Select genomic region:
Overview
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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

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

NZ_CP017717.1 ([Actinomadura] parvosata subsp. kistnae)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | terpene | 31,921 | 52,841 |
Region 2 | terpene,lanthipeptide-class-iii | 611,191 | 655,445 | Low | SAL-2242 | ribosomal:RiPP:Lanthipeptide
Region 3 | NAPAA | 688,007 | 721,837 | High | ε-Poly-L-lysine | NRPS:Type I
Region 4 | betalactone | 895,664 | 928,476 |  |
Region 5 | hydrogen-cyanide | 1,233,727 | 1,246,943 | Low | aborycin | ribosomal:RiPP
Region 6 | lassopeptide | 1,331,416 | 1,353,851 |
Region 7 | RRE-containing,azole-containing-RiPP | 1,817,713 | 1,849,326 |
Region 8 | proteusin,RiPP-like | 2,079,093 | 2,100,550 |
Region 9 | RRE-containing | 2,100,708 | 2,121,865 |  |
Region 10 | terpene | 2,390,421 | 2,411,563 | High | 2-methylisoborneol | terpene:Monoterpene
Region 11 | NRPS-like,NRP-metallophore,NRPS | 2,413,820 | 2,488,778 | Medium | coelichelin | NRPS:Type I
Region 12 | NRPS-like,lassopeptide,PKS-like,T1PKS | 2,521,005 | 2,607,980 | High | citrulassin E | ribosomal:RiPP
Region 13 | lassopeptide | 3,001,811 | 3,024,306 |
Region 14 | RiPP-like,RRE-containing | 3,167,162 | 3,193,571 |
Region 15 | lassopeptide | 3,504,849 | 3,527,401 |
Region 16 | hglE-KS | 4,171,747 | 4,213,108 |  |
Region 17 | terpene-precursor | 4,271,531 | 4,292,565 |  |
Region 18 | NRPS,T1PKS,phenazine,RiPP-like,PKS-like | 4,324,333 | 4,457,338 | Medium | phenazine SA/phenazine SB/phenazine SC | other:other
Region 19 | T1PKS,PKS-like | 4,821,966 | 4,868,135 |  |
Region 20 | CDPS | 4,947,263 | 4,968,063 |  |
Region 21 | T2PKS | 5,044,303 | 5,124,407 | Low | xantholipin | PKS
Region 22 | t3nrps-iterative | 5,727,621 | 5,770,669 |
Region 23 | NRPS | 5,961,208 | 6,017,646 | Low | salinamide A/salinamide B/salinamide C/salinamide D/salinamide E/salinamide F/desmethylsalinamide C/desmethylsalinamide E | NRPS:Type I+PKS:Type I
Region 24 | terpene-precursor | 6,379,937 | 6,401,004 | Low | pentamycin/filipin | PKS:Modular type I
Region 25 | terpene | 6,533,252 | 6,554,253 |  |
Region 26 | azole-containing-RiPP | 7,666,018 | 7,693,782 |
Region 27 | terpene | 8,110,733 | 8,131,839 | High | geosmin | terpene:Sesquiterpene
Region 28 | NRPS,arylpolyene,T1PKS | 10,086,900 | 10,191,750 | Low | kitacinnamycin A/kitacinnamycin B/kitacinnamycin C/kitacinnamycin D/kitacinnamycin E/kitacinnamycin F | NRPS:Type I
Region 29 | terpene | 10,468,179 | 10,493,960 |  |
Region 30 | NI-siderophore | 10,508,102 | 10,539,346 |  |
Region 31 | T1PKS | 10,881,004 | 10,926,625 |  |
Region 32 | RiPP-like | 11,337,351 | 11,348,166 |
Region 33 | NI-siderophore | 11,540,697 | 11,571,791 |  |
Region 34 | NRPS,T3PKS | 11,969,038 | 12,040,280 | High | kistamicin A | NRPS:Type I+PKS
Region 35 | NRPS | 12,340,018 | 12,393,654 |  |
Region 36 | T3PKS | 12,785,949 | 12,827,004 | Low | lagunapyrone A/lagunapyrone B/lagunapyrone C | PKS

NZ_CP017717.1 - Region 1 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 31,921 - 52,841 nt. (total: 20,921 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
BKM31_RS00185: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

BKM31_RS00215: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: kinase
BKM31_RS00225: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Lyases: cyclase
BKM31_RS00200: 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
--- | --- | --- | --- | --- | ---
BGC0001642.3 |  | 0.74 | terpene | koraiol | Fusarium fujikuroi IMI 58289
BGC0001746.3 |  | 0.74 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0001201.3 |  | 0.51 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0001294.5 |  | 0.40 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0000821.5 |  | 0.34 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0002387.2 |  | 0.33 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0002545.3 |  | 0.30 | PKS | sungeidine C, sungeidine B, sungeidine D, sungeidine H, sungeidine A, sungeidine E, sungeidine F, sungeidine G | Micromonospora sp.
BGC0000197.5 |  | 0.29 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0001514.5 |  | 0.29 | other (other) | aristeromycin | Streptomyces citricolor
BGC0000937.5 |  | 0.29 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001642.3 |  | 0.74 | terpene | koraiol | Fusarium fujikuroi IMI 58289
BGC0001746.3 |  | 0.74 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0001201.3 |  | 0.51 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0001294.5 |  | 0.40 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0000821.5 |  | 0.34 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0002387.2 |  | 0.33 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0002545.3 |  | 0.30 | PKS | sungeidine C, sungeidine B, sungeidine D, sungeidine H, sungeidine A, sungeidine E, sungeidine F, sungeidine G | Micromonospora sp.
BGC0000197.5 |  | 0.29 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0001514.5 |  | 0.29 | other (other) | aristeromycin | Streptomyces citricolor
BGC0000937.5 |  | 0.29 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372

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

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:
BKM31_RS00200: T1TS
Domain 1 (2 - 292): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.85 out of 23.79
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 (6):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.30 out of 27.55
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.60 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.12 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.40 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.15 out of 33.14
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
--- | ---
ANR | Anaerobic transcriptional regulator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism

NZ_CP017717.1 - Region 2 - lanthipeptide-class-iii,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: 611,191 - 655,445 nt. (total: 44,255 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
lanthipeptide-class-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
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 oxidoreductase oxygenase
BKM31_RS02790: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

BKM31_RS02805: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BKM31_RS02870: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BKM31_RS02910: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

BKM31_RS02920: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: esterase
BKM31_RS02800: putative esterase

smcogs
  SMCOG1104: putative esterase

Lyases: cyclase decarboxylase dehydratase
BKM31_RS02730: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

BKM31_RS02780: Terpene synthase/cyclase metal-binding domain protein

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

BKM31_RS02905: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: synthetase
BKM31_RS02795: 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 | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000551.5 |  |  | 0.32 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000496.5 |  |  | 0.32 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3 |  |  | 0.31 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  |  | 0.27 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  |  | 0.27 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0001910.4 |  |  | 0.23 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  |  | 0.22 | terpene | raimonol | Streptomyces anulatus
BGC0000553.3 |  |  | 0.22 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000197.5 |  |  | 0.21 | PKS, saccharide | aranciamycin | Streptomyces echinatus
BGC0001768.4 |  |  | 0.20 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.65 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000496.5 |  | 0.65 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3 |  | 0.65 | 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
BGC0000553.3 |  | 0.57 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0001910.4 |  | 0.56 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000518.3 |  | 0.56 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0001911.3 |  | 0.55 | terpene | raimonol | Streptomyces anulatus
BGC0002173.2 |  | 0.52 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

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
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 BKM31_RS02880

BKM31_RS59280
Leader:
MVLLDLQGLEAPAASDVAS
Core:
G G S T L T V L S C H S G K P S N L S V A L C H
Core with dehydrations:
G G Dha Dhb L Dhb V L Dha Cys H Dha G K P Dha N L Dha V A L Cys H

#### antiSMASH-DB 4.0 matches for BKM31_RS59280

100.0%
NZ_CP017717.1 and 2 others:
NZ_FNDJ01000002.1 Lanthipeptides: BLS95_RS05705_lanthipeptide NZ_FNVT01000002.1 Lanthipeptides: C4V41_RS07345_lanthipeptide
Lanthipeptides: BKM31_RS59280_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T V L S C H S G K P S N L S V A L C H
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
95.8%
NZ_CP084058.1:
Lanthipeptides: LCN96_RS39235_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T V L S C H S G P S N L S V A L C H
1
G G S T L T V L S C H S G A P S N L S V A L C H
24
95.8%
NZ_JACHIN010000017.1:
Lanthipeptides: HNR40_RS44190_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T V L+C H S G K P S N L S V A L C H
1
G G S T L T V L T C H S G K P S N L S V A L C H
24
with 66 more sequence matches
Only the first 10 are displayed here.
95.8%
NZ_JAIWLT010000005.1 and 1 other:
NZ_JAIWLU010000020.1 Lanthipeptides: LDL05_RS29535_lanthipeptide
Lanthipeptides: LDL08_RS14700_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T V L C H S G K P S N L S V A L C H
1
G G S T L T V L G C H S G K P S N L S V A L C H
24
87.5%
NZ_JABWGN010000023.1:
Lanthipeptides: HTZ77_RS41305_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T V L C H S G P S N L S V A+C H
1
G G S T L T V L G C H S G A P S N L S V A V C H
24
87.5%
NZ_JABWGO010000017.1:
Lanthipeptides: HT134_RS41585_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T V L C H S G P S N L S V A+C H
1
G G S T L T V L G C H S G T P S N L S V A V C H
24
87.5%
NZ_JACDUR010000006.1 and 2 others:
NZ_JPMW01000001.1 Lanthipeptides: EV45_RS41010_lanthipeptide NZ_JPMW01000001.1 Lanthipeptides: EV45_RS41005_lanthipeptide
Lanthipeptides: HNR30_RS31115_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T L+C+S G K P S N L S V A L C H
1
G G S T L T A L T C N S G K P S N L S V A L C H
24
87.5%
NZ_WBMT01000033.1:
Lanthipeptides: F8566_RS47085_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T+L+C H S G K P S N L S A L C H
1
G G S T L T L L T C H S G K P S N L S A A L C H
24
83.3%
NZ_JAHFZZ010000011.1:
Lanthipeptides: KLK06_RS32640_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T L+C S G P S N L S V A L C H
1
G G S T L T A L T C Q S G H P S N L S V A L C H
24
80.8%
NZ_JACHJJ010000014.1 and 1 other:
NZ_JACHJJ010000014.1 Lanthipeptides: FHS22_RS20800_lanthipeptide
Lanthipeptides: FHS22_RS20805_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T V S C H S G+P S N L S V L C H
3
G G S T L T V A S C H S G Q P S N L S V L L C H
26
76.9%
NZ_BBYJ01000032.1 and 1 other:
NZ_BBYM01000040.1 Lanthipeptides: AWQ70_RS39425_lanthipeptide
Lanthipeptides: AWQ71_RS42200_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S T L T V L+C S G+P S N L S+A L C H
3
G G S T L T V L T C Q S G R P S N L S I A L C H
26
75.0%
NZ_JACJIA010000018.1:
Lanthipeptides: HNR61_RS42145_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S+L T +C S K P S N L S V A L C H
1
G G S S L T A A T C G S T K P S N L S V A L C H
24
75.0%
NZ_JAKRKC020000001.1:
Lanthipeptides: MF672_RS25655_lanthipeptide
1
G G S T L T V L S C H S G K P S N L S V A L C H
24
G G S+L T V +C S P S N L S V A L C H
1
G G S S L T V A T C G S H T P S N L S V A L C H
24

#### MIBiG 4.0 matches for BKM31_RS59280

41.7%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
2
G S T L T V L S C H S G K P S N L S V A L C
23
G S +++L C S+L S V L C
2
G S Q V S L L V C E Y---S S L S V V L C
20

#### Legend:

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

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

Genes with terpene domains:
BKM31_RS02780: T1TS
Domain 1 (17 - 264): Type 1 terpene synthase
Subtype: unknown
BKM31_RS02785: T2TS
Domain 1 (8 - 498): Type 2 terpene synthase
Subtype: Diterpene synthase

Reactions:
  GGPP → diterpene_C6-C11/C10-C15_PP

BKM31_RS02795: PT_FPPS_like
Domain 1 (44 - 322): 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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (22):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.88 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.28 out of 29.38
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.31 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.75 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.68 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.59 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.75 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.15 out of 35.63
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.32 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.95 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.23 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.13 out of 31.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.83 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.26 out of 32.93
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.48 out of 26.06
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.56 out of 28.19
Confidence: weak
Lanthipeptides
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

BKM31_RS59280 - Class III
  Cleavage pHMM score: 11.30
  RODEO score: 0
  Monoisotopic mass: 2241.2 Da
  Molecular weight: 2242.5 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2260.6 Da N = 1
    2278.6 Da N = 2
    2296.6 Da N = 3
    2314.6 Da N = 4
    2332.6 Da N = 5

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
--- | ---
AbrC3 | Antibiotic production activator

NZ_CP017717.1 - Region 3 - NAPAA
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 688,007 - 721,837 nt. (total: 33,831 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
BKM31_RS03080: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

BKM31_RS03100: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS03130: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BKM31_RS64780: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

BKM31_RS64785: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

Hydrolases: hydrolase
BKM31_RS03105: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

BKM31_RS03215: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

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

Reference | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.19 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 26.66 out of 30.11
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.34 out of 20.01
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.54 out of 23.79
Confidence: medium
Additional weak hits (9):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.04 out of 21.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.87 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.92 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.85 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.81 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 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 5, location 688006 - 721837:
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).
BKM31_RS03155: X
AMP-binding (33..403): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAELFDASCEELSTIFGGEWNTYGPTEATVVASA
  Nearest Stachelhaus code(s):
    Lys DAEDIGTVVK (71% 8Å match)
    Gln or Tyr DAESVGTVVK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism

NZ_CP017717.1 - Region 4 - 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: 895,664 - 928,476 nt. (total: 32,813 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: kinase
BKM31_RS04075: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: hydrolase
BKM31_RS04115: hydrolase

smcogs
  SMCOG1179: hydrolase

Ligases: ligase synthase
BKM31_RS04090: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

BKM31_RS04160: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS04165: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

Translocases: transporter
BKM31_RS04050: 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 | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.52 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.52 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000830.5 |  | 0.44 | other (aminocoumarin) | violacein | uncultured bacterium
BGC0000831.3 |  | 0.43 | other (other) | violacein | Duganella sp. B2
BGC0000343.5 |  | 0.43 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001440.5 |  | 0.43 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0000595.3 |  | 0.42 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001441.5 |  | 0.41 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0000829.5 |  | 0.40 | other (other) | violacein | Chromobacterium violaceum
BGC0002462.3 |  | 0.40 | saccharide | coformycin | Streptomyces kaniharaensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.52 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.52 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000830.5 |  | 0.44 | other (aminocoumarin) | violacein | uncultured bacterium
BGC0000831.3 |  | 0.43 | other (other) | violacein | Duganella sp. B2
BGC0000343.5 |  | 0.43 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001440.5 |  | 0.43 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0000595.3 |  | 0.42 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001441.5 |  | 0.41 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0000829.5 |  | 0.40 | other (other) | violacein | Chromobacterium violaceum
BGC0002462.3 |  | 0.40 | saccharide | coformycin | Streptomyces kaniharaensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.22 out of 26.85
Confidence: medium
Additional weak hits (5):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.56 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.85 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.85 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.03 out of 27.78
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.86 out of 33.14
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_CP017717.1 - Region 5 - hydrogen-cyanide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,233,727 - 1,246,943 nt. (total: 13,217 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase reductase
BKM31_RS05565: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

BKM31_RS62015: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Hydrolases: deaminase
BKM31_RS05595: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

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

Reference | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002285.2 |  | 0.34 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000119.5 |  | 0.24 | PKS, saccharide | 7-deoxypactamycin | Streptomyces pactum
BGC0000135.5 |  | 0.22 | PKS | reveromycin A | Streptomyces sp. SN-593
BGC0000378.5 |  | 0.21 | NRPS | Kutzneride 1, Kutzneride 2, Kutzneride 3, Kutzneride 4, Kutzneride 5, Kutzneride 6, Kutzneride 7, Kutzneride 8 | Kutzneria sp. 744

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002285.2 |  | 0.34 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000119.5 |  | 0.24 | PKS, saccharide | 7-deoxypactamycin | Streptomyces pactum
BGC0000135.5 |  | 0.22 | PKS | reveromycin A | Streptomyces sp. SN-593
BGC0000378.5 |  | 0.21 | NRPS | Kutzneride 1, Kutzneride 2, Kutzneride 3, Kutzneride 4, Kutzneride 5, Kutzneride 6, Kutzneride 7, Kutzneride 8 | Kutzneria sp. 744

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:
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.44 out of 27.18
Confidence: medium
Additional weak hits (5):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.10 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.11 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.10 out of 29.38
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.89 out of 20.01
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.34 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NrdR | Represses ribonucleotide reductase encoding genes

NZ_CP017717.1 - Region 6 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,331,416 - 1,353,851 nt. (total: 22,436 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
BKM31_RS06020: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

BKM31_RS06045: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001539.4 |  | 0.49 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001548.4 |  | 0.49 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001506.5 |  | 0.49 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0002006.2 |  | 0.49 | ribosomal | albusnodin | Streptomyces albus
BGC0002053.3 |  | 0.49 | ribosomal | ulleungdin | Streptomyces sp.
BGC0002064.2 |  | 0.48 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0001493.5 |  | 0.47 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001552.3 |  | 0.47 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001307.3 |  | 0.47 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0002074.2 |  | 0.46 | ribosomal | huascopeptin | Streptomyces huasconensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001539.4 |  | 0.49 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001548.4 |  | 0.49 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001506.5 |  | 0.49 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0002006.2 |  | 0.49 | ribosomal | albusnodin | Streptomyces albus
BGC0002053.3 |  | 0.49 | ribosomal | ulleungdin | Streptomyces sp.
BGC0002064.2 |  | 0.48 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0001493.5 |  | 0.47 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001552.3 |  | 0.47 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001307.3 |  | 0.47 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0002074.2 |  | 0.46 | ribosomal | huascopeptin | Streptomyces huasconensis

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

No significant matches found.

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - 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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.30 out of 26.85
Confidence: medium
Additional weak hits (12):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.92 out of 30.22
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.14 out of 32.93
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.37 out of 32.74
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.55 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.26 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.38 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.19 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.02 out of 30.25
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
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.27 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.75 out of 28.19
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (1331415...1353851)
BKM31_RS06025
  RRE type: Stand_Alone_Lasso_RRE
  Location: 16 - 88
  Score: 33.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP017717.1 - Region 7 - RRE-containing,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: 1,817,713 - 1,849,326 nt. (total: 31,614 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])
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
BKM31_RS08280: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Lyases: dehydratase
BKM31_RS08220: 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001145.5 |  |  | 0.51 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001640.3 |  |  | 0.46 | ribosomal | kocurin | Kocuria rosea
BGC0001146.5 |  |  | 0.46 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000603.5 |  |  | 0.44 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001860.4 |  |  | 0.39 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0000605.5 |  |  | 0.37 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0000613.5 |  |  | 0.36 | ribosomal | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0000606.5 |  |  | 0.33 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0001155.5 |  |  | 0.32 | ribosomal | GE2270 | Planobispora rosea
BGC0002363.3 |  |  | 0.28 | ribosomal | berninamycin K, berninamycin J, berninamycin A, berninamycin B | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001145.5 |  | 0.59 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001640.3 |  | 0.57 | ribosomal | kocurin | Kocuria rosea
BGC0001146.5 |  | 0.56 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000603.5 |  | 0.54 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001860.4 |  | 0.52 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0001310.5 |  | 0.51 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0000613.5 |  | 0.50 | ribosomal | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0000605.5 |  | 0.49 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0002631.2 |  | 0.49 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000606.5 |  | 0.48 | ribosomal | lactazole | Streptomyces lactacystinaeus

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: 19.35 out of 20.47
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.58 out of 23.79
Confidence: medium
Additional weak hits (12):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.93 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.90 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.50 out of 28.14
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.54 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.57 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.87 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.70 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.31 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.32 out of 31.73
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.18 out of 32.74
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.

RRE-containing protocluster (1817712...1839806)
BKM31_RS08200
  RRE type: Thiopeptide_F_RRE
  Location: 0 - 81
  Score: 83.6
  RRE type: Heterocycloanthracin_C_RRE
  Location: 5 - 91
  Score: 42.7
azole-containing-RiPP protocluster (1819798...1849326)
BKM31_RS08200
  RRE type: Thiopeptide_F_RRE
  Location: 0 - 81
  Score: 83.6
  RRE type: Heterocycloanthracin_C_RRE
  Location: 5 - 91
  Score: 42.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

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_CP017717.1 - Region 8 - RiPP-like,proteusin
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: 2,079,093 - 2,100,550 nt. (total: 21,458 nt) Show pHMM detection rules used
proteusin: (PoyD or TIGR03793)
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: oxygenase
BKM31_RS09420: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acetyltransferase aminotransferase sulfotransferase
BKM31_RS09355: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

BKM31_RS09400: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

BKM31_RS09410: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

BKM31_RS09415: 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 | proteusin | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001485.4 |  |  | 0.34 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000513.3 |  |  | 0.30 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002150.2 |  |  | 0.27 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  |  | 0.27 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0000598.5 |  |  | 0.27 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0002303.3 |  |  | 0.26 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0000567.3 |  |  | 0.26 | ribosomal | trifolitoxin | Rhizobium leguminosarum
BGC0002330.2 |  |  | 0.26 | ribosomal | landornamide A | Kamptonema sp. PCC 6506
BGC0001157.6 |  |  | 0.25 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000468.5 |  |  | 0.25 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.50 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002458.3 |  | 0.49 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000513.3 |  | 0.45 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001682.3 |  | 0.45 | other (other) | N-acyl lysine, N-acyl ornithine | Pseudomonas aeruginosa LESB58
BGC0001148.5 |  | 0.43 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0000598.5 |  | 0.43 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0002073.3 |  | 0.43 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002347.3 |  | 0.42 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6

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
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.14 out of 23.79
Confidence: medium
Additional weak hits (17):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.36 out of 20.97
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.69 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.22 out of 29.38
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
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.01 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.67 out of 27.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.55 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.19 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.08 out of 32.93
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.29 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.75 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.55 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.15 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.58 out of 29.65
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

proteusin protocluster (2079092...2100550)
BKM31_RS09380
  RRE type: Proteusin_Epimerase_RRE
  Location: 384 - 476
  Score: 37.5
RiPP-like protocluster (2082039...2094073)
BKM31_RS09380
  RRE type: Proteusin_Epimerase_RRE
  Location: 384 - 476
  Score: 37.5

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_CP017717.1 - Region 9 - 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: 2,100,708 - 2,121,865 nt. (total: 21,158 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidase
BKM31_RS09500: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Hydrolases: hydrolase
BKM31_RS09445: isochorismatase

smcogs
  SMCOG1027: isochorismatase

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
--- | --- | --- | --- | --- | ---
BGC0000812.3 |  | 0.48 | other (other) | huperzine A | Shiraia sp. slf14
BGC0000585.5 |  | 0.46 | ribosomal | microcin C7 | Escherichia coli
BGC0000885.3 |  | 0.42 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0002305.2 |  | 0.42 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001453.5 |  | 0.41 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002508.2 |  | 0.41 | other (other) | 8-azaguanine | Streptomyces pathocidini
BGC0000940.5 |  | 0.41 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0002690.2 |  | 0.41 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0000583.5 |  | 0.41 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000662.5 |  | 0.40 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000812.3 |  | 0.48 | other (other) | huperzine A | Shiraia sp. slf14
BGC0000585.5 |  | 0.46 | ribosomal | microcin C7 | Escherichia coli
BGC0000885.3 |  | 0.42 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0002305.2 |  | 0.42 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001453.5 |  | 0.41 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002508.2 |  | 0.41 | other (other) | 8-azaguanine | Streptomyces pathocidini
BGC0000940.5 |  | 0.41 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0002690.2 |  | 0.41 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0000583.5 |  | 0.41 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000662.5 |  | 0.40 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.73 out of 36.53
Confidence: medium
Additional weak hits (12):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.94 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.22 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.44 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.22 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.74 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.77 out of 31.73
Confidence: weak
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
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.91 out of 27.78
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.82 out of 39.62
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.93 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (2100707...2121865)
BKM31_RS09480
  RRE type: Pantocin_Microcin_RRE
  Location: 0 - 90
  Score: 34.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor

NZ_CP017717.1 - Region 10 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,390,421 - 2,411,563 nt. (total: 21,143 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 electron transfer
BKM31_RS10730: flavodoxin

smcogs
  SMCOG1134: flavodoxin

BKM31_RS10755: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS10775: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
BKM31_RS10760: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
BKM31_RS10750: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BKM31_RS10780: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: cyclase
BKM31_RS10765: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: ligase
BKM31_RS10800: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease
BKM31_RS10805: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000657.5 |  | 0.74 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000659.3 |  | 0.63 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000658.3 |  | 0.61 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002276.2 |  | 0.57 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001160.5 |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.55 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000894.4 |  | 0.50 | other (other) | citrinin | Monascus aurantiacus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000657.5 |  | 0.74 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000659.3 |  | 0.63 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000658.3 |  | 0.61 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002276.2 |  | 0.57 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001160.5 |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.55 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000894.4 |  | 0.50 | other (other) | citrinin | Monascus aurantiacus

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
monoterpene |  | 2-methylisoborneol | C11 | C1-C6 | OH
monoterpene |  | 2-methylenebornane | C11 | C1-C6 | none

Genes with terpene domains:
BKM31_RS10765: T1TS
Domain 1 (64 - 378): Type 1 terpene synthase
Subtype: 2-Methylisoborneol synthase type

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.36 out of 25.31
Confidence: medium
Additional weak hits (9):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.14 out of 20.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.28 out of 28.14
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.75 out of 28.19
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.97 out of 27.18
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.95 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.60 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.58 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP017717.1 - Region 11 - NRP-metallophore,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: 2,413,820 - 2,488,778 nt. (total: 74,959 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)
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
BKM31_RS10845: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS10850: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

BKM31_RS10885: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

BKM31_RS10910: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BKM31_RS10940: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BKM31_RS10945: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BKM31_RS11010: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

BKM31_RS11015: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: formyltransferase
BKM31_RS11005: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: back translocase esterase hydrolase
BKM31_RS10975: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

BKM31_RS11000: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

BKM31_RS11060: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
BKM31_RS10915: argininosuccinate synthase

smcogs
  SMCOG1291: argininosuccinate synthase

BKM31_RS10920: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS10930: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BKM31_RS10990: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS-like | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002276.2 |  |  |  | 1.19 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000342.4 |  |  |  | 1.08 | NRPS | enniatin | Fusarium equiseti
BGC0001825.4 |  |  |  | 1.07 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  |  |  | 1.05 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  |  | 1.04 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  |  | 1.02 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 1.02 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 1.01 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000357.5 |  |  |  | 1.01 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001251.4 |  |  |  | 1.00 | NRPS | epichloenin A | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.72 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001825.4 |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0000357.5 |  | 0.69 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001251.4 |  | 0.68 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.68 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
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
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.20 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.03 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.90 out of 36.53
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.11 out of 25.31
Confidence: medium
Additional weak hits (20):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.80 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.32 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.04 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.18 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.26 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.49 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.38 out of 20.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.36 out of 20.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.02 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.13 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.24 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.97 out of 21.55
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.28 out of 19.26
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.26 out of 27.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.91 out of 29.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.78 out of 26.12
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.05 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.28 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 14, location 2413819 - 2488778:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Fo-OH-Orn - D-Thr - OH-Orn) + (X) + (Glu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 15, location 2413819 - 2456906:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Fo-OH-Orn - D-Thr - OH-Orn) + (X) + (Glu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 16, location 2417104 - 2488778:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Fo-OH-Orn - D-Thr - OH-Orn) + (X) + (Glu)

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).
BKM31_RS10920: Glu
Search NORINE for peptide: strict or relaxed
AMP-binding (35..442): Glu
nrpys: Glu

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:
    glu (Glu)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RAMSFDSSMWQWDFLIGGETNTFGPTECSIGSVF
  Nearest Stachelhaus code(s):
    Glu DVWHVGSIGK (53% 8Å match)
    Asp DSWKLGVVDK (47% 8Å match)
  Stachelhaus code match:
    60% (weak)

BKM31_RS10930: X
AMP-binding (497..890): X
nrpys: (unknown)

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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FTFSFDVSVSDSDIFIGMEHNGYGPTEVTVTCVD
  Nearest Stachelhaus code(s):
    dn-dohHep DVFDFGGVTK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BKM31_RS10990: Fo-OH-Orn - Thr - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (142..540): Fo-OH-Orn
nrpys: Fo-OH-Orn

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

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

AMP-binding (1632..2040): Thr
nrpys: Thr

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

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

AMP-binding (3057..3457): OH-Orn
nrpys: OH-Orn

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

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

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CatR | H2O2-responsive repressor
CelR | Cellobiose uptake repressor
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP017717.1 - Region 12 - NRPS-like,PKS-like,T1PKS,lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,521,005 - 2,607,980 nt. (total: 86,976 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)
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)
PKS-like: (t2pks2 or ksIII)
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
Lasso peptides
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase
BKM31_RS11380: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

BKM31_RS11405: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

BKM31_RS11520: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS11590: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BKM31_RS11595: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS11600: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

BKM31_RS11630: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS11645: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Transferases: acylase methyltransferase
BKM31_RS11675: methyltransferase

smcogs
  SMCOG1248: methyltransferase

BKM31_RS62235: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
BKM31_RS11445: HAD-superfamily hydrolase, subfamily IA, variant

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

BKM31_RS11450: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

BKM31_RS11460: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

BKM31_RS11670: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Lyases: cyclase dehydratase
BKM31_RS11360: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

BKM31_RS11635: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
BKM31_RS11610: 3-oxoacyl-(acyl carrier protein) synthase III

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

BKM31_RS11615: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | NRPS-like | lassopeptide | PKS-like | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001551.4 |  |  |  |  | 0.91 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001549.3 |  |  |  |  | 0.90 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001552.3 |  |  |  |  | 0.85 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001548.4 |  |  |  |  | 0.84 | ribosomal | citrulassin A | Streptomyces albulus
BGC0002318.2 |  |  |  |  | 0.83 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0002053.3 |  |  |  |  | 0.81 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001781.4 |  |  |  |  | 0.78 | ribosomal | sphaericin | Planomonospora sphaerica
BGC0001249.5 |  |  |  |  | 0.76 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001550.3 |  |  |  |  | 0.75 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001507.3 |  |  |  |  | 0.74 | ribosomal | anantin C | Streptomyces olindensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001551.4 |  | 0.76 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001549.3 |  | 0.75 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001552.3 |  | 0.74 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001548.4 |  | 0.73 | ribosomal | citrulassin A | Streptomyces albulus
BGC0002053.3 |  | 0.72 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001781.4 |  | 0.71 | ribosomal | sphaericin | Planomonospora sphaerica
BGC0001249.5 |  | 0.70 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001550.3 |  | 0.70 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001507.3 |  | 0.70 | ribosomal | anantin C | Streptomyces olindensis
BGC0001889.2 |  | 0.68 | ribosomal | fusilassin | Thermobifida fusca YX

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
Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - 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: 17.68 out of 20.47
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.48 out of 18.57
Confidence: strong
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.70 out of 27.55
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (22):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.95 out of 27.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.62 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.62 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.16 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.58 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.65 out of 27.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.15 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.00 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.63 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.95 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.80 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.66 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.55 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.88 out of 29.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.40 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.72 out of 20.01
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.80 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.63 out of 29.65
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.97 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Lasso peptides
NRPS/PKS products
NRPS/PKS substrates
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
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 2521004 - 2607980:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gln) + (pk)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 18, location 2521004 - 2564847:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gln)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 20, location 2561851 - 2607980:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BKM31_RS11420: Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (28..430): Gln
nrpys: Gln

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

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

BKM31_RS62235: pk
PKS_AT (600..893): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  Methylmalonyl-CoA: 70.8%
  Ethylmalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 122.0
  Ethylmalonyl-CoA: 104.6
  Malonyl-CoA: 92.2
  Methoxymalonyl-CoA: 91.6
  trans-1,2-CPDA: 58.6
  Propionyl-CoA: 53.3
  2-Methylbutyryl-CoA: 47.9
  Isobutyryl-CoA: 41.4
  Benzoyl-CoA: 39.9
  Acetyl-CoA: 37.8
  inactive: 33.0
  CHC-CoA: 26.9
  3-Methylbutyryl-CoA: 25.5
  fatty_acid: 20.2

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (2540824...2563487)
BKM31_RS11465
  RRE type: Stand_Alone_Lasso_RRE
  Location: 0 - 84
  Score: 74.1
  RRE type: Lasso_Fused_RRE
  Location: 0 - 52
  Score: 29.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
GnfM | Regulator of nitrogen-fixation genes
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP017717.1 - Region 13 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,001,811 - 3,024,306 nt. (total: 22,496 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
BKM31_RS13595: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

BKM31_RS13630: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: dehydratase
BKM31_RS13635: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Translocases: transporter
BKM31_RS13545: 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 | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000772.5 |  | 0.41 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0000706.3 |  | 0.36 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0002285.2 |  | 0.35 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000820.5 |  | 0.34 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0001782.3 |  | 0.33 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0000703.4 |  | 0.32 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001964.2 |  | 0.32 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0001707.5 |  | 0.32 | ribosomal | nosiheptide | Streptomyces sp.
BGC0001386.5 |  | 0.31 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77
BGC0000219.4 |  | 0.31 | PKS, saccharide | elloramycin | Streptomyces olivaceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000772.5 |  | 0.41 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0000706.3 |  | 0.36 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0002285.2 |  | 0.35 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000820.5 |  | 0.34 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0001782.3 |  | 0.33 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0000703.4 |  | 0.32 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001964.2 |  | 0.32 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0001707.5 |  | 0.32 | ribosomal | nosiheptide | Streptomyces sp.
BGC0001386.5 |  | 0.31 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77
BGC0000219.4 |  | 0.31 | PKS, saccharide | elloramycin | Streptomyces olivaceus

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

No significant matches found.

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (11):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.93 out of 19.26
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.58 out of 20.97
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.00 out of 26.85
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.27 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.81 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.61 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.36 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.80 out of 24.78
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.03 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.24 out of 33.14
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (3001810...3024306)
BKM31_RS13590
  RRE type: Stand_Alone_Lasso_RRE
  Location: 3 - 84
  Score: 46.2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP017717.1 - Region 14 - RRE-containing,RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,167,162 - 3,193,571 nt. (total: 26,410 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))
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
BKM31_RS14345: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS14365: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

BKM31_RS14370: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase
BKM31_RS14360: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

BKM31_RS14435: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

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 | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000885.3 |  |  | 0.28 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0001374.5 |  |  | 0.26 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0000937.5 |  |  | 0.21 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372
BGC0000313.4 |  |  | 0.21 | NRPS | beauvericin | Beauveria bassiana
BGC0002631.2 |  |  | 0.21 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001865.4 |  |  | 0.20 | PKS | elsinochrome C | Parastagonospora nodorum SN15
BGC0001007.5 |  |  | 0.20 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin b | Salinispora arenicola CNS-205
BGC0000154.4 |  |  | 0.20 | PKS | stipitatic acid | Talaromyces stipitatus ATCC 10500
BGC0001925.4 |  |  | 0.19 | other (other) | altemicidin, SB-203207, SB-203208 | Streptomyces sp.
BGC0001006.5 |  |  | 0.19 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin B | Salinispora tropica CNB-440

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001310.5 |  | 0.50 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001374.5 |  | 0.48 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001485.4 |  | 0.47 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002825.2 |  | 0.47 | ribosomal | nocapeptin A | Nocardia terpenica IFM 0406
BGC0002103.2 |  | 0.45 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0000885.3 |  | 0.45 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0001986.3 |  | 0.44 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0001223.5 |  | 0.43 | other (other) | hydroxysporine | uncultured bacterium

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
Additional weak hits (13):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.34 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.40 out of 26.33
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.61 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.04 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.91 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.82 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.77 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.27 out of 30.12
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 25.37 out of 32.93
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.62 out of 32.93
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (3173280...3193571)
BKM31_RS14390
  RRE type: PqqD_RRE
  Location: 21 - 88
  Score: 44.3
  RRE type: Stand_Alone_Lasso_RRE
  Location: 15 - 85
  Score: 39.6
  RRE type: Subtilosin_rSAM_RRE
  Location: 34 - 84
  Score: 27.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP017717.1 - Region 15 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,504,849 - 3,527,401 nt. (total: 22,553 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: deacetylase hydrolase
BKM31_RS16070: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

BKM31_RS16075: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002074.2 |  | 0.56 | ribosomal | huascopeptin | Streptomyces huasconensis
BGC0001549.3 |  | 0.55 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0002053.3 |  | 0.54 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001539.4 |  | 0.53 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001781.4 |  | 0.52 | ribosomal | sphaericin | Planomonospora sphaerica
BGC0001493.5 |  | 0.51 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001634.3 |  | 0.50 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001645.3 |  | 0.47 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0002307.3 |  | 0.45 | ribosomal | humidimycin | Streptomyces humidus
BGC0002064.2 |  | 0.44 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002074.2 |  | 0.56 | ribosomal | huascopeptin | Streptomyces huasconensis
BGC0001549.3 |  | 0.55 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0002053.3 |  | 0.54 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001539.4 |  | 0.53 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001781.4 |  | 0.52 | ribosomal | sphaericin | Planomonospora sphaerica
BGC0001493.5 |  | 0.51 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001634.3 |  | 0.50 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001645.3 |  | 0.47 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0002307.3 |  | 0.45 | ribosomal | humidimycin | Streptomyces humidus
BGC0002064.2 |  | 0.44 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10

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

No significant matches found.

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

No significant matches found.

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

#### Lassopeptide(s) for BKM31_RS59740

BKM31_RS59740
Leader:
MDHPTPAGYEAPHLSPVGSFATSTL
Full core:
G S Y S K D T S D D S D A G Q Y Y P S
Putative macrolactam:
G S Y S K D T S D

#### antiSMASH-DB 4.0 matches for BKM31_RS59740

100.0%
NZ_CP017717.1:
Lassopeptides: BKM31_RS59740_lassopeptide
1
G S Y S K D T S D D S D A G Q Y Y P S
19
G S Y S K D T S D D S D A G Q Y Y P S
1
G S Y S K D T S D D S D A G Q Y Y P S
19
57.9%
NZ_JAJKFK010000001.1:
Lassopeptides: LOZ83_RS01335_lassopeptide
1
G S Y S K D T S D D S D A G Q Y Y P
18
G Y S++ S D D D A G Y+P
1
G Q Y S R N R S D D G D A G G Y F P
18
52.6%
NZ_CP016354.1:
Lassopeptides: BAY61_RS33250_lassopeptide
1
G S Y S K D T S D D S D A G Q Y Y
17
G Y S+ S D D D A G Y+
1
G Q Y S R S I S D D G D A G G Y W
17
with 1 more sequence matches
44.4%
NZ_JACHJF010000012.1:
Lassopeptides: FHS36_RS19400_lassopeptide
1
G S Y S K D T S D D S D A G Q Y Y
17
G S S D D S D A G Q Y Y
1
G D V S V G Q S D D S D A G Q Y Y
17

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (5):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.10 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.83 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.01 out of 20.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

BKM31_RS59740 - Class II
  Cleavage pHMM score: -1.90
  RODEO score: 20
  Monoisotopic mass: 2023.8 Da
  Molecular weight: 2025.0 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (3504848...3527401)
BKM31_RS16080
  RRE type: Stand_Alone_Lasso_RRE
  Location: 11 - 80
  Score: 51.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP017717.1 - Region 16 - 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: 4,171,747 - 4,213,108 nt. (total: 41,362 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 domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase reductase
BKM31_RS19000: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

BKM31_RS19040: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: PPTase acylase carboxylase
BKM31_RS19020: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

BKM31_RS19025: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

BKM31_RS62710: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: synthase
BKM31_RS19035: 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 | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.57 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.57 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.57 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.56 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001164.3 |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.55 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000056.3 |  | 0.50 | PKS | esperamicin | Actinomadura verrucosospora
BGC0000044.3 |  | 0.45 | PKS | dawenol | Stigmatella aurantiaca DW4/3-1
BGC0002284.3 |  | 0.45 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0001264.3 |  | 0.43 | PKS | betaenone A, betaenone B, betaenone C | Phoma betae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.57 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.57 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.57 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.56 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001164.3 |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.55 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000056.3 |  | 0.50 | PKS | esperamicin | Actinomadura verrucosospora
BGC0000044.3 |  | 0.45 | PKS | dawenol | Stigmatella aurantiaca DW4/3-1
BGC0002284.3 |  | 0.45 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0001264.3 |  | 0.43 | PKS | betaenone A, betaenone B, betaenone C | Phoma betae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.98 out of 29.51
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.68 out of 30.12
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.22 out of 23.43
Confidence: medium
Additional weak hits (5):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.71 out of 36.54
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.30 out of 29.51
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.88 out of 27.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.18 out of 20.97
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.58 out of 32.93
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BKM31_RS62710: mal
PKS_AT (294..591): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 79.2%
  2-Methylbutyryl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 131.0
  inactive: 80.2
  Methoxymalonyl-CoA: 67.7
  Propionyl-CoA: 54.8
  Methylmalonyl-CoA: 52.7
  2-Methylbutyryl-CoA: 38.7
  Isobutyryl-CoA: 37.3
  trans-1,2-CPDA: 20.1
  Benzoyl-CoA: 18.4
  CHC-CoA: 14.9
  Ethylmalonyl-CoA: 13.3
  Acetyl-CoA: 11.7
  fatty_acid: 10.7
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
DosR | Hypoxia stress response regulator
OsdR | Development and stress management regulator

NZ_CP017717.1 - Region 17 - 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: 4,271,531 - 4,292,565 nt. (total: 21,035 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Ligases: synthetase
BKM31_RS19440: 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
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000829.5 |  | 0.40 | other (other) | violacein | Chromobacterium violaceum
BGC0002116.3 |  | 0.38 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0001779.5 |  | 0.37 | ribosomal | siamycin | Streptomyces nodosus
BGC0000541.5 |  | 0.37 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002447.3 |  | 0.37 | ribosomal | cerecyclin | Bacillus cereus
BGC0000043.5 |  | 0.37 | PKS | curacin A | Moorea producens 19L
BGC0002442.3 |  | 0.37 | ribosomal | toyoncin | Bacillus toyonensis
BGC0000487.5 |  | 0.36 | ribosomal | carnocyclin | Carnobacterium maltaromaticum
BGC0001289.5 |  | 0.36 | ribosomal | penisin | Paenibacillus ehimensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000829.5 |  | 0.40 | other (other) | violacein | Chromobacterium violaceum
BGC0002116.3 |  | 0.38 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0001779.5 |  | 0.37 | ribosomal | siamycin | Streptomyces nodosus
BGC0000541.5 |  | 0.37 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002447.3 |  | 0.37 | ribosomal | cerecyclin | Bacillus cereus
BGC0000043.5 |  | 0.37 | PKS | curacin A | Moorea producens 19L
BGC0002442.3 |  | 0.37 | ribosomal | toyoncin | Bacillus toyonensis
BGC0000487.5 |  | 0.36 | ribosomal | carnocyclin | Carnobacterium maltaromaticum
BGC0001289.5 |  | 0.36 | ribosomal | penisin | Paenibacillus ehimensis

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:
BKM31_RS19440: PT_FPPS_like
Domain 1 (92 - 342): 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: 19.19 out of 20.47
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.13 out of 23.79
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (4):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.16 out of 28.14
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.58 out of 21.55
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.60 out of 32.93
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.08 out of 36.53
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
--- | ---
AbrC3 | Antibiotic production activator
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP017717.1 - Region 18 - NRPS,PKS-like,RiPP-like,T1PKS,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: 4,324,333 - 4,457,338 nt. (total: 133,006 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))
phenazine: phzB
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))
PKS-like: (t2pks2 or ksIII)

#### 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 synthase
BKM31_RS19660: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

BKM31_RS19725: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

BKM31_RS19775: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

BKM31_RS19780: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

BKM31_RS19820: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

BKM31_RS19875: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

BKM31_RS19915: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS20090: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BKM31_RS20095: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

BKM31_RS20140: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS20160: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

BKM31_RS20170: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: acylase methyltransferase
BKM31_RS19805: methyltransferase

smcogs
  SMCOG1089: methyltransferase

BKM31_RS19850: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase synthase
BKM31_RS19780: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

BKM31_RS19970: isochorismatase

smcogs
  SMCOG1027: isochorismatase

BKM31_RS20065: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Isomerases: isomerase
BKM31_RS19965: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
BKM31_RS19735: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BKM31_RS19855: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS19865: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BKM31_RS20070: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS20085: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | NRPS | T1PKS | NRPS | phenazine | RiPP-like | T1PKS | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001276.3 |  |  |  |  |  |  |  | 1.49 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  |  |  |  |  |  |  | 1.33 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001273.3 |  |  |  |  |  |  |  | 1.21 | PKS | asperlactone | Aspergillus ochraceus
BGC0001284.4 |  |  |  |  |  |  |  | 1.13 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002191.2 |  |  |  |  |  |  |  | 1.12 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001160.5 |  |  |  |  |  |  |  | 1.12 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002175.3 |  |  |  |  |  |  |  | 1.10 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0002154.2 |  |  |  |  |  |  |  | 1.10 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001268.4 |  |  |  |  |  |  |  | 1.01 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001128.4 |  |  |  |  |  |  |  | 0.91 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.77 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000936.5 |  | 0.70 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.67 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.65 | 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:
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.59 out of 25.75
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.85 out of 20.97
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.60 out of 20.97
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.13 out of 23.79
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.67 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.91 out of 28.19
Confidence: medium
Additional weak hits (56):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.04 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.54 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.70 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.32 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.90 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.63 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.14 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
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.37 out of 30.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.72 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.36 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.44 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.27 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.63 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.95 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.32 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.52 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.01 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: 15.81 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.95 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.20 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.12 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.03 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.96 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.30 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.68 out of 26.06
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: 16.66 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.38 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.02 out of 26.85
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.08 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.54 out of 29.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.41 out of 20.97
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.22 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.32 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.48 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.82 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.96 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.75 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.65 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.14 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.14 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.98 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.95 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.00 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.03 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.96 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.55 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.60 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.52 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.77 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.58 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 28, location 4324332 - 4416067:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Cys) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 30, location 4352402 - 4402613:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Cys) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 32, location 4406337 - 4457338:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 34, location 4408192 - 4453415:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 35, location 4416267 - 4457338:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BKM31_RS19735: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (425..827): 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:
    TDITFDLSVYDGNTLMSGDISLGGATEASIWSIW
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

BKM31_RS19850: mal
PKS_AT (556..831): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 76.3
  Methoxymalonyl-CoA: 67.9
  Methylmalonyl-CoA: 61.2
  Ethylmalonyl-CoA: 40.3
  Propionyl-CoA: 30.7
  fatty_acid: 24.7
  Isobutyryl-CoA: 22.7
  inactive: 20.7
  2-Methylbutyryl-CoA: 20.3
  CHC-CoA: 16.2
  trans-1,2-CPDA: 14.9
  Acetyl-CoA: 11.5
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

BKM31_RS19855: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (567..969): 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:
    TDLSFDLSVYDSNTLLSADVSLGGATEASIWSIC
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

BKM31_RS20070: pk
PKS_AT (541..835): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  Methylmalonyl-CoA: 70.8%
  Methoxymalonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 117.2
  Methoxymalonyl-CoA: 99.0
  Ethylmalonyl-CoA: 95.5
  Isobutyryl-CoA: 85.1
  Malonyl-CoA: 81.6
  2-Methylbutyryl-CoA: 54.5
  Propionyl-CoA: 53.2
  trans-1,2-CPDA: 49.6
  3-Methylbutyryl-CoA: 41.1
  Acetyl-CoA: 38.3
  CHC-CoA: 35.7
  Benzoyl-CoA: 28.6
  fatty_acid: 26.2
  inactive: 14.4

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CcpA | Catabolite control protein A
IolR | Regulator of the inositol catabolism
MatP | Cell cycle regulator
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_CP017717.1 - Region 19 - PKS-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: 4,821,966 - 4,868,135 nt. (total: 46,170 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
PKS-like: (t2pks2 or ksIII)

#### 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: oxidoreductase
BKM31_RS21915: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: dehalogenase
BKM31_RS21870: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: dehydratase
BKM31_RS21875: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
BKM31_RS21860: 3-oxoacyl-(acyl carrier protein) synthase III

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

BKM31_RS21880: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS21890: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS21930: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS21935: 3-oxoacyl-(acyl carrier protein) synthase III

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

BKM31_RS21945: 3-oxoacyl-(acyl carrier protein) synthase III

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

Translocases: transport
BKM31_RS21865: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | T1PKS | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001275.3 |  |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  |  | 0.63 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  | 0.62 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001284.4 |  |  | 0.57 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001160.5 |  |  | 0.55 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001268.4 |  |  | 0.55 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002191.2 |  |  | 0.53 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000037.4 |  |  | 0.53 | PKS | cichorine | Aspergillus nidulans FGSC A4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001268.4 |  | 0.61 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002191.2 |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000037.4 |  | 0.60 | PKS | cichorine | Aspergillus nidulans FGSC A4

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.58 out of 25.88
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (11):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.69 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.40 out of 26.33
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 21.84
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.35 out of 25.88
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.16 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.59 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.23 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.32 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 36, location 4821965 - 4868135:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 37, location 4821965 - 4865727:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 38, location 4825773 - 4868135:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BKM31_RS21880: X
AMP-binding (12..433): 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:
    QLLL-------AFALTAGARSVYGATECLLVSMA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

BKM31_RS21930: pk
PKS_AT (526..816): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%
  Methylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 128.3
  Ethylmalonyl-CoA: 112.7
  Methoxymalonyl-CoA: 103.9
  Malonyl-CoA: 91.7
  Propionyl-CoA: 66.9
  Isobutyryl-CoA: 66.3
  2-Methylbutyryl-CoA: 61.9
  trans-1,2-CPDA: 55.2
  Benzoyl-CoA: 37.2
  Acetyl-CoA: 33.3
  CHC-CoA: 29.1
  3-Methylbutyryl-CoA: 28.1
  fatty_acid: 24.7
  inactive: 23.1

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
PsrA | Oleic acid responsive regulator
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP017717.1 - Region 20 - CDPS
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: 4,947,263 - 4,968,063 nt. (total: 20,801 nt) Show pHMM detection rules used
CDPS: CDPS

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
BKM31_RS22475: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS22490: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

Transferases: glycosyltransferase
BKM31_RS22505: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

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

Reference | CDPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000851.5 |  | 0.65 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0001986.3 |  | 0.59 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0001948.3 |  | 0.49 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0002150.2 |  | 0.42 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.42 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0001496.3 |  | 0.39 | ribosomal | actinokineosin | Actinokineospora spheciospongiae
BGC0000545.5 |  | 0.38 | ribosomal | ruminococcin A | [Ruminococcus] gnavus E1
BGC0000527.5 |  | 0.38 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001210.5 |  | 0.38 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000851.5 |  | 0.65 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0001986.3 |  | 0.59 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0001948.3 |  | 0.49 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0002150.2 |  | 0.42 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  | 0.42 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0001496.3 |  | 0.39 | ribosomal | actinokineosin | Actinokineospora spheciospongiae
BGC0000545.5 |  | 0.38 | ribosomal | ruminococcin A | [Ruminococcus] gnavus E1
BGC0000527.5 |  | 0.38 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001210.5 |  | 0.38 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.72 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.33 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.57 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.10 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.39 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.99 out of 27.55
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.31 out of 29.51
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.98 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP017717.1 - Region 21 - T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,044,303 - 5,124,407 nt. (total: 80,105 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
BKM31_RS22930: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BKM31_RS22955: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

BKM31_RS22965: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

BKM31_RS22970: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS22990: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS23010: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS23015: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS23025: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

BKM31_RS23040: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS23055: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS23105: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: carboxylase glycosyltransferase methyltransferase transferase
BKM31_RS22975: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

BKM31_RS22985: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

BKM31_RS23035: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

BKM31_RS23050: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

BKM31_RS23080: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

BKM31_RS23090: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Hydrolases: hydrolase
BKM31_RS22910: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase dehydratase
BKM31_RS22940: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

BKM31_RS23000: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

BKM31_RS23060: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

BKM31_RS23250: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
BKM31_RS23070: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS23110: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: transport
BKM31_RS23240: 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 | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.61 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000231.5 |  | 0.57 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001723.5 |  | 0.56 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000261.5 |  | 0.55 | PKS | R1128 | Streptomyces sp. R1128
BGC0001513.3 |  | 0.54 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000234.5 |  | 0.54 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001928.2 |  | 0.53 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000272.3 |  | 0.53 | PKS | spore pigment | Streptomyces collinus
BGC0002047.2 |  | 0.52 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000866.5 |  | 0.52 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.61 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000231.5 |  | 0.57 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001723.5 |  | 0.56 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000261.5 |  | 0.55 | PKS | R1128 | Streptomyces sp. R1128
BGC0001513.3 |  | 0.54 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000234.5 |  | 0.54 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001928.2 |  | 0.53 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000272.3 |  | 0.53 | PKS | spore pigment | Streptomyces collinus
BGC0002047.2 |  | 0.52 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000866.5 |  | 0.52 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242

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:
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: 18.00 out of 20.47
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.42 out of 23.43
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.86 out of 21.84
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.35 out of 23.79
Confidence: medium
Additional weak hits (23):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.49 out of 30.22
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.29 out of 32.74
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.62 out of 32.93
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.26 out of 31.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.65 out of 29.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.73 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.80 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.81 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.82 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.68 out of 27.78
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.20 out of 39.62
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.02 out of 32.74
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.44 out of 20.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.67 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.59 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.32 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.82 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.56 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.66 out of 29.65
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  5044302 to 5124407
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:
  11|12 (Score: 716.4; E-value: 1.8e-218)
Product class(es):
  pentangular polyphenol
Product molecular weight(s):
  acetyl-CoA_11: 690 Da
  acetyl-CoA_12: 732 Da

BKM31_RS22925
  OXY (Score: 16.2; E-value: 1e-05)
BKM31_RS22940
  CYC C9-C14 (Score: 238.3; E-value: 5.9e-74)
BKM31_RS22945
  ACP (Score: 94.1; E-value: 9.3e-30)
BKM31_RS22970
  KR C11 (Score: 414.0; E-value: 4.3e-127)
BKM31_RS22975
  MET C13O|C17O (Score: 453.9; E-value: 6.6e-139)
BKM31_RS22985
  MET (Score: 271.7; E-value: 2e-83)
BKM31_RS23015
  KR (Score: 178.5; E-value: 4.5e-55)
BKM31_RS23035
  MET (Score: 273.9; E-value: 4.1e-84)
BKM31_RS23050
  GT (Score: 334.2; E-value: 3.2e-102)
BKM31_RS23055
  KR (Score: 107.7; E-value: 1.8e-33)
BKM31_RS23060
  CYC C4-C21/C2-C23|C2-C19 (Score: 167.4; E-value: 1.8e-52)
BKM31_RS23065
  CYC C5-C18 (Score: 218.3; E-value: 6.3e-68)
BKM31_RS23070
  KS (Score: 774.5; E-value: 5.4e-236)
BKM31_RS23105
  KR C19 (Score: 381.2; E-value: 5e-117)
BKM31_RS23110
  CLF 11|12 (Score: 716.4; E-value: 1.8e-218)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
BldD | Development and antibiotic global regulator
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP017717.1 - Region 22 - t3nrps-iterative
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: 5,727,621 - 5,770,669 nt. (total: 43,049 nt) Show pHMM detection rules used
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
BKM31_RS25875: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BKM31_RS25975: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BKM31_RS26005: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Lyases: decarboxylase
BKM31_RS25960: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase
BKM31_RS25955: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport
BKM31_RS26000: 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 | t3nrps-iterative | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000307.4 |  | 0.59 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001249.5 |  | 0.59 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0000131.5 |  | 0.47 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000706.3 |  | 0.45 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000900.5 |  | 0.44 | other (other) | ferrichrome | Aspergillus oryzae
BGC0002284.3 |  | 0.44 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000207.5 |  | 0.43 | PKS | chartreusin | Streptomyces chartreusis
BGC0000597.4 |  | 0.43 | ribosomal | SWA-2138 | Streptomyces sp. e14

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000307.4 |  | 0.59 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001249.5 |  | 0.59 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0000131.5 |  | 0.47 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000706.3 |  | 0.45 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000900.5 |  | 0.44 | other (other) | ferrichrome | Aspergillus oryzae
BGC0002284.3 |  | 0.44 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000207.5 |  | 0.43 | PKS | chartreusin | Streptomyces chartreusis
BGC0000597.4 |  | 0.43 | ribosomal | SWA-2138 | Streptomyces sp. e14

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.98 out of 20.97
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.87 out of 29.72
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.52 out of 27.04
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
Additional weak hits (23):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.79 out of 31.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.10 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.30 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.66 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.89 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.27 out of 28.14
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.31 out of 20.97
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.81 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.14 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
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.59 out of 27.55
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: 13.98 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.24 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.31 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.35 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.43 out of 35.63
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.35 out of 33.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.47 out of 32.93
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BKM31_RS25955: X
AMP-binding (13..395): 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:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    VAIQFDVGLYQLPTTNTGAQLMYGLTECKRVSIM
  Nearest Stachelhaus code(s):
    Asp DYYPTTMRVK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
DasR | N-acetylglucosamine dependent repressor
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator

NZ_CP017717.1 - Region 23 - 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: 5,961,208 - 6,017,646 nt. (total: 56,439 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
BKM31_RS26870: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS26915: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

BKM31_RS27025: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS27035: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Hydrolases: hydrolase
BKM31_RS26910: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

BKM31_RS26960: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase synthase
BKM31_RS26975: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BKM31_RS26985: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS27015: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BKM31_RS27020: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS27065: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS60245: 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
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001249.5 |  | 0.74 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001249.5 |  | 0.74 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti

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

No significant matches found.

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: 19.53 out of 23.79
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.21 out of 27.78
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
Additional weak hits (24):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.95 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.79 out of 30.97
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.08 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.19 out of 21.55
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.67 out of 36.53
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.18 out of 29.25
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.94 out of 20.01
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.47 out of 23.43
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.01 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.65 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.22 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.92 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.55 out of 31.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.62 out of 18.57
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.44 out of 26.85
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.29 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.89 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.96 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.98 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.24 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 42, location 5961207 - 6017646:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (D-X) + (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).
BKM31_RS26975: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (14..378): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGQSWDAFALEGYLIVGGERNGYGPVEGMIFLTT
  Nearest Stachelhaus code(s):
    Val DALWIGGTFK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

BKM31_RS26985: X
AMP-binding (490..883): 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:
    LSLGFDISIGELLISSGADWNAYGPTETTVAASV
  Nearest Stachelhaus code(s):
    Leu DALHSGAVAK (59% 8Å match)
  Stachelhaus code match:
    70% (weak)

BKM31_RS60245: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (455..837): 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:
    LDHSFDAATYETWLWAGGDVNGYGPTETTTFATS
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

BKM31_RS27015: X
AMP-binding (463..842): 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:
    LAVVFDVAVSDFFLAIGGEVDAYGPSENTVYSTT
  Nearest Stachelhaus code(s):
    Trp DVSQVGAVAK (59% 8Å match)
    Leu or Ile DAFFNGAVYK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

BKM31_RS27065: X
AMP-binding (10..454): 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:
    AAVS-------GAAIFSWA--------TAIPVTT
  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
--- | ---
CRP | Cyclic AMP receptor protein
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
IolR | Regulator of the inositol catabolism

NZ_CP017717.1 - Region 24 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,379,937 - 6,401,004 nt. (total: 21,068 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
BKM31_RS28745: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS28810: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

BKM31_RS28815: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: phosphorylase
BKM31_RS28800: thiamine-phosphate pyrophosphorylase

smcogs
  SMCOG1280: thiamine-phosphate pyrophosphorylase

Ligases: synthetase
BKM31_RS28795: 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
--- | --- | --- | --- | --- | ---
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.46 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001910.4 |  | 0.43 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000665.5 |  | 0.43 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001521.3 |  | 0.42 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001911.3 |  | 0.42 | terpene | raimonol | Streptomyces anulatus
BGC0001529.5 |  | 0.41 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000285.5 |  | 0.41 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.46 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001910.4 |  | 0.43 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000665.5 |  | 0.43 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001521.3 |  | 0.42 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001911.3 |  | 0.42 | terpene | raimonol | Streptomyces anulatus
BGC0001529.5 |  | 0.41 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000285.5 |  | 0.41 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea

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:
BKM31_RS28795: PT_FPPS_like
Domain 1 (45 - 347): 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:
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 25.32 out of 29.65
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.64 out of 24.78
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.74 out of 24.78
Confidence: medium
Additional weak hits (10):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.91 out of 28.14
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.98 out of 27.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.91 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.29 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.92 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.22 out of 29.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.11 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.60 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
LexA variant 1 | Repressor of DNA damage response
LexA variant 2 | Repressor of DNA damage response

NZ_CP017717.1 - Region 25 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,533,252 - 6,554,253 nt. (total: 21,002 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
BKM31_RS29520: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase hydratase
BKM31_RS29545: Terpene synthase/cyclase metal-binding domain protein

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

BKM31_RS29575: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Ligases: synthase
BKM31_RS29515: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000503.5 |  | 0.41 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000583.5 |  | 0.41 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000903.3 |  | 0.39 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0000885.3 |  | 0.39 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0002313.3 |  | 0.39 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0001374.5 |  | 0.38 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0002346.3 |  | 0.38 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0002316.2 |  | 0.37 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002318.2 |  | 0.36 | ribosomal | canucin A, canucin B | Streptomyces canus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000503.5 |  | 0.41 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000583.5 |  | 0.41 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000903.3 |  | 0.39 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0000885.3 |  | 0.39 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0002313.3 |  | 0.39 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0001374.5 |  | 0.38 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0002346.3 |  | 0.38 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0002316.2 |  | 0.37 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002318.2 |  | 0.36 | ribosomal | canucin A, canucin B | Streptomyces canus

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
BKM31_RS29545: T1TS
Domain 1 (54 - 332): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.88 out of 29.72
Confidence: medium
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 30.40 out of 35.63
Confidence: medium
Additional weak hits (15):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.62 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.78 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.35 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.57 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.42 out of 26.33
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.68 out of 25.88
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.10 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.71 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.63 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.01 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.54 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.71 out of 29.65
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
--- | ---
NrtR | NAD synthesis repressor
NtrC | Nitrogen regulatory protein C

NZ_CP017717.1 - Region 26 - 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: 7,666,018 - 7,693,782 nt. (total: 27,765 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: dehydrogenase oxidase oxidoreductase
BKM31_RS34535: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

BKM31_RS34570: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

BKM31_RS34575: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BKM31_RS34580: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: protease
BKM31_RS34510: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Ligases: ligase
BKM31_RS34485: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS34490: 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
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.56 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  | 0.55 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.55 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000595.3 |  | 0.47 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001928.2 |  | 0.46 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000597.4 |  | 0.46 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000131.5 |  | 0.46 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0002711.2 |  | 0.44 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.56 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  | 0.55 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.55 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000595.3 |  | 0.47 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001928.2 |  | 0.46 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000597.4 |  | 0.46 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000131.5 |  | 0.46 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0002711.2 |  | 0.44 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102

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 (18):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.64 out of 29.51
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.29 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.70 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.51 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.96 out of 30.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.91 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.90 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.13 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.40 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.03 out of 23.43
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.58 out of 26.06
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.59 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.89 out of 25.88
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.89 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.58 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.44 out of 29.65
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
TFBS Finder
Azole RiPPs
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

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_CP017717.1 - Region 27 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,110,733 - 8,131,839 nt. (total: 21,107 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
BKM31_RS36540: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: acetyltransferase
BKM31_RS36630: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Lyases: cyclase
BKM31_RS36580: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.79 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000866.5 |  | 0.48 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.46 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000271.5 |  | 0.36 | PKS | spore pigment | Streptomyces avermitilis
BGC0002535.2 |  | 0.35 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002514.3 |  | 0.32 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0002467.2 |  | 0.30 | NRPS | thermochelin | Thermocrispum agreste DSM 44070
BGC0002012.4 |  | 0.29 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.79 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000866.5 |  | 0.48 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.46 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000271.5 |  | 0.36 | PKS | spore pigment | Streptomyces avermitilis
BGC0002535.2 |  | 0.35 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002514.3 |  | 0.32 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0002467.2 |  | 0.30 | NRPS | thermochelin | Thermocrispum agreste DSM 44070
BGC0002012.4 |  | 0.29 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772

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

No significant matches found.

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

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

Genes with terpene domains:
BKM31_RS36580: T1TS
Domain 1 (10 - 332): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 25.31
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
Additional weak hits (6):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.90 out of 23.43
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.10 out of 30.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.18 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.20 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.77 out of 35.63
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP017717.1 - Region 28 - NRPS,T1PKS,arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,086,900 - 10,191,750 nt. (total: 104,851 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
arylpolyene: (APE_KS1 or APE_KS2)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### 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
BKM31_RS46075: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BKM31_RS46145: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BKM31_RS46160: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS46200: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS46350: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: aminotransferase carbamoyltransferase carboxylase transferase
BKM31_RS46025: aminotransferase

smcogs
  SMCOG1019: aminotransferase

BKM31_RS46080: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

BKM31_RS46180: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

BKM31_RS46190: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Hydrolases: deaminase dehalogenase esterase
BKM31_RS46090: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

BKM31_RS46125: thioesterase

smcogs
  SMCOG1004: thioesterase

BKM31_RS46310: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: dehydratase
BKM31_RS46305: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
BKM31_RS46085: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BKM31_RS46095: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

BKM31_RS46105: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS46130: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS46135: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BKM31_RS46150: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS46195: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS46210: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS46225: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS46230: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS46235: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS46290: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BKM31_RS46295: 3-oxoacyl-(acyl carrier protein) synthase III

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

BKM31_RS46300: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport
BKM31_RS46050: 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 | arylpolyene | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001160.5 |  |  |  | 0.90 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  | 0.90 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001135.5 |  |  |  | 0.77 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  |  |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  |  | 0.68 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001276.3 |  |  |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  |  |  | 0.67 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001273.3 |  |  |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001249.5 |  | 0.75 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.75 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.67 out of 26.85
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.96 out of 23.79
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 24.35 out of 29.72
Confidence: medium
Additional weak hits (35):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.61 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.75 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.97 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.08 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.27 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.09 out of 28.14
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.32 out of 20.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.81 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.62 out of 18.57
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.71 out of 25.88
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.04 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.10 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.70 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.80 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.13 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.79 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.60 out of 26.12
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.46 out of 20.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.01 out of 20.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.06 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.32 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.50 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.64 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.00 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.74 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.97 out of 36.54
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.60 out of 35.63
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.54 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.71 out of 28.19
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.66 out of 27.18
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.84 out of 30.98
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.79 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 47, location 10086899 - 10191750:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-pk) + (Ser - Ser - D-X) + (Phe - Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 48, location 10086899 - 10147242:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - Ser - D-X) + (Phe - Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 49, location 10132179 - 10173325:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-pk)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 50, location 10144271 - 10191750:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-pk)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BKM31_RS46085: Phe - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (12..389): Phe
nrpys: Phe

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

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

AMP-binding (1042..1439): 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:
    LATHFDFSVWEGNQIFGGEINMYGITETTVHTTF
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

BKM31_RS46105: Ser - Ser - X
Search NORINE for peptide: strict or relaxed
AMP-binding (521..926): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LVAHFDVSVWEGNQVFAGELNMYGITETTVHTTF
  Nearest Stachelhaus code(s):
    Ser DVWNVAMVHK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1577..1979): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LVAHFDVSVWEGNQVFAGELNMYGITETTVHTTF
  Nearest Stachelhaus code(s):
    Ser DVWNVAMVHK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2624..3030): 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:
    LENANDVAVGEGDQLLGGEVNVYGNTEATSNSTF
  Nearest Stachelhaus code(s):
    Ac-OH-Orn DVWALGAVNK (59% 8Å match)
    Dpr DAQDLAVVNK (53% 8Å match)
    3Me-Glu or Glu DLGKTGVVNK (41% 8Å match)
  Stachelhaus code match:
    60% (weak)

BKM31_RS46130: AHBA
CAL_domain (36..453): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 21.2
  NH2: 11.7
  shikimic_acid: 5.4
  fatty_acid: 0.0
  Acetyl-CoA: -2.4

BKM31_RS46150: Acetyl-CoA
CAL_domain (36..460): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 52.6
  fatty_acid: 42.6
  NH2: 22.9
  AHBA: 10.9
  shikimic_acid: 0.0

BKM31_RS46290: pk
PKS_AT (533..827): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  CE-Malonyl-CoA: 66.7%
  Methylmalonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 112.7
  Methoxymalonyl-CoA: 93.1
  Malonyl-CoA: 84.7
  Ethylmalonyl-CoA: 81.0
  Isobutyryl-CoA: 57.4
  CHC-CoA: 48.3
  Propionyl-CoA: 48.0
  trans-1,2-CPDA: 43.2
  2-Methylbutyryl-CoA: 41.5
  Benzoyl-CoA: 32.6
  Acetyl-CoA: 30.7
  fatty_acid: 23.5
  inactive: 14.6
  3-Methylbutyryl-CoA: 2.2

BKM31_RS46300: X
AMP-binding (224..506): 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:
    QLLS---FLPFAFAAVAGALSVYGATECLPVAAI
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP017717.1 - Region 29 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,468,179 - 10,493,960 nt. (total: 25,782 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
BKM31_RS47830: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: acetyltransferase
BKM31_RS47745: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Lyases: cyclase dehydratase
BKM31_RS47835: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

BKM31_RS61650: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase synthetase
BKM31_RS47805: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

BKM31_RS47810: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000657.5 |  | 0.56 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002283.2 |  | 0.54 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.54 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0000665.5 |  | 0.52 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000677.5 |  | 0.49 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000666.5 |  | 0.48 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0000663.5 |  | 0.48 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0002309.2 |  | 0.47 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3 |  | 0.45 | terpene | raimonol | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000657.5 |  | 0.56 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002283.2 |  | 0.54 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.54 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0000665.5 |  | 0.52 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000677.5 |  | 0.49 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000666.5 |  | 0.48 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0000663.5 |  | 0.48 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0002309.2 |  | 0.47 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3 |  | 0.45 | terpene | raimonol | Streptomyces anulatus

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

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

Genes with terpene domains:
BKM31_RS61650: T1TS + T1TS
Domain 1 (2 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (341 - 691): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

BKM31_RS47805: PT_FPPS_like
Domain 1 (46 - 348): 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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.32 out of 27.78
Confidence: medium
Additional weak hits (13):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.96 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.63 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.68 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.67 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.11 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.41 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.74 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.41 out of 31.73
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.63 out of 25.75
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.86 out of 27.18
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.10 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria

NZ_CP017717.1 - Region 30 - 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: 10,508,102 - 10,539,346 nt. (total: 31,245 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 oxidoreductase oxygenase
BKM31_RS47920: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

BKM31_RS48035: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

BKM31_RS48040: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: acetyltransferase kinase
BKM31_RS47970: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

BKM31_RS48000: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.46 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002527.2 |  | 0.45 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001374.5 |  | 0.45 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0000231.5 |  | 0.44 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002493.3 |  | 0.44 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000234.5 |  | 0.42 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001810.3 |  | 0.42 | PKS | trehangelin | Polymorphospora rubra
BGC0001723.5 |  | 0.42 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001774.5 |  | 0.42 | other (other) | spicamycin | Streptomyces fimbriatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.46 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002527.2 |  | 0.45 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001374.5 |  | 0.45 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0000231.5 |  | 0.44 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002493.3 |  | 0.44 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000234.5 |  | 0.42 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001810.3 |  | 0.42 | PKS | trehangelin | Polymorphospora rubra
BGC0001723.5 |  | 0.42 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001774.5 |  | 0.42 | other (other) | spicamycin | Streptomyces fimbriatus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
Additional weak hits (9):
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.93 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.46 out of 25.88
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.93 out of 29.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.29 out of 36.53
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.82 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.83 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP017717.1 - Region 31 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,881,004 - 10,926,625 nt. (total: 45,622 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
BKM31_RS49650: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

BKM31_RS49670: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BKM31_RS49700: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase
BKM31_RS49595: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

Hydrolases: esterase glucosidase hydrolase
BKM31_RS49640: putative esterase

smcogs
  SMCOG1104: putative esterase

BKM31_RS49690: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

BKM31_RS49705: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BKM31_RS49710: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

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

Ligases: ligase synthase
BKM31_RS49580: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS49645: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transport transporter
BKM31_RS49585: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

BKM31_RS49605: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001164.3 |  | 0.68 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.67 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002277.2 |  | 0.66 | NRPS | atromentin | Suillus grevillei
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002175.3 |  | 0.63 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001164.3 |  | 0.68 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.67 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002277.2 |  | 0.66 | NRPS | atromentin | Suillus grevillei
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002175.3 |  | 0.63 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
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.

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:
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 24.63 out of 25.88
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.13 out of 23.79
Confidence: medium
Additional weak hits (11):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.82 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.96 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.99 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.31 out of 39.62
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.86 out of 27.18
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.21 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.74 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.65 out of 24.78
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.67 out of 20.01
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.71 out of 25.31
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 53, location 10881003 - 10926625:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-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).
BKM31_RS49580: NH2
CAL_domain (36..471): NH2
minowa: NH2

Prediction, score:
  NH2: 94.4
  fatty_acid: 32.5
  AHBA: 2.9
  shikimic_acid: 0.5
  Acetyl-CoA: -3.9

BKM31_RS49645: mmal
PKS_AT (604..861): mmal
ATSignature: Malonyl-CoA, Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 104.7
  Ethylmalonyl-CoA: 95.3
  Methoxymalonyl-CoA: 91.8
  Malonyl-CoA: 88.0
  fatty_acid: 69.4
  Propionyl-CoA: 68.1
  2-Methylbutyryl-CoA: 65.6
  Isobutyryl-CoA: 51.3
  Acetyl-CoA: 50.5
  trans-1,2-CPDA: 48.5
  CHC-CoA: 46.8
  inactive: 42.1
  3-Methylbutyryl-CoA: 27.6
  Benzoyl-CoA: 21.3

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

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
PsrA | Oleic acid responsive regulator

NZ_CP017717.1 - 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: 11,337,351 - 11,348,166 nt. (total: 10,816 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
--- | --- | --- | --- | --- | ---
BGC0002152.2 |  | 0.34 | other (other) | toxoflavin | Pseudomonas protegens Pf-5
BGC0002665.2 |  | 0.29 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001486.4 |  | 0.28 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001321.3 |  | 0.23 | terpene | monoterpenes-diterpenes | Solanum habrochaites
BGC0001322.3 |  | 0.19 | terpene | lycosantalonol, β-phellandrene | Solanum lycopersicum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002152.2 |  | 0.34 | other (other) | toxoflavin | Pseudomonas protegens Pf-5
BGC0002665.2 |  | 0.29 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001486.4 |  | 0.28 | ribosomal | 3-thiaglutamate | Pseudomonas syringae pv. maculicola str. ES4326
BGC0001321.3 |  | 0.23 | terpene | monoterpenes-diterpenes | Solanum habrochaites
BGC0001322.3 |  | 0.19 | terpene | lycosantalonol, β-phellandrene | Solanum lycopersicum

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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.51 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.39 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.86 out of 27.04
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.02 out of 29.51
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.41 out of 26.85
Confidence: medium
Additional weak hits (3):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.19 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.19 out of 28.14
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.63 out of 27.04
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
DosR | Hypoxia stress response regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP017717.1 - Region 33 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 11,540,697 - 11,571,791 nt. (total: 31,095 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
BKM31_RS52550: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase protease
BKM31_RS52525: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

BKM31_RS52595: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: decarboxylase
BKM31_RS52565: 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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.66 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002527.2 |  | 0.60 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001408.5 |  | 0.60 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0000947.5 |  | 0.52 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0002692.2 |  | 0.50 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002683.2 |  | 0.43 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002629.2 |  | 0.42 | ribosomal | limnothamide | Limnothrix sp. CACIAM 69d
BGC0001167.4 |  | 0.42 | ribosomal | piricyclamide 7005E1, piricyclamide 7005E2, piricyclamide 7005E3, piricyclamide 7005E4 | Microcystis aeruginosa PCC 7005
BGC0000943.5 |  | 0.42 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002466.3 |  | 0.37 | NRPS | peucechelin | Streptomyces peucetius subsp. caesius ATCC 27952

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.66 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002527.2 |  | 0.60 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001408.5 |  | 0.60 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0000947.5 |  | 0.52 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0002692.2 |  | 0.50 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002683.2 |  | 0.43 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002629.2 |  | 0.42 | ribosomal | limnothamide | Limnothrix sp. CACIAM 69d
BGC0001167.4 |  | 0.42 | ribosomal | piricyclamide 7005E1, piricyclamide 7005E2, piricyclamide 7005E3, piricyclamide 7005E4 | Microcystis aeruginosa PCC 7005
BGC0000943.5 |  | 0.42 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002466.3 |  | 0.37 | NRPS | peucechelin | Streptomyces peucetius subsp. caesius ATCC 27952

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.62 out of 36.53
Confidence: medium
Additional weak hits (13):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.94 out of 19.26
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.51 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.46 out of 31.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.38 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.66 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.54 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.97 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 35.63
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.14 out of 36.53
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.14 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.69 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.58 out of 23.43
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor

NZ_CP017717.1 - Region 34 - NRPS,T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 11,969,038 - 12,040,280 nt. (total: 71,243 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
BKM31_RS54575: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BKM31_RS54580: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: aminotransferase halogenase
BKM31_RS54585: aminotransferase

smcogs
  SMCOG1019: aminotransferase

BKM31_RS54610: flavin-dependent tyrosine-like hpg halogenase

halogenases
  flavin-dependent tyrosine-like hpg halogenase
MITE
  MITE0000028Halogenation (identity: 76.30%)
smcogs
  SMCOG1119: halogenase

Lyases: hydratase
BKM31_RS54595: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

BKM31_RS54600: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

BKM31_RS54605: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
BKM31_RS54550: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS54555: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS54560: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BKM31_RS54590: 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 | NRPS | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001635.4 |  |  | 1.29 | NRPS, PKS | kistamicin A | Nonomuraea sp. ATCC 55076
BGC0002341.2 |  |  | 0.94 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002608.2 |  |  | 0.92 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0002135.2 |  |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001758.4 |  |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001635.4 |  | 0.98 | NRPS, PKS | kistamicin A | Nonomuraea sp. ATCC 55076
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002608.2 |  | 0.76 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0000322.3 |  | 0.71 | NRPS | chloroeremomycin | Amycolatopsis orientalis
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001050.5 |  | 0.70 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
Additional weak hits (19):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.35 out of 30.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.98 out of 28.14
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.92 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.65 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.84 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.92 out of 23.43
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.38 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.81 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.81 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.31 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.56 out of 36.53
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.91 out of 29.65
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.35 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.37 out of 26.06
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.81 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.09 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 56, location 11969037 - 12040280:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Trp) + (D-Dhpg) + (Hpg - D-Hpg - Tyr) + (Hpg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 57, location 11969037 - 12034871:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Trp) + (D-Dhpg) + (Hpg - D-Hpg - Tyr) + (Hpg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 58, location 11999191 - 12040280:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpg - D-Hpg - Tyr) + (Hpg)

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).
BKM31_RS54550: Trp
Search NORINE for peptide: strict or relaxed
AMP-binding (638..1022): Trp
nrpys: Trp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FFRSFDVAMGDPIMVIGGEVNEYGVTEATITSTV
  Nearest Stachelhaus code(s):
    Trp DVGIVGEITK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

BKM31_RS54555: Dhpg
Search NORINE for peptide: strict or relaxed
AMP-binding (468..852): 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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    dhpg (Dhpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPAFDASLHDVQLATGGDRHTYGPTESTLYTTW
  Nearest Stachelhaus code(s):
    Dhpg DAHQAGTLYK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

BKM31_RS54560: Hpg - Hpg - Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (458..842): Hpg
nrpys: Hpg

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:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPAFDISLYEVHLLTGGDRHLYGPTEITLCGTW
  Nearest Stachelhaus code(s):
    Hpg DIYHLGLLCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1488..1878): Hpg
nrpys: Hpg

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:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LEPAFDISLYEVHLLTGGDRHMYGPTETTLCATW
  Nearest Stachelhaus code(s):
    Hpg DIYHLGMLCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2992..3376): Tyr
nrpys: Tyr

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

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

BKM31_RS54565: Hpg
Search NORINE for peptide: strict or relaxed
AMP-binding (451..848): Hpg
nrpys: Hpg

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:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPAFDASLYEVHLLTGGDRHLYGPTETTLCATW
  Nearest Stachelhaus code(s):
    Hpg DAYHLGLLCK (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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein

NZ_CP017717.1 - Region 35 - 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: 12,340,018 - 12,393,654 nt. (total: 53,637 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
BKM31_RS56105: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

BKM31_RS56115: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: kinase
BKM31_RS56070: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Hydrolases: hydrolase
BKM31_RS56145: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

BKM31_RS56260: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase synthase
BKM31_RS56155: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

BKM31_RS56170: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BKM31_RS63945: 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
--- | --- | --- | --- | --- | ---
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001133.4 |  | 0.68 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001133.4 |  | 0.68 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.37 out of 23.43
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.84 out of 30.12
Confidence: medium
Additional weak hits (16):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.30 out of 28.14
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.08 out of 30.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.92 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.11 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.57 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.34 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.12 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.10 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.22 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.13 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.76 out of 18.57
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.70 out of 29.51
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.68 out of 23.43
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 59, location 12340017 - 12393654:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Tyr) + (Asp - 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).
BKM31_RS63945: Asp - X
Search NORINE for peptide: strict or relaxed
AMP-binding (534..914): Asp
nrpys: Asp

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

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

AMP-binding (1608..2003): X
nrpys: Asp, Asn

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:
    asp,asn (Asp, Asn)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YGMSADFGLTCGKCILAGEQSHYGHTESTMICLV
  Nearest Stachelhaus code(s):
    Asp DLTKIGHVGK (59% 8Å match)
  Stachelhaus code match:
    60% (weak)

BKM31_RS56170: X - Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (22..401): X
nrpys: Ile, Leu

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:
    LWESFDASITQTFGLSGGELNMYGPTECTTGSTM
  Nearest Stachelhaus code(s):
    Leu or Ile DAFFLGMTFK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1065..1440): Tyr
nrpys: Tyr

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:
    LGMAFDASASESDLVAGGEWNAYGPTETTVTSTL
  Nearest Stachelhaus code(s):
    Tyr DAIDVGAVGK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
BldD | Development and antibiotic global regulator
OsdR | Development and stress management regulator

NZ_CP017717.1 - Region 36 - 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: 12,785,949 - 12,827,004 nt. (total: 41,056 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: oxidoreductase oxygenase
BKM31_RS58085: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

BKM31_RS58190: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: kinase methyltransferase
BKM31_RS58060: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

BKM31_RS58125: Methylation

MITE
  MITE0000155Methylation (identity: 66.50%)
smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Hydrolases: hydrolase
BKM31_RS58135: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: synthase
BKM31_RS58120: 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
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.72 | 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 |  | 0.55 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001962.3 |  | 0.50 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0001647.3 |  | 0.43 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0001964.2 |  | 0.42 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000571.3 |  | 0.41 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0000908.3 |  | 0.40 | other (other) | melanin | Streptomyces avermitilis
BGC0001223.5 |  | 0.40 | other (other) | hydroxysporine | uncultured bacterium
BGC0002390.2 |  | 0.40 | terpene | zealexin A1 | Zea mays

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.72 | 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 |  | 0.55 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001962.3 |  | 0.50 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0001647.3 |  | 0.43 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0001964.2 |  | 0.42 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000571.3 |  | 0.41 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0000908.3 |  | 0.40 | other (other) | melanin | Streptomyces avermitilis
BGC0001223.5 |  | 0.40 | other (other) | hydroxysporine | uncultured bacterium
BGC0002390.2 |  | 0.40 | terpene | zealexin A1 | Zea mays

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: 20.47 out of 20.47
Confidence: strong
Additional weak hits (16):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.47 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.68 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.43 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.43 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.58 out of 20.01
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.85 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.85 out of 30.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.98 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.85 out of 28.14
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.54 out of 30.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.26 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.81 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.10 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.54 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.87 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.42 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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