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

NZ_CP018145.1 (Brevibacillus formosus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | lanthipeptide-class-i | 737,485 | 762,010 |
Region 2 | NI-siderophore | 1,088,893 | 1,120,630 | High | petrobactin | other:other
Region 3 | terpene-precursor | 1,408,632 | 1,429,534 |  |
Region 4 | azole-containing-RiPP | 1,773,548 | 1,797,118 |
Region 5 | RiPP-like | 1,802,248 | 1,814,182 |
Region 6 | NRPS,opine-like-metallophore | 1,873,981 | 1,961,466 | High | tyrocidine | NRPS:Type I
Region 7 | NRPS | 1,993,607 | 2,102,223 | High | gramicidin | NRPS:Type I
Region 8 | NRPS,T1PKS,transAT-PKS | 2,127,394 | 2,314,194 | Low | zwittermicin A | NRPS:Type I+PKS
Region 9 | lanthipeptide-class-iii | 2,392,508 | 2,415,129 |
Region 10 | transAT-PKS,NRPS | 2,473,963 | 2,550,851 |  |
Region 11 | NRPS,transAT-PKS-like | 2,566,592 | 2,626,899 |
Region 12 | T3PKS | 2,999,473 | 3,040,537 |
Region 13 | terpene | 3,148,918 | 3,170,825 |
Region 14 | NRPS,transAT-PKS,cyclic-lactone-autoinducer | 3,335,100 | 3,446,455 | Low | aurantinin B/aurantinin C/aurantinin D | PKS
Region 15 | RiPP-like | 3,649,811 | 3,660,659 |
Region 16 | NRP-metallophore,NRPS | 3,883,377 | 3,943,892 | High | ulbactin F/ulbactin G | NRPS:Type I
Region 17 | lanthipeptide-class-iv | 4,761,845 | 4,784,205 |
Region 18 | azole-containing-RiPP | 6,315,021 | 6,338,583 |

NZ_CP018145.1 - Region 1 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 737,485 - 762,010 nt. (total: 24,526 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
BP422_RS03835: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

BP422_RS03840: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

BP422_RS03845: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Lyases: cyclase dehydratase
BP422_RS03795: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

BP422_RS03800: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Translocases: transporter
BP422_RS03820: 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 | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.60 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000542.3 |  | 0.59 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.59 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002640.2 |  | 0.59 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0000560.5 |  | 0.55 | ribosomal | subtilomycin | Bacillus subtilis
BGC0002635.2 |  | 0.55 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000506.4 |  | 0.54 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000515.4 |  | 0.53 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0002323.2 |  | 0.53 | ribosomal | nisin J | Staphylococcus capitis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.60 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000542.3 |  | 0.59 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.59 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002640.2 |  | 0.59 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0000560.5 |  | 0.55 | ribosomal | subtilomycin | Bacillus subtilis
BGC0002635.2 |  | 0.55 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000506.4 |  | 0.54 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000515.4 |  | 0.53 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0002323.2 |  | 0.53 | ribosomal | nisin J | Staphylococcus capitis

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

No significant matches found.

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.62 out of 21.55
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.17 out of 25.31
Confidence: medium
Additional weak hits (1):
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.37 out of 20.47
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (737484...762010)
BP422_RS03800
  RRE type: Lanthipeptide_LanB_RRE
  Location: 25 - 115
  Score: 46.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
CatR | H2O2-responsive repressor
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP018145.1 - Region 2 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,088,893 - 1,120,630 nt. (total: 31,738 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
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
Isomerases: mutase
BP422_RS05510: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase
BP422_RS05485: 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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000942.4 |  | 0.80 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0002469.2 |  | 0.50 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000295.5 |  | 0.50 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002692.2 |  | 0.49 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002694.2 |  | 0.48 | other (other) | roseobactin | Phaeobacter inhibens 2.10
BGC0001499.5 |  | 0.48 | other (other) | aerobactin | Pantoea ananatis
BGC0001713.5 |  | 0.47 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002633.2 |  | 0.47 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002471.3 |  | 0.45 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0002470.2 |  | 0.45 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000942.4 |  | 0.80 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0002469.2 |  | 0.50 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000295.5 |  | 0.50 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002692.2 |  | 0.49 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002694.2 |  | 0.48 | other (other) | roseobactin | Phaeobacter inhibens 2.10
BGC0001499.5 |  | 0.48 | other (other) | aerobactin | Pantoea ananatis
BGC0001713.5 |  | 0.47 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002633.2 |  | 0.47 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002471.3 |  | 0.45 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0002470.2 |  | 0.45 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.00 out of 20.47
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 23.37 out of 24.78
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.85 out of 29.38
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.11 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.27 out of 28.19
Confidence: medium
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.70 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.57 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.80 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.90 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.73 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.25 out of 31.73
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 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.17 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
FuR variant 1 | Ferric Uptake Regulator
LexA variant 2 | Repressor of DNA damage response
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_CP018145.1 - Region 3 - 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: 1,408,632 - 1,429,534 nt. (total: 20,903 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
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: carboxylase
BP422_RS07060: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Ligases: synthase synthetase
BP422_RS07105: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

BP422_RS07115: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000639.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000668.5 |  | 0.36 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000639.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000668.5 |  | 0.36 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830

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

Genes with terpene domains:
BP422_RS07105: PT_FPPS_like
Domain 1 (35 - 300): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  IPP, DMAPP → FPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.87 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
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP018145.1 - Region 4 - 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: 1,773,548 - 1,797,118 nt. (total: 23,571 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
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
Transferases: acetyltransferase aminotransferase
BP422_RS08955: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

BP422_RS08960: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

BP422_RS31990: 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002488.3 |  | 0.51 | other (other) | bacillopaline | Paenibacillus mucilaginosus KNP414
BGC0001638.4 |  | 0.51 | ribosomal | klebsazolicin | Klebsiella pneumoniae subsp. ozaenae
BGC0002487.3 |  | 0.46 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0000569.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001173.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0000925.5 |  | 0.43 | other (other) | quinolobactin | Pseudomonas fluorescens
BGC0000607.5 |  | 0.42 | ribosomal | micrococcin P1 | Macrococcus caseolyticus
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002285.2 |  | 0.41 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001146.5 |  | 0.41 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002488.3 |  | 0.51 | other (other) | bacillopaline | Paenibacillus mucilaginosus KNP414
BGC0001638.4 |  | 0.51 | ribosomal | klebsazolicin | Klebsiella pneumoniae subsp. ozaenae
BGC0002487.3 |  | 0.46 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0000569.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001173.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0000925.5 |  | 0.43 | other (other) | quinolobactin | Pseudomonas fluorescens
BGC0000607.5 |  | 0.42 | ribosomal | micrococcin P1 | Macrococcus caseolyticus
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002285.2 |  | 0.41 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001146.5 |  | 0.41 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908

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

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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.32 out of 25.88
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 26.61 out of 29.38
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.00 out of 28.19
Confidence: medium
Additional weak hits (8):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.22 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.69 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.95 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.06 out of 28.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.83 out of 36.53
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.06 out of 26.06
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.65 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.31 out of 25.88
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (1773547...1797118)
BP422_RS08940
  RRE type: Heterocycloanthracin_C_RRE
  Location: 0 - 99
  Score: 135.0
  RRE type: Thiopeptide_F_RRE
  Location: 7 - 88
  Score: 45.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
FuR variant 1 | Ferric Uptake Regulator
PsrA | Oleic acid responsive regulator
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

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_CP018145.1 - Region 5 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,802,248 - 1,814,182 nt. (total: 11,935 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
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
BP422_RS09055: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.38 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002161.2 |  | 0.35 | PKS | scytalone, T3HN | Pestalotiopsis fici W106-1
BGC0000598.5 |  | 0.31 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0000470.6 |  | 0.31 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.31 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.31 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.29 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001197.5 |  | 0.27 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001148.5 |  | 0.27 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus
BGC0001753.3 |  | 0.26 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.38 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002161.2 |  | 0.35 | PKS | scytalone, T3HN | Pestalotiopsis fici W106-1
BGC0000598.5 |  | 0.31 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0000470.6 |  | 0.31 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.31 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.31 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.29 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001197.5 |  | 0.27 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001148.5 |  | 0.27 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus
BGC0001753.3 |  | 0.26 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.80 out of 18.16
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.20 out of 25.88
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.51 out of 27.78
Confidence: medium
Additional weak hits (3):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.62 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.26 out of 29.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.15 out of 25.88
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
PsrA | Oleic acid responsive regulator

NZ_CP018145.1 - Region 6 - NRPS,opine-like-metallophore
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: 1,873,981 - 1,961,466 nt. (total: 87,486 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
opine-like-metallophore: (CntL and CntM)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: PPTase
BP422_RS09440: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase hydrolase
BP422_RS09445: thioesterase

smcogs
  SMCOG1004: thioesterase

BP422_RS09455: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase
BP422_RS09415: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BP422_RS09420: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BP422_RS09425: 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 | opine-like-metallophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002488.3 |  |  | 0.70 | other (other) | bacillopaline | Paenibacillus mucilaginosus KNP414
BGC0002487.3 |  |  | 0.51 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0000452.5 |  |  | 0.49 | NRPS | tyrocidine | Brevibacillus brevis NBRC 100599
BGC0000426.5 |  |  | 0.46 | NRPS | sevadicin | Paenibacillus larvae
BGC0001758.4 |  |  | 0.44 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  | 0.44 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002075.3 |  |  | 0.43 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  |  | 0.43 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  | 0.43 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  | 0.43 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002488.3 |  | 0.84 | other (other) | bacillopaline | Paenibacillus mucilaginosus KNP414
BGC0002487.3 |  | 0.79 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0000452.5 |  | 0.78 | NRPS | tyrocidine | Brevibacillus brevis NBRC 100599
BGC0000426.5 |  | 0.76 | NRPS | sevadicin | Paenibacillus larvae
BGC0001758.4 |  | 0.75 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.74 | 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.72 out of 20.97
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.00 out of 29.72
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.31 out of 28.19
Confidence: medium
Additional weak hits (5):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.21 out of 39.62
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.74 out of 30.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.18 out of 35.63
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.82 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 6, location 1873980 - 1961466:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Phe) + (Pro - X - D-Phe) + (Asn - Gln - Tyr - Val - Orn - Leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 1873980 - 1947688:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Phe) + (Pro - X - D-Phe) + (Asn - Gln - Tyr - Val - Orn - Leu)

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).
BP422_RS09415: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (37..430): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LFFAFDASVWEMTLITAGSVNAYGPTETSICATI
  Nearest Stachelhaus code(s):
    Phe DAWTIAAICK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS09420: Pro - X - Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (472..870): Pro
nrpys: Pro

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

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

AMP-binding (1512..1906): X
nrpys: (unknown)

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:
    SWNLFDGFVLTALCVLGGEVNAYGPTESSVIATY
  Nearest Stachelhaus code(s):
    3OH-Leu DALLVGAVAK (56% 8Å match)
    Leu DALLVGAVAK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2550..2940): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LVFAFDASVWDMTLITAGSINGYGPTESTVCATL
  Nearest Stachelhaus code(s):
    Phe DAWTIAGVCK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS09425: Asn - Gln - Tyr - Val - Orn - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (470..863): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDLTVTSTKLIVGGEFNEYGPTETVVGCMI
  Nearest Stachelhaus code(s):
    Asn DLTKIGEVGK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1505..1900): Gln
nrpys: Gln

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

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

AMP-binding (2542..2938): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    SWKLFDGFVLSTTCTLGGEANEYGPTESSVVATR
  Nearest Stachelhaus code(s):
    Tyr DGLTTGEVVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3582..3975): 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:
    LHTGFDAMTFEGWLIVGGEWNGYGPTENTTFSTC
  Nearest Stachelhaus code(s):
    Val DAFWIGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4617..5019): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VAWAFDVSTGDREAILGADVNSYGVTEACIDSSY
  Nearest Stachelhaus code(s):
    Orn DVGEIGSIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5663..6060): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    CWRFFDGFVASAYGTLGGENNEYGPTENSVVTTI
  Nearest Stachelhaus code(s):
    Leu DGAYTGEVVK (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
--- | ---
CcpA | Catabolite control protein A
NtrC | Nitrogen regulatory protein C
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP018145.1 - Region 7 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,993,607 - 2,102,223 nt. (total: 108,617 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
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
BP422_RS09895: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: back translocase esterase
BP422_RS09775: thioesterase

smcogs
  SMCOG1004: thioesterase

BP422_RS09890: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Ligases: ligase
BP422_RS09795: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BP422_RS09800: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BP422_RS32470: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BP422_RS32475: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: permease
BP422_RS09900: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000367.5 |  | 0.86 | NRPS | gramicidin | Brevibacillus brevis NBRC 100599
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.71 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000367.5 |  | 0.86 | NRPS | gramicidin | Brevibacillus brevis NBRC 100599
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.71 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001825.4 |  | 0.70 | 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.95 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.72 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.08 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.21 out of 27.78
Confidence: medium
Additional weak hits (10):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.86 out of 25.88
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.33 out of 25.88
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.97 out of 25.88
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.45 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.31 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.80 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.41 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.55 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: 21.14 out of 26.06
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 9, location 1993606 - 2102223:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - D-Gly) + (Ala - D-Leu - Ala - D-Val - Ala - D-Val) + (Val - D-Val - X - D-Leu - X - D-Leu) + (Trp - D-Leu - Trp - Gly)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BP422_RS09795: Leu - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (207..593): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWHSFDGSVLEPFFLTGGDYNLYGPTECTILATV
  Nearest Stachelhaus code(s):
    Leu DLLHLGLILK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1228..1625): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VAMTFDISVAEGNFLACGEENIYGPTEATIYTSR
  Nearest Stachelhaus code(s):
    Gly DIANLCIIYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS09800: Ala - Leu - Ala - Val - Ala - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (472..869): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    QALTFDVSVAEGNFMAAGEENIYGPTEATIYASS
  Nearest Stachelhaus code(s):
    Ala DVANFAIIYK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1535..1929): Leu
nrpys: Leu

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

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

AMP-binding (3052..3445): Ala
nrpys: Ala

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

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

AMP-binding (4107..4505): 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:
    LETSFDAATFEGWLLVGGDINGYGPTENTTFTCC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5632..6025): Ala
nrpys: Ala

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

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

AMP-binding (6687..7085): 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:
    LETSFDAATFEGWLLVGGDINGYGPTENTTFTCC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS32470: Val - Val - X - Leu - X - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (467..865): 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:
    LNTSFDAATFEGWLLVGGDINGYGPTENTTFTCC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1530..1928): 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:
    LNTSFDAATFEGWLLVGGDINGYGPTENTTFTCC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3057..3446): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  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:
    MYLCFDVSVAEMMTVIGGEFNCYGPTEATVCTTL
  Nearest Stachelhaus code(s):
    Trp DVAMVGAVCK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4108..4502): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHAFDASVWEPFLLTGGDVNQYGPTENAVVATA
  Nearest Stachelhaus code(s):
    Leu DAWFLGQVVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5631..6020): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSLTFDVSVSEMTMIVGGEFNCYGPTETTVTATL
  Nearest Stachelhaus code(s):
    Trp DVSAIGCVTK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (6688..7081): Leu
nrpys: Leu

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

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

BP422_RS32475: Trp - Leu - Trp - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (470..859): Trp
nrpys: Trp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MALTFDVSVSEMSMIVGGEFNCYGPTEATVCSTM
  Nearest Stachelhaus code(s):
    Trp DVSSIGCVCK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1524..1918): Leu
nrpys: Leu

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

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

AMP-binding (3050..3440): Trp
nrpys: Trp

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:
    MAYTFDVSISEQSMEVGGDYNCYGPTEATVGTVI
  Nearest Stachelhaus code(s):
    Trp DVSSEGCVGK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4104..4495): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWATFDLSVYEANTNLCGEFNLYGPTEDTVYSTH
  Nearest Stachelhaus code(s):
    Gly DLYNNCLVYK (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
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis

NZ_CP018145.1 - Region 8 - NRPS,T1PKS,transAT-PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,127,394 - 2,314,194 nt. (total: 186,801 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))
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
BP422_RS10215: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

BP422_RS10235: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

BP422_RS10315: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

BP422_RS10390: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

BP422_RS10440: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acetyltransferase acylase aminotransferase
BP422_RS10355: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

BP422_RS10400: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

BP422_RS10415: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

BP422_RS10420: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase hydrolase phosphatase
BP422_RS10210: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

BP422_RS10220: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

BP422_RS10330: thioesterase

smcogs
  SMCOG1004: thioesterase

BP422_RS10340: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: ligase synthase
BP422_RS10205: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BP422_RS10240: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10250: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10260: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10265: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BP422_RS10270: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10280: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10285: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10290: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10335: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10345: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10350: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10360: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10365: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

BP422_RS10370: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

BP422_RS10375: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10380: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS10405: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BP422_RS10410: 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 | T1PKS | transAT-PKS | T1PKS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  |  |  | 2.09 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  |  |  | 1.99 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  |  |  |  |  | 1.95 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  |  |  |  | 1.95 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  |  |  | 1.93 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  |  | 1.92 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  |  |  | 1.89 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  |  |  |  | 1.84 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  |  |  |  |  | 1.83 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  |  |  |  |  | 1.76 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001641.4 |  | 0.74 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.72 | 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:
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 26.79 out of 30.25
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 22.42 out of 26.33
Confidence: medium
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 23.83 out of 29.25
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.33 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.10 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.06 out of 28.19
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.43 out of 28.19
Confidence: medium
Additional weak hits (13):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.87 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.78 out of 36.54
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.12 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.41 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.46 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.53 out of 21.55
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.19 out of 30.11
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.27 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.51 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.73 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.10 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.75 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.10 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 10, location 2127393 - 2314194:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Asn) + (Gly - mal - Ser - Ser) + (ohmal) + (Thr) + (Gly - Cys) + (ohmal - ohmal) + (ohmal - Gly) + (pk) + (X) + (ohmal - Gly) + (ccmal) + (ccmal) + (ccmal - Gly) + (ccmal) + (ccmal) + (Ser) + (X - X - 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).
BP422_RS10205: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (461..855): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDLTITSTKLIVGGELNEYGPTETVVGCMI
  Nearest Stachelhaus code(s):
    Asn DLTKIGEVGK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS10240: Gly - mal - Ser - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (468..874): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGMTFDIFVLEAQALIGGEYNVYGPTETTVWSTV
  Nearest Stachelhaus code(s):
    Gly DILQLGVVWK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

PKS_AT (1599..1891): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 66.7%
  2-Rhyd-Malonyl-CoA: 58.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 82.6
  inactive: 54.7
  Methoxymalonyl-CoA: 51.7
  Methylmalonyl-CoA: 32.7
  Propionyl-CoA: 26.8
  Isobutyryl-CoA: 15.4
  Ethylmalonyl-CoA: 11.3
  Acetyl-CoA: 10.5
  trans-1,2-CPDA: 10.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

AMP-binding (2521..2917): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWELHFICSGEHNLYGPTEASIDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHISLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3561..3960): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWELHFICSGEHNLYGPTEASIDVSY
  Nearest Stachelhaus code(s):
    Ser DVWHISLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS10250: mal
PKS_AT (502..794): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 62.5%
  2-Rhyd-Malonyl-CoA: 58.3%
  inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 104.0
  Methoxymalonyl-CoA: 63.4
  inactive: 52.6
  Methylmalonyl-CoA: 43.1
  Propionyl-CoA: 26.7
  Benzoyl-CoA: 19.8
  Isobutyryl-CoA: 16.2
  2-Methylbutyryl-CoA: 12.4
  Ethylmalonyl-CoA: 11.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

BP422_RS10265: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (269..669): 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:
    LHEHFDFSVWEGNQIFGGEINMYGITETTVHTTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS10270: Gly - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (1850..2242): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGVTFDIFWLELQTLIGGEYNLYGPTETTIWSTI
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2904..3288): 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:
    TDISFDLSVYDGNSMLSGDVSLGGATEASIWSIY
  Nearest Stachelhaus code(s):
    Cys DLYNMSLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS10285: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (1705..2127): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWGTFDISVFEGHSMLGGEHNMYGPTETTIWISS
  Nearest Stachelhaus code(s):
    Gly DIFHMGMIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS10290: pk
PKS_AT (530..718): pk
ATSignature: (unknown)
No matches above 50%
minowa: inactive

Prediction, score:
  inactive: 31.6
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0
  Malonyl-CoA: -5.7

BP422_RS10335: X
AMP-binding (2189..2596): X
nrpys: Gly, Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YQFTHAIGILDGHSLLGGEVNFLGCSELMVISFF
  Nearest Stachelhaus code(s):
    Gly DILQLGVVWK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

BP422_RS10350: mal - Gly
Search NORINE for peptide: strict or relaxed
PKS_AT (531..817): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 77.5
  inactive: 54.2
  Methoxymalonyl-CoA: 43.5
  Methylmalonyl-CoA: 23.6
  Propionyl-CoA: 3.2
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

AMP-binding (1974..2368): Gly
nrpys: Gly

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

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

BP422_RS10355: mal
PKS_AT (6..293): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 66.7%
  2-Methylbutyryl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 100.1
  inactive: 44.2
  Methoxymalonyl-CoA: 18.5
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

BP422_RS10370: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (2006..2428): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWSTFDISVFEGHSLIGGEYNMYGPTEATIWATC
  Nearest Stachelhaus code(s):
    Gly DIFHMGMIWK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BP422_RS10405: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (553..963): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEGHFFASGEINLYGPTETTVEVSW
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

BP422_RS10410: X - X - X
AMP-binding (281..683): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWYAFDLAQKNANCFLGGEVNTYGPTECTDIASY
  Nearest Stachelhaus code(s):
    Hse DLKNVGSDVK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1323..1725): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWYAFDLAQKNANCFLGGEVNTYGPTECTDIASY
  Nearest Stachelhaus code(s):
    Hse DLKNVGSDVK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (2365..2767): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWYAFDLAQKNANCFLGGEVNTYGPTECTDIASY
  Nearest Stachelhaus code(s):
    Hse DLKNVGSDVK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ColR | Phenol-responsive regulator
MogR | Repressor of flagellar motility genes
SypG | Regulator of biofilm formation and host colonization
ZuR variant 1 | Zinc-responsive repressor

NZ_CP018145.1 - Region 9 - lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,392,508 - 2,415,129 nt. (total: 22,622 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
BP422_RS10975: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

BP422_RS10980: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Hydrolases: deacetylase hydrolase
BP422_RS10930: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

BP422_RS11010: 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 | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002700.2 |  | 0.54 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000551.5 |  | 0.53 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0001226.4 |  | 0.52 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0002111.3 |  | 0.51 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000501.3 |  | 0.51 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.51 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000496.5 |  | 0.50 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3 |  | 0.50 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000553.3 |  | 0.48 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002701.2 |  | 0.46 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002700.2 |  | 0.54 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000551.5 |  | 0.53 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0001226.4 |  | 0.52 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0002111.3 |  | 0.51 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000501.3 |  | 0.51 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.51 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000496.5 |  | 0.50 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3 |  | 0.50 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000553.3 |  | 0.48 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002701.2 |  | 0.46 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus

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

No significant matches found.

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

No significant matches found.

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

#### Lanthipeptide(s) for BP422_RS10970

allorf_2405271_2405375
Leader:
MNQVLNLQKLPQNEASEVAA
Core:
R W S L Y S N I C P W P W G
Core with dehydrations:
R W Dha L Y Dha N I Cys P W P W G

#### antiSMASH-DB 4.0 matches for allorf_2405271_2405375

100.0%
NZ_CP018145.1 and 1 other:
NZ_LMPN02000035.1 Lanthipeptides: allorf_21181_21285_lanthipeptide
Lanthipeptides: allorf_2405271_2405375_lanthipeptide
1
R W S L Y S N I C P W P W G
14
R W S L Y S N I C P W P W G
1
R W S L Y S N I C P W P W G
14
92.9%
NZ_BDFB01000004.1 and 1 other:
NZ_CP023474.1 Lanthipeptides: allorf_3553947_3554057_lanthipeptide
Lanthipeptides: allorf_0474880_0474990_lanthipeptide
2
W S L Y S N I C P W P W G
14
W S L Y S N I C P W P W G
1
W S L Y S N I C P W P W G
13
92.9%
NZ_CP042161.1:
Lanthipeptides: allorf_1767960_1768070_lanthipeptide
1
R W S L Y S N I C P W P W G
14
R W S L Y S N I C W P W G
1
R W S L Y S N I C H W P W G
14
with 2 more sequence matches
85.7%
NZ_CP030117.1:
Lanthipeptides: allorf_3078198_3078308_lanthipeptide
2
W S L Y S N I C P W P W G
14
W S L Y S N I C W P W G
1
W S L Y S N I C H W P W G
13
17.9%
NZ_LR134301.1:
Lanthipeptides: allorf_1738566_1738781_lanthipeptide
7
N I C P W P W G
14
C P W P G
2
G T C P W P G G
9

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.23 out of 21.55
Confidence: medium
Additional weak hits (1):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.01 out of 36.54
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

allorf_2405271_2405375 - Class III
  Cleavage pHMM score: 1.20
  RODEO score: 0
  Monoisotopic mass: 1727.8 Da
  Molecular weight: 1729.0 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1747.0 Da N = 1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation

NZ_CP018145.1 - Region 10 - NRPS,transAT-PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,473,963 - 2,550,851 nt. (total: 76,889 nt) Show pHMM detection rules used
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
BP422_RS11360: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

BP422_RS11375: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: acetyltransferase acylase aminotransferase phosphorylase
BP422_RS11425: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

BP422_RS11450: aminotransferase

smcogs
  SMCOG1019: aminotransferase

BP422_RS11565: thiamine-phosphate pyrophosphorylase

smcogs
  SMCOG1280: thiamine-phosphate pyrophosphorylase

BP422_RS11570: thiamine-phosphate pyrophosphorylase

smcogs
  SMCOG1280: thiamine-phosphate pyrophosphorylase

BP422_RS11585: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: deaminase hydrolase
BP422_RS11315: HAD-superfamily hydrolase, subfamily IA, variant

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

BP422_RS11325: isochorismatase

smcogs
  SMCOG1027: isochorismatase

BP422_RS11390: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

BP422_RS11400: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Ligases: ligase synthase
BP422_RS11405: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

BP422_RS11420: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS11430: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BP422_RS11435: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BP422_RS11440: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BP422_RS11445: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BP422_RS11455: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BP422_RS11465: 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 | transAT-PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001135.5 |  |  | 0.89 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.87 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  | 0.83 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  |  | 0.82 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001758.4 |  |  | 0.81 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  | 0.79 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.79 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  |  | 0.77 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001833.4 |  |  | 0.77 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  | 0.71 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.71 | 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.68 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.26 out of 27.78
Confidence: medium
Additional weak hits (9):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.31 out of 29.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.40 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.56 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.26 out of 30.22
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.91 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.52 out of 26.06
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.08 out of 32.38
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.48 out of 26.06
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 12, location 2473962 - 2550851:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Asn) + (X) + (X - X) + (X) + (Me-ccmal - Gly) + (mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BP422_RS11425: mal
PKS_AT (6..287): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 105.8
  Methoxymalonyl-CoA: 45.1
  Methylmalonyl-CoA: 37.6
  inactive: 32.5
  Propionyl-CoA: 23.9
  Acetyl-CoA: 11.8
  Ethylmalonyl-CoA: 8.9
  2-Methylbutyryl-CoA: 8.2
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

BP422_RS11430: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (2094..2487): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGITFDIFLLEVQLLIGGEYNLYGPTETTIWSTV
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS11435: X
AMP-binding (276..677): X
nrpys: Ser, Thr, Dhpg, Hpg

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTYDSSVWQWDFILGGETNLYGPTETSIGVIY
  Nearest Stachelhaus code(s):
    Glu DVWHIGSIGK (71% 8Å match)
    Orn DVWNIGLIHK (59% 8Å match)
  Stachelhaus code match:
    70% (weak)

BP422_RS11440: X
AMP-binding (275..693): X
nrpys: (unknown)

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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    HAKAFDISVWQAEVAVTGEVNMYGPTEASDDITH
  Nearest Stachelhaus code(s):
    Dpr DIWEMTADDK (91% 8Å match)
    Dab DIWELTADDK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

BP422_RS11445: X
AMP-binding (44..463): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TWLTFTDSVWEWQFFNGGEANIYGMTESAIYASV
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIDK (59% 8Å match)
  Stachelhaus code match:
    60% (weak)

BP422_RS11455: X
AMP-binding (470..865): 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:
    AWHAFDASVVECLVLCTGEYNLYGPTENSISASG
  Nearest Stachelhaus code(s):
    Hpg DAVHLGLLCK (47% 8Å match)
  Stachelhaus code match:
    60% (weak)

BP422_RS11465: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (446..839): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDLTVTSCKLIVGGELNEYGPTETVVGCMI
  Nearest Stachelhaus code(s):
    Asn DLTKIGEVGK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ToxT | Regulator of MSHA biosynthesis

NZ_CP018145.1 - Region 11 - NRPS,transAT-PKS-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: 2,566,592 - 2,626,899 nt. (total: 60,308 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
transAT-PKS-like: cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS) and not PKS_AT)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
BP422_RS11680: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

BP422_RS11715: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

BP422_RS11750: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

BP422_RS11825: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase sulfhydrylase
BP422_RS11675: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

BP422_RS11810: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

Hydrolases: protease
BP422_RS11690: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Ligases: ligase synthase
BP422_RS11735: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

BP422_RS11740: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | NRPS | transAT-PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  |  | 0.69 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001825.4 |  |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001133.4 |  |  | 0.68 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.68 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001133.4 |  | 0.67 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.66 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.83 out of 27.78
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 23.03 out of 26.33
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.56 out of 20.97
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.78 out of 28.19
Confidence: medium
Additional weak hits (7):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.42 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.18 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.83 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.12 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.51 out of 26.06
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.91 out of 30.22
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.13 out of 30.22
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 13, location 2566591 - 2626899:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - mal - Orn - D-X) + (Phe)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BP422_RS11735: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (469..862): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LFFAFDASVWEMTLITAGSINAYGPTETTICATT
  Nearest Stachelhaus code(s):
    Phe DAWTIAAICK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS11740: fatty_acid - Orn - X
Search NORINE for peptide: strict or relaxed
CAL_domain (34..480): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 244.5
  NH2: 35.1
  Acetyl-CoA: 8.8
  shikimic_acid: 0.0
  AHBA: 0.0

AMP-binding (3091..3492): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VTWAFDVFAGDRESILGSDINSYGVTEAAIDSSY
  Nearest Stachelhaus code(s):
    Orn DVGEIGSIDK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4137..4537): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTYDSAIWQWDFIIGGETNLYGPTEASIGCIA
  Nearest Stachelhaus code(s):
    Glu DVWHIGSIGK (62% 8Å match)
    Orn DVWNIGLIHK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ZuR variant 1 | Zinc-responsive repressor

NZ_CP018145.1 - Region 12 - 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: 2,999,473 - 3,040,537 nt. (total: 41,065 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
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: glycosyltransferase methyltransferase
BP422_RS14000: isoprenylcysteine carboxyl methyltransferase

smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

BP422_RS14095: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: peptidase
BP422_RS14040: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

Lyases: cyclase
BP422_RS13990: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: synthase
BP422_RS13995: 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 |  | 0.68 | 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 |  | 0.54 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001962.3 |  | 0.50 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0000779.3 |  | 0.47 | saccharide | lipopolysaccharide | Aeromonas piscicola
BGC0002332.2 |  | 0.45 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0001647.3 |  | 0.39 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0000249.5 |  | 0.39 | PKS | nogalamycin | Streptomyces nogalater
BGC0001586.3 |  | 0.36 | saccharide | EPS273 | Pseudomonas stutzeri
BGC0001964.2 |  | 0.35 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0000763.5 |  | 0.34 | saccharide | stewartan | Pantoea stewartii subsp. stewartii DC283

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.68 | 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 |  | 0.54 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001962.3 |  | 0.50 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0000779.3 |  | 0.47 | saccharide | lipopolysaccharide | Aeromonas piscicola
BGC0002332.2 |  | 0.45 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0001647.3 |  | 0.39 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0000249.5 |  | 0.39 | PKS | nogalamycin | Streptomyces nogalater
BGC0001586.3 |  | 0.36 | saccharide | EPS273 | Pseudomonas stutzeri
BGC0001964.2 |  | 0.35 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0000763.5 |  | 0.34 | saccharide | stewartan | Pantoea stewartii subsp. stewartii DC283

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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.86 out of 26.06
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.02 out of 23.79
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.11 out of 27.55
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.54 out of 18.46
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.86 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.52 out of 26.06
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.57 out of 23.79
Confidence: medium
Additional weak hits (4):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.02 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.61 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.49 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.18 out of 26.06
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
GnfM | Regulator of nitrogen-fixation genes
IolR | Regulator of the inositol catabolism
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis

NZ_CP018145.1 - Region 13 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,148,918 - 3,170,825 nt. (total: 21,908 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
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: reductase
BP422_RS14745: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase 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
--- | --- | --- | --- | --- | ---
BGC0002173.2 |  | 0.47 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000670.4 |  | 0.34 | terpene | thalianol, thaliandiol, thalianin | Arabidopsis thaliana
BGC0000663.5 |  | 0.30 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0001791.4 |  | 0.30 | NRPS | sunshinamide | Gynuella sunshinyii YC6258
BGC0002675.2 |  | 0.29 | PKS | prodigiosin | Pseudoalteromonas rubra
BGC0000258.3 |  | 0.28 | PKS | prodigiosin | Serratia sp.
BGC0002667.2 |  | 0.28 | ribosomal | estericin A | Clostridium estertheticum
BGC0002386.2 |  | 0.27 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0000969.5 |  | 0.26 | NRPS, PKS | chondramide A | Chondromyces crocatus
BGC0000765.3 |  | 0.25 | saccharide | exopolysaccharide | Lactobacillus johnsonii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002173.2 |  | 0.47 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000670.4 |  | 0.34 | terpene | thalianol, thaliandiol, thalianin | Arabidopsis thaliana
BGC0000663.5 |  | 0.30 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0001791.4 |  | 0.30 | NRPS | sunshinamide | Gynuella sunshinyii YC6258
BGC0002675.2 |  | 0.29 | PKS | prodigiosin | Pseudoalteromonas rubra
BGC0000258.3 |  | 0.28 | PKS | prodigiosin | Serratia sp.
BGC0002667.2 |  | 0.28 | ribosomal | estericin A | Clostridium estertheticum
BGC0002386.2 |  | 0.27 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0000969.5 |  | 0.26 | NRPS, PKS | chondramide A | Chondromyces crocatus
BGC0000765.3 |  | 0.25 | saccharide | exopolysaccharide | Lactobacillus johnsonii

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
BP422_RS14690: T2TS
Domain 1 (3 - 631): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.17 out of 25.31
Confidence: medium
Additional weak hits (9):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.83 out of 30.22
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.66 out of 26.85
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.72 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.08 out of 29.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.92 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.86 out of 30.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.78 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.16 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.19 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
--- | ---
CatR | H2O2-responsive repressor
ToxT | Regulator of MSHA biosynthesis

NZ_CP018145.1 - Region 14 - NRPS,cyclic-lactone-autoinducer,transAT-PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,335,100 - 3,446,455 nt. (total: 111,356 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
BP422_RS15690: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

BP422_RS15725: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acetyltransferase acylase methyltransferase
BP422_RS15635: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

BP422_RS15710: methyltransferase

smcogs
  SMCOG1089: methyltransferase

BP422_RS15735: methyltransferase

smcogs
  SMCOG1089: methyltransferase

BP422_RS15745: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

BP422_RS15750: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: dehalogenase hydrolase
BP422_RS15700: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

BP422_RS15740: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BP422_RS15875: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: ligase synthase
BP422_RS15705: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BP422_RS15715: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

BP422_RS15720: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BP422_RS15730: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | NRPS | transAT-PKS | cyclic-lactone-autoinducer | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000342.4 |  |  |  | 0.84 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  |  |  | 0.73 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  |  |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001833.4 |  |  |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001240.4 |  |  |  | 0.61 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0002286.3 |  |  |  | 0.61 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.73 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0002286.3 |  | 0.64 | 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.75 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.88 out of 26.06
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.71 out of 26.33
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.46 out of 27.55
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.72 out of 29.38
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.74 out of 24.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.03 out of 28.19
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.30 out of 25.31
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.73 out of 28.19
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 16.98 out of 18.16
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.37 out of 27.78
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
Additional weak hits (13):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.50 out of 39.62
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 25.27 out of 30.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.22 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.83 out of 26.06
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.34 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.85 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.68 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.98 out of 28.14
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.79 out of 32.93
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.48 out of 32.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.62 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.95 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.70 out of 39.62
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 16, location 3335099 - 3446455:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-ccmal) + (mal - ccmal - mal) + (Ala - ohmal - ccmal - ccmal - ohmal - mal) + (mal - ccmal) + (OMe-mal - mal) + (NMe-Ser)

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).
BP422_RS15705: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (523..922): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFICSGEHNLYGPTEAAIDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHISLIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS15720: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (500..909): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TFLTFDVSLSEGNFMVAGEENIYGPTEASIYAAW
  Nearest Stachelhaus code(s):
    Ala DVSNMAIIYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS15745: mal - mal
PKS_AT (7..294): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 61.4
  inactive: 31.3
  Isobutyryl-CoA: 25.6
  Methylmalonyl-CoA: 16.0
  Methoxymalonyl-CoA: 14.6
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (334..613): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 101.9
  inactive: 36.6
  Methoxymalonyl-CoA: 29.4
  Methylmalonyl-CoA: 21.5
  Propionyl-CoA: 14.7
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
GnfM | Regulator of nitrogen-fixation genes
LexA variant 2 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP018145.1 - Region 15 - 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: 3,649,811 - 3,660,659 nt. (total: 10,849 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
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
BP422_RS17110: aminotransferase

smcogs
  SMCOG1019: aminotransferase

BP422_RS17120: 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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000902.4 |  | 0.42 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001184.4 |  | 0.39 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000285.5 |  | 0.34 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000306.5 |  | 0.31 | NRPS | arylomycin | Streptomyces filamentosus NRRL 11379
BGC0000721.4 |  | 0.29 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000395.5 |  | 0.29 | NRPS | nocardicin A | Nocardia uniformis subsp. tsuyamanensis
BGC0001964.2 |  | 0.28 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0000993.4 |  | 0.26 | NRPS, PKS | FR901228 | Chromobacterium violaceum
BGC0001230.5 |  | 0.26 | NRPS, PKS | salinamide A, salinamide B, salinamide C, salinamide D, salinamide E, salinamide F, desmethylsalinamide C, desmethylsalinamide E | Streptomyces sp. CNB091
BGC0000388.5 |  | 0.26 | NRPS | mannopeptimycin | Streptomyces hygroscopicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000902.4 |  | 0.42 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001184.4 |  | 0.39 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000285.5 |  | 0.34 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000306.5 |  | 0.31 | NRPS | arylomycin | Streptomyces filamentosus NRRL 11379
BGC0000721.4 |  | 0.29 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000395.5 |  | 0.29 | NRPS | nocardicin A | Nocardia uniformis subsp. tsuyamanensis
BGC0001964.2 |  | 0.28 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0000993.4 |  | 0.26 | NRPS, PKS | FR901228 | Chromobacterium violaceum
BGC0001230.5 |  | 0.26 | NRPS, PKS | salinamide A, salinamide B, salinamide C, salinamide D, salinamide E, salinamide F, desmethylsalinamide C, desmethylsalinamide E | Streptomyces sp. CNB091
BGC0000388.5 |  | 0.26 | NRPS | mannopeptimycin | Streptomyces hygroscopicus

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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 28.43 out of 29.38
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.47 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.03 out of 29.38
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 20.10 out of 21.84
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.13 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.25 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.34 out of 29.38
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.53 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.75 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.27 out of 28.19
Confidence: medium
Additional weak hits (7):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.66 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.73 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.64 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.38 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.39 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.88 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.38 out of 32.74
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
FuR variant 1 | Ferric Uptake Regulator
MexT | Global virulence regulator
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP018145.1 - Region 16 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,883,377 - 3,943,892 nt. (total: 60,516 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase kinase
BP422_RS18250: aminotransferase

smcogs
  SMCOG1019: aminotransferase

BP422_RS18280: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: esterase hydrolase
BP422_RS18210: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BP422_RS18290: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

BP422_RS18325: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase
BP422_RS18295: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BP422_RS18310: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

BP422_RS18315: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
BP422_RS18225: 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 | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002472.2 |  |  | 1.28 | NRPS | ulbactin F, ulbactin G | Brevibacillus brevis
BGC0001641.4 |  |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.61 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  |  | 0.60 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.60 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  |  | 0.59 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.59 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002472.2 |  | 0.86 | NRPS | ulbactin F, ulbactin G | Brevibacillus brevis
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.45 out of 26.06
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.06 out of 19.26
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.19 out of 19.26
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.29 out of 27.78
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.19 out of 19.26
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.83 out of 29.38
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.46 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.06 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 28.19
Confidence: medium
Additional weak hits (18):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.04 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.24 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.16 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.73 out of 28.14
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.93 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.12 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.85 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.42 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.51 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.96 out of 29.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.47 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.02 out of 29.38
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.37 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.69 out of 39.62
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.99 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.33 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.24 out of 26.06
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 20.57 out of 30.12
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 19, location 3883376 - 3943892:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-Cys - Me-Cys) + (Cys)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BP422_RS18295: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (538..933): 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:
    TDMAFDLSVFDANSLLSGDVSLGGATEASIWSNY
  Nearest Stachelhaus code(s):
    Cys DLFNLSLIWK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS18310: Cys - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (566..964): 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:
    TEISFDLSVYDGNSMLSGDVAMGGATEASIWSNF
  Nearest Stachelhaus code(s):
    Cys DLYNMSMIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2028..2432): 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:
    TDISFDLSVYDGNTLLSGDIGLGGATEASIWSNL
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

BP422_RS18315: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (30..435): diOH-Bz
nrpys: diOH-Bz

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    NATLFPLCCPGGGLQVGGSQQVFGMAEGLICCTS
  Nearest Stachelhaus code(s):
    Sal TLPAQGVICK (82% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
MogR | Repressor of flagellar motility genes
ZuR variant 1 | Zinc-responsive repressor

NZ_CP018145.1 - Region 17 - lanthipeptide-class-iv
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,761,845 - 4,784,205 nt. (total: 22,361 nt) Show pHMM detection rules used
lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase
BP422_RS22580: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

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

Reference | lanthipeptide-class-iv | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001796.5 |  | 0.30 | NRPS | tauramamide | Brevibacillus laterosporus DSM 25
BGC0001835.2 |  | 0.22 | PKS | gynuellalide | Gynuella sunshinyii YC6258
BGC0002338.3 |  | 0.19 | PKS | Sorangipyranone | Myxococcales bacterium
BGC0002024.3 |  | 0.19 | PKS | nargenicin A1, nargenicin A1 | Nocardia argentinensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001796.5 |  | 0.30 | NRPS | tauramamide | Brevibacillus laterosporus DSM 25
BGC0001835.2 |  | 0.22 | PKS | gynuellalide | Gynuella sunshinyii YC6258
BGC0002338.3 |  | 0.19 | PKS | Sorangipyranone | Myxococcales bacterium
BGC0002024.3 |  | 0.19 | PKS | nargenicin A1, nargenicin A1 | Nocardia argentinensis

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

No significant matches found.

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.21 out of 27.78
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.11 out of 20.97
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 23.10 out of 24.78
Confidence: strong
Additional weak hits (3):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.73 out of 30.97
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.65 out of 27.18
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.38 out of 30.98
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2 | Repressor of DNA damage response
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis

NZ_CP018145.1 - Region 18 - azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,315,021 - 6,338,583 nt. (total: 23,563 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
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
Transferases: aminotransferase
BP422_RS30270: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Ligases: synthase
BP422_RS30305: Pseudouridine synthase

smcogs
  SMCOG1154: Pseudouridine 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000851.5 |  | 0.46 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0002013.4 |  | 0.46 | ribosomal | curacozole | Streptomyces curacoi
BGC0001145.5 |  | 0.44 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000569.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001146.5 |  | 0.43 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001173.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0000607.5 |  | 0.43 | ribosomal | micrococcin P1 | Macrococcus caseolyticus
BGC0000603.5 |  | 0.40 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001640.3 |  | 0.40 | ribosomal | kocurin | Kocuria rosea
BGC0000605.5 |  | 0.39 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000851.5 |  | 0.46 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0002013.4 |  | 0.46 | ribosomal | curacozole | Streptomyces curacoi
BGC0001145.5 |  | 0.44 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000569.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001146.5 |  | 0.43 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001173.5 |  | 0.43 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0000607.5 |  | 0.43 | ribosomal | micrococcin P1 | Macrococcus caseolyticus
BGC0000603.5 |  | 0.40 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001640.3 |  | 0.40 | ribosomal | kocurin | Kocuria rosea
BGC0000605.5 |  | 0.39 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.41 out of 23.79
Confidence: medium
Additional weak hits (3):
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.62 out of 29.51
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.05 out of 33.73
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 25.46 out of 30.98
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (6315020...6338583)
BP422_RS30285
  RRE type: Heterocycloanthracin_C_RRE
  Location: 0 - 99
  Score: 133.4
  RRE type: Thiopeptide_F_RRE
  Location: 7 - 88
  Score: 59.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

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.