.6 |  |  | 0.06 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000469.6 |  |  | 0.06 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001148.5 |  |  | 0.06 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus
BGC0002083.3 |  |  | 0.06 | PKS | gladiofungin A, gladiofungin B | Burkholderia gladioli
BGC0002146.2 |  |  | 0.05 | NRPS | FR901483 | Cladobotryum sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000657.5 |  | 0.58 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001485.4 |  | 0.40 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000468.5 |  | 0.31 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.31 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000470.6 |  | 0.31 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0001148.5 |  | 0.30 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus
BGC0000469.6 |  | 0.29 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001753.3 |  | 0.28 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus
BGC0002083.3 |  | 0.27 | PKS | gladiofungin A, gladiofungin B | Burkholderia gladioli

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

No significant matches found.

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:
AA314_RS11170: T1TS + T1TS
Domain 1 (6 - 335): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (336 - 717): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 23.28 out of 25.88
Confidence: strong
Additional weak hits (5):
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.53 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.72 out of 31.73
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
--- | ---
AbrC3 | Antibiotic production activator
PsrA | Oleic acid responsive regulator

NZ_CP011509.1 - Region 11 - NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,938,641 - 2,992,273 nt. (total: 53,633 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
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
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
AA314_RS11910: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

AA314_RS11955: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AA314_RS11965: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Ligases: ligase synthase
AA314_RS11960: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AA314_RS57030: 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 | NRPS-like | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  |  | 1.33 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001164.3 |  |  |  | 1.25 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  | 1.24 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001132.4 |  |  |  | 1.12 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  |  | 1.11 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 1.11 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  |  | 1.10 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  |  |  | 1.09 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  |  |  | 1.07 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  |  | 1.05 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001164.3 |  | 0.73 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.73 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.68 | 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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
Additional weak hits (7):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.36 out of 29.38
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.46 out of 20.01
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.78 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.25 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.54 out of 31.73
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.85 out of 26.12
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.07 out of 27.04
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 16, location 2938640 - 2992273:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (AHBA) + (mal) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 17, location 2938640 - 2980671:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (AHBA) + (mal) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 18, location 2942050 - >2986658:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (AHBA) + (mal) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 19, location 2947158 - 2992273:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (AHBA) + (mal) + (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).
AA314_RS11960: AHBA
CAL_domain (44..487): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 19.3
  fatty_acid: 8.3
  shikimic_acid: 4.4
  NH2: 3.6
  Acetyl-CoA: -1.5

AA314_RS57030: mal
PKS_AT (534..829): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 95.8%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 204.2
  inactive: 146.9
  Methoxymalonyl-CoA: 83.6
  Methylmalonyl-CoA: 80.5
  Propionyl-CoA: 63.0
  Ethylmalonyl-CoA: 60.1
  Isobutyryl-CoA: 51.3
  2-Methylbutyryl-CoA: 40.0
  Benzoyl-CoA: 35.9
  trans-1,2-CPDA: 28.5
  CHC-CoA: 27.0
  fatty_acid: 26.8
  Acetyl-CoA: 24.2
  3-Methylbutyryl-CoA: 6.8

AA314_RS57035: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (795..1197): 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:
    LSMTFDIAALELQALCGGEWNLYGPTETTIWSSA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

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

NZ_CP011509.1 - Region 12 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,029,565 - 3,074,862 nt. (total: 45,298 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
AA314_RS12270: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

Transferases: PPTase aminotransferase
AA314_RS12250: aminotransferase

smcogs
  SMCOG1019: aminotransferase

AA314_RS12280: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Ligases: synthase
AA314_RS12235: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

AA314_RS12285: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AA314_RS12295: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.63 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.63 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001238.3 |  | 0.58 | other (other) | biotin | Aspergillus nidulans
BGC0002192.3 |  | 0.58 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001239.3 |  | 0.56 | other (other) | biotin | Aspergillus nidulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.63 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.63 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001238.3 |  | 0.58 | other (other) | biotin | Aspergillus nidulans
BGC0002192.3 |  | 0.58 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001239.3 |  | 0.56 | other (other) | biotin | Aspergillus nidulans

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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (1):
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.03 out of 30.12
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 20, location 3029564 - 3074862:
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).
AA314_RS12295: mal
PKS_AT (1038..1328): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 44.2
  Methylmalonyl-CoA: 33.6
  Methoxymalonyl-CoA: 31.8
  inactive: 20.7
  Propionyl-CoA: 17.6
  Isobutyryl-CoA: 11.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

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

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

NZ_CP011509.1 - Region 13 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,583,681 - 3,605,564 nt. (total: 21,884 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
Translocases: transport
AA314_RS14340: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002805.2 |  | 0.22 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0000997.4 |  | 0.22 | NRPS, PKS | glidobactin, glidobactin B, glidobactin C | [Polyangium] brachysporum
BGC0000080.5 |  | 0.20 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0000106.5 |  | 0.18 | PKS | naphthomycin A | Streptomyces sp. CS

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002805.2 |  | 0.22 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0000997.4 |  | 0.22 | NRPS, PKS | glidobactin, glidobactin B, glidobactin C | [Polyangium] brachysporum
BGC0000080.5 |  | 0.20 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0000106.5 |  | 0.18 | PKS | naphthomycin A | Streptomyces sp. CS

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

No significant matches found.

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
No domains found
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (1):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.86 out of 27.78
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
--- | ---

NZ_CP011509.1 - Region 14 - microviridin
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: 3,624,566 - 3,644,760 nt. (total: 20,195 nt) Show pHMM detection rules used
microviridin: (mvd or mvnA)

#### 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 | microviridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000593.4 |  | 0.63 | ribosomal | microviridin J | Microcystis aeruginosa MRC
BGC0000592.5 |  | 0.53 | ribosomal | microviridin B | Microcystis aeruginosa NIES-298
BGC0000591.5 |  | 0.52 | ribosomal | marinostatin | Alteromonas sp. B-10-31
BGC0002049.3 |  | 0.49 | ribosomal | microviridin N9, microviridin N8, microviridin N7, microviridin N6, microviridin N5, microviridin N4, microviridin N3 | Nostoc punctiforme PCC 73102
BGC0002382.3 |  | 0.45 | ribosomal | grimoviridin | Grimontia marina
BGC0002725.3 |  | 0.43 | ribosomal | prunipeptin | Streptomyces prunicolor NBRC 13075
BGC0000594.5 |  | 0.43 | ribosomal | microviridin K | Planktothrix agardhii NIVA-CYA 126/8
BGC0002626.2 |  | 0.37 | ribosomal | microviridin 1688, microviridin 1739, microviridin 1748 | Nostoc sp. TH1S01
BGC0001122.4 |  | 0.31 | NRPS, PKS | dihydroisoflavipucine, isoflavipucine | Aspergillus terreus NIH2624
BGC0001591.4 |  | 0.31 | other (other) | fatty acid enol ester, N-tetradecanoyl tyrosine | uncultured bacterium CSLC2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000593.4 |  | 0.63 | ribosomal | microviridin J | Microcystis aeruginosa MRC
BGC0000592.5 |  | 0.53 | ribosomal | microviridin B | Microcystis aeruginosa NIES-298
BGC0000591.5 |  | 0.52 | ribosomal | marinostatin | Alteromonas sp. B-10-31
BGC0002049.3 |  | 0.49 | ribosomal | microviridin N9, microviridin N8, microviridin N7, microviridin N6, microviridin N5, microviridin N4, microviridin N3 | Nostoc punctiforme PCC 73102
BGC0002382.3 |  | 0.45 | ribosomal | grimoviridin | Grimontia marina
BGC0002725.3 |  | 0.43 | ribosomal | prunipeptin | Streptomyces prunicolor NBRC 13075
BGC0000594.5 |  | 0.43 | ribosomal | microviridin K | Planktothrix agardhii NIVA-CYA 126/8
BGC0002626.2 |  | 0.37 | ribosomal | microviridin 1688, microviridin 1739, microviridin 1748 | Nostoc sp. TH1S01
BGC0001122.4 |  | 0.31 | NRPS, PKS | dihydroisoflavipucine, isoflavipucine | Aspergillus terreus NIH2624
BGC0001591.4 |  | 0.31 | other (other) | fatty acid enol ester, N-tetradecanoyl tyrosine | uncultured bacterium CSLC2

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: 22.63 out of 26.85
Confidence: medium
Additional weak hits (5):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.63 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.51 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.26 out of 32.74
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP011509.1 - Region 15 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,684,431 - 3,728,837 nt. (total: 44,407 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
AA314_RS14830: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: transferase
AA314_RS14855: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: esterase glucanase
AA314_RS14905: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

AA314_RS50275: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

Lyases: cyclase dehydratase
AA314_RS14860: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

AA314_RS14865: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

AA314_RS14890: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
AA314_RS14870: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000871.4 |  | 0.80 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
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
BGC0001641.4 |  | 0.58 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001160.5 |  | 0.54 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.54 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001285.5 |  | 0.47 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0000826.5 |  | 0.46 | other (other) | staurosporine | Streptomyces clavuligerus ATCC 27064
BGC0000898.5 |  | 0.43 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0002711.2 |  | 0.43 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000825.5 |  | 0.42 | other (other) | staurosporine | Streptomyces sp. TP-A0274

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000871.4 |  | 0.80 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
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
BGC0001641.4 |  | 0.58 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001160.5 |  | 0.54 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.54 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001285.5 |  | 0.47 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0000826.5 |  | 0.46 | other (other) | staurosporine | Streptomyces clavuligerus ATCC 27064
BGC0000898.5 |  | 0.43 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0002711.2 |  | 0.43 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000825.5 |  | 0.42 | other (other) | staurosporine | Streptomyces sp. TP-A0274

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: 21.93 out of 27.55
Confidence: medium
Additional weak hits (5):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.69 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.43 out of 30.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.52 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.42 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 23, location 3684430 - 3728837:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AA314_RS14870: X
AMP-binding (566..1001): X
nrpys: 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:
    N/A
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LKLLFEFSAG-LIGVSGGSIEGYGLTEASPVLTV
  Nearest Stachelhaus code(s):
    Ala DLGIVGGMIK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

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

NZ_CP011509.1 - Region 16 - 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: 3,831,232 - 3,886,645 nt. (total: 55,414 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
Transferases: aminotransferase methyltransferase
AA314_RS15395: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

AA314_RS15405: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

AA314_RS15410: aminotransferase

smcogs
  SMCOG1019: aminotransferase

AA314_RS15430: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Ligases: ligase
AA314_RS15460: 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
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
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
BGC0001261.3 |  | 0.72 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
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
BGC0001261.3 |  | 0.72 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.69 | 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.

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (16):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.64 out of 32.74
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.02 out of 20.97
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.63 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.30 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.50 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.97 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.39 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.09 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.51 out of 27.78
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.47 out of 27.18
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.85 out of 36.53
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.55 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.51 out of 28.14
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.98 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 3831231 - 3886645:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X - X - Asn - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AA314_RS15460: X - X - X - Asn - X
Search NORINE for peptide: strict or relaxed
AMP-binding (37..446): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    NWLAFDISVWQGEMIIGGQANAYGPAECTDTTTL
  Nearest Stachelhaus code(s):
    Dab DIWELTADDK (59% 8Å match)
    Hpg DIWHVGAITK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1104..1510): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HGFAFDISVWQGDMITVGQINSYGPAECTDITTL
  Nearest Stachelhaus code(s):
    Lys DAEDIGSVIK (53% 8Å match)
  Stachelhaus code match:
    60% (weak)

AMP-binding (2168..2557): X
nrpys: Glu, Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    CAFGFDIHLEEFVIVTGGEVNTYGPTETSINVAA
  Nearest Stachelhaus code(s):
    N6-ohLys or Lys DIESIGTIVK (56% 8Å match)
    Hpg DIWHVGTIIK (53% 8Å match)
    Arg DVENVGAINK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (3216..3622): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDLTVTSAKLVIGGEINEYGPTETVVGCCV
  Nearest Stachelhaus code(s):
    Asn DLTKVGEVGK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4282..4686): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HALAFDAAAEDPSLAPGGDLNVYGPTECTITSAT
  Nearest Stachelhaus code(s):
    Arg DAEDIGAITK (59% 8Å match)
    Ahp DVENAGVVTK (59% 8Å match)
    Lys DAESVGTIIK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---

NZ_CP011509.1 - Region 17 - lanthipeptide-class-ii,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,020,820 - 4,055,797 nt. (total: 34,978 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)
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
Terpene
TFBS Finder
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
AA314_RS16245: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AA314_RS52660: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: glycosyltransferase
AA314_RS50320: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

AA314_RS50325: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

AA314_RS50330: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Lyases: cyclase
AA314_RS16160: Terpene synthase/cyclase metal-binding domain protein

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

AA314_RS16210: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | terpene | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000660.5 |  |  | 0.44 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0000554.4 |  |  | 0.39 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001555.4 |  |  | 0.39 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  |  | 0.38 | ribosomal | microcin N | Escherichia coli
BGC0001210.5 |  |  | 0.36 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002173.2 |  |  | 0.36 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000588.5 |  |  | 0.35 | ribosomal | microcin L | Escherichia coli
BGC0000623.3 |  |  | 0.34 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0002339.3 |  |  | 0.32 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0002698.2 |  |  | 0.31 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000554.4 |  | 0.57 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000660.5 |  | 0.57 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0002276.2 |  | 0.56 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001198.3 |  | 0.56 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0001210.5 |  | 0.55 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002339.3 |  | 0.53 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0002173.2 |  | 0.52 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000516.4 |  | 0.52 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli

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 AA314_RS16210

AA314_RS16215
Leader:
MSNIDVVRAWKDEQYRMSLTTEERAQLPQNPAGMVELTDSDLEGVAGG
Core:
Y A E A V D I D V S V T K T S C C T Y S T T A T A C C
Core with dehydrations:
Y A E A V D I D V Dha V Dhb K Dhb Dha Cys Cys Dhb Y Dha Dhb Dhb A Dhb A Cys Cys

#### antiSMASH-DB 4.0 matches for AA314_RS16215

100.0%
NZ_CP011509.1:
Lanthipeptides: AA314_RS16215_lanthipeptide
1
Y A E A V D I D V S V T K T S C C T Y S T T A T A C C
27
Y A E A V D I D V S V T K T S C C T Y S T T A T A C C
1
Y A E A V D I D V S V T K T S C C T Y S T T A T A C C
27
22.0%
NZ_BBYJ01000018.1:
Lanthipeptides: AWQ71_RS24060_lanthipeptide
3
E A V D I D V S V T K T S C C T Y S T T A T A C C
27
A D I D+S + T+ T+T C
3
P A G D I D L S T A A G A S N T W W I T S T P A C
27
15.6%
NZ_JAEKEJ010000007.1:
Lanthipeptides: JFU02_RS02780_lanthipeptide
1
Y A E A V D I D V S V T K T S C
16
Y A + I +++++ S C
17
Y A N G I T I G L A L S R Q S C
32
allorf_04046324_04046491
Leader:
MRGSTPGIRTPAYSPDALMLPVTAIPTRAHLLPLRPRKTRADSQGG
Core:
C L T T G L E G L
Core with dehydrations:
Cys L Dhb Dhb G L E G L

#### antiSMASH-DB 4.0 matches for allorf_04046324_04046491

100.0%
NZ_CP011509.1:
Lanthipeptides: allorf_04046324_04046491_lanthipeptide
1
C L T T G L E G L
9
C L T T G L E G L
1
C L T T G L E G L
9

#### Legend:

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
diterpene |  |  | C20 | C6-C11 + C10-C15 | PP

Genes with terpene domains:
AA314_RS16160: T1TS
Domain 1 (35 - 304): Type 1 terpene synthase
Subtype: unknown
AA314_RS16165: T2TS
Domain 1 (6 - 500): Type 2 terpene synthase
Subtype: Diterpene synthase

Reactions:
  GGPP → diterpene_C6-C11/C10-C15_PP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 25.31
Confidence: medium
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.79 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.03 out of 28.14
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
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
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.67 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.60 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.99 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.19 out of 28.19
Confidence: weak
Lanthipeptides
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

AA314_RS16215 - Class II
  Cleavage pHMM score: -0.30
  RODEO score: 0
  Monoisotopic mass: 2659.2 Da
  Molecular weight: 2660.9 Da
  Number of bridges: 4
  Additional modifications: OH
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2679.0 Da N = 1
    2697.0 Da N = 2
    2715.0 Da N = 3
    2733.0 Da N = 4
    2751.0 Da N = 5
allorf_04046324_04046491 - Class II
  Cleavage pHMM score: -2.30
  RODEO score: 0
  Monoisotopic mass: 885.5 Da
  Molecular weight: 886.0 Da
  Number of bridges: 1
  Additional modifications: OH
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    904.0 Da N = 1

Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
GGPP | Geranylgeranyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP011509.1 - Region 18 - proteusin,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: 4,443,765 - 4,478,787 nt. (total: 35,023 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)
proteusin: (PoyD or TIGR03793)

#### Legend:

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

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

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

Reference | terpene | proteusin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001198.3 |  |  | 0.18 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0001422.4 |  |  | 0.10 | NRPS, PKS | myxochromide A | Myxococcus fulvus HW-1
BGC0001424.4 |  |  | 0.09 | NRPS, PKS | myxochromide C | Myxococcus virescens
BGC0001423.4 |  |  | 0.09 | NRPS, PKS | myxochromide C | Myxococcus hansupus
BGC0001421.4 |  |  | 0.09 | NRPS, PKS | myxochromide B | Myxococcus sp.
BGC0001427.4 |  |  | 0.09 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001425.4 |  |  | 0.09 | NRPS, PKS | myxochromide A | Myxococcus xanthus DK 1622
BGC0001426.4 |  |  | 0.09 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001428.4 |  |  | 0.09 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0002339.3 |  |  | 0.08 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001198.3 |  | 0.50 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0002339.3 |  | 0.34 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0001422.4 |  | 0.28 | NRPS, PKS | myxochromide A | Myxococcus fulvus HW-1
BGC0001421.4 |  | 0.26 | NRPS, PKS | myxochromide B | Myxococcus sp.
BGC0001423.4 |  | 0.26 | NRPS, PKS | myxochromide C | Myxococcus hansupus
BGC0001424.4 |  | 0.26 | NRPS, PKS | myxochromide C | Myxococcus virescens
BGC0001427.4 |  | 0.26 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001425.4 |  | 0.26 | NRPS, PKS | myxochromide A | Myxococcus xanthus DK 1622
BGC0001426.4 |  | 0.26 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001428.4 |  | 0.26 | NRPS, PKS | myxochromide A | Myxococcus xanthus

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
diterpene |  |  | C20 | C6-C11 + C10-C15 | PP

Genes with terpene domains:
AA314_RS50390: T2TS
Domain 1 (10 - 502): Type 2 terpene synthase
Subtype: Diterpene synthase

Reactions:
  GGPP → diterpene_C6-C11/C10-C15_PP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.08 out of 18.57
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
Additional weak hits (11):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.25 out of 29.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.27 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.96 out of 26.33
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.64 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.94 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.17 out of 18.57
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.96 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.76 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.46 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.90 out of 20.01
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
GGPP | Geranylgeranyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CRP | Cyclic AMP receptor protein
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP011509.1 - Region 19 - 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: 4,701,952 - 4,712,794 nt. (total: 10,843 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
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
--- | --- | --- | --- | --- | ---
BGC0002665.2 |  | 0.33 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001486.4 |  | 0.31 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001902.3 |  | 0.21 | NRPS, PKS | bengamide | Myxococcus virescens
BGC0000721.4 |  | 0.20 | saccharide | tobramycin | Streptoalloteichus tenebrarius

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002665.2 |  | 0.33 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001486.4 |  | 0.31 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001902.3 |  | 0.21 | NRPS, PKS | bengamide | Myxococcus virescens
BGC0000721.4 |  | 0.20 | saccharide | tobramycin | Streptoalloteichus tenebrarius

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.

NZ_CP011509.1 - Region 20 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,767,513 - 4,778,355 nt. (total: 10,843 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
--- | --- | --- | --- | --- | ---
BGC0002665.2 |  | 0.29 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001486.4 |  | 0.28 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002665.2 |  | 0.29 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001486.4 |  | 0.28 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.26 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.83 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP011509.1 - Region 21 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,938,532 - 5,062,262 nt. (total: 123,731 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
AA314_RS19990: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase
AA314_RS19820: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

smcogs
  SMCOG1283: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

Ligases: ligase synthase
AA314_RS19840: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AA314_RS19945: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AA314_RS19950: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  | 1.38 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  | 1.37 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 1.32 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  | 1.31 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  |  |  | 1.31 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  |  | 1.29 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  | 1.29 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  |  | 1.28 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  |  | 1.17 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  |  |  | 1.16 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000342.4 |  | 0.76 | NRPS | enniatin | Fusarium equiseti
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.74 | 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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
Additional weak hits (15):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.92 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.90 out of 27.78
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.60 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.12 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.20 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.44 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.42 out of 18.57
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.38 out of 21.55
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 23.96 out of 30.12
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.84 out of 32.38
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.94 out of 27.04
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.48 out of 26.85
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.84 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 33, location 4938531 - 5062262:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-X - Ile - X) + (Ile - Ile - Ile - X) + (NH2 - Tyr - mal - Hpr - Hpr - Gln - Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 34, location 4938531 - 5004085:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Tyr - mal - Hpr - Hpr - Gln - Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 35, location 4997802 - 5062262:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-X - Ile - X) + (Ile - Ile - Ile - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AA314_RS19840: NH2 - Tyr - mal - X - Hpr - Hpr - Gln - Asp
Search NORINE for peptide: strict or relaxed
CAL_domain (39..484): NH2
minowa: NH2

Prediction, score:
  NH2: 167.7
  fatty_acid: 23.3
  AHBA: 3.2
  shikimic_acid: 0.0
  Acetyl-CoA: -2.5

AMP-binding (1147..1540): 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:
    TATAFDASVSESTAASVGELNFYGPTEATVCATM
  Nearest Stachelhaus code(s):
    Tyr DASTAAAVCK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

PKS_AT (2265..2563): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 143.0
  Methoxymalonyl-CoA: 73.9
  inactive: 73.5
  Methylmalonyl-CoA: 61.3
  Propionyl-CoA: 42.1
  Ethylmalonyl-CoA: 41.4
  Isobutyryl-CoA: 36.0
  CHC-CoA: 31.6
  Benzoyl-CoA: 23.0
  2-Methylbutyryl-CoA: 22.7
  fatty_acid: 16.5
  trans-1,2-CPDA: 11.0
  Acetyl-CoA: 10.0
  3-Methylbutyryl-CoA: 0.0

A-OX (3236..3956): X
No predictions made
AMP-binding (4461..4865): Hpr
nrpys: Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MWQSFDVSIQETFVVTAGEENQYGPSEAHVVTAH
  Nearest Stachelhaus code(s):
    Hpr DVQFVAQVVK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5529..5933): Hpr
nrpys: Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQAFDVSFQESFLVTAGEENQYGPSETHVVSAH
  Nearest Stachelhaus code(s):
    Hpr DVQFVAQVVK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6596..6996): Gln
nrpys: Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWLTFDASVWEAQVFCGGEVNLYGPTETTIDATW
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (7658..8063): 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:
    YGVSADLGHTAPKVVLGGDYNHYGPTETTVGVLA
  Nearest Stachelhaus code(s):
    Asp DLTKVGHVGK (82% 8Å match)
    OH-Asp DLTKVGHVGK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AA314_RS19945: Ile - Ile - Ile - X
Search NORINE for peptide: strict or relaxed
AMP-binding (494..890): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDTSFDAATFEGFLLFGGELHVYGPTENTTYSTW
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTYK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1549..1945): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDSSFDAATFEGFLLFGGELHVYGPTENTTFSTW
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2605..3001): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDTSFDAATFEGFLLFGGELHVYGPTENTTYSTW
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTYK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3660..4060): X
nrpys: Glu, Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWRAFDISVWEAHFFCGGEVHQYGPTEACIDCTA
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIDK (71% 8Å match)
    Hpg DIWHVGAITK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

AA314_RS19950: X - Ile - X
Search NORINE for peptide: strict or relaxed
AMP-binding (477..885): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HSLAFDVSLEEPNVIVGGEINAYGPTEATITSTL
  Nearest Stachelhaus code(s):
    Arg DVEEIGAITK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1968..2364): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNTSFDAATFEGFILAGGDLNGYGPTENTTFSTW
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (82% 8Å match)
    Ile DAFFLGVTFK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3021..3418): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSVAFDASTLEGHLLTGGDTACYGPTESTTFTSC
  Nearest Stachelhaus code(s):
    Ile DALFLGCTFK (56% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

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

NZ_CP011509.1 - Region 22 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,122,567 - 5,159,619 nt. (total: 37,053 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase synthase
AA314_RS20305: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AA314_RS20335: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

AA314_RS20350: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

AA314_RS20375: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

AA314_RS20385: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

AA314_RS20395: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acylase
AA314_RS20300: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: synthase
AA314_RS20335: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Lyases: cyclase
AA314_RS20390: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase
AA314_RS20295: 3-oxoacyl-(acyl carrier protein) synthase III

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

AA314_RS20315: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002175.3 |  | 0.60 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001201.3 |  | 0.57 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0001198.3 |  | 0.53 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002610.3 |  | 0.53 | terpene | stellatic acid | Aspergillus stellatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002175.3 |  | 0.60 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001201.3 |  | 0.57 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0001198.3 |  | 0.53 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002610.3 |  | 0.53 | terpene | stellatic acid | Aspergillus stellatus

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

No significant matches found.

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
AA314_RS20340: T2TS
Domain 1 (12 - 603): Type 2 terpene synthase
Subtype: unknown
AA314_RS20390: T1TS
Domain 1 (60 - 304): 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:
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.01 out of 29.51
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47
Confidence: medium
Additional weak hits (7):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.66 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.03 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.23 out of 21.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.11 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.81 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.69 out of 28.19
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
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
DosR | Hypoxia stress response regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP011509.1 - Region 23 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,318,262 - 5,339,152 nt. (total: 20,891 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
AA314_RS21220: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: synthase synthetase
AA314_RS21195: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

AA314_RS21200: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0000866.5 |  | 0.45 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.44 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000231.5 |  | 0.41 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001605.3 |  | 0.41 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000043.5 |  | 0.38 | PKS | curacin A | Moorea producens 19L

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0000866.5 |  | 0.45 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.44 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000231.5 |  | 0.41 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001605.3 |  | 0.41 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000043.5 |  | 0.38 | PKS | curacin A | Moorea producens 19L

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP

Genes with terpene domains:
AA314_RS21195: PT_FPPS_like
Domain 1 (36 - 295): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  IPP, DMAPP → FPP

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):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 25.75
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.97 out of 20.01
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP011509.1 - Region 24 - NRP-metallophore,NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,423,898 - 5,570,224 nt. (total: 146,327 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)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
AA314_RS21590: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

AA314_RS21655: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase
AA314_RS21670: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
AA314_RS21660: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
AA314_RS21665: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AA314_RS21675: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AA314_RS21770: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AA314_RS21775: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | NRP-metallophore | NRPS | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001758.4 |  |  |  |  | 1.50 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  |  |  | 1.49 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  |  |  |  | 1.43 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  | 1.43 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  |  | 0.94 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001806.4 |  |  |  |  | 0.93 | NRPS | tolaasin A | Pseudomonas tolaasii
BGC0001128.4 |  |  |  |  | 0.90 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  |  |  |  | 0.90 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0002324.3 |  |  |  |  | 0.89 | NRPS, PKS | myxochelin B, myxochelin N, myxochelin O, myxochelin P, myxochelin Q, myxochelin A | Archangium violaceum
BGC0001132.4 |  |  |  |  | 0.89 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001185.5 |  | 0.81 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0000343.5 |  | 0.78 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000401.5 |  | 0.76 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  | 0.75 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.75 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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

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:
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.14 out of 29.38
Confidence: medium
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 28.47 out of 32.74
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
Additional weak hits (31):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.58 out of 20.01
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.06 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.16 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.09 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.38 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.48 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.78 out of 29.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.50 out of 29.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.97 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.41 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.21 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.80 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.72 out of 29.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.50 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.39 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.24 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.67 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.77 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.65 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.89 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.98 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.24 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.45 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.98 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.27 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.60 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.68 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.61 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.03 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.98 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.87 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 38, location 5423897 - 5570224:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Acetyl-CoA - Val - Leu - Val - mal - D-Ser - Val - Ile - X - Ala) + (Acetyl-CoA - Val - Leu - Val - mal - D-Val - X - Ile - X - Ala)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 40, location 5456759 - 5570224:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Acetyl-CoA - Val - Leu - Val - mal - D-Ser - Val - Ile - X - Ala) + (Acetyl-CoA - Val - Leu - Val - mal - D-Val - X - Ile - X - Ala)

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).
AA314_RS21665: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (40..444): diOH-Bz
nrpys: diOH-Bz

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
  Small clusters prediction:
    Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
  Single AA prediction:
    dhb (diOH-Bz)

Stachelhaus prediction details:
  Stachelhaus sequence:
    SASLFPLSSPGGALQVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPAQGVVNK (100% 8Å match)
    diOH-Bz or Sal PLPAQGVVNK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AA314_RS21675: X
AMP-binding (467..709): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGAAFDASVEELDL-------------------Y
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

AA314_RS21770: Acetyl-CoA - Val - Leu - Val - mal - X - Ser - Val - Ile - X - Ala
Search NORINE for peptide: strict or relaxed
CAL_domain (43..492): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 55.3
  NH2: 13.6
  fatty_acid: 12.0
  AHBA: 5.8
  shikimic_acid: 0.0

AMP-binding (1170..1568): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDASTLEGHLLTGGDTACYGPTESTLFTSC
  Nearest Stachelhaus code(s):
    Hpg DALHLGLLCK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2229..2622): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWYVFDVSVWELFMFTGGDVNVYGPAENTVATTI
  Nearest Stachelhaus code(s):
    Leu or Arg DVWFFGLVDK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (3285..3682): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGASFDATTLEGYLLTGGDANCYGPTEGTVIASC
  Nearest Stachelhaus code(s):
    Val DAFWLGCVFK (68% 8Å match)
    Leu DALYLGMMCK (62% 8Å match)
  Stachelhaus code match:
    70% (weak)

PKS_AT (4409..4707): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 131.8
  Methoxymalonyl-CoA: 66.0
  inactive: 60.3
  Methylmalonyl-CoA: 52.7
  Propionyl-CoA: 33.4
  Ethylmalonyl-CoA: 26.6
  Isobutyryl-CoA: 20.4
  CHC-CoA: 20.2
  Benzoyl-CoA: 18.5
  2-Methylbutyryl-CoA: 16.1
  fatty_acid: 12.9
  trans-1,2-CPDA: 10.6
  Acetyl-CoA: 10.5
  3-Methylbutyryl-CoA: 0.0

A-OX (5400..6120): X
No predictions made
AMP-binding (6628..7030): 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:
    RWMTFDVSVWEWHFVCSGEHNLYGPTEAAVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (8156..8556): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSSSFDAATFEGFLVVGGEVNGYGPTESTTFATW
  Nearest Stachelhaus code(s):
    Val DAFFVGGTFK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (9231..9631): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSSSFDAATFEGFLLFGGELNAYGPTESTTFATW
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (82% 8Å match)
    Val DAFWLGATFK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (10306..10696): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TQFLFDGSICEPSFVSAGEINAYGPTEASICATL
  Nearest Stachelhaus code(s):
    bOH-Tyr DTSKVAAICK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (11371..11756): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TQCAFDVSIWEPNFSVAGEINAYGPTEVSIIATL
  Nearest Stachelhaus code(s):
    Ala DVWVTAAIIK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AA314_RS21775: Acetyl-CoA - Val - Leu - Val - mal - X - Val - X - Ile - X - Ala
Search NORINE for peptide: strict or relaxed
CAL_domain (43..492): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 55.3
  fatty_acid: 12.0
  NH2: 7.7
  AHBA: 3.8
  shikimic_acid: 0.0

AMP-binding (1170..1568): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDASTLEGHLLTGGDTACYGPTESTLFTSC
  Nearest Stachelhaus code(s):
    Hpg DALHLGLLCK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2229..2622): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWYVFDVSVWELFMFTGGDVNVYGPAENTVATTI
  Nearest Stachelhaus code(s):
    Leu or Arg DVWFFGLVDK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (3284..3682): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDATTLEGHLLTGGDTACYGPTESTLFTSC
  Nearest Stachelhaus code(s):
    Hpg DALHLGLLCK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

PKS_AT (4409..4707): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 129.0
  Methoxymalonyl-CoA: 64.3
  inactive: 56.0
  Methylmalonyl-CoA: 52.2
  Propionyl-CoA: 30.1
  Isobutyryl-CoA: 26.8
  Ethylmalonyl-CoA: 25.0
  Benzoyl-CoA: 21.9
  CHC-CoA: 17.0
  2-Methylbutyryl-CoA: 15.7
  fatty_acid: 14.6
  Acetyl-CoA: 12.4
  trans-1,2-CPDA: 10.2
  3-Methylbutyryl-CoA: 0.0

A-OX (5391..6115): X
No predictions made
AMP-binding (6623..7021): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDASTLEGHLLTGGDTACYGPTESTLFTSC
  Nearest Stachelhaus code(s):
    Hpg DALHLGLLCK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (8155..8541): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TETAFDASIVEPTFAAAGELNIYGPTEVSIASTV
  Nearest Stachelhaus code(s):
    Phe DAWTIAAIAK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (9202..9602): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSSSFDAATFEGFLLFGGELNAYGPTESTTFATW
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (82% 8Å match)
    Val DAFWLGATFK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (10278..10678): X
nrpys: Glu, Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWRAFDISVWEAHFFCGGEVHQYGPTEACIDCTA
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIDK (71% 8Å match)
    Hpg DIWHVGAITK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (11353..11738): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TQCAFDVSIWEPNFSVAGEINAYGPTEVSIIATL
  Nearest Stachelhaus code(s):
    Ala DVWVTAAIIK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
FuR variant 1 | Ferric Uptake Regulator
FuR variant 2 | Ferric Uptake Regulator

NZ_CP011509.1 - Region 25 - azole-containing-RiPP
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: 6,040,054 - 6,065,091 nt. (total: 25,038 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### 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
Azole RiPPs
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: dehalogenase
AA314_RS23895: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002116.3 |  | 0.42 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0001485.4 |  | 0.41 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000598.5 |  | 0.40 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0000470.6 |  | 0.36 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.34 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.34 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.34 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000841.5 |  | 0.33 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate, clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0001753.3 |  | 0.32 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus
BGC0001148.5 |  | 0.32 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002116.3 |  | 0.42 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0001485.4 |  | 0.41 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000598.5 |  | 0.40 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0000470.6 |  | 0.36 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.34 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.34 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.34 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000841.5 |  | 0.33 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate, clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0001753.3 |  | 0.32 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus
BGC0001148.5 |  | 0.32 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus

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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.65 out of 18.46
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.71 out of 23.43
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (4):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.79 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.25 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.29 out of 30.25
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
TFBS Finder
Azole RiPPs
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
BldD | Development and antibiotic global regulator
RpoN | Regulator of nitrogen assimilation and virulence

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_CP011509.1 - Region 26 - oligosaccharide
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: 6,096,866 - 6,139,943 nt. (total: 43,078 nt) Show pHMM detection rules used
oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))

#### 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
AA314_RS24190: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: glycosyltransferase
AA314_RS24085: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

AA314_RS24130: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

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 | oligosaccharide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000277.5 |  | 0.41 | PKS | urdamycin | Streptomyces fradiae
BGC0001526.4 |  | 0.41 | other (other) | bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K | Synechocystis salina LEGE 06099
BGC0001022.5 |  | 0.38 | NRPS, PKS | myxalamid, myxalamid A, myxalamid C, myxalamid D | Stigmatella aurantiaca
BGC0001525.3 |  | 0.37 | other (other) | bartoloside B, bartoloside C, bartoloside D | Synechocystis salina LEGE 06155
BGC0001417.4 |  | 0.37 | NRPS, PKS | myxochromide D | Cystobacterineae bacterium
BGC0002535.2 |  | 0.35 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0000662.5 |  | 0.35 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.35 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.33 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001573.3 |  | 0.33 | other (other) | dihydrolysergic acid | Claviceps africana

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000277.5 |  | 0.41 | PKS | urdamycin | Streptomyces fradiae
BGC0001526.4 |  | 0.41 | other (other) | bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K | Synechocystis salina LEGE 06099
BGC0001022.5 |  | 0.38 | NRPS, PKS | myxalamid, myxalamid A, myxalamid C, myxalamid D | Stigmatella aurantiaca
BGC0001525.3 |  | 0.37 | other (other) | bartoloside B, bartoloside C, bartoloside D | Synechocystis salina LEGE 06155
BGC0001417.4 |  | 0.37 | NRPS, PKS | myxochromide D | Cystobacterineae bacterium
BGC0002535.2 |  | 0.35 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0000662.5 |  | 0.35 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.35 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.33 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001573.3 |  | 0.33 | other (other) | dihydrolysergic acid | Claviceps africana

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
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
Additional weak hits (6):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.46 out of 29.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.44 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.38 out of 30.25
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.59 out of 24.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.13 out of 36.53
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CRP | Cyclic AMP receptor protein

NZ_CP011509.1 - Region 27 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,173,716 - 6,233,063 nt. (total: 59,348 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
AA314_RS24395: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

AA314_RS24405: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AA314_RS24415: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
AA314_RS24450: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Lyases: dehydratase
AA314_RS24495: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

AA314_RS24500: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: isomerase
AA314_RS24435: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
AA314_RS24420: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AA314_RS24425: 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
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.72 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.72 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  | 0.71 | NRPS | AM-toxin | Alternaria alternata
BGC0002071.2 |  | 0.71 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0000307.4 |  | 0.71 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.72 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.72 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  | 0.71 | NRPS | AM-toxin | Alternaria alternata
BGC0002071.2 |  | 0.71 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0000307.4 |  | 0.71 | NRPS | AbT1 | Aureobasidium pullulans

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

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.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (5):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.38 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
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.10 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 43, location 6173715 - 6233063:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (NH2 - X - Asp - Ser - Thr)

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).
AA314_RS24420: NH2 - X - Asp - Ser - Thr
Search NORINE for peptide: strict or relaxed
CAL_domain (37..483): NH2
minowa: NH2

Prediction, score:
  NH2: 233.7
  AHBA: 4.6
  shikimic_acid: 0.0
  Acetyl-CoA: -1.0
  fatty_acid: -2.4

AMP-binding (1141..1532): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LVMAFDTSVEEVNEITGGEINVYGQTETTIEVTT
  Nearest Stachelhaus code(s):
    Lys DTENIGTISK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2190..2589): 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:
    YGISADLGHTSPKIVLGGEFNHYGPTETTVGVTT
  Nearest Stachelhaus code(s):
    Asp DLTKVGHVGK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3244..3643): 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:
    RWATFDVSVWEWHFICSGEHNLYGPTEAAVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHISLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4303..4709): 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:
    LATHFDFSVWEGNQIFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AA314_RS24425: X
AMP-binding (508..911): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

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

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

Regulator | Description
--- | ---

NZ_CP011509.1 - Region 28 - 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: 6,283,311 - 6,294,168 nt. (total: 10,858 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
--- | --- | --- | --- | --- | ---
BGC0001838.4 |  | 0.29 | NRPS | WLIP | Pseudomonas putida
BGC0001588.3 |  | 0.24 | saccharide | exopolysaccharides | Burkholderia pseudomallei 1026b
BGC0000714.5 |  | 0.22 | saccharide | sisomicin | Micromonospora inyonensis
BGC0001603.3 |  | 0.22 | saccharide | gentamicin | Micromonospora echinospora
BGC0001589.3 |  | 0.22 | saccharide | exopolysaccharides | Burkholderia cenocepacia J2315
BGC0002025.4 |  | 0.21 | NRPS, PKS | thaxteramide C | Jahnella sp. MSr9139
BGC0001093.3 |  | 0.21 | NRPS, PKS | disorazol A | Sorangium cellulosum
BGC0000080.5 |  | 0.21 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0000696.5 |  | 0.21 | saccharide | gentamicin | Micromonospora echinospora

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001838.4 |  | 0.29 | NRPS | WLIP | Pseudomonas putida
BGC0001588.3 |  | 0.24 | saccharide | exopolysaccharides | Burkholderia pseudomallei 1026b
BGC0000714.5 |  | 0.22 | saccharide | sisomicin | Micromonospora inyonensis
BGC0001603.3 |  | 0.22 | saccharide | gentamicin | Micromonospora echinospora
BGC0001589.3 |  | 0.22 | saccharide | exopolysaccharides | Burkholderia cenocepacia J2315
BGC0002025.4 |  | 0.21 | NRPS, PKS | thaxteramide C | Jahnella sp. MSr9139
BGC0001093.3 |  | 0.21 | NRPS, PKS | disorazol A | Sorangium cellulosum
BGC0000080.5 |  | 0.21 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0000696.5 |  | 0.21 | saccharide | gentamicin | Micromonospora echinospora

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.26 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.39 out of 20.97
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP011509.1 - 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: 6,323,536 - 6,344,627 nt. (total: 21,092 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001483.4 |  | 0.32 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001430.4 |  | 0.29 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca Sg a15
BGC0000845.5 |  | 0.26 | other (non-nrp beta-lactam) | clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0000997.4 |  | 0.26 | NRPS, PKS | glidobactin, glidobactin B, glidobactin C | [Polyangium] brachysporum
BGC0002025.4 |  | 0.26 | NRPS, PKS | thaxteramide C | Jahnella sp. MSr9139
BGC0001057.4 |  | 0.25 | NRPS, PKS | zearalenone | Fusarium graminearum
BGC0000080.5 |  | 0.25 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0002288.2 |  | 0.24 | NRPS | ashimide A, ashimide B | Streptomyces sp. NA03103
BGC0001281.3 |  | 0.24 | PKS | ustilagic acid | Ustilago maydis 521
BGC0002657.2 |  | 0.22 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001483.4 |  | 0.32 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001430.4 |  | 0.29 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca Sg a15
BGC0000845.5 |  | 0.26 | other (non-nrp beta-lactam) | clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0000997.4 |  | 0.26 | NRPS, PKS | glidobactin, glidobactin B, glidobactin C | [Polyangium] brachysporum
BGC0002025.4 |  | 0.26 | NRPS, PKS | thaxteramide C | Jahnella sp. MSr9139
BGC0001057.4 |  | 0.25 | NRPS, PKS | zearalenone | Fusarium graminearum
BGC0000080.5 |  | 0.25 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0002288.2 |  | 0.24 | NRPS | ashimide A, ashimide B | Streptomyces sp. NA03103
BGC0001281.3 |  | 0.24 | PKS | ustilagic acid | Ustilago maydis 521
BGC0002657.2 |  | 0.22 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis

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

No significant matches found.

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
No domains 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 (3):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.16 out of 32.74
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.17 out of 28.19
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
--- | ---

NZ_CP011509.1 - Region 30 - NRPS,T1PKS,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: 6,376,546 - 6,492,237 nt. (total: 115,692 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### 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
AA314_RS50715: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
AA314_RS25270: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
AA314_RS25340: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase synthetase
AA314_RS25135: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

AA314_RS25245: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AA314_RS25250: 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 | terpene | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  | 0.95 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  | 0.90 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  |  |  | 0.89 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  |  | 0.87 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  |  | 0.84 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  |  |  | 0.84 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  |  | 0.83 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  |  | 0.82 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  | 0.82 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  |  | 0.81 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.77 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.77 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001133.4 |  | 0.75 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001825.4 |  | 0.74 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

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:
AA314_RS25120: TS_Pyr4
Domain 1 (27 - 228): Pyr4 type terpene synthase
Subtype: unknown
AA314_RS25135: PT_FPPS_like
Domain 1 (48 - 339): 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: 18.57 out of 18.57
Confidence: strong
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.28 out of 27.55
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.12 out of 23.79
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.97 out of 23.79
Confidence: medium
Additional weak hits (9):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.09 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.60 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.39 out of 27.04
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.52 out of 26.12
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.84 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.70 out of 26.06
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.00 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.81 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
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 46, location 6376545 - 6492237:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - X - D-Ser - Ile - Val) + (mal - X - bLys) + (Ser - bLys - Val - X - Val - Ala - Val - Val - Val - Ala)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 48, location 6389198 - 6492237:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - X - D-Ser - Ile - Val) + (mal - X - bLys) + (Ser - bLys - Val - X - Val - Ala - Val - Val - Val - Ala)

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).
AA314_RS25240: fatty_acid - X - Ser - Ile - Val
Search NORINE for peptide: strict or relaxed
CAL_domain (41..489): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 30.8
  NH2: 13.8
  shikimic_acid: 7.9
  AHBA: 7.3
  Acetyl-CoA: 1.2

A-OX (1172..1936): X
No predictions made
AMP-binding (2573..2972): 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:
    RWMTFDVSVWEWHFICSGEHNLYGPTEAAVDVTF
  Nearest Stachelhaus code(s):
    Ser DVWHISLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4058..4457): Ile
nrpys: Ile

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

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

AMP-binding (5121..5517): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGSAFDAATLEGWLLAGGDVNAYGPTENTTFTTC
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (91% 8Å match)
    bOH-Val DALWLGGTFK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AA314_RS25245: mal - X - X - bLys
Search NORINE for peptide: strict or relaxed
PKS_AT (532..829): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 119.3
  Methoxymalonyl-CoA: 56.8
  inactive: 46.3
  Methylmalonyl-CoA: 44.3
  Propionyl-CoA: 28.6
  Ethylmalonyl-CoA: 26.2
  CHC-CoA: 20.5
  Isobutyryl-CoA: 19.4
  Benzoyl-CoA: 18.9
  2-Methylbutyryl-CoA: 12.8
  fatty_acid: 9.5
  Acetyl-CoA: 2.5
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

A-OX (1503..2222): X
No predictions made
AMP-binding (2732..3136): X
nrpys: OH-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:
    YGVSADLGNTAPKIVLGGDFNHYGPTETTVGVLT
  Nearest Stachelhaus code(s):
    OH-Asp DLTKVGHVGK (85% 8Å match)
    Asp DLTKVGHVGK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3799..4204): bLys
nrpys: bLys

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 with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAAAWDTSAEEPNLVIGGELNTYGLTEVTAVATS
  Nearest Stachelhaus code(s):
    bLys DTENVGTAVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AA314_RS25250: Ser - bLys - Val - X - Val - Ala - Val - Val - Val - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (495..892): 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:
    RWMTFDVSVWEWHFFSSGEHNLYGPTEAAVDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1554..1959): bLys
nrpys: bLys

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 with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAAAWDTSAEEPNLVIGGELNTYGLTEVTAVATS
  Nearest Stachelhaus code(s):
    bLys DTENVGTAVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2622..3017): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDASTLEGWLLAGGDINGYGPTENTTFSCC
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (88% 8Å match)
    bOH-Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3680..4084): X
nrpys: OH-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:
    YGVSADLGNTAPKIVLGGDFNHYGPTETTVGVLT
  Nearest Stachelhaus code(s):
    OH-Asp DLTKVGHVGK (85% 8Å match)
    Asp DLTKVGHVGK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4748..5143): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDASTLEGWLLAGGDINGYGPTENTTFSCC
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (88% 8Å match)
    bOH-Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5805..6195): 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:
    FWATFDLSVFEANTNLAGELNLYGPTEDTTYSTY
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6853..7248): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDASTLEGWLLAGGDINGYGPTENTTFSCC
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (88% 8Å match)
    bOH-Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (7910..8301): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDASTLEGWLLAGGDINGYGPTENTTFSCC
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (88% 8Å match)
    bOH-Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (8960..9349): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGAAFDASTLEGWLLAGGDINGYGPTENTTFSCC
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (88% 8Å match)
    bOH-Val DALWLGGTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (10007..10397): 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:
    FWATFDLSVFEANTNLAGELNLYGPTEDTTYSTY
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
GnfM | Regulator of nitrogen-fixation genes
IolR | Regulator of the inositol catabolism
ToxT | Regulator of MSHA biosynthesis

NZ_CP011509.1 - Region 31 - 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: 6,502,735 - 6,523,739 nt. (total: 21,005 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Ligases: synthetase
AA314_RS25445: 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 |  | 0.45 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.42 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.37 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000676.5 |  | 0.28 | terpene | aphidicolin, aphidicolan-16β-ol, 3-deoxyaphidicolin, 17-deoxyaphidicolin | Phoma betae
BGC0000688.4 |  | 0.28 | terpene | copalyl diphosphate | Diaporthe amygdali
BGC0001756.3 |  | 0.28 | terpene | retigeranin, arathanatriene | Arabidopsis thaliana
BGC0001075.5 |  | 0.27 | PKS, terpene | aurachin RE | Rhodococcus erythropolis
BGC0001529.5 |  | 0.27 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000665.5 |  | 0.26 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000678.5 |  | 0.25 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.45 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.42 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.37 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000676.5 |  | 0.28 | terpene | aphidicolin, aphidicolan-16β-ol, 3-deoxyaphidicolin, 17-deoxyaphidicolin | Phoma betae
BGC0000688.4 |  | 0.28 | terpene | copalyl diphosphate | Diaporthe amygdali
BGC0001756.3 |  | 0.28 | terpene | retigeranin, arathanatriene | Arabidopsis thaliana
BGC0001075.5 |  | 0.27 | PKS, terpene | aurachin RE | Rhodococcus erythropolis
BGC0001529.5 |  | 0.27 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000665.5 |  | 0.26 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000678.5 |  | 0.25 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
AA314_RS25445: PT_FPPS_like
Domain 1 (46 - 319): 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.33 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.21 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
Additional weak hits (4):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.54 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.58 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.25 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.49 out of 26.85
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP011509.1 - Region 32 - NRPS,T1PKS,microviridin,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: 6,533,679 - 6,580,989 nt. (total: 47,311 nt) Show pHMM detection rules used
phenazine: phzB
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
microviridin: (mvd or mvnA)

#### 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 reductase
AA314_RS25600: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

AA314_RS25710: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: acylase glycosyltransferase
AA314_RS25590: sugar transferase

smcogs
  SMCOG1146: sugar transferase

AA314_RS25730: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: glucanase glucosidase hydrolase
AA314_RS25575: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

AA314_RS25625: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

AA314_RS25745: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

AA314_RS25755: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Ligases: synthase
AA314_RS25670: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AA314_RS25685: 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 | phenazine | NRPS | T1PKS | microviridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001164.3 |  |  |  |  | 0.84 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  |  | 0.82 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002154.2 |  |  |  |  | 0.82 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  |  |  |  | 0.82 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001244.3 |  |  |  |  | 0.78 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  |  |  |  | 0.78 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  |  |  | 0.77 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  |  |  | 0.77 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002135.2 |  |  |  |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.00 out of 20.47
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 26.35 out of 29.65
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.52 out of 24.78
Confidence: medium
Additional weak hits (5):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.58 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.03 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.24 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 50, location 6533678 - 6580989:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 52, location 6534143 - 6580989:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).
AA314_RS25670: X - mal
AMP-binding (469..859): 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:
    LVQAFDMAVQESVLMVGGEINGYGPTEATIYATA
  Nearest Stachelhaus code(s):
    Hty DAQSMGAIIK (62% 8Å match)
  Stachelhaus code match:
    60% (weak)

PKS_AT (1579..1869): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 163.8
  inactive: 98.8
  Methylmalonyl-CoA: 63.9
  Methoxymalonyl-CoA: 63.5
  Propionyl-CoA: 46.6
  Isobutyryl-CoA: 36.6
  Ethylmalonyl-CoA: 35.8
  2-Methylbutyryl-CoA: 26.2
  CHC-CoA: 25.4
  fatty_acid: 23.2
  Benzoyl-CoA: 22.2
  trans-1,2-CPDA: 9.6
  Acetyl-CoA: 9.6
  3-Methylbutyryl-CoA: 0.0

AA314_RS25730: mmal
PKS_AT (18..312): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 70.8%
  Ethylmalonyl-CoA: 62.5%
  Isobutyryl-CoA: 62.5%

minowa: Benzoyl-CoA

Prediction, score:
  Benzoyl-CoA: 138.3
  Methylmalonyl-CoA: 130.7
  Isobutyryl-CoA: 130.7
  Methoxymalonyl-CoA: 113.5
  Ethylmalonyl-CoA: 94.6
  Acetyl-CoA: 89.3
  Malonyl-CoA: 86.9
  Propionyl-CoA: 81.2
  trans-1,2-CPDA: 80.8
  2-Methylbutyryl-CoA: 65.7
  3-Methylbutyryl-CoA: 55.8
  CHC-CoA: 46.7
  fatty_acid: 29.9
  inactive: 27.0

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
LexA variant 1 | Repressor of DNA damage response
LexA variant 2 | Repressor of DNA damage response
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP011509.1 - Region 33 - RRE-containing,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: 6,669,690 - 6,710,332 nt. (total: 40,643 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])
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase kinase
AA314_RS26115: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

AA314_RS26285: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Ligases: synthase synthetase
AA314_RS26250: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

AA314_RS26270: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

Translocases: transport
AA314_RS26275: 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 | RRE-containing | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000948.5 |  |  | 0.22 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0001701.4 |  |  | 0.15 | ribosomal | nisin O | Blautia obeum
BGC0000677.5 |  |  | 0.13 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002674.2 |  |  | 0.12 | ribosomal | enterocin F4-9 | Enterococcus faecalis
BGC0001206.5 |  |  | 0.12 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0001485.4 |  |  | 0.12 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002826.2 |  |  | 0.12 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0000616.4 |  |  | 0.12 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0001910.4 |  |  | 0.11 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000664.5 |  |  | 0.11 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000948.5 |  | 0.54 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000677.5 |  | 0.45 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001206.5 |  | 0.44 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0001485.4 |  | 0.42 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001896.4 |  | 0.42 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0002309.2 |  | 0.42 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000665.5 |  | 0.41 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000678.5 |  | 0.41 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001910.4 |  | 0.40 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002674.2 |  | 0.40 | ribosomal | enterocin F4-9 | Enterococcus faecalis

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
AA314_RS26250: PT_FPPS_like
Domain 1 (35 - 340): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
Additional weak hits (11):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.65 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.83 out of 26.12
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.08 out of 29.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.14 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.36 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.57 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.89 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.17 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.67 out of 20.01
Confidence: weak
RREFinder
Terpene
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (6669689...6689980)
AA314_RS26150
  RRE type: Stand_Alone_Lasso_RRE
  Location: 17 - 90
  Score: 44.3
  RRE type: PqqD_RRE
  Location: 22 - 90
  Score: 33.2

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
--- | ---
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP011509.1 - Region 34 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,320,981 - 7,397,535 nt. (total: 76,555 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
AA314_RS28615: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

AA314_RS28710: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Lyases: dehydratase
AA314_RS28610: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
AA314_RS28620: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

AA314_RS28685: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AA314_RS28690: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AA314_RS28695: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.94 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.93 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  | 0.90 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002075.3 |  |  | 0.89 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  |  | 0.89 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.89 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  |  | 0.88 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001133.4 |  |  | 0.87 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  | 0.86 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.85 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.75 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001133.4 |  | 0.74 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.25 out of 28.19
Confidence: medium
Additional weak hits (15):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.79 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.21 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.70 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 26.11 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.35 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.49 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.99 out of 29.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.07 out of 36.54
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.86 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.62 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.44 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.68 out of 24.78
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.60 out of 20.01
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.82 out of 20.01
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 57, location 7320980 - 7397535:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Phe) + (mal - D-X) + (D-Gln - X - X - Phe - Phe)

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).
AA314_RS28685: Gln - X - X - Phe - Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (470..870): Gln
nrpys: Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWITFDASVWEAQLFCGGEVNLYGPTEATIDATF
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2000..2394): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TASAFDVSVFEGVLMVAGEVNAYGPTEISIYATL
  Nearest Stachelhaus code(s):
    Ala DVWVTAAIIK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (3103..3502): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LALGFDTSVKQQDCLVGGEFNVYGPTECTVDATV
  Nearest Stachelhaus code(s):
    Glu DAKDLGVVDK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4731..5117): Phe
nrpys: Phe

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    Unpolar aromatic ring (Phe, Trp)
  Single AA prediction:
    phe (Phe)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGKAFDASIWEMTLMSVGEVNGYGPTEASVCVTW
  Nearest Stachelhaus code(s):
    Leu or Phe DAWTIGGVCK (71% 8Å match)
    Phe DAWTIAGVCK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (5780..6166): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGKAFDASIWELTLMVAGEVNGYGPTEVSVLATW
  Nearest Stachelhaus code(s):
    Phe DAWTIAGVCK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AA314_RS28690: mal - X - X
PKS_AT (528..825): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 128.4
  Methoxymalonyl-CoA: 62.5
  inactive: 55.7
  Methylmalonyl-CoA: 50.2
  Ethylmalonyl-CoA: 38.1
  Isobutyryl-CoA: 22.9
  Propionyl-CoA: 20.3
  Benzoyl-CoA: 17.0
  CHC-CoA: 13.3
  2-Methylbutyryl-CoA: 10.4
  3-Methylbutyryl-CoA: 8.2
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Acetyl-CoA: 0.0

A-OX (1502..2225): X
No predictions made
AMP-binding (2731..3125): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AARSFDASLAGWIGTVGGEFNEYGPTEATIWSTV
  Nearest Stachelhaus code(s):
    Trp DAAIIGEIWK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AA314_RS28695: NH2 - Phe
Search NORINE for peptide: strict or relaxed
CAL_domain (49..485): NH2
minowa: NH2

Prediction, score:
  NH2: 181.1
  fatty_acid: 30.1
  AHBA: 6.8
  shikimic_acid: 0.0
  Acetyl-CoA: -1.6

AMP-binding (1170..1558): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LARAFDSSVWEVTLMSVGELNGYGPTEVSVAVSW
  Nearest Stachelhaus code(s):
    dmeaTrp or 1Me-Trp DVWTHGGVAK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
ZuR variant 1 | Zinc-responsive repressor

NZ_CP011509.1 - Region 35 - 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: 7,604,383 - 7,616,032 nt. (total: 11,650 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
AA314_RS29695: HAD-superfamily hydrolase, subfamily IA, variant

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

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

No matches found.

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.73 out of 23.79
Confidence: medium
Additional weak hits (3):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.30 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.17 out of 29.65
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.56 out of 29.25
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP011509.1 - Region 36 - lanthipeptide-class-ii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,166,194 - 8,189,421 nt. (total: 23,228 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
AA314_RS31775: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase hydratase
AA314_RS31790: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

AA314_RS31825: 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 | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001210.5 |  | 0.53 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000554.4 |  | 0.53 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.52 | ribosomal | microcin N | Escherichia coli
BGC0002005.2 |  | 0.51 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0000525.5 |  | 0.51 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002698.2 |  | 0.50 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001579.4 |  | 0.49 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0000527.5 |  | 0.49 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001210.5 |  | 0.53 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000554.4 |  | 0.53 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.52 | ribosomal | microcin N | Escherichia coli
BGC0002005.2 |  | 0.51 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0000525.5 |  | 0.51 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002698.2 |  | 0.50 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001579.4 |  | 0.49 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0000527.5 |  | 0.49 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728

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

No significant matches found.

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

No significant matches found.

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

#### Lanthipeptide(s) for AA314_RS31790

AA314_RS31785
Leader:
MKKEWIVRAWKDPAFRANLSAEERASLPESPSGRALTELDESELLGITGG
Core:
R A A L E P S T G C T D G S Q P T C G I V L C S V L E A A
Core with dehydrations:
R A A L E P Dha Dhb G Cys Dhb D G Dha Q P Dhb Cys G I V L Cys Dha V L E A A

#### antiSMASH-DB 4.0 matches for AA314_RS31785

100.0%
NZ_CP011509.1:
Lanthipeptides: AA314_RS31785_lanthipeptide
1
R A A L E P S T G C T D G S Q P T C G I V L C S V L E A A
29
R A A L E P S T G C T D G S Q P T C G I V L C S V L E A A
1
R A A L E P S T G C T D G S Q P T C G I V L C S V L E A A
29
41.4%
NZ_CP069396.1:
Lanthipeptides: JRI60_RS31715_lanthipeptide
2
A A L E P S T G C T D G S Q P T C G I V L C S V L E A
28
A ++P+T G C + T C G I+ C S+L++
3
A E M Q P A T G C D G P E R Q T C G I I N C S L L D S
29
24.1%
NZ_CP051627.1 and 1 other:
NZ_CP051627.1 Lanthipeptides: FOF52_RS17520_lanthipeptide
Lanthipeptides: FOF52_RS17520_lanthipeptide
9
G C T D G S Q P T C
18
G D G Q P T C
9
G T N D G C Q P T C
18
with 2 more sequence matches
16.0%
NZ_QSFS01000023.1:
Lanthipeptides: DW924_RS15110_lanthipeptide
1
R A A L E P S T G C T D G S Q P T C
18
R+ P T G + G S Q C
33
R S Q C A P C T G S S K G S Q A R C
50
15.4%
NZ_VXKQ01000008.1:
Lanthipeptides: F3D62_RS12715_lanthipeptide
6
P S T G C T D G S Q P T C G
19
P C T+ + P+C G
26
P G G H C T E T T D P S C G
39

#### MIBiG 4.0 matches for AA314_RS31785

16.2%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
2
A A L E P S T G C T D
12
A A P+T C T
25
A A F C P T T K C T S
35
13.8%
BGC0002110.3 (QKV49894.1):
Lanthipeptide: birimositide
6
P S T G C T D
12
P+T C T
18
P T T K C T S
24
allorf_08181116_08181184
Leader:
MWVELVSPQGS
Core:
S S Y R S A P S T T C
Core with dehydrations:
Dha Dha Y R Dha A P Dha Dhb Dhb Cys

#### antiSMASH-DB 4.0 matches for allorf_08181116_08181184

100.0%
NZ_CP011509.1:
Lanthipeptides: allorf_08181116_08181184_lanthipeptide
1
S S Y R S A P S T T C
11
S S Y R S A P S T T C
1
S S Y R S A P S T T C
11
16.1%
NZ_QLLX01000002.1 and 1 other:
NZ_QLLX01000002.1 Lanthipeptides: allorf_335035_335211_lanthipeptide
Lanthipeptides: allorf_335035_335211_lanthipeptide
1
S S Y R S A P S T T C
11
+++R S P+ T C
12
A A H R S V P T R T C
22
allorf_08187294_08187419
Leader:
MNPPHPIPIEPRTSCLRLMGQLPAG
Core:
Y S C S W G G P G T D Y N R R P
Core with dehydrations:
Y Dha Cys Dha W G G P G Dhb D Y N R R P

#### antiSMASH-DB 4.0 matches for allorf_08187294_08187419

100.0%
NZ_CP011509.1:
Lanthipeptides: allorf_08187294_08187419_lanthipeptide
1
Y S C S W G G P G T D Y N R R P
16
Y S C S W G G P G T D Y N R R P
1
Y S C S W G G P G T D Y N R R P
16
30.0%
NZ_CM000951.1:
Lassopeptides: SSEG_RS44950_lassopeptide
3
C S W G G P G T D Y
12
C W G G T D+
1
C V W G G D C T D F
10
23.1%
NZ_SNWS01000006.1 and 2 others:
NZ_SODT01000015.1 Lanthipeptides: EV647_RS42365_lanthipeptide NZ_SODU01000003.1 Lanthipeptides: EV137_RS40830_lanthipeptide
Lanthipeptides: EV651_RS42965_lanthipeptide
1
Y S C S W G G P G T D Y N R R P
16
Y+C G P G + P
7
Y T C W C G A P G A K V V K G P
22

#### MIBiG 4.0 matches for allorf_08187294_08187419

21.1%
BGC0000503.5 (cinA):
Lanthipeptide: cinnamycin
2
S C S W G
6
S C S+G
4
S C S F G
8
allorf_08187456_08187584
Leader:
MEPVPLLRTSEPRDLVGA
Core:
H A S W R G G T R A D W E G C R E T Q H L G K C
Core with dehydrations:
H A Dha W R G G Dhb R A D W E G Cys R E Dhb Q H L G K Cys

#### antiSMASH-DB 4.0 matches for allorf_08187456_08187584

100.0%
NZ_CP011509.1:
Lanthipeptides: allorf_08187456_08187584_lanthipeptide
1
H A S W R G G T R A D W E G C R E T Q H L G K C
24
H A S W R G G T R A D W E G C R E T Q H L G K C
1
H A S W R G G T R A D W E G C R E T Q H L G K C
24
29.2%
NZ_CP072634.1:
Lassopeptides: allorf_1182129_1182365_lassopeptide
6
G G T R A D W E G C R E T Q H
20
G T R A D G R +
4
G S T R A D R V G P R P N R F
18
22.0%
NZ_FNVT01000019.1:
Lanthipeptides: C4V41_RS61165_lanthipeptide
7
G T R A D W E G-C R E T Q H L G K C
24
G T+ W G C T Q G C
10
G T Q V S W S G T C S G T Q D C G T C
28
with 3 more sequence matches
20.7%
NZ_CP030771.1:
Lanthipeptides: C9F11_RS36615_lanthipeptide
7
G T R A D W E G C R E T Q H L G K C
24
G+ ++W C+ T L C
1
G S S S N W L S C K G T C S L S L C
18
19.1%
NZ_JAGGRJ010000002.1:
Lanthipeptides: allorf_19530_19697_lanthipeptide
5
R G G T R A D W E G C R E T Q H L G
22
R G G R A D G R G
15
R G G R R A D S S G H R G A D R T G
32
13.3%
NZ_AUBN01000022.1:
Lanthipeptides: allorf_10193_10369_lanthipeptide
7
G T R A D W E G C
15
G R A W G C
26
G A R A P W S G C
34
allorf_08187499_08187591
Leader:
MGDGARTSASNFG
Core:
T A R P R W G T R L V A R G H T C
Core with dehydrations:
Dhb A R P R W G Dhb R L V A R G H Dhb Cys

#### antiSMASH-DB 4.0 matches for allorf_08187499_08187591

100.0%
NZ_CP011509.1:
Lanthipeptides: allorf_08187499_08187591_lanthipeptide
1
T A R P R W G T R L V A R G H T C
17
T A R P R W G T R L V A R G H T C
1
T A R P R W G T R L V A R G H T C
17

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.49 out of 28.19
Confidence: medium
Additional weak hits (6):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.87 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.51 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.49 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.56 out of 28.14
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.94 out of 19.26
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.36 out of 29.65
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.

AA314_RS31785 - Class II
  Cleavage pHMM score: -1.00
  RODEO score: 0
  Monoisotopic mass: 2740.3 Da
  Molecular weight: 2742.1 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2760.1 Da N = 1
    2778.1 Da N = 2
    2796.1 Da N = 3
allorf_08181116_08181184 - Class II
  Cleavage pHMM score: -3.50
  RODEO score: 0
  Monoisotopic mass: 1050.5 Da
  Molecular weight: 1051.1 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1069.1 Da N = 1
    1087.1 Da N = 2
    1105.2 Da N = 3
    1123.2 Da N = 4
    1141.2 Da N = 5
allorf_08187294_08187419 - Class II
  Cleavage pHMM score: -6.20
  RODEO score: 0
  Monoisotopic mass: 1760.8 Da
  Molecular weight: 1761.9 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1779.9 Da N = 1
    1797.9 Da N = 2
allorf_08187456_08187584 - Class II
  Cleavage pHMM score: -1.50
  RODEO score: 0
  Monoisotopic mass: 2686.2 Da
  Molecular weight: 2687.9 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2705.9 Da N = 1
allorf_08187499_08187591 - Class II
  Cleavage pHMM score: -5.30
  RODEO score: 0
  Monoisotopic mass: 1883.0 Da
  Molecular weight: 1884.2 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1902.2 Da N = 1
    1920.2 Da N = 2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
ZuR variant 1 | Zinc-responsive repressor

NZ_CP011509.1 - Region 37 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,274,361 - 8,298,826 nt. (total: 24,466 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: electron transfer
AA314_RS32215: flavodoxin

smcogs
  SMCOG1134: flavodoxin

Transferases: methyltransferase
AA314_RS32225: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase dehydratase
AA314_RS32240: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

AA314_RS32245: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase 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 | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002640.2 |  | 0.76 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.49 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0001727.3 |  | 0.39 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0002120.3 |  | 0.35 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000380.5 |  | 0.21 | NRPS, PKS | Leupyrrin A1, Leupyrrin A2, Leupyrrin B1, Leupyrrin B2, Leupyrrin C, Leupyrrin D | Sorangium cellulosum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002640.2 |  | 0.76 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.49 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0001727.3 |  | 0.39 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0002120.3 |  | 0.35 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000380.5 |  | 0.21 | NRPS, PKS | Leupyrrin A1, Leupyrrin A2, Leupyrrin B1, Leupyrrin B2, Leupyrrin C, Leupyrrin D | Sorangium cellulosum

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

No significant matches found.

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.50 out of 23.79
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
Additional weak hits (17):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.56 out of 26.85
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.40 out of 26.06
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.26 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.96 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.71 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.52 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.07 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.07 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.99 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.25 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.18 out of 18.57
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.33 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.90 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.18 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.60 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.27 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.51 out of 35.63
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (8274360...8298826)
AA314_RS32245
  RRE type: Lanthipeptide_LanB_RRE
  Location: 173 - 263
  Score: 33.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C

NZ_CP011509.1 - Region 38 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,416,505 - 8,476,008 nt. (total: 59,504 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
AA314_RS32760: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Lyases: dehydratase
AA314_RS32810: L-carnitine dehydratase/bile acid-inducible

smcogs
  SMCOG1189: L-carnitine dehydratase/bile acid-inducible

Ligases: ligase synthase
AA314_RS32795: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AA314_RS32800: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AA314_RS32805: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

AA314_RS32835: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.63 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001284.4 |  | 0.63 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.63 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001284.4 |  | 0.63 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.21 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.72 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.57 out of 23.79
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.29 out of 27.18
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (8):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.53 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.07 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.81 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.37 out of 32.93
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.32 out of 25.88
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 61, location 8416504 - 8476008:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ohmal)

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).
AA314_RS32800: mal
PKS_AT (556..849): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 83.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 193.1
  inactive: 144.0
  Methoxymalonyl-CoA: 84.0
  Methylmalonyl-CoA: 76.9
  Propionyl-CoA: 68.2
  Isobutyryl-CoA: 53.5
  2-Methylbutyryl-CoA: 48.6
  Ethylmalonyl-CoA: 40.6
  Acetyl-CoA: 33.0
  CHC-CoA: 32.5
  trans-1,2-CPDA: 27.7
  Benzoyl-CoA: 27.7
  3-Methylbutyryl-CoA: 24.9
  fatty_acid: 22.8

AA314_RS32805: mxmal - mmal
PKS_AT (559..775): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 42.3
  Methylmalonyl-CoA: 28.7
  Isobutyryl-CoA: 24.6
  Propionyl-CoA: 21.5
  fatty_acid: 19.7
  Benzoyl-CoA: 18.9
  3-Methylbutyryl-CoA: 17.8
  Acetyl-CoA: 15.5
  trans-1,2-CPDA: 13.8
  CHC-CoA: 13.8
  2-Methylbutyryl-CoA: 13.1
  Ethylmalonyl-CoA: 11.3
  inactive: 0.0
  Malonyl-CoA: -1.8

PKS_AT (913..1208): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 83.3%
  Malonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 176.0
  Ethylmalonyl-CoA: 159.7
  Methoxymalonyl-CoA: 126.2
  Isobutyryl-CoA: 114.8
  Malonyl-CoA: 101.7
  Benzoyl-CoA: 100.7
  2-Methylbutyryl-CoA: 84.3
  Propionyl-CoA: 74.5
  trans-1,2-CPDA: 72.9
  CHC-CoA: 69.2
  Acetyl-CoA: 61.8
  fatty_acid: 33.2
  inactive: 26.2
  3-Methylbutyryl-CoA: 23.6

AA314_RS32835: X
AMP-binding (21..480): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    EGVLFGQVVK-APAANGSA-----------FSLF
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP011509.1 - Region 39 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,585,532 - 8,607,100 nt. (total: 21,569 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 oxidase
AA314_RS33300: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

AA314_RS33305: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

Hydrolases: protease
AA314_RS33280: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

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
--- | --- | --- | --- | --- | ---
BGC0000597.4 |  | 0.38 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000595.3 |  | 0.38 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000313.4 |  | 0.36 | NRPS | beauvericin | Beauveria bassiana
BGC0002339.3 |  | 0.34 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0001440.5 |  | 0.31 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0000842.5 |  | 0.31 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0002315.2 |  | 0.31 | PKS | accramycin A | Streptomyces sp.
BGC0001338.4 |  | 0.30 | PKS | citrinin | Monascus ruber
BGC0001791.4 |  | 0.29 | NRPS | sunshinamide | Gynuella sunshinyii YC6258

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000597.4 |  | 0.38 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000595.3 |  | 0.38 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000313.4 |  | 0.36 | NRPS | beauvericin | Beauveria bassiana
BGC0002339.3 |  | 0.34 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0001440.5 |  | 0.31 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0000842.5 |  | 0.31 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0002315.2 |  | 0.31 | PKS | accramycin A | Streptomyces sp.
BGC0001338.4 |  | 0.30 | PKS | citrinin | Monascus ruber
BGC0001791.4 |  | 0.29 | NRPS | sunshinamide | Gynuella sunshinyii YC6258

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene | drimane-type |  | C15 | C2-C7 + C6-C11 | PP

Genes with terpene domains:
AA314_RS33320: T2TS
Domain 1 (3 - 494): Type 2 terpene synthase
Subtype: Sesquiterpene synthase, group b

Reactions:
  FPP → sesquiterpene_C2-C7/C6-C11_PP

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):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.85 out of 28.14
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.82 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.56 out of 27.78
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
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.34 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.96 out of 32.93
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP011509.1 - Region 40 - hserlactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,122,031 - 9,142,663 nt. (total: 20,633 nt) Show pHMM detection rules used
hserlactone: Autoind_synth

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer oxygenase
AA314_RS35490: flavodoxin

smcogs
  SMCOG1134: flavodoxin

AA314_RS35525: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

AA314_RS35555: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

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

Reference | hserlactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000918.3 |  | 0.40 | other (other) | ochronotic pigment | Streptomyces avermitilis
BGC0001485.4 |  | 0.37 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002496.3 |  | 0.36 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000272.3 |  | 0.35 | PKS | spore pigment | Streptomyces collinus
BGC0001736.3 |  | 0.35 | NRPS | pepteridine A, pepteridine B | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001223.5 |  | 0.35 | other (other) | hydroxysporine | uncultured bacterium
BGC0001810.3 |  | 0.34 | PKS | trehangelin | Polymorphospora rubra
BGC0001723.5 |  | 0.34 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000384.6 |  | 0.34 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0001336.5 |  | 0.33 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000918.3 |  | 0.40 | other (other) | ochronotic pigment | Streptomyces avermitilis
BGC0001485.4 |  | 0.37 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002496.3 |  | 0.36 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000272.3 |  | 0.35 | PKS | spore pigment | Streptomyces collinus
BGC0001736.3 |  | 0.35 | NRPS | pepteridine A, pepteridine B | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001223.5 |  | 0.35 | other (other) | hydroxysporine | uncultured bacterium
BGC0001810.3 |  | 0.34 | PKS | trehangelin | Polymorphospora rubra
BGC0001723.5 |  | 0.34 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000384.6 |  | 0.34 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0001336.5 |  | 0.33 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.63 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.87 out of 24.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.99 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP011509.1 - Region 41 - lanthipeptide-class-v,thioamitides
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,290,987 - 9,333,228 nt. (total: 42,242 nt) Show pHMM detection rules used
lanthipeptide-class-v: (APH and HopA1)
thioamitides: ((YcaO or TIGR03604) and TfuA)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase
AA314_RS36255: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-v | thioamitides | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002560.3 |  |  | 0.48 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0001849.4 |  |  | 0.41 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0001802.5 |  |  | 0.35 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0001696.5 |  |  | 0.35 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0000625.5 |  |  | 0.35 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0002669.2 |  |  | 0.29 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87
BGC0000471.4 |  |  | 0.24 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112
BGC0000480.5 |  |  | 0.24 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000475.5 |  |  | 0.24 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0000473.4 |  |  | 0.24 | ribosomal | aerucyclamide A, aerucyclamide B, aerucyclamide C, aerucyclamide D | Microcystis aeruginosa NIES-298

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002560.3 |  | 0.57 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0001849.4 |  | 0.53 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0001802.5 |  | 0.49 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0001696.5 |  | 0.49 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0000625.5 |  | 0.49 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0002669.2 |  | 0.44 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87
BGC0000471.4 |  | 0.40 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112
BGC0000480.5 |  | 0.40 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000475.5 |  | 0.40 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0000473.4 |  | 0.40 | ribosomal | aerucyclamide A, aerucyclamide B, aerucyclamide C, aerucyclamide D | Microcystis aeruginosa NIES-298

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

No significant matches found.

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.84 out of 28.19
Confidence: medium
Additional weak hits (14):
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
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.58 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.20 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.48 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.40 out of 27.04
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.36 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.00 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.36 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.36 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.00 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.36 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.38 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ZuR variant 1 | Zinc-responsive repressor

NZ_CP011509.1 - Region 42 - thioamitides
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 9,383,722 - 9,406,072 nt. (total: 22,351 nt) Show pHMM detection rules used
thioamitides: ((YcaO or TIGR03604) and TfuA)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase reductase
AA314_RS36680: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

AA314_RS36730: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Hydrolases: hydrolase
AA314_RS36720: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: synthase
AA314_RS36710: 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 | thioamitides | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002284.3 |  | 0.42 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000918.3 |  | 0.41 | other (other) | ochronotic pigment | Streptomyces avermitilis
BGC0002560.3 |  | 0.40 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0001696.5 |  | 0.38 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0002669.2 |  | 0.38 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87
BGC0001802.5 |  | 0.38 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0002326.2 |  | 0.36 | NRPS | endopyrrole B, endopyrrole C, endopyrrole A | Mycetohabitans rhizoxinica
BGC0001474.4 |  | 0.36 | ribosomal | thiopeptin | Streptomyces tateyamensis
BGC0001850.4 |  | 0.35 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0001471.5 |  | 0.34 | ribosomal | saalfelduracin | Amycolatopsis saalfeldensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002284.3 |  | 0.42 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000918.3 |  | 0.41 | other (other) | ochronotic pigment | Streptomyces avermitilis
BGC0002560.3 |  | 0.40 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0001696.5 |  | 0.38 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0002669.2 |  | 0.38 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87
BGC0001802.5 |  | 0.38 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0002326.2 |  | 0.36 | NRPS | endopyrrole B, endopyrrole C, endopyrrole A | Mycetohabitans rhizoxinica
BGC0001474.4 |  | 0.36 | ribosomal | thiopeptin | Streptomyces tateyamensis
BGC0001850.4 |  | 0.35 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0001471.5 |  | 0.34 | ribosomal | saalfelduracin | Amycolatopsis saalfeldensis

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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.79 out of 29.72
Confidence: medium
Additional weak hits (4):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.81 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.43 out of 29.38
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.43 out of 32.93
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP011509.1 - Region 43 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,228,405 - 10,279,069 nt. (total: 50,665 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
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
AA314_RS40135: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: sulfotransferase
AA314_RS40155: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

Hydrolases: hydrolase
AA314_RS40165: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
AA314_RS40140: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

AA314_RS40145: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AA314_RS51465: 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 | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  | 0.85 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
Additional weak hits (9):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.27 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.16 out of 30.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.75 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.16 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.78 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19
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: 19.14 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 67, location 10228404 - 10279069:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-ccmal) + (Ala)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 68, location 10228404 - 10275070:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-ccmal) + (Ala)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 69, location 10235094 - 10279069:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-ccmal) + (Ala)

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).
AA314_RS40140: mal
PKS_AT (535..830): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 79.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 145.6
  inactive: 90.1
  Methoxymalonyl-CoA: 55.7
  Methylmalonyl-CoA: 46.3
  Propionyl-CoA: 31.5
  Ethylmalonyl-CoA: 21.0
  CHC-CoA: 15.9
  Isobutyryl-CoA: 15.2
  2-Methylbutyryl-CoA: 13.6
  fatty_acid: 10.9
  Benzoyl-CoA: 10.7
  trans-1,2-CPDA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

AA314_RS40145: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (470..868): 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:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    MDTSFDTSAFEGWLLAGGDINGYGPTESSTFTTC
  Nearest Stachelhaus code(s):
    Ala DTFWLGGTFK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

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

NZ_CP011509.1 - Region 44 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,561,540 - 10,609,297 nt. (total: 47,758 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
AA314_RS41290: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AA314_RS41370: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase
AA314_RS41355: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Ligases: ligase synthase
AA314_RS41330: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AA314_RS41340: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AA314_RS41380: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

AA314_RS54330: 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
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.33 out of 20.97
Confidence: medium
Additional weak hits (5):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.07 out of 32.74
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: 14.29 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.93 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 70, location 10561539 - 10609297:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val - Val)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AA314_RS54330: Val - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (479..881): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDPSVFEGFCFFGGEVNGYGPTECTVFSTY
  Nearest Stachelhaus code(s):
    Val DAFFFGGTFK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1547..1949): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDPSTFEGFVVFGGEVNGYGPTECTVFSTF
  Nearest Stachelhaus code(s):
    Val DGFFVGGVFK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AA314_RS41330: X
AMP-binding (31..382): 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:
    NRHLYSMVAQAAALGVGGDYLTYGLSEAGVATLA
  Nearest Stachelhaus code(s):
    Lys DNESGGTVAK (29% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
CcpA | Catabolite control protein A

NZ_CP011509.1 - Region 45 - 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: 10,689,840 - 10,710,151 nt. (total: 20,312 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
AA314_RS41840: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

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
--- | --- | --- | --- | --- | ---
BGC0002284.3 |  | 0.39 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000706.3 |  | 0.38 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001778.5 |  | 0.38 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000207.5 |  | 0.35 | PKS | chartreusin | Streptomyces chartreusis
BGC0001786.3 |  | 0.35 | ribosomal | subterisin | Novosphingobium subterraneum
BGC0000003.3 |  | 0.34 | PKS | AF-toxin | Alternaria alternata
BGC0000244.4 |  | 0.33 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0002412.2 |  | 0.32 | NRPS | holomycin | Photobacterium galatheae
BGC0000312.4 |  | 0.32 | NRPS | bassianolide | Beauveria bassiana
BGC0000783.3 |  | 0.31 | saccharide | O-antigen | Xanthomonas oryzae pv. oryzae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002284.3 |  | 0.39 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000706.3 |  | 0.38 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001778.5 |  | 0.38 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000207.5 |  | 0.35 | PKS | chartreusin | Streptomyces chartreusis
BGC0001786.3 |  | 0.35 | ribosomal | subterisin | Novosphingobium subterraneum
BGC0000003.3 |  | 0.34 | PKS | AF-toxin | Alternaria alternata
BGC0000244.4 |  | 0.33 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0002412.2 |  | 0.32 | NRPS | holomycin | Photobacterium galatheae
BGC0000312.4 |  | 0.32 | NRPS | bassianolide | Beauveria bassiana
BGC0000783.3 |  | 0.31 | saccharide | O-antigen | Xanthomonas oryzae pv. oryzae

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 (9):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.87 out of 26.85
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.90 out of 33.73
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.42 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.04 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.22 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.27 out of 28.19
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (10689839...10710151)
AA314_RS41820
  RRE type: PqqD_RRE
  Location: 46 - 99
  Score: 30.5
  RRE type: Stand_Alone_Lasso_RRE
  Location: 47 - 99
  Score: 30.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP011509.1 - Region 46 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,875,544 - 10,897,769 nt. (total: 22,226 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: hydrolase
AA314_RS42650: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: cyclase
AA314_RS42645: 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 |  | 0.79 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002403.2 |  | 0.42 | PKS | β-Diketones | Hordeum vulgare subsp. vulgare
BGC0000843.5 |  | 0.38 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0000030.3 |  | 0.37 | PKS | bikaverin | Fusarium fujikuroi IMI 58289
BGC0001483.4 |  | 0.37 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002313.3 |  | 0.36 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0002509.3 |  | 0.35 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0001521.3 |  | 0.35 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001162.3 |  | 0.34 | PKS | 1-heptadecene | Moorea producens JHB
BGC0001161.5 |  | 0.34 | PKS | 1-heptadecene | Moorea bouillonii PNG

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.79 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002403.2 |  | 0.42 | PKS | β-Diketones | Hordeum vulgare subsp. vulgare
BGC0000843.5 |  | 0.38 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0000030.3 |  | 0.37 | PKS | bikaverin | Fusarium fujikuroi IMI 58289
BGC0001483.4 |  | 0.37 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002313.3 |  | 0.36 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0002509.3 |  | 0.35 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0001521.3 |  | 0.35 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001162.3 |  | 0.34 | PKS | 1-heptadecene | Moorea producens JHB
BGC0001161.5 |  | 0.34 | PKS | 1-heptadecene | Moorea bouillonii PNG

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

Genes with terpene domains:
AA314_RS42645: T1TS + T1TS
Domain 1 (2 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (374 - 702): 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.37 out of 20.47
Confidence: strong
Additional weak hits (2):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.59 out of 30.97
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.06 out of 35.63
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
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP011509.1 - Region 47 - 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: 11,561,755 - 11,619,860 nt. (total: 58,106 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 reductase
AA314_RS45350: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

AA314_RS45385: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AA314_RS45445: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

Transferases: methyltransferase
AA314_RS45375: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

AA314_RS45460: isoprenylcysteine carboxyl methyltransferase

smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Hydrolases: esterase
AA314_RS45430: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

smcogs
  SMCOG1283: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

Ligases: ligase synthase
AA314_RS45400: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

AA314_RS45405: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AA314_RS45450: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AA314_RS45465: 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
--- | --- | --- | --- | --- | ---
BGC0001831.3 |  | 0.78 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000282.3 |  | 0.75 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001310.5 |  | 0.53 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001962.3 |  | 0.51 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0002127.3 |  | 0.50 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.49 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001831.3 |  | 0.78 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000282.3 |  | 0.75 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001310.5 |  | 0.53 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001962.3 |  | 0.51 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0002127.3 |  | 0.50 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.49 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 25.46 out of 32.38
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.92 out of 29.65
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
Additional weak hits (19):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.62 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.05 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.39 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.96 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.88 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.70 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.26 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.23 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.49 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.80 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.77 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.74 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.88 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.99 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.95 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.97 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.65 out of 24.78
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AA314_RS45405: AHBA
CAL_domain (74..517): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 18.7
  shikimic_acid: 14.5
  fatty_acid: 9.7
  NH2: 0.7
  Acetyl-CoA: 0.0

AA314_RS45450: AHBA
CAL_domain (40..476): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 13.9
  Acetyl-CoA: 10.2
  shikimic_acid: 6.7
  NH2: 2.0
  fatty_acid: -2.4

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

Regulator | Description
--- | ---
CsoR | Copper-responsive repressor
LexA variant 1 | Repressor of DNA damage response
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP011509.1 - Region 48 - terpene,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: 12,003,229 - 12,032,766 nt. (total: 29,538 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)
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
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
AA314_RS58730: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Lyases: cyclase
AA314_RS47260: Terpene synthase/cyclase metal-binding domain protein

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

Isomerases: mutase
AA314_RS47350: 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 | terpene | triceptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002707.2 |  |  | 0.32 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0001400.3 |  |  | 0.12 | PKS | citreoviridin | Aspergillus terreus NIH2624
BGC0002338.3 |  |  | 0.10 | PKS | Sorangipyranone | Myxococcales bacterium
BGC0001728.4 |  |  | 0.09 | NRPS, PKS | paenilipoheptin | Paenibacillus polymyxa E681
BGC0001523.5 |  |  | 0.09 | PKS | azalomycin F3a | Streptomyces sp. 211726
BGC0001755.5 |  |  | 0.06 | PKS | reedsmycin A, reedsmycin B, reedsmycin C, reedsmycin D, reedsmycin E | Streptomyces sp.
BGC0000842.5 |  |  | 0.06 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0000080.5 |  |  | 0.05 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0000014.5 |  |  | 0.04 | PKS | ambruticin | Sorangium cellulosum
BGC0000035.5 |  |  | 0.04 | PKS | chalcomycin A | Streptomyces bikiniensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002707.2 |  | 0.47 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0001400.3 |  | 0.39 | PKS | citreoviridin | Aspergillus terreus NIH2624
BGC0000842.5 |  | 0.26 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0001755.5 |  | 0.25 | PKS | reedsmycin A, reedsmycin B, reedsmycin C, reedsmycin D, reedsmycin E | Streptomyces sp.
BGC0002338.3 |  | 0.24 | PKS | Sorangipyranone | Myxococcales bacterium
BGC0000080.5 |  | 0.23 | PKS | jerangolid A, jerangolid D | Sorangium cellulosum
BGC0001728.4 |  | 0.22 | NRPS, PKS | paenilipoheptin | Paenibacillus polymyxa E681
BGC0001523.5 |  | 0.22 | PKS | azalomycin F3a | Streptomyces sp. 211726
BGC0000014.5 |  | 0.21 | PKS | ambruticin | Sorangium cellulosum
BGC0002501.3 |  | 0.20 | other (other) | penigainamide A, penigainamide B, penigainamide C, adametizine A, FA2097, outovirin A, outovirin C, pretrichodermamide C | Penicillium steckii

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

No significant matches found.

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
AA314_RS47260: T1TS
Domain 1 (5 - 307): 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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.21 out of 20.97
Confidence: medium
Additional weak hits (2):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.58 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.33 out of 35.63
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
--- | ---
CcpA | Catabolite control protein A

NZ_CP011509.1 - Region 49 - 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: 12,173,873 - 12,194,847 nt. (total: 20,975 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
AA314_RS47915: methyltransferase

smcogs
  SMCOG1089: methyltransferase

AA314_RS51860: methyltransferase

smcogs
  SMCOG1248: methyltransferase

AA314_RS58135: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: deaminase
AA314_RS47995: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: cyclase
AA314_RS47955: 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
--- | --- | --- | --- | --- | ---
BGC0000675.5 |  | 0.44 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0001198.3 |  | 0.43 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0002449.2 |  | 0.42 | other (other) | sarasinoside | uncultured bacterium
BGC0000936.5 |  | 0.37 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1
BGC0002561.3 |  | 0.36 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0002439.3 |  | 0.36 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0002509.3 |  | 0.35 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0001444.5 |  | 0.34 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0000821.5 |  | 0.34 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0001529.5 |  | 0.34 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000675.5 |  | 0.44 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0001198.3 |  | 0.43 | terpene | (+)-O-methylkolavelool | Herpetosiphon aurantiacus DSM 785
BGC0002449.2 |  | 0.42 | other (other) | sarasinoside | uncultured bacterium
BGC0000936.5 |  | 0.37 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1
BGC0002561.3 |  | 0.36 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0002439.3 |  | 0.36 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0002509.3 |  | 0.35 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0001444.5 |  | 0.34 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0000821.5 |  | 0.34 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0001529.5 |  | 0.34 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18

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

No significant matches found.

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
AA314_RS47955: T1TS
Domain 1 (4 - 309): 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.
No hits above weak threshold.
Weak hits (2):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.20 out of 30.11
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
--- | ---