Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
1.11
1.12
1.13
1.14
1.15
1.16
1.17
1.18
1.19
1.20
1.21
1.22
1.23
1.24
1.25
1.26
1.27
1.28
1.29
1.30
1.31
1.32
1.33
1.34
1.35
1.36
1.37
1.38
1.39
2.1
2.2
5.1

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

NZ_CP117709.1 (Streptomyces sp. MMBL 11-1)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | butyrolactone | 34,962 | 45,906 |  |
Region 1.2 | terpene | 69,578 | 91,791 | High | geosmin | terpene:Sesquiterpene
Region 1.3 | terpene | 121,251 | 149,616 | High | isorenieratene | terpene
Region 1.4 | NRP-metallophore,NRPS | 150,916 | 205,954 | High | griseobactin | NRPS:Type I
Region 1.5 | T3PKS | 277,866 | 318,996 |  |
Region 1.6 | NRPS,NRPS-like | 391,001 | 441,938 | Low | deoxyhangtaimycin | PKS+NRPS:Type I
Region 1.7 | hglE-KS | 518,717 | 571,685 |  |
Region 1.8 | NRPS-like,transAT-PKS | 770,647 | 842,733 | Medium | cycloheximide | PKS:Trans-AT type I
Region 1.9 | NRPS-like,betalactone,terpene | 911,108 | 973,592 | Low | steffimycin D | PKS:Type II+saccharide:hybrid/tailoring
Region 1.10 | ectoine | 1,398,740 | 1,409,138 | High | ectoine | other:other
Region 1.11 | NRPS | 1,445,668 | 1,521,009 | Low | kitacinnamycin A/kitacinnamycin B/kitacinnamycin C/kitacinnamycin D/kitacinnamycin E/kitacinnamycin F | NRPS:Type I
Region 1.12 | NI-siderophore | 2,071,407 | 2,101,218 | Low | coelichelin | NRPS:Type I
Region 1.13 | lanthipeptide-class-ii,lanthipeptide-class-iii | 2,439,541 | 2,471,158 |
Region 1.14 | NI-siderophore | 2,522,676 | 2,552,454 | High | desferrioxamin B | other:other
Region 1.15 | lanthipeptide-class-i | 3,146,041 | 3,172,357 |  |
Region 1.16 | lanthipeptide-class-v | 4,193,213 | 4,235,518 |  |
Region 1.17 | NRPS,T1PKS | 4,248,489 | 4,302,115 | Low | skyllamycin D/skyllamycin E | NRPS:Type I
Region 1.18 | lanthipeptide-class-iii | 4,324,808 | 4,347,483 | Medium | catenulipeptin | ribosomal:RiPP:Lanthipeptide
Region 1.19 | NRPS-like,T1PKS | 5,292,167 | 5,346,941 | Low | rotihibin A | NRPS:Type I
Region 1.20 | azole-containing-RiPP | 5,355,576 | 5,384,464 |  |
Region 1.21 | melanin | 5,402,259 | 5,412,678 | High | melanin | other:other
Region 1.22 | lanthipeptide-class-iii | 5,455,011 | 5,477,707 | High | AmfS | ribosomal:RiPP:Lanthipeptide
Region 1.23 | terpene-precursor | 5,600,010 | 5,621,053 |  |
Region 1.24 | terpene | 5,814,826 | 5,835,803 |
Region 1.25 | NI-siderophore | 6,206,509 | 6,239,232 | Low | kinamycin | PKS
Region 1.26 | T2PKS,PKS-like,betalactone,RiPP-like,arylpolyene,NRPS-like,hydrogen-cyanide | 6,399,179 | 6,491,844 | Low | LL-D49194α1 (LLD)/LL-D49194β2 | PKS
Region 1.27 | NRPS | 6,559,702 | 6,602,983 | Medium | pyrroloformamide A/pyrroloformamide B/pyrroloformamide D/pyrroloformamide C | NRPS:Type I+other:other
Region 1.28 | RiPP-like | 6,656,170 | 6,667,507 | Low | 14-hydroxyisochainin | PKS:Modular type I
Region 1.29 | NRPS-like,NRPS,T3PKS,ectoine,phenazine | 6,872,403 | 7,006,263 | High | phenazine SA/phenazine SB/phenazine SC | other:other
Region 1.30 | terpene | 7,266,776 | 7,293,348 | Medium | hopene | terpene
Region 1.31 | NRPS,T1PKS | 7,392,445 | 7,441,936 | High | 10-epi-HSAF/10-epi-3-deOH-HSAF/10-epi-maltophilin/10-epi-xanthobaccin C/10-epi-hydroxymaltophilin/10-epi-FI-2 | other:other+PKS
Region 1.32 | RiPP-like | 7,548,920 | 7,559,717 |
Region 1.33 | NRPS-like,T1PKS,NI-siderophore,betalactone | 7,659,821 | 7,739,434 | Low | legonoxamine A/desferrioxamine B/legonoxamine B | other:other
Region 1.34 | RiPP-like | 7,747,839 | 7,759,206 | Medium | streptamidine | ribosomal:unmodified
Region 1.35 | melanin | 7,759,924 | 7,770,409 |  |
Region 1.36 | terpene-precursor | 7,772,413 | 7,793,462 |  |
Region 1.37 | T3PKS | 7,803,570 | 7,844,622 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 1.38 | NRPS,T1PKS | 7,897,547 | 7,950,191 |  |
Region 1.39 | azole-containing-RiPP | 7,984,328 | 8,003,288 | Low | lactazole | ribosomal:RiPP:Thiopeptide

NZ_CP117710.1 (Streptomyces sp. MMBL 11-1)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | RRE-containing | 143,551 | 166,691 |
Region 2.2 | nucleoside | 211,788 | 232,708 |  |

NZ_CP117713.1 (Streptomyces sp. MMBL 11-1)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | RRE-containing | 2,333 | 14,055 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | butyrolactone | 34,962 | 45,906 |  |
Region 1.2 | terpene | 69,578 | 91,791 | High | geosmin | terpene:Sesquiterpene
Region 1.3 | terpene | 121,251 | 149,616 | High | isorenieratene | terpene
Region 1.4 | NRP-metallophore,NRPS | 150,916 | 205,954 | High | griseobactin | NRPS:Type I
Region 1.5 | T3PKS | 277,866 | 318,996 |  |
Region 1.6 | NRPS,NRPS-like | 391,001 | 441,938 | Low | deoxyhangtaimycin | PKS+NRPS:Type I
Region 1.7 | hglE-KS | 518,717 | 571,685 |  |
Region 1.8 | NRPS-like,transAT-PKS | 770,647 | 842,733 | Medium | cycloheximide | PKS:Trans-AT type I
Region 1.9 | NRPS-like,betalactone,terpene | 911,108 | 973,592 | Low | steffimycin D | PKS:Type II+saccharide:hybrid/tailoring
Region 1.10 | ectoine | 1,398,740 | 1,409,138 | High | ectoine | other:other
Region 1.11 | NRPS | 1,445,668 | 1,521,009 | Low | kitacinnamycin A/kitacinnamycin B/kitacinnamycin C/kitacinnamycin D/kitacinnamycin E/kitacinnamycin F | NRPS:Type I
Region 1.12 | NI-siderophore | 2,071,407 | 2,101,218 | Low | coelichelin | NRPS:Type I
Region 1.13 | lanthipeptide-class-ii,lanthipeptide-class-iii | 2,439,541 | 2,471,158 |
Region 1.14 | NI-siderophore | 2,522,676 | 2,552,454 | High | desferrioxamin B | other:other
Region 1.15 | lanthipeptide-class-i | 3,146,041 | 3,172,357 |  |
Region 1.16 | lanthipeptide-class-v | 4,193,213 | 4,235,518 |  |
Region 1.17 | NRPS,T1PKS | 4,248,489 | 4,302,115 | Low | skyllamycin D/skyllamycin E | NRPS:Type I
Region 1.18 | lanthipeptide-class-iii | 4,324,808 | 4,347,483 | Medium | catenulipeptin | ribosomal:RiPP:Lanthipeptide
Region 1.19 | NRPS-like,T1PKS | 5,292,167 | 5,346,941 | Low | rotihibin A | NRPS:Type I
Region 1.20 | azole-containing-RiPP | 5,355,576 | 5,384,464 |  |
Region 1.21 | melanin | 5,402,259 | 5,412,678 | High | melanin | other:other
Region 1.22 | lanthipeptide-class-iii | 5,455,011 | 5,477,707 | High | AmfS | ribosomal:RiPP:Lanthipeptide
Region 1.23 | terpene-precursor | 5,600,010 | 5,621,053 |  |
Region 1.24 | terpene | 5,814,826 | 5,835,803 |
Region 1.25 | NI-siderophore | 6,206,509 | 6,239,232 | Low | kinamycin | PKS
Region 1.26 | T2PKS,PKS-like,betalactone,RiPP-like,arylpolyene,NRPS-like,hydrogen-cyanide | 6,399,179 | 6,491,844 | Low | LL-D49194α1 (LLD)/LL-D49194β2 | PKS
Region 1.27 | NRPS | 6,559,702 | 6,602,983 | Medium | pyrroloformamide A/pyrroloformamide B/pyrroloformamide D/pyrroloformamide C | NRPS:Type I+other:other
Region 1.28 | RiPP-like | 6,656,170 | 6,667,507 | Low | 14-hydroxyisochainin | PKS:Modular type I
Region 1.29 | NRPS-like,NRPS,T3PKS,ectoine,phenazine | 6,872,403 | 7,006,263 | High | phenazine SA/phenazine SB/phenazine SC | other:other
Region 1.30 | terpene | 7,266,776 | 7,293,348 | Medium | hopene | terpene
Region 1.31 | NRPS,T1PKS | 7,392,445 | 7,441,936 | High | 10-epi-HSAF/10-epi-3-deOH-HSAF/10-epi-maltophilin/10-epi-xanthobaccin C/10-epi-hydroxymaltophilin/10-epi-FI-2 | other:other+PKS
Region 1.32 | RiPP-like | 7,548,920 | 7,559,717 |
Region 1.33 | NRPS-like,T1PKS,NI-siderophore,betalactone | 7,659,821 | 7,739,434 | Low | legonoxamine A/desferrioxamine B/legonoxamine B | other:other
Region 1.34 | RiPP-like | 7,747,839 | 7,759,206 | Medium | streptamidine | ribosomal:unmodified
Region 1.35 | melanin | 7,759,924 | 7,770,409 |  |
Region 1.36 | terpene-precursor | 7,772,413 | 7,793,462 |  |
Region 1.37 | T3PKS | 7,803,570 | 7,844,622 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 1.38 | NRPS,T1PKS | 7,897,547 | 7,950,191 |  |
Region 1.39 | azole-containing-RiPP | 7,984,328 | 8,003,288 | Low | lactazole | ribosomal:RiPP:Thiopeptide
Region 2.1 | RRE-containing | 143,551 | 166,691 |
Region 2.2 | nucleoside | 211,788 | 232,708 |  |
Region 5.1 | RRE-containing | 2,333 | 14,055 |

No secondary metabolite regions were found in these records:
  NZ_CP117711.1 (Streptomyces sp. MMBL 11-1)
  NZ_CP117712.1 (Streptomyces sp. MMBL 11-1)

Compact view
NZ_CP117709.1 - Region 1 - butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 34,962 - 45,906 nt. (total: 10,945 nt) Show pHMM detection rules used
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
PSQ21_RS00170: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: acyltransferase
PSQ21_RS00215: acyltransferase

smcogs
  SMCOG1141: acyltransferase

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

Reference | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.87 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.62 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.52 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001364.3 |  | 0.40 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001633.3 |  | 0.40 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0002578.2 |  | 0.40 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000189.4 |  | 0.34 | 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
BGC0001458.4 |  | 0.33 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0001776.3 |  | 0.32 | terpene | shearinine D | Penicillium janthinellum
BGC0001177.4 |  | 0.31 | PKS | mensacaricin | Streptomyces bottropensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.87 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.62 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.52 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001364.3 |  | 0.40 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001633.3 |  | 0.40 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0002578.2 |  | 0.40 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000189.4 |  | 0.34 | 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
BGC0001458.4 |  | 0.33 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0001776.3 |  | 0.32 | terpene | shearinine D | Penicillium janthinellum
BGC0001177.4 |  | 0.31 | PKS | mensacaricin | Streptomyces bottropensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72
Confidence: medium
Additional weak hits (3):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.43 out of 28.14
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.01 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP117709.1 - 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: 69,578 - 91,791 nt. (total: 22,214 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
Lyases: cyclase
PSQ21_RS00385: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: ligase
PSQ21_RS00410: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS00415: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.83 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.75 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002826.2 |  | 0.51 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0002128.3 |  | 0.47 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0002405.2 |  | 0.45 | saccharide | mid-chain acyl sugars | Solanum lycopersicum
BGC0000933.3 |  | 0.44 | other (other) | xiamenmycin A | Streptomyces xiamenensis
BGC0000597.4 |  | 0.40 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000595.3 |  | 0.39 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0002238.3 |  | 0.39 | PKS | 2,4'-dihydroxy-3'-methoxypropiophenone | Aspergillus oryzae RIB40

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.83 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.75 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002826.2 |  | 0.51 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0002128.3 |  | 0.47 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0002405.2 |  | 0.45 | saccharide | mid-chain acyl sugars | Solanum lycopersicum
BGC0000933.3 |  | 0.44 | other (other) | xiamenmycin A | Streptomyces xiamenensis
BGC0000597.4 |  | 0.40 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000595.3 |  | 0.39 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0002238.3 |  | 0.39 | PKS | 2,4'-dihydroxy-3'-methoxypropiophenone | Aspergillus oryzae RIB40

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:
PSQ21_RS00385: T1TS + T1TS
Domain 1 (2 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (336 - 697): 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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.85 out of 27.04
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.86 out of 18.57
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.02 out of 23.79
Confidence: medium
Additional weak hits (7):
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
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.02 out of 25.88
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.52 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.46 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.56 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.81 out of 29.65
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
ToxT | Regulator of MSHA biosynthesis

NZ_CP117709.1 - Region 3 - 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: 121,251 - 149,616 nt. (total: 28,366 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
PSQ21_RS00600: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

PSQ21_RS00645: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

PSQ21_RS00655: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: methyltransferase
PSQ21_RS00555: methyltransferase

smcogs
  SMCOG1089: methyltransferase

PSQ21_RS00620: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
PSQ21_RS00545: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: synthetase
PSQ21_RS00595: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.87 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.79 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.74 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.71 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.71 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000645.3 |  | 0.55 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.53 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.51 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.50 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000639.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC260

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.87 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.79 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.74 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.71 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.71 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000645.3 |  | 0.55 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.53 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.51 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.50 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000639.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC260

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:
PSQ21_RS00595: PT_FPPS_like
Domain 1 (75 - 371): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

PSQ21_RS00605: PT_phytoene_like
Domain 1 (16 - 324): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

PSQ21_RS00625: Lycopene_cycl
Domain 1 (6 - 384): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.50 out of 21.55
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP117709.1 - Region 4 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 150,916 - 205,954 nt. (total: 55,039 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
PSQ21_RS00800: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: esterase hydrolase
PSQ21_RS00770: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

PSQ21_RS00790: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

PSQ21_RS00815: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
PSQ21_RS00805: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
PSQ21_RS00775: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS00810: 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 | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000368.5 |  |  | 1.09 | NRPS | griseobactin | Streptomyces sp. ATCC 700974
BGC0000343.5 |  |  | 0.78 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0000401.5 |  |  | 0.69 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001833.4 |  |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001185.5 |  |  | 0.66 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0002286.3 |  |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000368.5 |  | 0.81 | NRPS | griseobactin | Streptomyces sp. ATCC 700974
BGC0000343.5 |  | 0.71 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0000401.5 |  | 0.68 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
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
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001185.5 |  | 0.66 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.52 out of 23.79
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.07 out of 36.53
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.63 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.00 out of 27.04
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.21 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.62 out of 36.53
Confidence: medium
Additional weak hits (17):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.78 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.80 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.28 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.44 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.71 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.24 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.40 out of 36.53
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.14 out of 39.62
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.13 out of 28.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.16 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.23 out of 36.53
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
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.24 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
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 4, location 150915 - 205954:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Arg - 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).
PSQ21_RS00775: Arg - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (477..915): Arg
nrpys: Arg

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:
    LGHAFDASWDPWDVVVGGEVNLYGPTETTVDAYY
  Nearest Stachelhaus code(s):
    Arg DADDVGLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1611..2018): 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:
    LATHFDFSVWEGNQVFGGEVNMYGITETTVHVSH
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

PSQ21_RS00810: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (32..439): 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:
    SGSLFPLSSPGGGLLVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPGLGVVNK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator

NZ_CP117709.1 - Region 5 - 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: 277,866 - 318,996 nt. (total: 41,131 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
PSQ21_RS01210: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

PSQ21_RS01240: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

PSQ21_RS01305: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: kinase
PSQ21_RS01255: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: protease
PSQ21_RS01295: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Ligases: synthase
PSQ21_RS01230: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

PSQ21_RS01245: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

PSQ21_RS01250: 3-oxoacyl-(acyl carrier protein) synthase III

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

PSQ21_RS01300: 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
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.83 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.71 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000280.5 |  | 0.53 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002711.2 |  | 0.52 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000281.3 |  | 0.52 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002476.2 |  | 0.51 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0002073.3 |  | 0.50 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0001987.2 |  | 0.49 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.83 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.71 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000280.5 |  | 0.53 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002711.2 |  | 0.52 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000281.3 |  | 0.52 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002476.2 |  | 0.51 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0002073.3 |  | 0.50 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0001987.2 |  | 0.49 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.21 out of 27.78
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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.62 out of 36.53
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.62 out of 25.88
Confidence: medium
Additional weak hits (15):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.31 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.12 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.50 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.92 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.13 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.04 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.94 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.50 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.33 out of 30.97
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.73 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.76 out of 24.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.38 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.06 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.07 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.45 out of 35.63
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
DmdR1 | Iron(II)-dependent repressor
PsrA | Oleic acid responsive regulator

NZ_CP117709.1 - Region 6 - NRPS,NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 391,001 - 441,938 nt. (total: 50,938 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
PSQ21_RS01830: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: methyltransferase sulfotransferase
PSQ21_RS01795: methyltransferase

smcogs
  SMCOG1089: methyltransferase

PSQ21_RS01835: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

PSQ21_RS01880: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

PSQ21_RS01885: methyltransferase

smcogs
  SMCOG1089: methyltransferase

PSQ21_RS01895: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
PSQ21_RS01770: HAD-superfamily hydrolase, subfamily IA, variant

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

PSQ21_RS01950: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: ligase
PSQ21_RS01840: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS01855: 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 | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002164.2 |  |  | 0.74 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002164.2 |  | 0.70 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.36 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
Additional weak hits (15):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.28 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.81 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.70 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.83 out of 20.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.66 out of 29.65
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.40 out of 27.04
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
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
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.26 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.46 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.45 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.07 out of 30.98
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 391000 - 441938:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X - Lys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 391000 - 438431:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X - Lys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 400258 - 441938:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X - Lys)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
PSQ21_RS01840: X - Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (446..796): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MRSTFDISVWEAQVVSVGEWNAYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQVGVIWK (71% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1517..1892): Lys
nrpys: Lys

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    lys (Lys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAFPFDAAFGDPDTMVGGDHNHYGPTEATVCATS
  Nearest Stachelhaus code(s):
    CysA DATKMGHVGK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

PSQ21_RS01855: X
AMP-binding (4..375): X
nrpys: Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDVAVADMCMIVAGEINAYGPTETTACATM
  Nearest Stachelhaus code(s):
    Ala DVWCIAAIYK (68% 8Å match)
    Tyr DAAIIAAVCK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator

NZ_CP117709.1 - Region 7 - hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 518,717 - 571,685 nt. (total: 52,969 nt) Show pHMM detection rules used
hglE-KS: (hglE or hglD)

#### 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: acylase methyltransferase
PSQ21_RS02350: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

PSQ21_RS02435: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Lyases: dehydratase
PSQ21_RS02345: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: racemase
PSQ21_RS02445: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: synthase
PSQ21_RS02355: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

PSQ21_RS02360: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

PSQ21_RS02450: cysteine synthase

smcogs
  SMCOG1081: cysteine 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 | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.62 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000863.3 |  | 0.62 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  | 0.60 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002154.2 |  | 0.59 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001872.3 |  | 0.54 | PKS | fabclavine-polyamine | Xenorhabdus bovienii SS-2004
BGC0002648.2 |  | 0.54 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.62 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000863.3 |  | 0.62 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  | 0.60 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002154.2 |  | 0.59 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001872.3 |  | 0.54 | PKS | fabclavine-polyamine | Xenorhabdus bovienii SS-2004
BGC0002648.2 |  | 0.54 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.71 out of 23.79
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.25 out of 27.04
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (7):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.70 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.62 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.75 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.61 out of 32.93
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.95 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 9, location 518716 - 571685:
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).
PSQ21_RS02355: mal
PKS_AT (573..870): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 66.7%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 99.7
  Methoxymalonyl-CoA: 35.5
  Methylmalonyl-CoA: 33.7
  inactive: 26.3
  2-Methylbutyryl-CoA: 18.2
  Ethylmalonyl-CoA: 17.7
  Isobutyryl-CoA: 17.4
  fatty_acid: 16.5
  Propionyl-CoA: 14.8
  CHC-CoA: 14.7
  Benzoyl-CoA: 10.8
  trans-1,2-CPDA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PSQ21_RS02360: mxmal
PKS_AT (935..1173): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 31.9
  Methylmalonyl-CoA: 25.2
  Malonyl-CoA: 16.5
  Propionyl-CoA: 10.3
  2-Methylbutyryl-CoA: 9.4
  Ethylmalonyl-CoA: 8.9
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP117709.1 - Region 8 - NRPS-like,transAT-PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 770,647 - 842,733 nt. (total: 72,087 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)
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
PSQ21_RS03265: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

PSQ21_RS03295: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

PSQ21_RS03300: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

PSQ21_RS03325: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

PSQ21_RS03330: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

PSQ21_RS03335: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: acylase aminotransferase
PSQ21_RS03360: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

PSQ21_RS03395: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: hydrolase
PSQ21_RS03350: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: ligase synthase
PSQ21_RS03220: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

PSQ21_RS03320: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS03345: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | NRPS-like | transAT-PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002276.2 |  |  | 0.85 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000175.5 |  |  | 0.57 | PKS | cycloheximide | Streptomyces sp. YIM 56141
BGC0002099.3 |  |  | 0.48 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  |  | 0.48 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0001310.5 |  |  | 0.39 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001928.2 |  |  | 0.38 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000384.6 |  |  | 0.36 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0001948.3 |  |  | 0.35 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0001374.5 |  |  | 0.35 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0002127.3 |  |  | 0.34 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.73 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000175.5 |  | 0.70 | PKS | cycloheximide | Streptomyces sp. YIM 56141
BGC0000107.3 |  | 0.62 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
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
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002462.3 |  | 0.54 | saccharide | coformycin | Streptomyces kaniharaensis
BGC0002083.3 |  | 0.53 | PKS | gladiofungin A, gladiofungin B | Burkholderia gladioli
BGC0001374.5 |  | 0.53 | other (other) | thienodolin | Streptomyces albogriseolus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
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 (10):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.91 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.90 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.65 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.72 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.12 out of 35.63
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.63 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.28 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.95 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 10, location 770646 - 842733:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (ccmal - mal - ccmal - mal - Me-ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 11, location 770646 - 814084:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (ccmal - mal - ccmal - mal - Me-ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 12, location 778904 - 842733:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (ccmal - mal - ccmal - mal - Me-ccmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
PSQ21_RS03320: X
AMP-binding (63..491): 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:
    AGFLHLAGRYAGTMFVGTAYTGYGSTEAGGVLLD
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

PSQ21_RS03360: mal
PKS_AT (4..275): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 70.8%
  inactive: 58.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 83.0
  Methoxymalonyl-CoA: 30.6
  inactive: 28.9
  Methylmalonyl-CoA: 28.0
  Propionyl-CoA: 20.6
  2-Methylbutyryl-CoA: 14.7
  Isobutyryl-CoA: 8.2
  CHC-CoA: 6.1
  Acetyl-CoA: 4.9
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP117709.1 - Region 9 - NRPS-like,betalactone,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: 911,108 - 973,592 nt. (total: 62,485 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)
betalactone: (HMGL-like and AMP-binding)
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase synthase
PSQ21_RS03780: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

PSQ21_RS03810: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

PSQ21_RS03920: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: formyltransferase
PSQ21_RS03950: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: amidase deaminase hydrolase peptidase synthase
PSQ21_RS03780: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

PSQ21_RS03850: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

PSQ21_RS03860: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

PSQ21_RS03870: amidase

smcogs
  SMCOG1105: amidase

PSQ21_RS03890: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

PSQ21_RS03895: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: cyclase dehydratase hydratase
PSQ21_RS03815: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

PSQ21_RS03910: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

PSQ21_RS03930: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase
PSQ21_RS03825: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

PSQ21_RS03855: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate 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 | betalactone | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001633.3 |  |  |  | 0.48 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001268.4 |  |  |  | 0.47 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002708.2 |  |  |  | 0.45 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0002034.3 |  |  |  | 0.35 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0001338.4 |  |  |  | 0.31 | PKS | citrinin | Monascus ruber
BGC0001006.5 |  |  |  | 0.31 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin B | Salinispora tropica CNB-440
BGC0001440.5 |  |  |  | 0.29 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0000319.5 |  |  |  | 0.28 | NRPS | cephamycin C | Streptomyces clavuligerus ATCC 27064
BGC0002169.3 |  |  |  | 0.27 | NRPS, PKS | acurin A | Aspergillus aculeatus ATCC 16872
BGC0001441.5 |  |  |  | 0.27 | other (other) | belactosin A, belactosin C | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002708.2 |  | 0.76 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0001268.4 |  | 0.57 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001633.3 |  | 0.51 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0002707.2 |  | 0.51 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0001302.5 |  | 0.49 | other (other) | lomofungin | Streptomyces lomondensis
BGC0001440.5 |  | 0.46 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0002499.2 |  | 0.46 | NRPS, PKS | enteromycin | Streptomyces achromogenes subsp. streptozoticus
BGC0002034.3 |  | 0.46 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0000927.3 |  | 0.44 | other (flavin) | roseoflavin | Streptomyces davaonensis JCM 4913
BGC0001965.4 |  | 0.44 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
monoterpene |  |  | C10 | C1-C10 | none
sesquiterpene |  |  | C15 | C1-C10 | none

Genes with terpene domains:
PSQ21_RS03930: T1TS
Domain 1 (4 - 315): Type 1 terpene synthase
Subtype: Germacrene A synthase type

Reactions:
  GPP → monoterpene_C1-C10
  FPP → sesquiterpene_C1-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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.25 out of 27.04
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.95 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.13 out of 27.04
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.03 out of 26.85
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.10 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.50 out of 23.79
Confidence: medium
Additional weak hits (24):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.99 out of 20.97
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.35 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.57 out of 27.78
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.94 out of 25.88
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.10 out of 28.14
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.23 out of 20.97
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.15 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.18 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.59 out of 27.04
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.36 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.76 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.15 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.70 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.60 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.65 out of 32.74
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.65 out of 26.12
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.51 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.81 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.90 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.72 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 13, location 911107 - 973592:
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

For candidate cluster 14, location 911107 - 954623:
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).
PSQ21_RS03815: X
AMP-binding (82..515): 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:
    MNAMHNGRAWLGSLALCGSIDCYGSTETTRAIVV
  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
--- | ---
FPP | Farnesyl diphosphate
GPP | Geranyl diphoshate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP117709.1 - Region 10 - ectoine
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,398,740 - 1,409,138 nt. (total: 10,399 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
PSQ21_RS05965: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

PSQ21_RS05975: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

PSQ21_RS05995: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

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

Reference | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.94 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.85 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.59 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.94 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.85 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.59 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (8):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.46 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.64 out of 26.06
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.46 out of 27.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.75 out of 21.55
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.04 out of 26.12
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.51 out of 27.78
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_CP117709.1 - Region 11 - 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: 1,445,668 - 1,521,009 nt. (total: 75,342 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
PSQ21_RS06270: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acyltransferase transketolase
PSQ21_RS06240: transketolase

smcogs
  SMCOG1204: transketolase

PSQ21_RS06295: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

PSQ21_RS06300: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

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
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001133.4 |  | 0.73 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.73 | NRPS | enniatin | Fusarium equiseti
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001133.4 |  | 0.73 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.73 | NRPS | enniatin | Fusarium equiseti
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.72 | 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:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.23 out of 23.43
Confidence: medium
Additional weak hits (9):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.66 out of 26.06
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.83 out of 30.22
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.93 out of 19.26
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.76 out of 25.75
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.94 out of 33.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 17, location 1445667 - 1521009:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Thr - D-Asn - Thr - NMe-Phe) + (Val - Gly - Gly - D-Val - 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).
PSQ21_RS06295: Val - Gly - Gly - Val - X
Search NORINE for peptide: strict or relaxed
AMP-binding (465..861): 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:
    LDRSFDASTYEVWMWTGGDVDGYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1525..1924): 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:
    FGMTFDIAGLELQGLVGGEVNLYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2585..2984): 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:
    FGMTFDIAGLELQGLVGGEVNLYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3646..4052): 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:
    LDRSFDASTYEVWLWTGGDVDGYGPTETTTFASH
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5198..5595): X
nrpys: cycHexAla, Leu, Val

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:
    LGLAFDASVLELSLVIGGDVNGYGPTETTVAATI
  Nearest Stachelhaus code(s):
    Leu DALFVGAVAK (76% 8Å match)
    Val DALFVGLVAK (71% 8Å match)
    cycHexAla DLLSVGGVFK (59% 8Å match)
  Stachelhaus code match:
    80% (moderate)

PSQ21_RS06300: Thr - Asn - Thr - Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (531..944): 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:
    LATHFDFSVWEGNQVFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2087..2488): 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:
    YWASFDLTVTAGKVVVGGEINEYGPTETTVGCIE
  Nearest Stachelhaus code(s):
    Asn DLTKVGEVGK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3627..4042): 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:
    LATHFDFSVWEGNQVFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4702..5093): 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:
    LAQFFDGAFWEMTLSVAGEINSYGPSEATVCATM
  Nearest Stachelhaus code(s):
    Trp DGWAVASVCK (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
--- | ---
BldD | Development and antibiotic global regulator

NZ_CP117709.1 - Region 12 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,071,407 - 2,101,218 nt. (total: 29,812 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
PSQ21_RS08915: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

PSQ21_RS08970: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: aminotransferase
PSQ21_RS08960: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: decarboxylase
PSQ21_RS08965: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0001478.5 |  | 0.64 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.62 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002073.3 |  | 0.61 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002305.2 |  | 0.60 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002464.3 |  | 0.55 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0000940.5 |  | 0.55 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.55 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0001478.5 |  | 0.64 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.62 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002073.3 |  | 0.61 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002305.2 |  | 0.60 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002464.3 |  | 0.55 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0000940.5 |  | 0.55 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.55 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.73 out of 18.46
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.30 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.03 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.77 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.77 out of 36.53
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 25.31
Confidence: medium
Additional weak hits (5):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
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: 16.40 out of 21.84
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.08 out of 30.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.12 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
DmdR1 | Iron(II)-dependent repressor
NtrC | Nitrogen regulatory protein C
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP117709.1 - Region 13 - lanthipeptide-class-ii,lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,439,541 - 2,471,158 nt. (total: 31,618 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
PSQ21_RS10470: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Hydrolases: protease
PSQ21_RS10550: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Lyases: cyclase
PSQ21_RS10490: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-ii | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002700.2 |  |  | 0.38 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000496.5 |  |  | 0.37 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  |  | 0.37 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000525.5 |  |  | 0.36 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000519.4 |  |  | 0.35 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000501.3 |  |  | 0.35 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000518.3 |  |  | 0.35 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000553.3 |  |  | 0.34 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000554.4 |  |  | 0.34 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002111.3 |  |  | 0.34 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000496.5 |  | 0.50 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.50 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000519.4 |  | 0.49 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000501.3 |  | 0.49 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000518.3 |  | 0.49 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000553.3 |  | 0.48 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002111.3 |  | 0.48 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139

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 PSQ21_RS10510

PSQ21_RS10520
Leader:
MSENTKPTADETPEVEAHSVLDLQETSVQGG
Core:
D Q T D G N C I S V L S V V E T Q P L
Core with dehydrations:
D Q Dhb D G N Cys I Dha V L Dha V V E Dhb Q P L

#### antiSMASH-DB 4.0 matches for PSQ21_RS10520

100.0%
NZ_CP117709.1:
Lanthipeptides: PSQ21_RS10520_lanthipeptide
1
D Q T D G N C I S V L S V V E T Q P L
19
D Q T D G N C I S V L S V V E T Q P L
1
D Q T D G N C I S V L S V V E T Q P L
19
78.9%
NZ_BMRY01000010.1 and 58 others:
NZ_BMRY01000010.1 Lanthipeptides: IE140_RS27680_lanthipeptide NZ_BMRY01000010.1 Lanthipeptides: IE140_RS27680_lanthipeptide NZ_BMRY01000010.1 Lanthipeptides: IE140_RS27680_lanthipeptide NZ_BMSZ01000004.1 Lanthipeptides: IE135_RS08610_lanthipeptide NZ_BMSZ01000004.1 Lanthipeptides: IE135_RS08610_lanthipeptide NZ_BMSZ01000004.1 Lanthipeptides: IE135_RS08610_lanthipeptide NZ_BMSZ01000004.1 Lanthipeptides: IE135_RS08610_lanthipeptide NZ_CP010833.1 Lanthipeptides: TK78_RS36080_lanthipeptide NZ_CP010833.1 Lanthipeptides: TK78_RS36080_lanthipeptide NZ_CP010833.1 Lanthipeptides: TK78_RS36080_lanthipeptide NZ_CP010833.1 Lanthipeptides: TK78_RS36080_lanthipeptide NZ_CP013738.1 Lanthipeptides: WQO_RS36380_lanthipeptide NZ_CP013738.1 Lanthipeptides: WQO_RS36380_lanthipeptide NZ_CP013738.1 Lanthipeptides: WQO_RS36380_lanthipeptide NZ_CP013738.1 Lanthipeptides: WQO_RS36380_lanthipeptide NZ_CP021707.1 Lanthipeptides: CCZ36_RS34740_lanthipeptide NZ_CP021707.1 Lanthipeptides: CCZ36_RS34740_lanthipeptide NZ_CP021707.1 Lanthipeptides: CCZ36_RS34740_lanthipeptide NZ_CP021707.1 Lanthipeptides: CCZ36_RS34740_lanthipeptide NZ_CP029361.1 Lanthipeptides: DIJ69_RS34965_lanthipeptide NZ_CP029361.1 Lanthipeptides: DIJ69_RS34965_lanthipeptide NZ_CP029361.1 Lanthipeptides: DIJ69_RS34965_lanthipeptide NZ_CP029361.1 Lanthipeptides: DIJ69_RS34965_lanthipeptide NZ_CP084357.1 Lanthipeptides: LEL86_RS06820_lanthipeptide NZ_CP084357.1 Lanthipeptides: LEL86_RS06820_lanthipeptide NZ_CP084357.1 Lanthipeptides: LEL86_RS06820_lanthipeptide NZ_CP084357.1 Lanthipeptides: LEL86_RS06820_lanthipeptide NZ_CP090837.1 Lanthipeptides: LZ559_RS11615_lanthipeptide NZ_CP090837.1 Lanthipeptides: LZ559_RS11615_lanthipeptide NZ_CP090837.1 Lanthipeptides: LZ559_RS11615_lanthipeptide NZ_CP090837.1 Lanthipeptides: LZ559_RS11615_lanthipeptide NZ_JAJUKK010000002.1 Lanthipeptides: LXH09_RS05290_lanthipeptide NZ_JAJUKK010000002.1 Lanthipeptides: LXH09_RS05290_lanthipeptide NZ_JAJUKK010000002.1 Lanthipeptides: LXH09_RS05290_lanthipeptide NZ_JAJUKK010000002.1 Lanthipeptides: LXH09_RS05290_lanthipeptide NZ_JNLT01000008.1 Lanthipeptides: CD02_RS38865_lanthipeptide NZ_JNLT01000008.1 Lanthipeptides: CD02_RS38865_lanthipeptide NZ_JNLT01000008.1 Lanthipeptides: CD02_RS38865_lanthipeptide NZ_JNLT01000008.1 Lanthipeptides: CD02_RS38865_lanthipeptide NZ_KZ679082.1 Lanthipeptides: allorf_2505302_2505508_lanthipeptide NZ_KZ679082.1 Lanthipeptides: allorf_2505302_2505508_lanthipeptide NZ_KZ679082.1 Lanthipeptides: allorf_2505302_2505508_lanthipeptide NZ_KZ819154.1 Lanthipeptides: allorf_5241449_5241619_lanthipeptide NZ_KZ819154.1 Lanthipeptides: allorf_5241449_5241619_lanthipeptide NZ_KZ819178.1 Lanthipeptides: DBP20_RS35630_lanthipeptide NZ_KZ819178.1 Lanthipeptides: DBP20_RS35630_lanthipeptide NZ_KZ819178.1 Lanthipeptides: DBP20_RS35630_lanthipeptide NZ_KZ819178.1 Lanthipeptides: DBP20_RS35630_lanthipeptide NZ_LIXK01000002.1 Lanthipeptides: AMK23_RS37800_lanthipeptide NZ_LIXK01000002.1 Lanthipeptides: AMK23_RS37800_lanthipeptide NZ_LIXK01000002.1 Lanthipeptides: AMK23_RS37800_lanthipeptide NZ_LIXK01000002.1 Lanthipeptides: AMK23_RS37800_lanthipeptide NZ_NNBN01000010.1 Lanthipeptides: CG717_RS33255_lanthipeptide NZ_NNBN01000010.1 Lanthipeptides: CG717_RS33255_lanthipeptide NZ_WWGD01000003.1 Lanthipeptides: GTY72_RS37120_lanthipeptide NZ_WWGD01000003.1 Lanthipeptides: GTY72_RS37120_lanthipeptide NZ_WWGD01000003.1 Lanthipeptides: GTY72_RS37120_lanthipeptide NZ_WWGD01000003.1 Lanthipeptides: GTY72_RS37120_lanthipeptide
Lanthipeptides: IE140_RS27680_lanthipeptide
1
D Q T D G N C I S V L S V V E T Q
17
D T D G N C I S V L S V V E Q
1
D T T D G N C I S V L S V V E Q Q
17
78.9%
NZ_BNBJ01000007.1 and 21 others:
NZ_BNBJ01000007.1 Lanthipeptides: IE304_RS13825_lanthipeptide NZ_BNBJ01000007.1 Lanthipeptides: IE304_RS13825_lanthipeptide NZ_BNBJ01000007.1 Lanthipeptides: IE304_RS13825_lanthipeptide NZ_CP079114.1 Lanthipeptides: KV381_RS11695_lanthipeptide NZ_CP079114.1 Lanthipeptides: KV381_RS11695_lanthipeptide NZ_CP079114.1 Lanthipeptides: KV381_RS11695_lanthipeptide NZ_CP079114.1 Lanthipeptides: KV381_RS11695_lanthipeptide NZ_DS999644.1 Lanthipeptides: SSGG_RS37575_lanthipeptide NZ_JALDPQ010000065.1 Lanthipeptides: MQC87_RS27525_lanthipeptide NZ_JALDPQ010000065.1 Lanthipeptides: MQC87_RS27525_lanthipeptide NZ_JALDPQ010000065.1 Lanthipeptides: MQC87_RS27525_lanthipeptide NZ_JALDPQ010000065.1 Lanthipeptides: MQC87_RS27525_lanthipeptide NZ_JAMFLF010000007.1 Lanthipeptides: M1212_RS18745_lanthipeptide NZ_JAMFLF010000007.1 Lanthipeptides: M1212_RS18745_lanthipeptide NZ_JAMFLF010000007.1 Lanthipeptides: M1212_RS18745_lanthipeptide NZ_JAMFLF010000007.1 Lanthipeptides: M1212_RS18745_lanthipeptide NZ_KL573557.1 Lanthipeptides: BG84_RS1000000140065_lanthipeptide NZ_LACR01000026.1 Lanthipeptides: YW5_RS36735_lanthipeptide NZ_LACR01000026.1 Lanthipeptides: YW5_RS36735_lanthipeptide NZ_LACR01000026.1 Lanthipeptides: YW5_RS36735_lanthipeptide NZ_LACR01000026.1 Lanthipeptides: YW5_RS36735_lanthipeptide
Lanthipeptides: IE304_RS13825_lanthipeptide
1
D Q T D G N C I S V L S V V E T Q
17
D T D G N C I S V L S V V E+Q
1
D T T D G N C I S V L S V V E S Q
17
with 12 more sequence matches
Only the first 10 are displayed here.
63.2%
NZ_LZRD01000043.1:
Lanthipeptides: A3Q37_RS37410_lanthipeptide
5
G N C I S V L S V V E T Q
17
G N C I S V L S V V E+Q
1
G N C I S V L S V V E S Q
13
57.9%
NZ_BNBJ01000007.1 and 8 others:
NZ_CP079114.1 Lanthipeptides: KV381_RS11700_lanthipeptide NZ_JALDPQ010000065.1 Lanthipeptides: MQC87_RS27530_lanthipeptide NZ_JALDPQ010000065.1 Lanthipeptides: MQC87_RS27530_lanthipeptide NZ_JALDPQ010000065.1 Lanthipeptides: MQC87_RS27530_lanthipeptide NZ_JALDPQ010000065.1 Lanthipeptides: MQC87_RS27530_lanthipeptide NZ_JAMFLF010000007.1 Lanthipeptides: M1212_RS18750_lanthipeptide NZ_KL573557.1 Lanthipeptides: BG84_RS1000000140060_lanthipeptide NZ_LZRD01000043.1 Lanthipeptides: A3Q37_RS37415_lanthipeptide
Lanthipeptides: IE304_RS13830_lanthipeptide
5
G N C I S V L S V V E T
16
G N C I S V L S V V E
2
G N C I S V L S V V E N
13
47.4%
NZ_LMFT01000038.1 and 1 other:
NZ_LMFT01000038.1 Lanthipeptides: ASD51_RS37395_lanthipeptide
Lanthipeptides: ASD51_RS37395_lanthipeptide
7
C I S V L S V V E
15
C I S V L S V V E
1
C I S V L S V V E
9
29.2%
NZ_ML142907.1 and 1 other:
NZ_ML142907.1 Lanthipeptides: DN53_RS02460_lanthipeptide
Lanthipeptides: DN53_RS02460_lanthipeptide
1
D Q T D G N C I S V L S V V
14
D T+G+C S S+V
7
D T T N G D C T S G T S I V
20
23.5%
NC_021177.1 and 9 others:
NC_021177.1 Lanthipeptides: SFUL_RS36595_lanthipeptide NZ_BMUG01000001.1 Lanthipeptides: IE264_RS01515_lanthipeptide NZ_BMUG01000001.1 Lanthipeptides: IE264_RS01515_lanthipeptide NZ_CP054926.1 Lanthipeptides: HUT09_RS11275_lanthipeptide NZ_CP054926.1 Lanthipeptides: HUT09_RS11275_lanthipeptide NZ_CP071044.1 Lanthipeptides: JHY03_RS11255_lanthipeptide NZ_CP071044.1 Lanthipeptides: JHY03_RS11255_lanthipeptide NZ_JOJC01000008.1 Lanthipeptides: IO23_RS1000000137100_lanthipeptide NZ_JOJC01000008.1 Lanthipeptides: IO23_RS1000000137100_lanthipeptide
Lanthipeptides: SFUL_RS36595_lanthipeptide
5
G N C I S V L S V V
14
G+C+S V L S V V
22
G S C V S V L S V V
31
22.2%
NZ_CP058552.1:
Lanthipeptides: HW560_RS06640_lanthipeptide
3
T D G N C I S V L S V
13
T D G N C+S ++
7
T D G N C V S T I T A
17
20.0%
NZ_BDHJ01000009.1 and 1 other:
NZ_CP076457.1 Lanthipeptides: KME66_RS23045_lanthipeptide
Lanthipeptides: BHQ08_RS34920_lanthipeptide
5
G N C I S V L S V V
14
G N C+S +S+V
19
G N C V S T V S L V
28
19.2%
NZ_BMLN01000009.1:
Lanthipeptides: IEX28_RS15335_lanthipeptide
3
T D G N C I S V L S V
13
T D G N C+ ++
7
T D G N C L K S I T A
17
19.2%
NZ_JABRUZ010000012.1:
Lanthipeptides: HRF55_RS15035_lanthipeptide
3
T D G N C I S V L S V
13
T D G N C++ ++
7
T D G N C L A S I T A
17
19.2%
NZ_JH600294.1 and 1 other:
NZ_JH600294.1 Lanthipeptides: GYU_RS0115740_lanthipeptide
Lanthipeptides: GYU_RS0115745_lanthipeptide
3
T D G N C I S V L S V
13
T D G N C++ ++
7
T D G N C L T T I T A
17
allorf_2463560_2463742
Leader:
MPAVAEKVRKPGLAIASAAVWRRYRASSEGG
Core:
K H C F P A S P T A P A P A P T W A H T A A E A P P D R P
Core with dehydrations:
K H Cys F P A Dha P Dhb A P A P A P Dhb W A H Dhb A A E A P P D R P

#### antiSMASH-DB 4.0 matches for allorf_2463560_2463742

100.0%
NZ_CP117709.1:
Lanthipeptides: allorf_2463560_2463742_lanthipeptide
1
K H C F P A S P T A P A P A P T W A H T A A E A P P D R P
29
K H C F P A S P T A P A P A P T W A H T A A E A P P D R P
1
K H C F P A S P T A P A P A P T W A H T A A E A P P D R P
29
40.0%
NZ_KZ819159.1 and 2 others:
NZ_KZ819159.1 Lanthipeptides: allorf_2152839_2153060_lanthipeptide NZ_KZ819159.1 Lanthipeptides: allorf_2152839_2153060_lanthipeptide
Lanthipeptides: allorf_2152839_2153060_lanthipeptide
3
C F P A S P T A P A P A P T W A H T A A E A P P D R
28
C P P+ T W A+T E A P D R
4
C R A E G P G G F L P S L T W A Y T G P E A M P D R
29
27.6%
NZ_BMRB01000009.1 and 1 other:
NZ_CP031087.1 Lanthipeptides: allorf_5861679_5861834_lanthipeptide
Lanthipeptides: allorf_009813_009968_lanthipeptide
8
P T A P A P A P T W A H T A A E A P P D R
28
P P W A H A + P R
2
P R C L L S M P Q W A H R R A L S N P I R
22
with 3 more sequence matches
27.4%
NZ_CP054926.1 and 1 other:
NZ_CP071044.1 Lanthipeptides: allorf_2567238_2567450_lanthipeptide
Lanthipeptides: allorf_2557855_2558067_lanthipeptide
4
F P A S P T A P A P A P-----------T W A H T A A E A P P D R
28
+ A S T A P A P T A H T A A E A D R
26
Y G A S S T A P A P V S R G R P P P S G P S L T C A H T A A E A M T D R
61
25.8%
NZ_JOJC01000008.1 and 1 other:
NZ_JOJC01000008.1 Lanthipeptides: allorf_025681_025893_lanthipeptide
Lanthipeptides: allorf_025681_025893_lanthipeptide
4
F P A S P T A P A P A P T W-----------A H T A A E A P P D R
28
+ A S T A P A P A H T A A E A D R
26
Y G A S S T A P A P V S R G R P P P S G P S L A C A H T A A E A M A D R
61
20.7%
NZ_AUBN01000022.1:
Lanthipeptides: allorf_02867_02956_lanthipeptide
3
C F P A S P T A P A
12
C F P+ P P A
6
C F P S G P V G P A
15

#### MIBiG 4.0 matches for allorf_2463560_2463742

13.8%
BGC0000582.4 (ADR72962.1):
Linaridin: cypemycin
5
P A S P T A
10
P A+P T
3
P A T P T V
8

#### 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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.64 out of 27.04
Confidence: medium
Additional weak hits (7):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.85 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.48 out of 28.14
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.11 out of 26.85
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.83 out of 20.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.00 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.77 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.70 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.

PSQ21_RS10520 - Class II
  Cleavage pHMM score: -4.20
  RODEO score: 0
  Monoisotopic mass: 1945.0 Da
  Molecular weight: 1946.1 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1964.1 Da N = 1
    1982.2 Da N = 2
    2000.2 Da N = 3
allorf_2463560_2463742 - Class II
  Cleavage pHMM score: -4.00
  RODEO score: 0
  Monoisotopic mass: 2919.4 Da
  Molecular weight: 2921.2 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2939.3 Da N = 1
    2957.3 Da N = 2
    2975.3 Da N = 3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor

NZ_CP117709.1 - Region 14 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,522,676 - 2,552,454 nt. (total: 29,779 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
PSQ21_RS10770: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

PSQ21_RS10830: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: acetyltransferase
PSQ21_RS10815: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase
PSQ21_RS10855: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: decarboxylase
PSQ21_RS10825: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.82 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  | 0.74 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.74 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002305.2 |  | 0.73 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.62 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002690.2 |  | 0.62 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002073.3 |  | 0.58 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0000244.4 |  | 0.55 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.82 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  | 0.74 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.74 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002305.2 |  | 0.73 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.62 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002690.2 |  | 0.62 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002073.3 |  | 0.58 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0000244.4 |  | 0.55 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.19 out of 20.47
Confidence: strong
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.98 out of 29.51
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.04 out of 27.04
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.29 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 26.66 out of 30.11
Confidence: medium
Additional weak hits (14):
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.72 out of 23.43
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.97 out of 39.62
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.69 out of 30.97
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.27 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 36.53
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.63 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.25 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.29 out of 36.54
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.52 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.37 out of 24.78
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.23 out of 23.43
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.58 out of 30.11
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
DmdR1 | Iron(II)-dependent repressor
DosR | Hypoxia stress response regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP117709.1 - Region 15 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,146,041 - 3,172,357 nt. (total: 26,317 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: dehydrogenase
PSQ21_RS13610: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
PSQ21_RS13535: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: hydrolase
PSQ21_RS13590: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: cyclase dehydratase
PSQ21_RS13555: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

PSQ21_RS13560: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Isomerases: mutase
PSQ21_RS13530: 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 | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002276.2 |  | 0.56 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002635.2 |  | 0.52 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001289.5 |  | 0.50 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002425.3 |  | 0.48 | ribosomal | stlassin | Streptomyces sp.
BGC0000894.4 |  | 0.46 | other (other) | citrinin | Monascus aurantiacus
BGC0002120.3 |  | 0.45 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000231.5 |  | 0.44 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002276.2 |  | 0.56 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002635.2 |  | 0.52 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001289.5 |  | 0.50 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002425.3 |  | 0.48 | ribosomal | stlassin | Streptomyces sp.
BGC0000894.4 |  | 0.46 | other (other) | citrinin | Monascus aurantiacus
BGC0002120.3 |  | 0.45 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000231.5 |  | 0.44 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
Additional weak hits (2):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.91 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
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 (3146040...3172357)
PSQ21_RS13560
  RRE type: Lanthipeptide_LanB_RRE
  Location: 115 - 207
  Score: 65.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP117709.1 - Region 16 - lanthipeptide-class-v
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: 4,193,213 - 4,235,518 nt. (total: 42,306 nt) Show pHMM detection rules used
lanthipeptide-class-v: (APH and HopA1)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
PSQ21_RS18565: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: aminotransferase glycosyltransferase methyltransferase
PSQ21_RS18470: sugar transferase

smcogs
  SMCOG1146: sugar transferase

PSQ21_RS18550: methyltransferase

smcogs
  SMCOG1248: methyltransferase

PSQ21_RS18610: 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 | lanthipeptide-class-v | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002110.3 |  | 0.45 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908
BGC0001896.4 |  | 0.45 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0000513.3 |  | 0.45 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002701.2 |  | 0.45 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0002151.2 |  | 0.44 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0002150.2 |  | 0.44 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002303.3 |  | 0.43 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002635.2 |  | 0.43 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000882.5 |  | 0.43 | other (other) | mildiomycin | Streptomyces rimofaciens
BGC0001206.5 |  | 0.42 | other (other) | indolmycin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002110.3 |  | 0.45 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908
BGC0001896.4 |  | 0.45 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0000513.3 |  | 0.45 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002701.2 |  | 0.45 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0002151.2 |  | 0.44 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0002150.2 |  | 0.44 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002303.3 |  | 0.43 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002635.2 |  | 0.43 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000882.5 |  | 0.43 | other (other) | mildiomycin | Streptomyces rimofaciens
BGC0001206.5 |  | 0.42 | other (other) | indolmycin | Streptomyces griseus subsp. griseus

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

No significant matches found.

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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.22 out of 27.04
Confidence: medium
Additional weak hits (13):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.00 out of 32.74
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.05 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.95 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.15 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.45 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.38 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.51 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.93 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.39 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.05 out of 33.14
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
--- | ---
DasR | N-acetylglucosamine dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP117709.1 - Region 17 - 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: 4,248,489 - 4,302,115 nt. (total: 53,627 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
PSQ21_RS18760: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

PSQ21_RS18765: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

PSQ21_RS18815: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: methyltransferase
PSQ21_RS18810: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: hydrolase
PSQ21_RS18755: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

PSQ21_RS18880: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
PSQ21_RS18775: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS18780: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS18785: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

PSQ21_RS18800: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS18805: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  | 0.68 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001833.4 |  |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000307.4 |  |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  |  | 0.61 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.61 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.66 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.37 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.91 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.22 out of 27.04
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
Additional weak hits (27):
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.15 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.37 out of 28.14
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.11 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.59 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.45 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.33 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.61 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.34 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.42 out of 29.65
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.54 out of 32.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.91 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.18 out of 35.63
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.95 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.49 out of 33.14
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 30.11
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.22 out of 20.01
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.63 out of 26.06
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.87 out of 26.85
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.50 out of 33.14
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.74 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 25, location 4248488 - 4302115:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Fo-OH-Orn) + (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).
PSQ21_RS18775: X
AMP-binding (15..416): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWTSFDLSTFDGYAAFAGEYNLYGPTETNVCTFE
  Nearest Stachelhaus code(s):
    Pro DLFYLALVCK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

PSQ21_RS18780: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (33..442): 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:
    NAALYTMNCPGGAIQIGSAQQVFGMAEGLLCLTR
  Nearest Stachelhaus code(s):
    Hpa TWPSQGVLCK (82% 8Å match)
    diOH-Bz PLPAQGVLCK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

PSQ21_RS18785: X
AMP-binding (556..951): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    TCLSFDLSVYDGNCVLGGDAGLGGTTEAAIHSTV
  Nearest Stachelhaus code(s):
    Ser DLYNLGLIHK (91% 8Å match)
  Stachelhaus code match:
    90% (moderate)

PSQ21_RS18800: Fo-OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (534..937): Fo-OH-Orn
nrpys: Fo-OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWQAFDISINELYLWCGGEYHGYGPAEATIGVTC
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DINYWGGIGK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

PSQ21_RS18805: mal
PKS_AT (536..822): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 82.4
  Methoxymalonyl-CoA: 64.9
  inactive: 47.1
  Methylmalonyl-CoA: 36.2
  Propionyl-CoA: 25.1
  Isobutyryl-CoA: 19.6
  Ethylmalonyl-CoA: 14.8
  fatty_acid: 13.4
  Benzoyl-CoA: 13.4
  2-Methylbutyryl-CoA: 11.1
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP117709.1 - Region 18 - lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,324,808 - 4,347,483 nt. (total: 22,676 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
PSQ21_RS19025: methyltransferase

smcogs
  SMCOG1089: methyltransferase

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

Reference | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.65 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.65 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000496.5 |  | 0.63 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000501.3 |  | 0.60 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000518.3 |  | 0.51 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000553.3 |  | 0.50 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002111.3 |  | 0.48 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000546.3 |  | 0.48 | ribosomal | SAL-2242 | Streptomyces albidoflavus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.65 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.65 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000496.5 |  | 0.63 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000501.3 |  | 0.60 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000518.3 |  | 0.51 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000553.3 |  | 0.50 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002111.3 |  | 0.48 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000546.3 |  | 0.48 | ribosomal | SAL-2242 | Streptomyces albidoflavus

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 PSQ21_RS19065

PSQ21_RS19055
Leader:
MSVLDLQEMELPVESPEEE
PSQ21_RS19060
Leader:
MSLLDLQEMELPVESPEEE
Shared core:
L L G S G R S Q H C S D A S W V F C
Core with dehydrations:
L L G Dha G R Dha Q H Cys Dha D A Dha W V F Cys

#### antiSMASH-DB 4.0 matches for PSQ21_RS19055

100.0%
NZ_CP117709.1 and 1 other:
NZ_CP117709.1 Lanthipeptides: PSQ21_RS19055_lanthipeptide
Lanthipeptides: PSQ21_RS19060_lanthipeptide
1
L L G S G R S Q H C S D A S W V F C
18
L L G S G R S Q H C S D A S W V F C
1
L L G S G R S Q H C S D A S W V F C
18
94.4%
NZ_CP058693.1 and 1 other:
NZ_CP058693.1 Lanthipeptides: HYQ63_RS44925_lanthipeptide
Lanthipeptides: HYQ63_RS44930_lanthipeptide
1
L L G S G R S Q H C S D A S W V F C
18
+L G S G R S Q H C S D A S W V F C
1
V L G S G R S Q H C S D A S W V F C
18
80.0%
NZ_BMUN01000002.1 and 4 others:
NZ_CP027297.1 Lanthipeptides: C1N79_RS19645_lanthipeptide NZ_CP039123.1 Lanthipeptides: E5N77_RS19350_lanthipeptide NZ_CP104697.1 Lanthipeptides: N6Q81_RS18965_lanthipeptide NZ_JACWAA010000005.1 Lanthipeptides: ICA23_RS27195_lanthipeptide
Lanthipeptides: IE238_RS05610_lanthipeptide
1
L L G S G R S Q H C S D A S W V F C
18
+L G S G+S Q H C S D A S W V F C
3
V L G S G K S Q H C S D A S W V F C
20
with 10 more sequence matches
80.0%
NZ_BMUN01000002.1 and 5 others:
NZ_CP027297.1 Lanthipeptides: C1N79_RS36515_lanthipeptide NZ_CP039123.1 Lanthipeptides: E5N77_RS37620_lanthipeptide NZ_CP104697.1 Lanthipeptides: N6Q81_RS18960_lanthipeptide NZ_JACWAA010000005.1 Lanthipeptides: ICA23_RS34925_lanthipeptide NZ_KZ819185.1 Lanthipeptides: DBP22_RS30620_lanthipeptide
Lanthipeptides: IE238_RS37930_lanthipeptide
1
L L G S G R S Q H C S D A S W V F C
18
+L G S G+S Q H C S D A S W V F C
3
V L G S G Q S Q H C S D A S W V F C
20
55.6%
NZ_CP047146.1 and 1 other:
NZ_CP047146.1 Lanthipeptides: GR130_RS07915_lanthipeptide
Lanthipeptides: GR130_RS07915_lanthipeptide
4
S G R S Q H C S D A S W--V F C
18
S G S H C+D S V F C
1
S G N S A H C N D T S G I S V F C
17
50.0%
NZ_BNBY01000001.1 and 1 other:
NZ_BNBY01000001.1 Lanthipeptides: IE332_RS00510_lanthipeptide
Lanthipeptides: IE332_RS00515_lanthipeptide
2
L G S G R S Q H C S D A S W V F C
18
+G S G+S C S++S W++C
1
M G S G Q S T D C S N S S W L W C
17
38.9%
NZ_AP018365.1 and 8 others:
NZ_AP018365.1 Lanthipeptides: allorf_8005631_8005744_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8005631_8005744_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8005631_8005744_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide
Lanthipeptides: allorf_8005631_8005744_lanthipeptide
10
C S D A S W V F C
18
C S D A S W C
4
C S D A S W F L C
12
38.9%
NZ_CP063374.1:
Lanthipeptides: allorf_6445065_6445196_lanthipeptide
1
L L G S G R S Q H C S D A S
14
L G S S H C+D +
1
F L G S L L S N H C T D V A
14
38.9%
NZ_CP094264.1:
Lanthipeptides: LUW75_RS07675_lanthipeptide
6
R S Q H C S D A S W--V F C
18
+S H C+D S +F C
2
Q S N H C N D T S G I S I F C
16
36.4%
NZ_BNBY01000001.1:
Lanthipeptides: IE332_RS00505_lanthipeptide
2
L G S G R S Q H C S D A S W V F C
18
+ S G+S C S++S W++C
5
M D S G K S T D C S N S S W L W C
21
27.8%
NZ_CP047146.1 and 1 other:
NZ_CP047146.1 Lanthipeptides: GR130_RS07920_lanthipeptide
Lanthipeptides: GR130_RS07920_lanthipeptide
7
S Q H C S D A S W V
16
S+H C+D S +
1
S E H C N D T S G I
10
18.8%
NZ_MUXN01000027.1:
Lanthipeptides: allorf_018463_018597_lanthipeptide
4
S G R S Q H C S D A S W V
16
+G R S+ C D + V
6
A G R S R R C G D D A P V
18
8.7%
NZ_LMEQ01000012.1:
Lanthipeptides: ASD48_RS22460_lanthipeptide
2
L G S G R S Q H C S D A S
14
L G+ H C S S
53
L G A S A E P H C S P V S
65

#### 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:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.49 out of 23.43
Confidence: medium
Additional weak hits (2):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.34 out of 20.97
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.03 out of 25.88
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.

PSQ21_RS19055 - Class III
  Cleavage pHMM score: 6.30
  RODEO score: 0
  Monoisotopic mass: 1879.9 Da
  Molecular weight: 1881.1 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1899.1 Da N = 1
    1917.1 Da N = 2
PSQ21_RS19060 - Class III
  Cleavage pHMM score: 6.30
  RODEO score: 0
  Monoisotopic mass: 1879.9 Da
  Molecular weight: 1881.1 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1899.1 Da N = 1
    1917.1 Da N = 2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator

NZ_CP117709.1 - Region 19 - 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: 5,292,167 - 5,346,941 nt. (total: 54,775 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))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase reductase
PSQ21_RS23800: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

PSQ21_RS23865: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

PSQ21_RS23925: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

Transferases: aminotransferase
PSQ21_RS23880: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: esterase
PSQ21_RS23870: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: lyase
PSQ21_RS23850: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
PSQ21_RS23860: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS23885: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: permease
PSQ21_RS23940: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | NRPS-like | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  | 0.83 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  |  | 0.69 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  |  | 0.68 | NRPS | AM-toxin | Alternaria alternata
BGC0001641.4 |  |  | 0.67 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001276.3 |  |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  | 0.67 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001641.4 |  | 0.67 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.91 out of 23.79
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 25.31
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.88 out of 36.53
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
Additional weak hits (17):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.44 out of 39.62
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.94 out of 36.54
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.59 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.36 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.79 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.61 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.67 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.83 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.92 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.25 out of 20.01
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.32 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.95 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.60 out of 32.93
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.36 out of 27.18
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 27, location 5292166 - 5346941:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (aThr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 28, location 5292166 - 5334752:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (aThr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 29, location 5303614 - 5346941:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (aThr)

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).
PSQ21_RS23860: aThr
Search NORINE for peptide: strict or relaxed
AMP-binding (294..677): aThr
nrpys: aThr

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:
    LSVHFDFSVWEGSQVLGGEVNMYGITETTVHVTA
  Nearest Stachelhaus code(s):
    aThr DFWSVGMVHK (91% 8Å match)
    Thr DFWSVGMVHK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

PSQ21_RS23885: mal
PKS_AT (556..848): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 122.7
  inactive: 78.2
  Methylmalonyl-CoA: 56.2
  Methoxymalonyl-CoA: 54.1
  Isobutyryl-CoA: 37.5
  Ethylmalonyl-CoA: 34.9
  Propionyl-CoA: 30.9
  CHC-CoA: 28.4
  fatty_acid: 23.4
  Benzoyl-CoA: 21.0
  trans-1,2-CPDA: 17.8
  2-Methylbutyryl-CoA: 14.9
  Acetyl-CoA: 13.8
  3-Methylbutyryl-CoA: 11.8

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

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP117709.1 - Region 20 - 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: 5,355,576 - 5,384,464 nt. (total: 28,889 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
Oxidoreductases: oxygenase
PSQ21_RS24090: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: aminotransferase glycosyltransferase methyltransferase transferase
PSQ21_RS24015: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

PSQ21_RS24025: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

PSQ21_RS24030: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

PSQ21_RS24035: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

PSQ21_RS24040: methyltransferase

smcogs
  SMCOG1089: methyltransferase

PSQ21_RS24045: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Lyases: dehydratase
PSQ21_RS24020: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
PSQ21_RS24120: 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000898.5 |  | 0.54 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0001295.5 |  | 0.52 | other (other) | cremeomycin | Streptomyces cremeus
BGC0000813.3 |  | 0.51 | other (other) | K-252a | Nonomuraea longicatena
BGC0000278.3 |  | 0.51 | PKS | urdamycin | Streptomyces fradiae
BGC0000825.5 |  | 0.51 | other (other) | staurosporine | Streptomyces sp. TP-A0274
BGC0000826.5 |  | 0.50 | other (other) | staurosporine | Streptomyces clavuligerus ATCC 27064
BGC0002311.3 |  | 0.50 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0000193.3 |  | 0.49 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0000899.4 |  | 0.49 | saccharide | desosamine | Streptomyces narbonensis
BGC0000827.3 |  | 0.49 | other (other) | staurosporine | Salinispora arenicola CNS-205

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000898.5 |  | 0.54 | saccharide | desosamine, pikromycin, neomethymycin, narbomycin | Streptomyces venezuelae
BGC0001295.5 |  | 0.52 | other (other) | cremeomycin | Streptomyces cremeus
BGC0000813.3 |  | 0.51 | other (other) | K-252a | Nonomuraea longicatena
BGC0000278.3 |  | 0.51 | PKS | urdamycin | Streptomyces fradiae
BGC0000825.5 |  | 0.51 | other (other) | staurosporine | Streptomyces sp. TP-A0274
BGC0000826.5 |  | 0.50 | other (other) | staurosporine | Streptomyces clavuligerus ATCC 27064
BGC0002311.3 |  | 0.50 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0000193.3 |  | 0.49 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0000899.4 |  | 0.49 | saccharide | desosamine | Streptomyces narbonensis
BGC0000827.3 |  | 0.49 | other (other) | staurosporine | Salinispora arenicola CNS-205

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.99 out of 20.47
Confidence: medium
Additional weak hits (21):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.54 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.85 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.28 out of 29.65
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.74 out of 29.72
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.81 out of 23.43
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.65 out of 19.26
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.16 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.71 out of 29.38
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.29 out of 23.43
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.51 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.88 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.56 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.10 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.72 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.11 out of 29.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.62 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.19 out of 24.78
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
(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.
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (5355575...5384464)
PSQ21_RS24060
  RRE type: Thiopeptide_F_RRE
  Location: 0 - 82
  Score: 32.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

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_CP117709.1 - Region 21 - melanin
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,402,259 - 5,412,678 nt. (total: 10,420 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: esterase
PSQ21_RS24240: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily 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 | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000912.3 |  | 0.86 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000911.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.59 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.53 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.49 | other (other) | melanin | Streptomyces avermitilis
BGC0000662.5 |  | 0.37 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.37 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.36 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.35 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.35 | other (other) | iso-A82775C | Pestalotiopsis fici

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000912.3 |  | 0.86 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000911.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.59 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.53 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.49 | other (other) | melanin | Streptomyces avermitilis
BGC0000662.5 |  | 0.37 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.37 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.36 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.35 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.35 | other (other) | iso-A82775C | Pestalotiopsis fici

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.36 out of 23.79
Confidence: medium
Additional weak hits (7):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.00 out of 39.62
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.64 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.21 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.62 out of 29.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.55 out of 33.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.08 out of 32.93
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.37 out of 30.98
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism

NZ_CP117709.1 - Region 22 - lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,455,011 - 5,477,707 nt. (total: 22,697 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase aminotransferase
PSQ21_RS24510: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

PSQ21_RS24565: 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 | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.90 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000553.3 |  | 0.72 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.60 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000518.3 |  | 0.55 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000546.3 |  | 0.53 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0001226.4 |  | 0.52 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.90 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000553.3 |  | 0.72 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.60 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000518.3 |  | 0.55 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000546.3 |  | 0.53 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0001226.4 |  | 0.52 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai

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

No significant matches found.

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

#### Lanthipeptide(s) for PSQ21_RS24525

PSQ21_RS24530
Leader:
MALLDLQAMDTPAEDSFGELAT
Core:
G S Q V S L L V C E Y S S L S V V L C T P
Core with dehydrations:
G Dha Q V Dha L L V Cys E Y Dha Dha L Dha V V L Cys Dhb P

#### antiSMASH-DB 4.0 matches for PSQ21_RS24530

100.0%
NC_010572.1 and 60 others:
NC_021177.1 Lanthipeptides: SFUL_RS24355_lanthipeptide NZ_AQRK01000102.1 Lanthipeptides: YUW_RS30025_lanthipeptide NZ_ARPF01000003.1 Lanthipeptides: B083_RS0107255_lanthipeptide NZ_BMRY01000001.1 Lanthipeptides: IE140_RS02070_lanthipeptide NZ_BMSP01000003.1 Lanthipeptides: IE150_RS06495_lanthipeptide NZ_BMSZ01000003.1 Lanthipeptides: IE135_RS07550_lanthipeptide NZ_BMTW01000017.1 Lanthipeptides: IE134_RS28550_lanthipeptide NZ_BMUG01000009.1 Lanthipeptides: IE264_RS25430_lanthipeptide NZ_BMVK01000002.1 Lanthipeptides: IE272_RS07115_lanthipeptide NZ_BNBJ01000002.1 Lanthipeptides: IE304_RS05195_lanthipeptide NZ_CM003601.1 Lanthipeptides: JI76_RS25200_lanthipeptide NZ_CP010833.1 Lanthipeptides: TK78_RS10875_lanthipeptide NZ_CP011522.1 Lanthipeptides: ABE83_RS11805_lanthipeptide NZ_CP013738.1 Lanthipeptides: WQO_RS23525_lanthipeptide NZ_CP015362.1 Lanthipeptides: A6E92_RS09975_lanthipeptide NZ_CP020563.1 Lanthipeptides: B7C62_RS24450_lanthipeptide NZ_CP020570.1 Lanthipeptides: B1H20_RS34690_lanthipeptide NZ_CP024957.1 Lanthipeptides: CVT27_RS22730_lanthipeptide NZ_CP029361.1 Lanthipeptides: DIJ69_RS10225_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS22865_lanthipeptide NZ_CP061072.1 Lanthipeptides: HYC88_RS10560_lanthipeptide NZ_CP079114.1 Lanthipeptides: KV381_RS24895_lanthipeptide NZ_CP084357.1 Lanthipeptides: LEL86_RS29435_lanthipeptide NZ_CP086102.1 Lanthipeptides: LK895_RS11660_lanthipeptide NZ_CP090837.1 Lanthipeptides: LZ559_RS24025_lanthipeptide NZ_CP096281.1 Lanthipeptides: MWG59_RS25685_lanthipeptide NZ_CP101397.1 Lanthipeptides: NLU04_RS06465_lanthipeptide NZ_CP110539.1 Lanthipeptides: OH133_RS12690_lanthipeptide NZ_CP112880.1 Lanthipeptides: N7925_RS11185_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS22935_lanthipeptide NZ_CP117709.1 Lanthipeptides: PSQ21_RS24530_lanthipeptide NZ_DS999644.1 Lanthipeptides: SSGG_RS09925_lanthipeptide NZ_GL877172.1 Lanthipeptides: SACT1_RS12960_lanthipeptide NZ_JAAWWP010000002.1 Lanthipeptides: HFV08_RS04115_lanthipeptide NZ_JAGGOV010000004.1 Lanthipeptides: J7E92_RS02930_lanthipeptide NZ_JAHHWT010000009.1 Lanthipeptides: KM153_RS24430_lanthipeptide NZ_JALDPQ010000064.1 Lanthipeptides: MQC87_RS23965_lanthipeptide NZ_JAMFLF010000002.1 Lanthipeptides: M1212_RS07295_lanthipeptide NZ_JANRMN010000004.1 Lanthipeptides: NW249_RS08610_lanthipeptide NZ_JNLT01000003.1 Lanthipeptides: CD02_RS0108685_lanthipeptide NZ_KB890925.1 Lanthipeptides: B053_RS0113845_lanthipeptide NZ_KL573549.1 Lanthipeptides: BG84_RS0119125_lanthipeptide NZ_KQ257779.1 Lanthipeptides: IQ60_RS22540_lanthipeptide NZ_KZ195572.1 Lanthipeptides: B9W61_RS11940_lanthipeptide NZ_KZ679082.1 Lanthipeptides: C6W96_RS24050_lanthipeptide NZ_KZ819154.1 Lanthipeptides: DBP12_RS10285_lanthipeptide NZ_KZ819178.1 Lanthipeptides: DBP20_RS23960_lanthipeptide NZ_KZ819182.1 Lanthipeptides: DBP21_RS24660_lanthipeptide NZ_LACR01000009.1 Lanthipeptides: YW5_RS12280_lanthipeptide NZ_LIPB01000001.1 Lanthipeptides: AMK17_RS03280_lanthipeptide NZ_LIPE01000001.1 Lanthipeptides: AMK12_RS03355_lanthipeptide NZ_LIVT01000001.1 Lanthipeptides: AMK24_RS01700_lanthipeptide NZ_LIVW01000001.1 Lanthipeptides: AMK28_RS03165_lanthipeptide NZ_LIXK01000001.1 Lanthipeptides: AMK23_RS04085_lanthipeptide NZ_LMEL01000012.1 Lanthipeptides: ASD29_RS10010_lanthipeptide NZ_LZRD01000054.1 Lanthipeptides: A3Q37_RS33745_lanthipeptide NZ_ML123117.1 Lanthipeptides: EES46_RS10300_lanthipeptide NZ_NNBN01000004.1 Lanthipeptides: CG717_RS12310_lanthipeptide NZ_VEHK01000004.1 Lanthipeptides: FS984_RS13530_lanthipeptide NZ_WWGD01000029.1 Lanthipeptides: GTY72_RS23245_lanthipeptide
Lanthipeptides: SGR_RS11800_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E Y S S L S V V L C T P
1
G S Q V S L L V C E Y S S L S V V L C T P
21
95.2%
NZ_BDHJ01000008.1 and 4 others:
NZ_CP032543.1 Lanthipeptides: D6270_RS22715_lanthipeptide NZ_CP076457.1 Lanthipeptides: KME66_RS09945_lanthipeptide NZ_CP077652.1 Lanthipeptides: KRR37_RS22855_lanthipeptide NZ_WUEJ01000001.1 Lanthipeptides: GRQ63_RS04560_lanthipeptide
Lanthipeptides: BHQ08_RS03045_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E Y S S L S V L C T P
1
G S Q V S L L V C E Y S S L S V T L C T P
21
95.2%
NZ_CP010519.1 and 1 other:
NZ_CP092644.1 Lanthipeptides: MID12_RS21330_lanthipeptide
Lanthipeptides: SLNWT_RS22370_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E Y S S L S V V L C+P
1
G S Q V S L L V C E Y S S L S V V L C S P
21
with 77 more sequence matches
Only the first 10 are displayed here.
95.2%
NZ_CP045178.1:
Lanthipeptides: GBW32_RS28450_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L+C E Y S S L S V V L C T P
1
G S Q V S L L I C E Y S S L S V V L C T P
21
95.2%
NZ_CP054926.1 and 11 others:
NZ_CP068598.1 Lanthipeptides: IFE09_RS23820_lanthipeptide NZ_CP071044.1 Lanthipeptides: JHY03_RS23495_lanthipeptide NZ_CP080029.1 Lanthipeptides: KZO11_RS24935_lanthipeptide NZ_JAJUKK010000008.1 Lanthipeptides: LXH09_RS27635_lanthipeptide NZ_JOJC01000009.1 Lanthipeptides: IO23_RS0108435_lanthipeptide NZ_KB891296.1 Lanthipeptides: B061_RS0103425_lanthipeptide NZ_KZ268499.1 Lanthipeptides: CE422_RS23450_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS22830_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS10975_lanthipeptide NZ_LZQS01000001.1 Lanthipeptides: STIB_RS05225_lanthipeptide NZ_RCOL01000001.1 Lanthipeptides: STAN_RS24840_lanthipeptide
Lanthipeptides: HUT09_RS23550_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E+S S L S V V L C T P
1
G S Q V S L L V C E F S S L S V V L C T P
21
95.2%
NZ_CP058556.1 and 5 others:
NZ_CP059898.1 Lanthipeptides: H3V39_RS22935_lanthipeptide NZ_CP070242.1 Lanthipeptides: I6J39_RS23755_lanthipeptide NZ_CP070260.1 Lanthipeptides: I6J40_RS10935_lanthipeptide NZ_JAJDST010000047.1 Lanthipeptides: LJC81_RS16960_lanthipeptide NZ_WWGL01000003.1 Lanthipeptides: GTY38_RS03410_lanthipeptide
Lanthipeptides: HXS80_RS11105_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S+L V C E Y S S L S V V L C T P
1
G S Q V S V L V C E Y S S L S V V L C T P
21
90.5%
NZ_CM001165.1 and 4 others:
NZ_CP021118.1 Lanthipeptides: CAC01_RS28155_lanthipeptide NZ_CP049945.1 Lanthipeptides: G9U55_RS17850_lanthipeptide NZ_CP119149.1 Lanthipeptides: P0D76_RS02270_lanthipeptide NZ_RWGV01000033.1 Lanthipeptides: EJA11_RS20985_lanthipeptide
Lanthipeptides: STTU_RS29395_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L+C E Y S S L S V L C T P
1
G S Q V S L L I C E Y S S L S V T L C T P
21
85.7%
NC_020990.1 and 26 others:
NZ_AMPN02000002.1 Lanthipeptides: SM8_RS12785_lanthipeptide NZ_AP025692.1 Lanthipeptides: MTP06_RS18190_lanthipeptide NZ_CM002273.1 Lanthipeptides: B590_RS12280_lanthipeptide NZ_CP009802.1 Lanthipeptides: SFR_RS12925_lanthipeptide NZ_CP014485.1 Lanthipeptides: Salbus254_RS12710_lanthipeptide NZ_CP016824.1 Lanthipeptides: BEN82_RS18165_lanthipeptide NZ_CP026490.1 Lanthipeptides: C3K23_RS19520_lanthipeptide NZ_CP031742.1 Lanthipeptides: D0C37_RS13445_lanthipeptide NZ_CP047147.1 Lanthipeptides: GR131_RS18520_lanthipeptide NZ_CP053539.1 Lanthipeptides: HN026_RS11800_lanthipeptide NZ_CP056773.1 Lanthipeptides: HWN34_RS12245_lanthipeptide NZ_CP063844.1 Lanthipeptides: IPZ55_RS12410_lanthipeptide NZ_CP064783.1 Lanthipeptides: IT782_RS12060_lanthipeptide NZ_CP076385.1 Lanthipeptides: KNZ81_RS12450_lanthipeptide NZ_CP079112.1 Lanthipeptides: STALF2_RS18135_lanthipeptide NZ_CP091820.1 Lanthipeptides: L2I08_RS02835_lanthipeptide NZ_CP106650.1 Lanthipeptides: B591_RS12385_lanthipeptide NZ_CP113103.1 Lanthipeptides: OSU72_RS17905_lanthipeptide NZ_JAHUVY010000001.1 Lanthipeptides: STALF3_RS17905_lanthipeptide NZ_JALLPQ010000001.1 Lanthipeptides: MWG58_RS12385_lanthipeptide NZ_KB890715.1 Lanthipeptides: B048_RS0115750_lanthipeptide NZ_KN549183.1 Lanthipeptides: D076_RS30740_lanthipeptide NZ_KZ195583.1 Lanthipeptides: B9W68_RS12440_lanthipeptide NZ_MNPQ01000004.1 Lanthipeptides: BGV78_RS11170_lanthipeptide NZ_OX371412.1 Lanthipeptides: OZE77_RS18215_lanthipeptide NZ_VOGX01000092.1 Lanthipeptides: FRZ02_RS31600_lanthipeptide
Lanthipeptides: XNR_RS11575_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q+S L L+C E Y S S L S V L C T P
1
G S Q I S L L I C E Y S S L S V T L C T P
21
85.7%
NZ_AQRJ01000051.1 and 1 other:
NZ_LFBV01000002.1 Lanthipeptides: AB852_RS09920_lanthipeptide
Lanthipeptides: YW7_RS14945_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L+V C E Y S S L S +L C T P
1
G S Q V S L I V C E Y S S L S A L L C T P
21
85.7%
NZ_CP045702.1:
Lanthipeptides: F0344_RS33200_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E+S S L S+ L C T P
1
G S Q V S L L V C E H S S L S L T L C T P
21
85.7%
NZ_ML123034.1:
Lanthipeptides: EES43_RS19795_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L+C E+S S L S V L C T P
1
G S Q V S L L I C E F S S L S V T L C T P
21
81.0%
NZ_LWLE01000019.1:
Lanthipeptides: A6A29_RS44250_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L+C E+S S L S+ L C T P
1
G S Q V S L L I C E H S S L S L T L C T P
21
61.9%
NZ_QGGR01000008.1:
Lanthipeptides: BC793_RS19230_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T
20
G S Q S L L+C S S L S V C
2
G S Q A S L L L C G D S S L S V T T C N
21

#### MIBiG 4.0 matches for PSQ21_RS24530

95.5%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E Y S S L S V V L C T P
2
G S Q V S L L V C E Y S S L S V V L C T P
22

#### 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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.25 out of 20.01
Confidence: medium
Additional weak hits (7):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.19 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.78 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.12 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.05 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.05 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.84 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
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.

PSQ21_RS24530 - Class III
  Cleavage pHMM score: 31.80
  RODEO score: 0
  Monoisotopic mass: 2075.1 Da
  Molecular weight: 2076.4 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2094.4 Da N = 1
    2112.4 Da N = 2
    2130.5 Da N = 3
    2148.5 Da N = 4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
ArgR | Regulator of arginine biosynthesis genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP117709.1 - 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: 5,600,010 - 5,621,053 nt. (total: 21,044 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
Lyases: dehydratase
PSQ21_RS25215: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthetase
PSQ21_RS25180: 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
--- | --- | --- | --- | --- | ---
BGC0000673.3 |  | 0.53 | terpene | pimara-8(14),15-diene | Aspergillus nidulans FGSC A4
BGC0000948.5 |  | 0.45 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001910.4 |  | 0.35 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000678.5 |  | 0.35 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000664.5 |  | 0.35 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000644.3 |  | 0.35 | terpene | carotenoid | Dietzia sp. CQ4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000673.3 |  | 0.53 | terpene | pimara-8(14),15-diene | Aspergillus nidulans FGSC A4
BGC0000948.5 |  | 0.45 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001910.4 |  | 0.35 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000678.5 |  | 0.35 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000664.5 |  | 0.35 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000644.3 |  | 0.35 | terpene | carotenoid | Dietzia sp. CQ4

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:
PSQ21_RS25180: PT_FPPS_like
Domain 1 (58 - 345): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.11 out of 23.79
Confidence: medium
Additional weak hits (11):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.44 out of 29.51
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.12 out of 31.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.67 out of 24.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.43 out of 35.63
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.32 out of 29.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.12 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.32 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.43 out of 35.63
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
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP117709.1 - Region 24 - 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: 5,814,826 - 5,835,803 nt. (total: 20,978 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)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: deacetylase hydrolase
PSQ21_RS26065: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

PSQ21_RS26075: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: cyclase hydratase
PSQ21_RS26055: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

PSQ21_RS26085: 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
--- | --- | --- | --- | --- | ---
BGC0002651.2 |  | 0.37 | terpene | sordaricin B | Rosellinia necatrix
BGC0000885.3 |  | 0.32 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0002196.2 |  | 0.30 | PKS | clavatol | Penicillium crustosum
BGC0000913.3 |  | 0.29 | other (other) | MK-8 | Enterobacter cloacae
BGC0002553.2 |  | 0.29 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0001866.4 |  | 0.29 | PKS | viriditoxin | Byssochlamys spectabilis
BGC0002034.3 |  | 0.28 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0000252.5 |  | 0.28 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0000518.3 |  | 0.28 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000875.4 |  | 0.28 | other (nucleoside), saccharide | caprazamycin, caprazamycin aglycon | Streptomyces sp. MK730-62F2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002651.2 |  | 0.37 | terpene | sordaricin B | Rosellinia necatrix
BGC0000885.3 |  | 0.32 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0002196.2 |  | 0.30 | PKS | clavatol | Penicillium crustosum
BGC0000913.3 |  | 0.29 | other (other) | MK-8 | Enterobacter cloacae
BGC0002553.2 |  | 0.29 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0001866.4 |  | 0.29 | PKS | viriditoxin | Byssochlamys spectabilis
BGC0002034.3 |  | 0.28 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0000252.5 |  | 0.28 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0000518.3 |  | 0.28 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000875.4 |  | 0.28 | other (nucleoside), saccharide | caprazamycin, caprazamycin aglycon | Streptomyces sp. MK730-62F2

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:
PSQ21_RS26085: T1TS
Domain 1 (1 - 305): 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 (8):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
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: 15.04 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.82 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.23 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.12 out of 30.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP117709.1 - Region 25 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,206,509 - 6,239,232 nt. (total: 32,724 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
PSQ21_RS27825: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
PSQ21_RS27780: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
PSQ21_RS27830: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.52 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002683.2 |  | 0.51 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002633.2 |  | 0.51 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0001531.5 |  | 0.50 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002469.2 |  | 0.50 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002470.2 |  | 0.50 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0001572.3 |  | 0.50 | other (other) | desferrioxamine E | Pantoea agglomerans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.52 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002683.2 |  | 0.51 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002633.2 |  | 0.51 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0001531.5 |  | 0.50 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002469.2 |  | 0.50 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002470.2 |  | 0.50 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0001572.3 |  | 0.50 | other (other) | desferrioxamine E | Pantoea agglomerans

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.17 out of 27.18
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.03 out of 27.18
Confidence: medium
Additional weak hits (8):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.39 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.25 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.65 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.61 out of 23.43
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.88 out of 24.78
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP117709.1 - Region 26 - NRPS-like,PKS-like,RiPP-like,T2PKS,arylpolyene,betalactone,hydrogen-cyanide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,399,179 - 6,491,844 nt. (total: 92,666 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)
PKS-like: (t2pks2 or ksIII)
betalactone: (HMGL-like and AMP-binding)
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))
arylpolyene: (APE_KS1 or APE_KS2)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase reductase
PSQ21_RS28450: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

PSQ21_RS28485: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

PSQ21_RS28505: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

PSQ21_RS28615: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

PSQ21_RS28650: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

PSQ21_RS28815: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

PSQ21_RS28820: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

PSQ21_RS28830: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: PPTase acylase acyltransferase aminotransferase glycosyltransferase methyltransferase transferase
PSQ21_RS28435: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

PSQ21_RS28455: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

PSQ21_RS28475: methyltransferase

smcogs
  SMCOG1248: methyltransferase

PSQ21_RS28495: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

PSQ21_RS28520: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

PSQ21_RS28525: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

PSQ21_RS28600: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

PSQ21_RS28750: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

PSQ21_RS28780: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: deaminase esterase hydrolase
PSQ21_RS28695: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

PSQ21_RS28725: thioesterase

smcogs
  SMCOG1004: thioesterase

PSQ21_RS28850: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: cyclase dehydratase
PSQ21_RS28465: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

PSQ21_RS28515: L-carnitine dehydratase/bile acid-inducible

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

PSQ21_RS28530: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

PSQ21_RS28545: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

PSQ21_RS28770: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase synthetase
PSQ21_RS28535: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

PSQ21_RS28540: 3-oxoacyl-(acyl carrier protein) synthase III

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

PSQ21_RS28555: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS28585: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

PSQ21_RS28590: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

PSQ21_RS28635: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

PSQ21_RS28670: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

PSQ21_RS28705: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

PSQ21_RS28710: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

PSQ21_RS28775: 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 | T2PKS | PKS-like | betalactone | RiPP-like | arylpolyene | NRPS-like | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000231.5 |  |  |  |  |  |  |  | 1.73 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000272.3 |  |  |  |  |  |  |  | 1.48 | PKS | spore pigment | Streptomyces collinus
BGC0000234.5 |  |  |  |  |  |  |  | 1.48 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  |  |  |  |  |  |  | 1.40 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001513.3 |  |  |  |  |  |  |  | 1.29 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000275.4 |  |  |  |  |  |  |  | 1.27 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0000271.5 |  |  |  |  |  |  |  | 1.25 | PKS | spore pigment | Streptomyces avermitilis
BGC0001197.5 |  |  |  |  |  |  |  | 1.24 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002477.3 |  |  |  |  |  |  |  | 1.18 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0001366.5 |  |  |  |  |  |  |  | 1.15 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002277.2 |  | 0.78 | NRPS | atromentin | Suillus grevillei
BGC0002274.2 |  | 0.77 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002193.2 |  | 0.76 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0000231.5 |  | 0.69 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000234.5 |  | 0.62 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000272.3 |  | 0.61 | PKS | spore pigment | Streptomyces collinus
BGC0001723.5 |  | 0.61 | PKS | oviedomycin | Streptomyces antibioticus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.71 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40
Confidence: strong
Additional weak hits (14):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.53 out of 31.73
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.89 out of 27.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.04 out of 32.74
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.20 out of 27.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.57 out of 32.93
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.60 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.93 out of 39.62
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.44 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.35 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 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
RREFinder
Type II PKS
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 36, location 6399178 - 6474740:
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

For candidate cluster 37, location 6399178 - 6471685:
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

For candidate cluster 40, location 6433600 - 6474740:
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

For candidate cluster 41, location 6448970 - 6491844:
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).
PSQ21_RS28555: NH2
CAL_domain (41..473): NH2
minowa: NH2

Prediction, score:
  NH2: 107.6
  AHBA: 25.1
  Acetyl-CoA: 9.6
  fatty_acid: 7.3
  shikimic_acid: 1.5

PSQ21_RS28600: mal
PKS_AT (23..303): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 45.8
  Propionyl-CoA: 36.6
  Methoxymalonyl-CoA: 28.7
  Methylmalonyl-CoA: 27.0
  fatty_acid: 12.3
  inactive: 11.0
  trans-1,2-CPDA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PSQ21_RS28775: X
AMP-binding (38..450): X
nrpys: Ppa

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    SAKVHVAALLELFMVSGGEWPAFGMTETCAGSVY
  Nearest Stachelhaus code(s):
    Ppa VALFVGAAGK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

RiPP-like protocluster (6425384...6437697)
PSQ21_RS28570
  RRE type: Goadsporin_CD_RRE
  Location: 18 - 115
  Score: 77.7
  RRE type: NHLP_CD_RRE
  Location: 18 - 111
  Score: 69.5
  RRE type: Cyanobactin_D_RRE
  Location: 19 - 94
  Score: 45.3

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

Cluster section:
  6399178 to 6471685
Starter unit(s):
  2-methylbutyryl-CoA (Score: 772.0; E-value: 4.63e-171)
Malonyl elongations:
  8|9 (Score: 664.7; E-value: 9.7e-203)
Product class(es):
  angucycline
  anthracycline
  aureolic acid
  tetracycline
Product molecular weight(s):
  2-methylbutyryl-CoA_8: 769 Da
  2-methylbutyryl-CoA_9: 811 Da

PSQ21_RS28455
  GT (Score: 398.7; E-value: 8.1e-122)
PSQ21_RS28495
  GT (Score: 331.5; E-value: 2.1e-101)
PSQ21_RS28505
  KR (Score: 205.9; E-value: 2e-63)
PSQ21_RS28540
  KSIII (Score: 463.6; E-value: 8.8e-142)
  KSIII AKT74268.1_Trioxacarcin_2-methylbutyryl-CoA (Score: 470.0; E-value: 4.63e-171)
PSQ21_RS28545
  CYC C7-C12 (Score: 421.6; E-value: 3.5e-129)
PSQ21_RS28585
  KS (Score: 740.1; E-value: 1.5e-225)
PSQ21_RS28590
  CLF 8|9 (Score: 664.7; E-value: 9.7e-203)
PSQ21_RS28595
  ACP (Score: 108.8; E-value: 2.4e-34)
PSQ21_RS28600
  AT (Score: 412.9; E-value: 2.2e-126)
  AT ADB23379.1_TLN-05220/TLN-05223_2-methylbutyryl-CoA (Score: 302.0; E-value: 8.87e-101)
PSQ21_RS28650
  KR (Score: 208.1; E-value: 4.3e-64)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
HypR | L-hydroxyproline utilization repressor
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP117709.1 - 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: 6,559,702 - 6,602,983 nt. (total: 43,282 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 reductase
PSQ21_RS29235: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

PSQ21_RS29265: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

PSQ21_RS29275: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: methyltransferase
PSQ21_RS29210: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase hydrolase
PSQ21_RS29205: thioesterase

smcogs
  SMCOG1004: thioesterase

PSQ21_RS29260: thioesterase

smcogs
  SMCOG1004: thioesterase

PSQ21_RS29330: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase
PSQ21_RS29250: 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
--- | --- | --- | --- | --- | ---
BGC0002340.3 |  | 0.75 | NRPS, other (other) | pyrroloformamide A, pyrroloformamide B, pyrroloformamide D, pyrroloformamide C | Streptomyces sp. CB02980
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002340.3 |  | 0.75 | NRPS, other (other) | pyrroloformamide A, pyrroloformamide B, pyrroloformamide D, pyrroloformamide C | Streptomyces sp. CB02980
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.72 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.85 out of 23.79
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 (12):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.94 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.21 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.44 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.37 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 25.75
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.76 out of 26.85
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.79 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.96 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.82 out of 24.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.87 out of 26.85
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 43, location 6559701 - 6602983:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Cys)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
PSQ21_RS29250: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (503..903): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDIAFDLSVYDGNSLLSGDISLGGATEGSIWSIH
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

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

NZ_CP117709.1 - 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: 6,656,170 - 6,667,507 nt. (total: 11,338 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
PSQ21_RS29535: dehydrogenase

smcogs
  SMCOG1222: 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
--- | --- | --- | --- | --- | ---
BGC0002298.2 |  | 0.34 | ribosomal | lassomycin-like peptide | Sanguibacter keddieii DSM 10542
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000351.5 |  | 0.32 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155
BGC0000306.5 |  | 0.31 | NRPS | arylomycin | Streptomyces filamentosus NRRL 11379
BGC0002579.2 |  | 0.31 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum
BGC0002303.3 |  | 0.30 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002788.2 |  | 0.30 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0002387.2 |  | 0.30 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0002490.2 |  | 0.30 | other (other) | yersinopine | Yersinia pestis CO92
BGC0000461.5 |  | 0.30 | NRPS | WAP-8294A2 | Lysobacter enzymogenes

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002298.2 |  | 0.34 | ribosomal | lassomycin-like peptide | Sanguibacter keddieii DSM 10542
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000351.5 |  | 0.32 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155
BGC0000306.5 |  | 0.31 | NRPS | arylomycin | Streptomyces filamentosus NRRL 11379
BGC0002579.2 |  | 0.31 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum
BGC0002303.3 |  | 0.30 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002788.2 |  | 0.30 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0002387.2 |  | 0.30 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0002490.2 |  | 0.30 | other (other) | yersinopine | Yersinia pestis CO92
BGC0000461.5 |  | 0.30 | NRPS | WAP-8294A2 | Lysobacter enzymogenes

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: 20.91 out of 26.85
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
Additional weak hits (1):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.00 out of 20.97
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP117709.1 - Region 29 - NRPS,NRPS-like,T3PKS,ectoine,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: 6,872,403 - 7,006,263 nt. (total: 133,861 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
ectoine: ectoine_synt
phenazine: phzB

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS 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
PSQ21_RS30475: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

PSQ21_RS30530: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

PSQ21_RS30705: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

PSQ21_RS30770: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: aminotransferase
PSQ21_RS30610: aminotransferase

smcogs
  SMCOG1019: aminotransferase

PSQ21_RS30760: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: amidase deaminase esterase hydrolase peptidase
PSQ21_RS30455: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

PSQ21_RS30550: thioesterase

smcogs
  SMCOG1004: thioesterase

PSQ21_RS30555: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

PSQ21_RS30580: thioesterase

smcogs
  SMCOG1004: thioesterase

PSQ21_RS30635: isochorismatase

smcogs
  SMCOG1027: isochorismatase

PSQ21_RS30660: thioesterase

smcogs
  SMCOG1004: thioesterase

PSQ21_RS30725: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

PSQ21_RS30730: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

PSQ21_RS30740: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

PSQ21_RS30795: isochorismatase

smcogs
  SMCOG1027: isochorismatase

PSQ21_RS30885: amidase

smcogs
  SMCOG1105: amidase

Lyases: hydratase lyase
PSQ21_RS30535: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

PSQ21_RS30590: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

PSQ21_RS30605: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

PSQ21_RS30755: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Isomerases: isomerase
PSQ21_RS30800: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
PSQ21_RS30540: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS30570: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

PSQ21_RS30585: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

PSQ21_RS30595: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

PSQ21_RS30650: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS30655: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS30670: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

PSQ21_RS30675: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS30680: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

PSQ21_RS30695: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS30860: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

Translocases: transport
PSQ21_RS30870: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | NRPS-like | NRPS | NRPS-like | T3PKS | NRPS | ectoine | phenazine | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  |  |  |  |  |  |  | 2.11 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002075.3 |  |  |  |  |  |  |  |  | 2.08 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  |  |  |  |  |  |  |  | 2.00 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  |  |  |  |  |  | 1.99 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  |  |  |  |  | 1.97 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  |  |  |  |  |  | 1.90 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  |  |  |  |  |  |  | 1.86 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  |  |  |  |  |  |  |  | 1.84 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  |  |  |  |  |  |  | 1.80 | NRPS | AM-toxin | Alternaria alternata
BGC0001758.4 |  |  |  |  |  |  |  |  | 1.80 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002561.3 |  | 0.82 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.76 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.41 out of 20.97
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.76 out of 23.79
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.50 out of 28.19
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.75 out of 23.05
Confidence: medium
Additional weak hits (29):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.42 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.07 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.97 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.24 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.08 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.33 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.29 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.55 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.44 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.26 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.19 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.64 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.37 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.15 out of 26.06
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.41 out of 24.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.79 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.22 out of 35.63
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.27 out of 36.53
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.38 out of 25.75
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.96 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.06 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.04 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.86 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.96 out of 23.43
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.91 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
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 45, location 6872402 - 7006263:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr) + (Thr) + (X - X) + (Thr) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 46, location 6872402 - 6915123:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 47, location 6881081 - 6925026:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 48, location 6887212 - 6929768:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr) + (Thr) + (X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 49, location 6892296 - 6933403:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr) + (Thr) + (X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 50, location 6906199 - 6965501:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X) + (Thr) + (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).
PSQ21_RS30540: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (326..722): 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:
    LATHFDFSVWEGNQILGGEVNMFGITETTVHVTA
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

PSQ21_RS30570: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (465..878): 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:
    IATHFDMSVWEGCQVFGGEVNMYGITETTIHATY
  Nearest Stachelhaus code(s):
    Thr DFWSVGMIHK (76% 8Å match)
  Stachelhaus code match:
    80% (moderate)

PSQ21_RS30580: Dhpg
Search NORINE for peptide: strict or relaxed
AMP-binding (266..657): Dhpg
nrpys: Dhpg

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:
    LAMAFDGSVLDVSVVLGAEWNTYGPTEATVITTA
  Nearest Stachelhaus code(s):
    Dhpg DALSVGTVIK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

PSQ21_RS30650: X
AMP-binding (380..781): 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:
    LTVAFDMSVWDMTLITGGEHNSYGPTETTVVSTL
  Nearest Stachelhaus code(s):
    His DTWTIASVDK (76% 8Å match)
    Lys DTEDIGSVVK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

PSQ21_RS30655: X - X
AMP-binding (39..357): X
No predictions made
AMP-binding (938..1326): 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:
    TALSEQTFVTEGRLLTGADLSGYGPAENTGLTTC
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

PSQ21_RS30670: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (471..884): 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:
    LATHFDMAVWEGCQVFGGEVNMYGITETTIHTTY
  Nearest Stachelhaus code(s):
    Thr DFWSVGMIHK (76% 8Å match)
  Stachelhaus code match:
    80% (moderate)

PSQ21_RS30675: X
AMP-binding (553..937): 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:
    LWYSFDTSAFEFNLAQGGEDNYYGPTETHLAIAH
  Nearest Stachelhaus code(s):
    bLys DTENVGTLVK (47% 8Å match)
    Dhpg DAYNAGTLCK (44% 8Å match)
  Stachelhaus code match:
    60% (weak)

PSQ21_RS30695: X
AMP-binding (33..423): 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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    SARAIDAAAAGFDGITGGEHNEYGPTESTVWATT
  Nearest Stachelhaus code(s):
    Trp DAAIIGEVWK (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
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A
IolR | Regulator of the inositol catabolism
ZuR variant 1 | Zinc-responsive repressor

NZ_CP117709.1 - Region 30 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,266,776 - 7,293,348 nt. (total: 26,573 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
PSQ21_RS32065: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

PSQ21_RS32100: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: aminotransferase transferase
PSQ21_RS32060: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

PSQ21_RS32125: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: dehydratase
PSQ21_RS32050: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthetase
PSQ21_RS32105: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.69 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002508.2 |  | 0.48 | other (other) | 8-azaguanine | Streptomyces pathocidini
BGC0000644.3 |  | 0.47 | terpene | carotenoid | Dietzia sp. CQ4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.69 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002508.2 |  | 0.48 | other (other) | 8-azaguanine | Streptomyces pathocidini
BGC0000644.3 |  | 0.47 | terpene | carotenoid | Dietzia sp. CQ4

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
--- | --- | --- | --- | --- | ---
triterpene | hopanoid |  | C30 | hopanoid skeleton | unknown
triterpene | polypodane |  | C30 | polypodane skeleton | unknown

Genes with terpene domains:
PSQ21_RS32090: PT_phytoene_like
Domain 1 (16 - 277): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

PSQ21_RS32095: PT_phytoene_like
Domain 1 (13 - 296): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

PSQ21_RS32105: PT_FPPS_like
Domain 1 (74 - 363): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

PSQ21_RS32110: T2TS
Domain 1 (25 - 652): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.09 out of 23.79
Confidence: medium
Additional weak hits (10):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.59 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.72 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.37 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.04 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.12 out of 26.06
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.38 out of 26.85
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.27 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.72 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.67 out of 22.40
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator

NZ_CP117709.1 - Region 31 - 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: 7,392,445 - 7,441,936 nt. (total: 49,492 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 oxygenase
PSQ21_RS32580: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

PSQ21_RS32590: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

PSQ21_RS32635: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

PSQ21_RS32640: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

PSQ21_RS32645: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

PSQ21_RS32650: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

PSQ21_RS32670: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

PSQ21_RS32680: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
PSQ21_RS32625: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Hydrolases: hydrolase
PSQ21_RS32665: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: dehydratase
PSQ21_RS32675: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
PSQ21_RS32630: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: transport
PSQ21_RS32600: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001043.4 |  |  | 1.03 | NRPS, PKS | SGR PTMs, SGR PTM Compound b, SGR PTM Compound c, SGR PTM Compound d | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002365.2 |  |  | 0.95 | PKS, other (other) | 10-epi-HSAF, 10-epi-3-deOH-HSAF, 10-epi-maltophilin, 10-epi-xanthobaccin C, 10-epi-hydroxymaltophilin, 10-epi-FI-2 | Streptomyces sp.
BGC0001273.3 |  |  | 0.94 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.93 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.92 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000996.5 |  |  | 0.78 | NRPS, PKS | frontalamide B, frontalamide A | Streptomyces sp. SPB78
BGC0001276.3 |  |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001641.4 |  |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.62 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  |  | 0.62 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001043.4 |  | 0.79 | NRPS, PKS | SGR PTMs, SGR PTM Compound b, SGR PTM Compound c, SGR PTM Compound d | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002365.2 |  | 0.77 | PKS, other (other) | 10-epi-HSAF, 10-epi-3-deOH-HSAF, 10-epi-maltophilin, 10-epi-xanthobaccin C, 10-epi-hydroxymaltophilin, 10-epi-FI-2 | Streptomyces sp.
BGC0001273.3 |  | 0.77 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000996.5 |  | 0.71 | NRPS, PKS | frontalamide B, frontalamide A | Streptomyces sp. SPB78
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.65 | 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:
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 28.35 out of 35.63
Confidence: medium
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 26.77 out of 35.63
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47
Confidence: medium
Additional weak hits (10):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.01 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.51 out of 30.22
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.32 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.25 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.46 out of 32.74
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.33 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.19 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.40 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.69 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 55, location 7392444 - 7441936:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk - Orn)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
PSQ21_RS32630: pk - Orn
Search NORINE for peptide: strict or relaxed
PKS_AT (551..847): pk
ATSignature: Malonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 130.0
  Malonyl-CoA: 126.6
  Methoxymalonyl-CoA: 125.4
  Ethylmalonyl-CoA: 101.4
  Isobutyryl-CoA: 94.8
  2-Methylbutyryl-CoA: 81.0
  Propionyl-CoA: 77.8
  Acetyl-CoA: 71.5
  trans-1,2-CPDA: 67.7
  Benzoyl-CoA: 60.7
  CHC-CoA: 47.4
  3-Methylbutyryl-CoA: 42.1
  fatty_acid: 39.4
  inactive: 37.1

AMP-binding (2338..2750): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAWAFDVFTGDREFVVGSDVNSYGLTEATIDSAY
  Nearest Stachelhaus code(s):
    Orn DVGEVGSIDK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
NrtR | NAD synthesis repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP117709.1 - Region 32 - 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: 7,548,920 - 7,559,717 nt. (total: 10,798 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
Lyases: decarboxylase
PSQ21_RS33315: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001778.5 |  | 0.34 | other (other) | showdomycin | Streptomyces showdoensis
BGC0001891.3 |  | 0.32 | other (other) | closthioamide | Ruminiclostridium cellulolyticum H10
BGC0001575.4 |  | 0.30 | NRPS | PZN5, PZN6, PZN7, PZN9, PZN10, PZN11 | Ruminococcus sp. 5_1_39BFAA
BGC0000975.5 |  | 0.27 | NRPS, PKS | Cryptophycin A | Nostoc sp. ATCC 53789
BGC0001882.3 |  | 0.27 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0001707.5 |  | 0.25 | ribosomal | nosiheptide | Streptomyces sp.
BGC0002718.2 |  | 0.23 | NRPS | madurastatin A2, madurastatin E1, madurastatin F, madurastatin G1, madurastatin A1 | Actinomadura sp. RB99
BGC0002409.3 |  | 0.23 | NRPS | frankobactin A1, frankobactin A2, frankobactin A3, frankobactin B1, frankobactin B2, frankobactin B3, frankobactin C1 | Frankia sp. CH37
BGC0000159.5 |  | 0.22 | PKS | tautomycin | Streptomyces spiroverticillatus
BGC0000291.5 |  | 0.21 | NRPS | A54145 | Streptomyces fradiae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001778.5 |  | 0.34 | other (other) | showdomycin | Streptomyces showdoensis
BGC0001891.3 |  | 0.32 | other (other) | closthioamide | Ruminiclostridium cellulolyticum H10
BGC0001575.4 |  | 0.30 | NRPS | PZN5, PZN6, PZN7, PZN9, PZN10, PZN11 | Ruminococcus sp. 5_1_39BFAA
BGC0000975.5 |  | 0.27 | NRPS, PKS | Cryptophycin A | Nostoc sp. ATCC 53789
BGC0001882.3 |  | 0.27 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0001707.5 |  | 0.25 | ribosomal | nosiheptide | Streptomyces sp.
BGC0002718.2 |  | 0.23 | NRPS | madurastatin A2, madurastatin E1, madurastatin F, madurastatin G1, madurastatin A1 | Actinomadura sp. RB99
BGC0002409.3 |  | 0.23 | NRPS | frankobactin A1, frankobactin A2, frankobactin A3, frankobactin B1, frankobactin B2, frankobactin B3, frankobactin C1 | Frankia sp. CH37
BGC0000159.5 |  | 0.22 | PKS | tautomycin | Streptomyces spiroverticillatus
BGC0000291.5 |  | 0.21 | NRPS | A54145 | Streptomyces fradiae

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

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 (4):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.33 out of 20.01
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.83 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.67 out of 20.01
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP117709.1 - Region 33 - NI-siderophore,NRPS-like,T1PKS,betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,659,821 - 7,739,434 nt. (total: 79,614 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))
NI-siderophore: IucA_IucC
betalactone: (HMGL-like and AMP-binding)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: electron transfer oxidase oxidoreductase oxygenase
PSQ21_RS33980: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

PSQ21_RS34000: flavodoxin

smcogs
  SMCOG1134: flavodoxin

PSQ21_RS34005: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

PSQ21_RS34025: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

PSQ21_RS34095: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: PPTase aminotransferase halogenase
PSQ21_RS33850: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

PSQ21_RS34020: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

PSQ21_RS34035: flavin-dependent trp 6 7 halogenase

halogenases
  flavin-dependent trp 6 7 halogenase
MITE
  MITE0000029Halogenation (identity: 66.70%)
smcogs
  SMCOG1119: halogenase

PSQ21_RS34080: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Hydrolases: deaminase hydrolase
PSQ21_RS33925: HAD-superfamily hydrolase, subfamily IA, variant

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

PSQ21_RS34040: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

PSQ21_RS34150: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Ligases: ligase synthase
PSQ21_RS33935: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

PSQ21_RS33945: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS33950: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

PSQ21_RS34015: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS34060: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS34090: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

PSQ21_RS34105: 3-oxoacyl-(acyl carrier protein) synthase III

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

PSQ21_RS34130: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

PSQ21_RS34140: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate 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 | NI-siderophore | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001478.5 |  |  |  |  | 1.32 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  |  |  |  | 1.17 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  |  |  |  | 1.10 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001164.3 |  |  |  |  | 1.00 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  |  | 1.00 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000940.5 |  |  |  |  | 1.00 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  |  |  |  | 1.00 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001273.3 |  |  |  |  | 0.96 | PKS | asperlactone | Aspergillus ochraceus
BGC0001572.3 |  |  |  |  | 0.90 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002191.2 |  |  |  |  | 0.87 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.75 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.71 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.69 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000940.5 |  | 0.68 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.68 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001273.3 |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0001572.3 |  | 0.64 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002464.3 |  | 0.63 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.27 out of 26.85
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.31 out of 23.43
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.88 out of 26.85
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.55 out of 26.85
Confidence: medium
Additional weak hits (17):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 21.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.34 out of 32.74
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.42 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.58 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.14 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.40 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.51 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.12 out of 30.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.92 out of 20.01
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.22 out of 32.93
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.65 out of 23.43
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: 17.85 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 57, location 7659820 - 7709672:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 58, location 7659820 - 7706218:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (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).
PSQ21_RS33945: X
AMP-binding (49..411): 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:
    VGLHFGYSMCEGCLLLSGEVNTYAATETAGQITA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

PSQ21_RS33950: mal
PKS_AT (511..788): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 33.3
  Methoxymalonyl-CoA: 16.3
  Propionyl-CoA: 13.1
  Methylmalonyl-CoA: 12.9
  inactive: 12.8
  Isobutyryl-CoA: 9.0
  Ethylmalonyl-CoA: 8.8
  2-Methylbutyryl-CoA: 8.2
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PSQ21_RS34015: X
AMP-binding (7..399): 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:
    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:
    MSWNH-GSITAHWMMFGASRNIYGMTEAGTFCTW
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

PSQ21_RS34060: NH2
CAL_domain (155..460): NH2
minowa: NH2

Prediction, score:
  NH2: 30.4
  Acetyl-CoA: 18.8
  fatty_acid: 10.0
  shikimic_acid: 0.0
  AHBA: 0.0

PSQ21_RS34090: X
AMP-binding (18..425): 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:
    LHLVHARMWPLIEAINTFDIQGYGQSETGPICLR
  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
--- | ---
BldD | Development and antibiotic global regulator
CRP | Cyclic AMP receptor protein
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP117709.1 - Region 34 - 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: 7,747,839 - 7,759,206 nt. (total: 11,368 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
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.75 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.42 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001639.3 |  | 0.41 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0001579.4 |  | 0.40 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000616.4 |  | 0.39 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000571.3 |  | 0.37 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001863.4 |  | 0.35 | ribosomal, terpene | bacillicn CER074 | Bacillus mycoides
BGC0002289.2 |  | 0.35 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.75 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.42 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001639.3 |  | 0.41 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0001579.4 |  | 0.40 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000616.4 |  | 0.39 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000571.3 |  | 0.37 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001863.4 |  | 0.35 | ribosomal, terpene | bacillicn CER074 | Bacillus mycoides
BGC0002289.2 |  | 0.35 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii

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
Additional weak hits (2):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 19.69 out of 32.74
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.28 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator

NZ_CP117709.1 - Region 35 - melanin
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,759,924 - 7,770,409 nt. (total: 10,486 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
PSQ21_RS34290: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: glycosyltransferase
PSQ21_RS34320: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

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

Reference | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000911.3 |  | 0.86 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.79 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.64 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.48 | other (other) | melanin | Streptomyces avermitilis
BGC0000902.4 |  | 0.41 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0002031.3 |  | 0.41 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000662.5 |  | 0.37 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.37 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.36 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000911.3 |  | 0.86 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.79 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.64 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.48 | other (other) | melanin | Streptomyces avermitilis
BGC0000902.4 |  | 0.41 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0002031.3 |  | 0.41 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000662.5 |  | 0.37 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.37 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.36 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
Additional weak hits (3):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.10 out of 26.85
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.50 out of 35.63
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.61 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP117709.1 - Region 36 - 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: 7,772,413 - 7,793,462 nt. (total: 21,050 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: oxidoreductase oxygenase
PSQ21_RS34355: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

PSQ21_RS34425: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: glycosyltransferase
PSQ21_RS34340: sugar transferase

smcogs
  SMCOG1146: sugar transferase

PSQ21_RS34345: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: hydrolase
PSQ21_RS34375: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Ligases: synthetase
PSQ21_RS34380: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.49 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000742.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000743.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000868.5 |  | 0.45 | other (other) | teichuronic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0000800.5 |  | 0.45 | saccharide | xanthan | Xanthomonas campestris
BGC0002403.2 |  | 0.45 | PKS | β-Diketones | Hordeum vulgare subsp. vulgare
BGC0000741.3 |  | 0.43 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000744.3 |  | 0.43 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000745.3 |  | 0.43 | saccharide | capsular polysaccharide | Streptococcus agalactiae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.49 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000742.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000743.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000868.5 |  | 0.45 | other (other) | teichuronic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0000800.5 |  | 0.45 | saccharide | xanthan | Xanthomonas campestris
BGC0002403.2 |  | 0.45 | PKS | β-Diketones | Hordeum vulgare subsp. vulgare
BGC0000741.3 |  | 0.43 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000744.3 |  | 0.43 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000745.3 |  | 0.43 | saccharide | capsular polysaccharide | Streptococcus agalactiae

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:
PSQ21_RS34380: PT_FPPS_like
Domain 1 (58 - 341): 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
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.14 out of 27.18
Confidence: medium
Additional weak hits (7):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.01 out of 26.85
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.20 out of 21.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.81 out of 30.98
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.44 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NrdR | Represses ribonucleotide reductase encoding genes
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP117709.1 - Region 37 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,803,570 - 7,844,622 nt. (total: 41,053 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
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
PSQ21_RS34595: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

PSQ21_RS34670: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: methyltransferase
PSQ21_RS34590: Methylation

MITE
  MITE0000155Methylation (identity: 91.00%)
smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Ligases: ligase synthase
PSQ21_RS34585: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

PSQ21_RS34635: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

Translocases: transporter
PSQ21_RS34685: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.89 | 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
BGC0001831.3 |  | 0.53 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001077.4 |  | 0.48 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431
BGC0001647.3 |  | 0.45 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0002358.3 |  | 0.42 | PKS | cyclofaulknamycin | Streptomyces albidoflavus
BGC0001366.5 |  | 0.41 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2
BGC0001453.5 |  | 0.41 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002305.2 |  | 0.41 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001553.5 |  | 0.40 | NRPS, PKS | clifednamide A | Streptomyces sp. JV178
BGC0001336.5 |  | 0.40 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.89 | 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
BGC0001831.3 |  | 0.53 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001077.4 |  | 0.48 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431
BGC0001647.3 |  | 0.45 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0002358.3 |  | 0.42 | PKS | cyclofaulknamycin | Streptomyces albidoflavus
BGC0001366.5 |  | 0.41 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2
BGC0001453.5 |  | 0.41 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002305.2 |  | 0.41 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001553.5 |  | 0.40 | NRPS, PKS | clifednamide A | Streptomyces sp. JV178
BGC0001336.5 |  | 0.40 | 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.
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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.64 out of 26.33
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.80 out of 29.51
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.20 out of 23.79
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.19 out of 36.53
Confidence: medium
Additional weak hits (5):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.19 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.81 out of 18.57
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.70 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 36.53
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
DmdR1 | Iron(II)-dependent repressor
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism

NZ_CP117709.1 - Region 38 - 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: 7,897,547 - 7,950,191 nt. (total: 52,645 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
PSQ21_RS35015: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

PSQ21_RS35125: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acetyltransferase acylase methyltransferase
PSQ21_RS34990: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

PSQ21_RS35055: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

PSQ21_RS35150: methyltransferase

smcogs
  SMCOG1248: methyltransferase

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

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000307.4 |  |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.58 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
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
BGC0002631.2 |  |  | 0.41 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000842.5 |  |  | 0.33 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0001364.3 |  |  | 0.31 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002000.4 |  |  | 0.31 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0002103.2 |  |  | 0.30 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
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
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000842.5 |  | 0.48 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0001364.3 |  | 0.46 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002000.4 |  | 0.46 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0002103.2 |  | 0.45 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.48 out of 25.88
Confidence: medium
Additional weak hits (10):
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.15 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.39 out of 23.43
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.68 out of 29.38
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.85 out of 20.01
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.14 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.28 out of 29.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.31 out of 30.22
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.10 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 65, location 7897546 - 7950191:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - ohmal - 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).
PSQ21_RS35055: fatty_acid - mal - X
CAL_domain (139..455): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 36.2
  NH2: 36.1
  shikimic_acid: 0.0
  Acetyl-CoA: 0.0
  AHBA: 0.0

PKS_AT (1229..1511): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 62.5%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 114.4
  Methylmalonyl-CoA: 75.1
  Methoxymalonyl-CoA: 71.2
  inactive: 41.3
  Ethylmalonyl-CoA: 38.0
  fatty_acid: 30.1
  Propionyl-CoA: 29.7
  2-Methylbutyryl-CoA: 22.9
  trans-1,2-CPDA: 20.6
  Isobutyryl-CoA: 19.7
  CHC-CoA: 16.3
  Benzoyl-CoA: 7.7
  Acetyl-CoA: 6.7
  3-Methylbutyryl-CoA: 0.0

AMP-binding (2696..3119): 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:
    YWAAFDASVRQASSHVGGEANLYGPTEATINTSC
  Nearest Stachelhaus code(s):
    Gln DACSTGVINK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
PsrA | Oleic acid responsive regulator

NZ_CP117709.1 - Region 39 - 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: 7,984,328 - 8,003,288 nt. (total: 18,961 nt) Show pHMM detection rules used
Region on contig edge.
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
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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000606.5 |  | 0.54 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0002311.3 |  | 0.51 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001146.5 |  | 0.50 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001145.5 |  | 0.47 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001174.4 |  | 0.47 | ribosomal | corynazolicin | Corynebacterium urealyticum DSM 7111
BGC0000603.5 |  | 0.47 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001640.3 |  | 0.45 | ribosomal | kocurin | Kocuria rosea
BGC0001173.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0000569.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001860.4 |  | 0.41 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000606.5 |  | 0.54 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0002311.3 |  | 0.51 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001146.5 |  | 0.50 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001145.5 |  | 0.47 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001174.4 |  | 0.47 | ribosomal | corynazolicin | Corynebacterium urealyticum DSM 7111
BGC0000603.5 |  | 0.47 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001640.3 |  | 0.45 | ribosomal | kocurin | Kocuria rosea
BGC0001173.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0000569.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001860.4 |  | 0.41 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833

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
Additional weak hits (3):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.47 out of 23.43
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.32 out of 30.22
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.
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (7984327...8003288)
PSQ21_RS35355
  RRE type: Thiopeptide_F_RRE
  Location: 28 - 109
  Score: 35.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator

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_CP117710.1 - Region 1 - 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: 143,551 - 166,691 nt. (total: 23,141 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
Lyases: dehydratase
PSQ21_RS36090: 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 | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.70 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001727.3 |  | 0.34 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000529.5 |  | 0.28 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000197.5 |  | 0.27 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0001755.5 |  | 0.27 | PKS | reedsmycin A, reedsmycin B, reedsmycin C, reedsmycin D, reedsmycin E | Streptomyces sp.
BGC0002064.2 |  | 0.26 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0001647.3 |  | 0.26 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0000495.5 |  | 0.26 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0000204.5 |  | 0.24 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.70 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001727.3 |  | 0.34 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000541.5 |  | 0.33 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000529.5 |  | 0.28 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000197.5 |  | 0.27 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0001755.5 |  | 0.27 | PKS | reedsmycin A, reedsmycin B, reedsmycin C, reedsmycin D, reedsmycin E | Streptomyces sp.
BGC0002064.2 |  | 0.26 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0001647.3 |  | 0.26 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0000495.5 |  | 0.26 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0000204.5 |  | 0.24 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200

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: 17.92 out of 20.47
Confidence: medium
Additional weak hits (2):
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.28 out of 30.98
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.41 out of 29.25
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (143550...166691)
PSQ21_RS36090
  RRE type: Lanthipeptide_LanB_RRE
  Location: 157 - 249
  Score: 28.8

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP117710.1 - Region 2 - nucleoside
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 211,788 - 232,708 nt. (total: 20,921 nt) Show pHMM detection rules used
nucleoside: (LipM or LipV or LipU or TunD or pur6 or pur10 or nikJ or nikO or truD)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
PSQ21_RS36380: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

PSQ21_RS36400: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

Lyases: dehydratase
PSQ21_RS36385: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

PSQ21_RS36420: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
PSQ21_RS36395: 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 | nucleoside | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.45 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000880.4 |  | 0.44 | other (nucleoside) | tunicamycin B1 | Streptomyces chartreusis NRRL 3882
BGC0001458.4 |  | 0.44 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0002553.2 |  | 0.40 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0001168.5 |  | 0.39 | NRPS | Livipeptin | Streptomyces lividans 1326
BGC0001903.3 |  | 0.39 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0000871.4 |  | 0.38 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
BGC0001627.4 |  | 0.36 | NRPS | isonitrile lipopeptides | Mycobacterium tuberculosis H37Rv
BGC0001895.4 |  | 0.36 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0000791.3 |  | 0.35 | saccharide | O-antigen | Cronobacter sakazakii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.45 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000880.4 |  | 0.44 | other (nucleoside) | tunicamycin B1 | Streptomyces chartreusis NRRL 3882
BGC0001458.4 |  | 0.44 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0002553.2 |  | 0.40 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0001168.5 |  | 0.39 | NRPS | Livipeptin | Streptomyces lividans 1326
BGC0001903.3 |  | 0.39 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0000871.4 |  | 0.38 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
BGC0001627.4 |  | 0.36 | NRPS | isonitrile lipopeptides | Mycobacterium tuberculosis H37Rv
BGC0001895.4 |  | 0.36 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0000791.3 |  | 0.35 | saccharide | O-antigen | Cronobacter sakazakii

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP117713.1 - Region 1 - RRE-containing
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,333 - 14,055 nt. (total: 11,723 nt) Show pHMM detection rules used
Region on contig edge.
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

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

Reference | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000606.5 |  | 0.36 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0002675.2 |  | 0.27 | PKS | prodigiosin | Pseudoalteromonas rubra
BGC0001791.4 |  | 0.27 | NRPS | sunshinamide | Gynuella sunshinyii YC6258
BGC0000258.3 |  | 0.26 | PKS | prodigiosin | Serratia sp.
BGC0002386.2 |  | 0.25 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0000260.3 |  | 0.24 | PKS | prodigiosin | Hahella chejuensis KCTC 2396
BGC0000969.5 |  | 0.24 | NRPS, PKS | chondramide A | Chondromyces crocatus
BGC0001186.4 |  | 0.22 | PKS | misakinolide A | Candidatus Entotheonella serta
BGC0001212.4 |  | 0.22 | NRPS, PKS | nannocystin a | Nannocystis sp. MB1016
BGC0001110.5 |  | 0.22 | NRPS, PKS | psymberin, irciniastatin B | uncultured bacterium psy1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000606.5 |  | 0.36 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0002675.2 |  | 0.27 | PKS | prodigiosin | Pseudoalteromonas rubra
BGC0001791.4 |  | 0.27 | NRPS | sunshinamide | Gynuella sunshinyii YC6258
BGC0000258.3 |  | 0.26 | PKS | prodigiosin | Serratia sp.
BGC0002386.2 |  | 0.25 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0000260.3 |  | 0.24 | PKS | prodigiosin | Hahella chejuensis KCTC 2396
BGC0000969.5 |  | 0.24 | NRPS, PKS | chondramide A | Chondromyces crocatus
BGC0001186.4 |  | 0.22 | PKS | misakinolide A | Candidatus Entotheonella serta
BGC0001212.4 |  | 0.22 | NRPS, PKS | nannocystin a | Nannocystis sp. MB1016
BGC0001110.5 |  | 0.22 | NRPS, PKS | psymberin, irciniastatin B | uncultured bacterium psy1

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: 19.46 out of 20.47
Confidence: strong
Additional weak hits (4):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.82 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.00 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.60 out of 29.65
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.54 out of 28.14
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (2332...14055)
PSQ21_RS37790
  RRE type: Thiopeptide_F_RRE
  Location: 28 - 109
  Score: 35.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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