Select genomic region:
Overview
1.1
2.1
2.2
2.3
4.1
4.2
8.1
8.2
13.1
14.1
14.2
14.3
14.4
14.5
14.6
14.7
15.1
17.1
19.1
20.1
27.1
27.2
31.1
31.2

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

NZ_BFCH01000001.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | terpene-precursor | 109,792 | 130,976 |

NZ_BFCH01000002.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | NRPS,betalactone | 46,784 | 117,976 |  |
Region 2.2 | T1PKS | 153,171 | 195,150 | Low | 4-hexadecanoyl-3-hydroxy-2-(hydroxymethyl)-2H-furan-5-one | PKS
Region 2.3 | RiPP-like | 458,258 | 469,058 |

NZ_BFCH01000007.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | T1PKS | 1 | 53,416 | Low | microsclerodermin | NRPS:Type I+PKS:Type I
Region 4.2 | NRPS-like,NRPS | 339,729 | 388,872 | High | isonitrile lipopeptides | NRPS:Type I

NZ_BFCH01000011.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 8.1 | terpene-precursor | 17,333 | 38,382 |
Region 8.2 | RiPP-like | 44,827 | 56,242 |

NZ_BFCH01000017.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 13.1 | NRPS-like | 197,035 | 240,616 |

NZ_BFCH01000018.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 14.1 | NRPS-like | 60,614 | 104,129 |
Region 14.2 | NRPS | 323,721 | 381,656 | Low | glycopeptidolipid | NRPS:Type I
Region 14.3 | T3PKS,T1PKS | 489,172 | 547,491 | High | methylated alkyl-resorcinol/methylated acyl-phloroglucinol | PKS
Region 14.4 | lanthipeptide-class-ii | 573,976 | 597,191 |  |
Region 14.5 | NRPS-like | 615,161 | 658,670 |
Region 14.6 | NRPS-like | 688,306 | 731,809 |
Region 14.7 | T1PKS | 1,148,667 | 1,201,152 |

NZ_BFCH01000019.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 15.1 | T3PKS | 157,223 | 198,323 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III

NZ_BFCH01000021.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 17.1 | terpene | 222,378 | 243,037 |  |

NZ_BFCH01000023.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 19.1 | NRP-metallophore,NRPS,T1PKS | 1 | 123,211 | High | mycobactin | NRPS:Type I+PKS

NZ_BFCH01000024.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 20.1 | NRPS | 1 | 6,792 |

NZ_BFCH01000036.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 27.1 | CDPS | 198,776 | 220,704 |
Region 27.2 | redox-cofactor | 391,093 | 413,802 |

NZ_BFCH01000048.1 (Mycobacterium montefiorense)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 31.1 | NAPAA | 1 | 28,051 | High | ε-Poly-L-lysine | NRPS:Type I
Region 31.2 | t3nrps-iterative,T1PKS | 78,066 | 140,662 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | terpene-precursor | 109,792 | 130,976 |
Region 2.1 | NRPS,betalactone | 46,784 | 117,976 |  |
Region 2.2 | T1PKS | 153,171 | 195,150 | Low | 4-hexadecanoyl-3-hydroxy-2-(hydroxymethyl)-2H-furan-5-one | PKS
Region 2.3 | RiPP-like | 458,258 | 469,058 |
Region 4.1 | T1PKS | 1 | 53,416 | Low | microsclerodermin | NRPS:Type I+PKS:Type I
Region 4.2 | NRPS-like,NRPS | 339,729 | 388,872 | High | isonitrile lipopeptides | NRPS:Type I
Region 8.1 | terpene-precursor | 17,333 | 38,382 |
Region 8.2 | RiPP-like | 44,827 | 56,242 |
Region 13.1 | NRPS-like | 197,035 | 240,616 |
Region 14.1 | NRPS-like | 60,614 | 104,129 |
Region 14.2 | NRPS | 323,721 | 381,656 | Low | glycopeptidolipid | NRPS:Type I
Region 14.3 | T3PKS,T1PKS | 489,172 | 547,491 | High | methylated alkyl-resorcinol/methylated acyl-phloroglucinol | PKS
Region 14.4 | lanthipeptide-class-ii | 573,976 | 597,191 |  |
Region 14.5 | NRPS-like | 615,161 | 658,670 |
Region 14.6 | NRPS-like | 688,306 | 731,809 |
Region 14.7 | T1PKS | 1,148,667 | 1,201,152 |
Region 15.1 | T3PKS | 157,223 | 198,323 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 17.1 | terpene | 222,378 | 243,037 |  |
Region 19.1 | NRP-metallophore,NRPS,T1PKS | 1 | 123,211 | High | mycobactin | NRPS:Type I+PKS
Region 20.1 | NRPS | 1 | 6,792 |
Region 27.1 | CDPS | 198,776 | 220,704 |
Region 27.2 | redox-cofactor | 391,093 | 413,802 |
Region 31.1 | NAPAA | 1 | 28,051 | High | ε-Poly-L-lysine | NRPS:Type I
Region 31.2 | t3nrps-iterative,T1PKS | 78,066 | 140,662 |

No secondary metabolite regions were found in these records:
  NZ_BFCH01000006.1 (Mycobacterium montefiorense)
  NZ_BFCH01000008.1 (Mycobacterium montefiorense)
  NZ_BFCH01000009.1 (Mycobacterium montefiorense)
  NZ_BFCH01000010.1 (Mycobacterium montefiorense)
  NZ_BFCH01000012.1 (Mycobacterium montefiorense)
  NZ_BFCH01000013.1 (Mycobacterium montefiorense)
  NZ_BFCH01000014.1 (Mycobacterium montefiorense)
  NZ_BFCH01000016.1 (Mycobacterium montefiorense)
  NZ_BFCH01000020.1 (Mycobacterium montefiorense)
  NZ_BFCH01000022.1 (Mycobacterium montefiorense)
  NZ_BFCH01000026.1 (Mycobacterium montefiorense)
  NZ_BFCH01000027.1 (Mycobacterium montefiorense)
  NZ_BFCH01000028.1 (Mycobacterium montefiorense)
  NZ_BFCH01000030.1 (Mycobacterium montefiorense)
  NZ_BFCH01000031.1 (Mycobacterium montefiorense)
  NZ_BFCH01000032.1 (Mycobacterium montefiorense)
  NZ_BFCH01000041.1 (Mycobacterium montefiorense)
  NZ_BFCH01000043.1 (Mycobacterium montefiorense)
  NZ_BFCH01000045.1 (Mycobacterium montefiorense)

Compact view
NZ_BFCH01000001.1 - Region 1 - 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: 109,792 - 130,976 nt. (total: 21,185 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: Oxidation
DB708_RS00560: Oxidation

MITE
  MITE0000068Oxidation (identity: 64.30%)

Ligases: ligase synthetase
DB708_RS00585: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

DB708_RS00605: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000467.5 |  | 0.37 | NRPS | yersiniabactin | Yersinia enterocolitica
BGC0001878.2 |  | 0.36 | NRPS, PKS | detoxin N2, detoxin N3 | Streptomyces sp. NRRL B-1347
BGC0002505.3 |  | 0.36 | NRPS, PKS | xenoacremone A | Xenoacremonium sp. BF-2018a
BGC0000648.3 |  | 0.34 | terpene | carotenoid | Myxococcus xanthus
BGC0001841.2 |  | 0.34 | NRPS, PKS | detoxin P1, detoxin P2, detoxin P3 | Amycolatopsis jejuensis
BGC0001806.4 |  | 0.34 | NRPS | tolaasin A | Pseudomonas tolaasii
BGC0000384.6 |  | 0.34 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0000871.4 |  | 0.33 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
BGC0000632.5 |  | 0.33 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001760.5 |  | 0.32 | NRPS | rimosamide | Streptomyces rimosus subsp. rimosus ATCC 10970

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000467.5 |  | 0.37 | NRPS | yersiniabactin | Yersinia enterocolitica
BGC0001878.2 |  | 0.36 | NRPS, PKS | detoxin N2, detoxin N3 | Streptomyces sp. NRRL B-1347
BGC0002505.3 |  | 0.36 | NRPS, PKS | xenoacremone A | Xenoacremonium sp. BF-2018a
BGC0000648.3 |  | 0.34 | terpene | carotenoid | Myxococcus xanthus
BGC0001841.2 |  | 0.34 | NRPS, PKS | detoxin P1, detoxin P2, detoxin P3 | Amycolatopsis jejuensis
BGC0001806.4 |  | 0.34 | NRPS | tolaasin A | Pseudomonas tolaasii
BGC0000384.6 |  | 0.34 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0000871.4 |  | 0.33 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
BGC0000632.5 |  | 0.33 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001760.5 |  | 0.32 | NRPS | rimosamide | Streptomyces rimosus subsp. rimosus ATCC 10970

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
DB708_RS00585: PT_FPPS_like
Domain 1 (57 - 390): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 28.63 out of 29.65
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.11 out of 24.78
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 26.85
Confidence: medium
Additional weak hits (3):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.48 out of 25.88
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.39 out of 32.74
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.72 out of 30.98
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
LexA variant 1 | Repressor of DNA damage response
LexA variant 2 | Repressor of DNA damage response
RutR | Regulator of the pyrimidine and purine metabolism

NZ_BFCH01000002.1 - Region 1 - NRPS,betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 46,784 - 117,976 nt. (total: 71,193 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
betalactone: (HMGL-like and AMP-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
Transferases: aminotransferase methyltransferase
DB708_RS01440: aminotransferase

smcogs
  SMCOG1019: aminotransferase

DB708_RS01450: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: hydratase
DB708_RS01420: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
DB708_RS01520: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

DB708_RS28285: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

DB708_RS28290: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

DB708_RS28295: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: permease
DB708_RS01410: 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 | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.78 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000307.4 |  |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001133.4 |  | 0.72 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  | 0.71 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.94 out of 25.88
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
Additional weak hits (6):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.76 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.68 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.17 out of 18.57
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.21 out of 39.62
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.19 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 46783 - 117976:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
DB708_RS28285: Thr - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (787..1174): 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:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSGHFDFSVWEGTQLLGGEINAYGPTEVTVYASM
  Nearest Stachelhaus code(s):
    Phe DFWTVAAVCK (74% 8Å match)
    Val DFESLAAVYK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1843..2247): 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:
    LSLHFDFSVWEGSRVFGGEINMYGITETTVHASF
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

DB708_RS28290: X - Thr - Thr - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (450..839): X
nrpys: Gly, Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSLHFDFSIWEGTQVIGAEINVYGPTETTMWASK
  Nearest Stachelhaus code(s):
    Phe DFWTVAAVCK (71% 8Å match)
    Thr DFWNVGMVHK (62% 8Å match)
  Stachelhaus code match:
    60% (weak)

AMP-binding (1501..1893): 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:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSTHFDFSVWEATQLLGGELNAYGPTEGTVYASM
  Nearest Stachelhaus code(s):
    Phe DFWTVAAVCK (74% 8Å match)
    Val DFESLAAVYK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (2991..3377): 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:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSTHFDFSVWEATQLLGGEINAYGPTEATVYASM
  Nearest Stachelhaus code(s):
    Phe DFWTVAAVCK (71% 8Å match)
    Val DFESLAAVYK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (4044..4430): 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:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    ISTHFDFSVWEATQLLGGEINAYGPSEATVYASM
  Nearest Stachelhaus code(s):
    Phe DFWTVAAVCK (65% 8Å match)
    Val DFESLAAVYK (44% 8Å match)
  Stachelhaus code match:
    70% (weak)

DB708_RS28295: X - X
AMP-binding (451..839): 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:
    QSLHFDFSVWEGTQLIGGEINAYGPTETTIYAAM
  Nearest Stachelhaus code(s):
    bOH-Tyr DASTLGAICK (62% 8Å match)
    Hpg DIWHLGAISK (41% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1501..1891): X
nrpys: Gly, Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSLHFDFSVWEGTQVIGAEVNVYGPTETTMWASK
  Nearest Stachelhaus code(s):
    Phe DFWTVAAVCK (74% 8Å match)
    Thr DFWNVGMVHK (68% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
PsrA | Oleic acid responsive regulator
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_BFCH01000002.1 - Region 2 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 153,171 - 195,150 nt. (total: 41,980 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
DB708_RS01800: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

DB708_RS01815: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

DB708_RS01820: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: PPTase acylase
DB708_RS01785: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

DB708_RS27495: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase hydrolase phosphatase
DB708_RS01770: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

DB708_RS01795: thioesterase

smcogs
  SMCOG1004: thioesterase

DB708_RS01925: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

DB708_RS01960: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
DB708_RS01810: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

DB708_RS01880: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

DB708_RS27490: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transport
DB708_RS01830: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.65 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001161.5 |  | 0.60 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0000140.5 |  | 0.56 | PKS | 4-hexadecanoyl-3-hydroxy-2-(hydroxymethyl)-2H-furan-5-one | Streptomyces sp. 88-682
BGC0001163.3 |  | 0.54 | PKS | 1-heptadecene | Moorea producens 3L
BGC0001162.3 |  | 0.54 | PKS | 1-heptadecene | Moorea producens JHB

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.65 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001161.5 |  | 0.60 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0000140.5 |  | 0.56 | PKS | 4-hexadecanoyl-3-hydroxy-2-(hydroxymethyl)-2H-furan-5-one | Streptomyces sp. 88-682
BGC0001163.3 |  | 0.54 | PKS | 1-heptadecene | Moorea producens 3L
BGC0001162.3 |  | 0.54 | PKS | 1-heptadecene | Moorea producens JHB

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.63 out of 32.74
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.66 out of 25.75
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.15 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 2, location 153170 - 195150:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal)
Non-colinear ordering:
  DB708_RS27490 + DB708_RS27495

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).
DB708_RS01810: NH2
CAL_domain (44..480): NH2
minowa: NH2

Prediction, score:
  NH2: 112.7
  AHBA: 19.0
  shikimic_acid: 9.4
  Acetyl-CoA: 0.5
  fatty_acid: -1.0

DB708_RS27495: mal
PKS_AT (196..474): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 70.8%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 119.1
  Methoxymalonyl-CoA: 68.2
  Methylmalonyl-CoA: 64.5
  inactive: 52.9
  Propionyl-CoA: 34.6
  Isobutyryl-CoA: 30.4
  2-Methylbutyryl-CoA: 20.1
  Ethylmalonyl-CoA: 16.5
  trans-1,2-CPDA: 13.4
  CHC-CoA: 11.7
  fatty_acid: 9.6
  Acetyl-CoA: 9.1
  Benzoyl-CoA: 8.2
  3-Methylbutyryl-CoA: 7.2

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

Regulator | Description
--- | ---

NZ_BFCH01000002.1 - Region 3 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 458,258 - 469,058 nt. (total: 10,801 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
DB708_RS03300: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: dehalogenase
DB708_RS03295: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002007.2 |  | 0.38 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000285.5 |  | 0.36 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000594.5 |  | 0.35 | ribosomal | microviridin K | Planktothrix agardhii NIVA-CYA 126/8
BGC0002729.2 |  | 0.34 | PKS | sordarial | Neurospora crassa OR74A
BGC0000236.5 |  | 0.33 | PKS | kinamycin | Streptomyces murayamaensis
BGC0002473.3 |  | 0.31 | NRPS | propanochelin, butanochelin, pentanochelin | Acinetobacter bouvetii DSM 14964 = CIP 107468
BGC0000264.5 |  | 0.31 | PKS | resistomycin, resistoflavine | Streptomyces resistomycificus
BGC0001882.3 |  | 0.31 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0001657.4 |  | 0.27 | NRPS | lysocin | Lysobacter sp. RH2180-5
BGC0000819.5 |  | 0.27 | NRPS, other (other) | paraherquamide | Penicillium fellutanum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002007.2 |  | 0.38 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000285.5 |  | 0.36 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000594.5 |  | 0.35 | ribosomal | microviridin K | Planktothrix agardhii NIVA-CYA 126/8
BGC0002729.2 |  | 0.34 | PKS | sordarial | Neurospora crassa OR74A
BGC0000236.5 |  | 0.33 | PKS | kinamycin | Streptomyces murayamaensis
BGC0002473.3 |  | 0.31 | NRPS | propanochelin, butanochelin, pentanochelin | Acinetobacter bouvetii DSM 14964 = CIP 107468
BGC0000264.5 |  | 0.31 | PKS | resistomycin, resistoflavine | Streptomyces resistomycificus
BGC0001882.3 |  | 0.31 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0001657.4 |  | 0.27 | NRPS | lysocin | Lysobacter sp. RH2180-5
BGC0000819.5 |  | 0.27 | NRPS, other (other) | paraherquamide | Penicillium fellutanum

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_BFCH01000007.1 - Region 1 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 53,416 nt. (total: 53,416 nt) Show pHMM detection rules used
Region on contig edge.
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
DB708_RS03715: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS03855: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

DB708_RS03860: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: carboxylase
DB708_RS03835: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Hydrolases: hydrolase
DB708_RS03850: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Ligases: synthase
DB708_RS03720: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

DB708_RS03730: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

DB708_RS03735: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

DB708_RS03740: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

DB708_RS03765: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.77 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.77 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.77 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.68 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002192.3 |  | 0.64 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.63 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.77 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.77 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.77 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.68 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002192.3 |  | 0.64 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.63 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 26.04 out of 29.38
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 25.36 out of 28.19
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.91 out of 28.19
Confidence: medium
Additional weak hits (12):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.15 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.24 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.84 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.05 out of 20.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.82 out of 27.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.41 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.05 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.23 out of 26.06
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.61 out of 29.65
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.27 out of 32.93
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 53416:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-ohmal) + (Me-redmal) + (Me-ccmal) + (D-mal) + (Me-redmal)
Non-colinear ordering:
  DB708_RS03720 + DB708_RS03725 + DB708_RS03730 + DB708_RS03735 + DB708_RS03740 + DB708_RS03765

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).
DB708_RS03720: mmal
PKS_AT (561..797): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 66.7%
  Malonyl-CoA: 62.5%
  Ethylmalonyl-CoA: 54.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 82.6
  Methoxymalonyl-CoA: 68.1
  Ethylmalonyl-CoA: 66.6
  Malonyl-CoA: 61.5
  Propionyl-CoA: 53.5
  Benzoyl-CoA: 50.9
  trans-1,2-CPDA: 48.5
  Isobutyryl-CoA: 42.3
  fatty_acid: 40.5
  CHC-CoA: 35.9
  2-Methylbutyryl-CoA: 33.1
  inactive: 24.9
  Acetyl-CoA: 19.3
  3-Methylbutyryl-CoA: 0.0

DB708_RS03730: mmal
PKS_AT (569..864): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 75.0%
  Malonyl-CoA: 70.8%
  Ethylmalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 118.0
  Methoxymalonyl-CoA: 97.2
  Ethylmalonyl-CoA: 91.5
  Malonyl-CoA: 88.3
  Propionyl-CoA: 74.1
  Isobutyryl-CoA: 67.8
  trans-1,2-CPDA: 60.8
  fatty_acid: 51.5
  2-Methylbutyryl-CoA: 48.5
  Benzoyl-CoA: 42.5
  Acetyl-CoA: 41.5
  CHC-CoA: 38.2
  inactive: 30.3
  3-Methylbutyryl-CoA: 26.2

DB708_RS03735: mmal
PKS_AT (560..852): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 75.0%
  Malonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 140.5
  Ethylmalonyl-CoA: 118.2
  Methoxymalonyl-CoA: 115.2
  Malonyl-CoA: 107.4
  Isobutyryl-CoA: 82.3
  Propionyl-CoA: 81.8
  2-Methylbutyryl-CoA: 75.1
  trans-1,2-CPDA: 68.6
  Acetyl-CoA: 61.4
  fatty_acid: 52.2
  Benzoyl-CoA: 51.5
  CHC-CoA: 49.8
  inactive: 38.9
  3-Methylbutyryl-CoA: 34.9

DB708_RS03740: mal
PKS_AT (546..827): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 120.8
  Methoxymalonyl-CoA: 72.2
  inactive: 62.9
  Methylmalonyl-CoA: 57.1
  Propionyl-CoA: 39.5
  Ethylmalonyl-CoA: 32.4
  Benzoyl-CoA: 24.2
  2-Methylbutyryl-CoA: 16.0
  Isobutyryl-CoA: 13.8
  trans-1,2-CPDA: 12.4
  fatty_acid: 12.1
  CHC-CoA: 10.7
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

DB708_RS03765: mmal
PKS_AT (532..825): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 70.8%
  Methoxymalonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 127.8
  Ethylmalonyl-CoA: 108.2
  Methoxymalonyl-CoA: 107.2
  Malonyl-CoA: 99.5
  2-Methylbutyryl-CoA: 82.3
  Propionyl-CoA: 72.3
  trans-1,2-CPDA: 60.0
  Isobutyryl-CoA: 51.9
  CHC-CoA: 51.6
  Acetyl-CoA: 46.0
  fatty_acid: 43.9
  inactive: 31.7
  3-Methylbutyryl-CoA: 26.1
  Benzoyl-CoA: 19.3

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

Regulator | Description
--- | ---
FuR variant 1 | Ferric Uptake Regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_BFCH01000007.1 - Region 2 - NRPS,NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 339,729 - 388,872 nt. (total: 49,144 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
DB708_RS05360: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

DB708_RS05365: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS05475: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

Transferases: formyltransferase methyltransferase
DB708_RS05405: methyltransferase

smcogs
  SMCOG1089: methyltransferase

DB708_RS05425: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: dehalogenase glucanase
DB708_RS05375: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

DB708_RS05410: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: cyclase dehydratase hydratase
DB708_RS05335: L-carnitine dehydratase/bile acid-inducible

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

DB708_RS05340: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

DB708_RS05370: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: ligase
DB708_RS05415: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

DB708_RS05420: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

DB708_RS05485: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

DB708_RS05495: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001627.4 |  |  | 0.70 | NRPS | isonitrile lipopeptides | Mycobacterium tuberculosis H37Rv
BGC0000426.5 |  |  | 0.64 | NRPS | sevadicin | Paenibacillus larvae
BGC0001135.5 |  |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  |  | 0.61 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002164.2 |  |  | 0.60 | NRPS | peramine | Epichloe festucae
BGC0001133.4 |  |  | 0.60 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0002135.2 |  |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000357.5 |  |  | 0.59 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001166.5 |  |  | 0.59 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001627.4 |  | 0.77 | NRPS | isonitrile lipopeptides | Mycobacterium tuberculosis H37Rv
BGC0000426.5 |  | 0.65 | NRPS | sevadicin | Paenibacillus larvae
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002164.2 |  | 0.64 | NRPS | peramine | Epichloe festucae
BGC0001133.4 |  | 0.63 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000357.5 |  | 0.63 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.00 out of 20.47
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.03 out of 36.53
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.70 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.70 out of 23.79
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.79 out of 21.84
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47
Confidence: medium
Additional weak hits (11):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 out of 26.12
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.18 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.67 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.22 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.26 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.37 out of 29.38
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.72 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.88 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.71 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 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 2, location 339728 - 388872:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 339728 - >382610:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 342875 - 388872:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-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).
DB708_RS05415: X
AMP-binding (0..339): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSLYFDASVEEGHQVVAAETNAYGPTESTLCATV
  Nearest Stachelhaus code(s):
    Phe DAWTVAAICK (71% 8Å match)
    Tyr DASTVAAVCK (62% 8Å match)
  Stachelhaus code match:
    70% (weak)

DB708_RS05420: X
AMP-binding (453..844): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LPLYFDASVEEGHQVVAAETNAYGPTETTLCVTV
  Nearest Stachelhaus code(s):
    Phe DAWTVAAICK (68% 8Å match)
    Tyr DASTVAAVCK (62% 8Å match)
  Stachelhaus code match:
    70% (weak)

DB708_RS05485: X
AMP-binding (15..422): X
nrpys: Pen, C4:0

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:
    GWIPHIGGLWWTCLGYGGSVQVYGLSETGCTAMC
  Nearest Stachelhaus code(s):
    Pen or C4:0 IGWCGGVCTK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

DB708_RS05495: X
AMP-binding (489..848): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    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:
    FAVASDVSVEEGDLVIGGEVSTYGPTEATVVVTH
  Nearest Stachelhaus code(s):
    Lys DIEDVGSVVK (82% 8Å match)
    bLys DTEDVGTMVK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_BFCH01000011.1 - Region 1 - 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: 17,333 - 38,382 nt. (total: 21,050 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
DB708_RS07745: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

Ligases: synthetase
DB708_RS07720: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.39 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3 |  | 0.35 | terpene | raimonol | Streptomyces anulatus
BGC0001456.3 |  | 0.34 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001910.4 |  | 0.33 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000665.5 |  | 0.33 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000664.5 |  | 0.33 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000936.5 |  | 0.32 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1
BGC0000633.3 |  | 0.32 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.32 | terpene | isorenieratene | Streptomyces collinus Tu 365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.39 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3 |  | 0.35 | terpene | raimonol | Streptomyces anulatus
BGC0001456.3 |  | 0.34 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001910.4 |  | 0.33 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000665.5 |  | 0.33 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000664.5 |  | 0.33 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000936.5 |  | 0.32 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1
BGC0000633.3 |  | 0.32 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.32 | terpene | isorenieratene | Streptomyces collinus Tu 365

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
DB708_RS07720: PT_FPPS_like
Domain 1 (33 - 347): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
Additional weak hits (6):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.17 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.59 out of 27.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.62 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.76 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.59 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_BFCH01000011.1 - Region 2 - 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: 44,827 - 56,242 nt. (total: 11,416 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
No tailoring functions detected.
Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000470.6 |  | 0.37 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.36 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.36 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.35 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001903.3 |  | 0.27 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0002097.3 |  | 0.22 | NRPS, PKS, saccharide | kosinostatin | Micromonospora sp. 28ISP2-46
BGC0001406.5 |  | 0.22 | NRPS | telomycin | Streptomyces canus
BGC0000315.5 |  | 0.22 | NRPS | CDA1b, CDA2a, CDA2b, CDA3a, CDA3b, CDA4a, CDA4b | Streptomyces coelicolor A3(2)
BGC0002440.3 |  | 0.21 | NRPS | longicatenamide B, longicatenamide C, longicatenamide A, longicatenamide D | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000470.6 |  | 0.37 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.36 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.36 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.35 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001903.3 |  | 0.27 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0002097.3 |  | 0.22 | NRPS, PKS, saccharide | kosinostatin | Micromonospora sp. 28ISP2-46
BGC0001406.5 |  | 0.22 | NRPS | telomycin | Streptomyces canus
BGC0000315.5 |  | 0.22 | NRPS | CDA1b, CDA2a, CDA2b, CDA3a, CDA3b, CDA4a, CDA4b | Streptomyces coelicolor A3(2)
BGC0002440.3 |  | 0.21 | NRPS | longicatenamide B, longicatenamide C, longicatenamide A, longicatenamide D | Streptomyces sp.

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

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
Additional weak hits (2):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.32 out of 31.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.74 out of 24.78
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ToxT | Regulator of MSHA biosynthesis

NZ_BFCH01000017.1 - Region 1 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 197,035 - 240,616 nt. (total: 43,582 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase
DB708_RS10900: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS10915: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS10930: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

DB708_RS10955: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

DB708_RS10980: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

DB708_RS11050: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

DB708_RS11055: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: acyltransferase
DB708_RS10935: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Hydrolases: back translocase esterase glucosidase
DB708_RS10990: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

DB708_RS11005: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

DB708_RS11020: putative esterase

smcogs
  SMCOG1104: putative esterase

Lyases: dehydratase
DB708_RS10920: L-carnitine dehydratase/bile acid-inducible

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

Ligases: ligase
DB708_RS10965: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001928.2 |  | 0.50 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000888.5 |  | 0.48 | other (other) | bacilysin | Bacillus sp. CS93
BGC0002285.2 |  | 0.47 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000706.3 |  | 0.47 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001184.4 |  | 0.45 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0001625.5 |  | 0.45 | PKS | Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F | Streptomyces sp. CB01883
BGC0001797.3 |  | 0.45 | ribosomal | telomestatin | Streptomyces anulatus
BGC0001736.3 |  | 0.44 | NRPS | pepteridine A, pepteridine B | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001386.5 |  | 0.44 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77
BGC0000248.5 |  | 0.44 | PKS | α naphtocyclinoic acid, fogacin | Streptomyces arenae DSM 40737

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001928.2 |  | 0.50 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000888.5 |  | 0.48 | other (other) | bacilysin | Bacillus sp. CS93
BGC0002285.2 |  | 0.47 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000706.3 |  | 0.47 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001184.4 |  | 0.45 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0001625.5 |  | 0.45 | PKS | Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F | Streptomyces sp. CB01883
BGC0001797.3 |  | 0.45 | ribosomal | telomestatin | Streptomyces anulatus
BGC0001736.3 |  | 0.44 | NRPS | pepteridine A, pepteridine B | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001386.5 |  | 0.44 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77
BGC0000248.5 |  | 0.44 | PKS | α naphtocyclinoic acid, fogacin | Streptomyces arenae DSM 40737

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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.52 out of 19.26
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31
Confidence: medium
Additional weak hits (6):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.70 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.56 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.63 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.20 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.44 out of 21.55
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 197034 - 240616:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
DB708_RS10965: X
AMP-binding (95..527): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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:
    LTEMHVGGRIPSGMGQGAEI-------TSFSTTA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor

NZ_BFCH01000018.1 - Region 1 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 60,614 - 104,129 nt. (total: 43,516 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
DB708_RS13110: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: hydrolase
DB708_RS13155: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Ligases: ligase
DB708_RS13105: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0000853.3 |  | 0.45 | other (other) | ectoine | Streptomyces anulatus
BGC0000919.5 |  | 0.44 | other (other) | phaseolotoxin | Pseudomonas syringae
BGC0002535.2 |  | 0.40 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002382.3 |  | 0.39 | ribosomal | grimoviridin | Grimontia marina
BGC0000313.4 |  | 0.39 | NRPS | beauvericin | Beauveria bassiana
BGC0001627.4 |  | 0.37 | NRPS | isonitrile lipopeptides | Mycobacterium tuberculosis H37Rv
BGC0001483.4 |  | 0.37 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000384.6 |  | 0.36 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0002706.2 |  | 0.36 | NRPS | saframycin Mx1 | Myxococcus xanthus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0000853.3 |  | 0.45 | other (other) | ectoine | Streptomyces anulatus
BGC0000919.5 |  | 0.44 | other (other) | phaseolotoxin | Pseudomonas syringae
BGC0002535.2 |  | 0.40 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002382.3 |  | 0.39 | ribosomal | grimoviridin | Grimontia marina
BGC0000313.4 |  | 0.39 | NRPS | beauvericin | Beauveria bassiana
BGC0001627.4 |  | 0.37 | NRPS | isonitrile lipopeptides | Mycobacterium tuberculosis H37Rv
BGC0001483.4 |  | 0.37 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000384.6 |  | 0.36 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0002706.2 |  | 0.36 | NRPS | saframycin Mx1 | Myxococcus xanthus

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.91 out of 19.26
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.67 out of 28.19
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 27.38 out of 29.65
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 23.11 out of 24.78
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.05 out of 24.78
Confidence: medium
Additional weak hits (9):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.25 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.29 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.79 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.85 out of 29.65
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.80 out of 26.85
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.11 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 60613 - 104129:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
DB708_RS13105: X
AMP-binding (83..514): 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:
    MRSMHVMGRGIGNFAMTGSLDGYGSTEAG-MVLF
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
LexA variant 1 | Repressor of DNA damage response
LexA variant 2 | Repressor of DNA damage response
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_BFCH01000018.1 - Region 2 - 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: 323,721 - 381,656 nt. (total: 57,936 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: dehydrogenase
DB708_RS14365: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS14370: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase methyltransferase transferase
DB708_RS14215: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

DB708_RS14220: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

DB708_RS14320: methyltransferase

smcogs
  SMCOG1089: methyltransferase

DB708_RS14325: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: decarboxylase dehydratase
DB708_RS14225: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

DB708_RS14235: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

DB708_RS14240: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

DB708_RS14300: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: ligase synthase
DB708_RS14250: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

DB708_RS14290: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

DB708_RS14295: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

DB708_RS14345: pseudouridine synthase

smcogs
  SMCOG1279: pseudouridine synthase

Translocases: transport
DB708_RS14270: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

DB708_RS14275: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000426.5 |  | 0.66 | NRPS | sevadicin | Paenibacillus larvae
BGC0002276.2 |  | 0.65 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001133.4 |  | 0.64 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000357.5 |  | 0.62 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000426.5 |  | 0.66 | NRPS | sevadicin | Paenibacillus larvae
BGC0002276.2 |  | 0.65 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001133.4 |  | 0.64 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000357.5 |  | 0.62 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.16 out of 20.97
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.13 out of 20.97
Confidence: medium
Additional weak hits (10):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.95 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.62 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.94 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.57 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.65 out of 20.97
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 19.26
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.37 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.07 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.25 out of 36.53
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.85 out of 27.18
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 323720 - 381656:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Phe - D-Thr - D-Ala) + (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).
DB708_RS14290: Phe - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (463..847): 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:
    LSFHFDFSVWEATQVVAGEINGYGPTETTVCVAI
  Nearest Stachelhaus code(s):
    Phe DFWTVAAVCK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1952..2353): 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:
    LSLHFDYSVWEGSQVFGGEINMYGITETTVHASF
  Nearest Stachelhaus code(s):
    Thr DYWSVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

DB708_RS14295: Ala - X
Search NORINE for peptide: strict or relaxed
AMP-binding (43..428): 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:
    LKLHFDVSVWEGCQFVAGEINAYGPTEGTIYAAM
  Nearest Stachelhaus code(s):
    Ala DVWCIAAIYK (91% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1539..1926): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSPHFDVSVWENGQVMAGEINAYGPTEATIYAAI
  Nearest Stachelhaus code(s):
    Aol DVWYVAAIYK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

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

NZ_BFCH01000018.1 - Region 3 - T1PKS,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: 489,172 - 547,491 nt. (total: 58,320 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase phosphate reductase
DB708_RS14905: N-acetyl-gamma-glutamyl-phosphate reductase

smcogs
  SMCOG1219: N-acetyl-gamma-glutamyl-phosphate reductase

DB708_RS14970: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: acylase aminotransferase carbamoyltransferase kinase
DB708_RS14915: acetylglutamate kinase

smcogs
  SMCOG1174: acetylglutamate kinase

DB708_RS14920: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

DB708_RS14925: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

DB708_RS14950: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Lyases: lyase
DB708_RS14940: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
DB708_RS14935: argininosuccinate synthase

smcogs
  SMCOG1291: argininosuccinate synthase

DB708_RS14945: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

DB708_RS14955: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

DB708_RS14960: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

DB708_RS14965: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

DB708_RS14985: 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 | T3PKS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001665.3 |  |  | 1.06 | PKS | methylated alkyl-resorcinol, methylated acyl-phloroglucinol | Mycobacterium marinum M
BGC0001273.3 |  |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  |  | 0.57 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  |  | 0.56 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001665.3 |  | 0.80 | PKS | methylated alkyl-resorcinol, methylated acyl-phloroglucinol | Mycobacterium marinum M
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.13 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.77 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 19.49 out of 20.01
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.67 out of 23.79
Confidence: medium
Additional weak hits (12):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.65 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 21.55
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.37 out of 27.04
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.78 out of 39.62
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 22.59 out of 36.54
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.38 out of 31.73
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.71 out of 25.88
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.52 out of 27.55
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.04 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.03 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.41 out of 29.65
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.48 out of 23.43
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 3, location 489171 - 547491:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (pk) + (redmal)
Non-colinear ordering:
  DB708_RS14960 + DB708_RS14950 + DB708_RS14955

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).
DB708_RS14950: pk
PKS_AT (568..861): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 222.0
  Methylmalonyl-CoA: 219.0
  Methoxymalonyl-CoA: 185.7
  2-Methylbutyryl-CoA: 155.0
  trans-1,2-CPDA: 133.9
  Propionyl-CoA: 115.4
  Malonyl-CoA: 110.2
  Isobutyryl-CoA: 96.9
  CHC-CoA: 94.2
  Benzoyl-CoA: 76.0
  3-Methylbutyryl-CoA: 52.0
  inactive: 50.0
  Acetyl-CoA: 46.8
  fatty_acid: 41.4

DB708_RS14955: mal
PKS_AT (562..848): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 177.4
  inactive: 87.6
  Methoxymalonyl-CoA: 77.0
  Methylmalonyl-CoA: 72.2
  Propionyl-CoA: 40.2
  Ethylmalonyl-CoA: 32.2
  CHC-CoA: 25.5
  fatty_acid: 23.5
  2-Methylbutyryl-CoA: 22.6
  Isobutyryl-CoA: 19.5
  trans-1,2-CPDA: 19.1
  Benzoyl-CoA: 18.4
  Acetyl-CoA: 16.5
  3-Methylbutyryl-CoA: 0.0

DB708_RS14960: mal
PKS_AT (500..790): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 177.0
  inactive: 95.5
  Methoxymalonyl-CoA: 78.5
  Methylmalonyl-CoA: 63.6
  Propionyl-CoA: 46.0
  CHC-CoA: 32.3
  fatty_acid: 31.0
  Benzoyl-CoA: 30.4
  2-Methylbutyryl-CoA: 24.9
  Isobutyryl-CoA: 23.3
  Ethylmalonyl-CoA: 23.3
  trans-1,2-CPDA: 22.0
  Acetyl-CoA: 18.2
  3-Methylbutyryl-CoA: 0.0

DB708_RS14985: X
AMP-binding (464..873): 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:
    SGTTHESALLVGSYLFIGSVEFFATTDGQAVLAN
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_BFCH01000018.1 - Region 4 - lanthipeptide-class-ii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 573,976 - 597,191 nt. (total: 23,216 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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: oxygenase
DB708_RS15235: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

DB708_RS15250: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Lyases: cyclase
DB708_RS15215: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002043.3 |  | 0.53 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0000528.5 |  | 0.53 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000503.5 |  | 0.53 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0001948.3 |  | 0.48 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000504.5 |  | 0.46 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001210.5 |  | 0.45 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000669.3 |  | 0.45 | terpene | marneral | Arabidopsis thaliana
BGC0000675.5 |  | 0.44 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002043.3 |  | 0.53 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0000528.5 |  | 0.53 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000503.5 |  | 0.53 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0001948.3 |  | 0.48 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000504.5 |  | 0.46 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001210.5 |  | 0.45 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000669.3 |  | 0.45 | terpene | marneral | Arabidopsis thaliana
BGC0000675.5 |  | 0.44 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064

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

No significant matches found.

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

#### Lanthipeptide(s) for DB708_RS15215

allorf_0576386_0576550
Leader:
MSCPENMDIARA
Core:
A G E S A G Y V L R V C T F T P V T A A A T C D L G D V L V L T T G G W P G E C I N
Core with dehydrations:
A G E Dha A G Y V L R V Cys Dhb F Dhb P V Dhb A A A Dhb Cys D L G D V L V L Dhb Dhb G G W P G E Cys I N

#### antiSMASH-DB 4.0 matches for allorf_0576386_0576550

100.0%
NZ_BFCH01000018.1:
Lanthipeptides: allorf_0576386_0576550_lanthipeptide
1
A G E S A G Y V L R V C T F T P V T A A A T C D L G D V L V L T T G G W P G E C I N
42
A G E S A G Y V L R V C T F T P V T A A A T C D L G D V L V L T T G G W P G E C I N
1
A G E S A G Y V L R V C T F T P V T A A A T C D L G D V L V L T T G G W P G E C I N
42
19.0%
NZ_CP035758.1:
Lanthipeptides: EPA93_RS35150_lanthipeptide
1
A G E S A G Y V L R V C T F T P V T A A A T C D L G D
27
A G+ + + +C + A A A C+ G
5
A G Q Q S Y N A I L I C N T L A I L A A A Q C N N G S
31
17.6%
NZ_KZ859514.1:
Lanthipeptides: DPQ64_RS06990_lanthipeptide
24
D L G D V L V L T T G G W-P G E C I
41
D L G D V + G W G C+
20
D L G D V H T V E W S G W C T G S C L
38
with 3 more sequence matches
16.7%
NZ_LXQN01000007.1:
Lassopeptides: allorf_3937798_3937932_lassopeptide
3
E S A G Y V L R V C T F T P V T A A A T C
23
+ G L C F P T C
3
K G G G E K L D Y C P F R P S K Y D G T C
23
16.0%
NZ_CP023465.1:
Lanthipeptides: allorf_4131827_4132054_lanthipeptide
5
A G Y V L R V C T F T P V T A A A
21
A +V R C +P T A A
26
A R H V S R H C R Q S P A T P A A
42
14.5%
NZ_KQ061217.1:
Lanthipeptides: allorf_4229632_4229841_lanthipeptide
9
L R V C T F T P V T A A A T C D L G D V L V L T T G G W
36
+V ++T + +C L D+ L G W
3
F K V N S W T F L P H D P S C A L Y D I C R L R R G P W
30

#### MIBiG 4.0 matches for allorf_0576386_0576550

9.5%
BGC0000503.5 (cinA):
Lanthipeptide: cinnamycin
10
R V C T F T P V T
18
+ C+F P T
3
Q S C S F G P F T
11
allorf_0578448_0578525
Leader:
MNLRPLDPQEVAAA
Core:
C L R S S R A V F V A
Core with dehydrations:
Cys L R Dha Dha R A V F V A

#### antiSMASH-DB 4.0 matches for allorf_0578448_0578525

100.0%
NZ_BFCH01000018.1:
Lanthipeptides: allorf_0578448_0578525_lanthipeptide
1
C L R S S R A V F V A
11
C L R S S R A V F V A
1
C L R S S R A V F V A
11
allorf_0580148_0580336
Leader:
MLSVIAAS
Core:
R Y A L V R L A V S A K G M P A G T F W T T S T G S I E I H R S A K S L S D T G P A C G P G A A M P W S P T
Core with dehydrations:
R Y A L V R L A V Dha A K G M P A G Dhb F W Dhb Dhb Dha Dhb G Dha I E I H R Dha A K Dha L Dha D Dhb G P A Cys G P G A A M P W Dha P Dhb

#### antiSMASH-DB 4.0 matches for allorf_0580148_0580336

100.0%
NZ_BFCH01000018.1:
Lanthipeptides: allorf_0580148_0580336_lanthipeptide
1
R Y A L V R L A V S A K G M P A G T F W T T S T G S I E I H R S A K S L S D T G P A C G P G A A M P W S P T
54
R Y A L V R L A V S A K G M P A G T F W T T S T G S I E I H R S A K S L S D T G P A C G P G A A M P W S P T
1
R Y A L V R L A V S A K G M P A G T F W T T S T G S I E I H R S A K S L S D T G P A C G P G A A M P W S P T
54
81.5%
NZ_JACKVL010000013.1:
Lanthipeptides: allorf_1185244_1185420_lanthipeptide
1
R Y A L V R L A V S A K G M P A G T F W T T S T G S I E I H R S A K S L S D T G P A C G P G A A M P
50
R Y A L V R L A V+A K M P A G W T T S T G+I E I H R S A K S L S D T G P A C G P G A M P
1
R Y A L V R L A V A A K R M P A G A S W T T S T G N I E I H R S A K S L S D T G P A C G P G A D M P
50
21.4%
NZ_BMUG01000001.1:
Lanthipeptides: allorf_0372936_0373142_lanthipeptide
23
S T G S I E I H R S A K S L S D T G P A C G P G A A M P
50
T G E H R A D C G G A P
1
D T G E Y E-H R L A A D E E D A V A R C G D G P A S P
27
with 4 more sequence matches
18.5%
NZ_KN196470.1:
Lanthipeptides: LF63_RS03635_lanthipeptide
12
K G M P A G T F W T T S T G S I E I H R S A K S--L S D T G P
41
K G P A G+ +T S ++ + + + +T G P
1
K G N P A G S L F T V S N V D L K A V G N T R E Y G V L N T G P
32
14.8%
NC_009621.1 and 4 others:
NZ_CP088111.1 Lanthipeptides: allorf_0787499_0787681_lanthipeptide NZ_NBUK01000063.1 Lanthipeptides: allorf_5939_6121_lanthipeptide NZ_VISX01000063.1 Lanthipeptides: allorf_2635_2817_lanthipeptide NZ_VITA01000039.1 Lanthipeptides: allorf_05894_06076_lanthipeptide
Lanthipeptides: allorf_1021255_1021437_lanthipeptide
6
R L A V S A K G M P A G T F W T T
22
R L A V++ P F W T
30
R L A V A S C N P P L S R F W F T
46
14.5%
NZ_FOYL01000002.1:
Lanthipeptides: allorf_0629508_0629729_lanthipeptide
26
S I E I H R S A K S L S D T G P A C G P G A A M P
50
S I +H L +G P C G +P
17
S I G M H L R V V V L G V S G P V C G L A Q N L P
41
13.0%
NZ_GG657757.1 and 1 other:
NZ_GG657757.1 Lanthipeptides: SSQG_RS42820_lanthipeptide
Lanthipeptides: SSQG_RS42820_lanthipeptide
15
P A G T F W T T S T G S I E I H R S A
33
P G W + + + H R S A
2
P T G C R W A S G S R F V R C H R S A
20

#### MIBiG 4.0 matches for allorf_0580148_0580336

13.0%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
13
G M P A G T F W T T S T G S I E I H R S
32
G G T+T I H S
14
G A L M G C N M K T A T C H C S I H V S
33
allorf_0587891_0587971
Leader:
MRRITVVAS
Core:
R S H L I W H Q C M Q S G G S T R
Core with dehydrations:
R Dha H L I W H Q Cys M Q Dha G G Dha Dhb R

#### antiSMASH-DB 4.0 matches for allorf_0587891_0587971

100.0%
NZ_BFCH01000018.1 and 1 other:
NZ_JACKVL010000013.1 Lanthipeptides: allorf_1192978_1193058_lanthipeptide
Lanthipeptides: allorf_0587891_0587971_lanthipeptide
1
R S H L I W H Q C M Q S G G S T R
17
R S H L I W H Q C M Q S G G S T R
1
R S H L I W H Q C M Q S G G S T R
17
allorf_0593429_0593524
Leader:
MEAAGNSVIRGS
Core:
R G A N G V S V G L P C C G V Q M F T
Core with dehydrations:
R G A N G V Dha V G L P Cys Cys G V Q M F Dhb

#### antiSMASH-DB 4.0 matches for allorf_0593429_0593524

100.0%
NZ_BFCH01000018.1:
Lanthipeptides: allorf_0593429_0593524_lanthipeptide
1
R G A N G V S V G L P C C G V Q M F T
19
R G A N G V S V G L P C C G V Q M F T
1
R G A N G V S V G L P C C G V Q M F T
19
59.3%
NZ_JACKVL010000013.1:
Lanthipeptides: allorf_1198506_1198685_lanthipeptide
1
R G A N G V S V G L P C C G V Q M F T
19
R G A+G V V G L P C C G V Q+F T
9
R G A S G V W V G L P C C G V Q I F T
27

#### MIBiG 4.0 matches for allorf_0593429_0593524

10.8%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
5
G V S V G L
10
G V+V G+
18
G V A V G V
23
7.8%
BGC0002120.3 (NQE92413.1):
Lanthipeptide: nocathioamide A
9
G L P C C G
14
L P C C
45
S L P C C A
50
allorf_0596314_0596454
Leader:
MSIIAGA
Core:
S R R H C Y R L V S I R L D V E R V I P E E R E T C R A C P Y H Q P G K H S G
Core with dehydrations:
Dha R R H Cys Y R L V Dha I R L D V E R V I P E E R E Dhb Cys R A Cys P Y H Q P G K H Dha G

#### antiSMASH-DB 4.0 matches for allorf_0596314_0596454

100.0%
NZ_BFCH01000018.1:
Lanthipeptides: allorf_0596314_0596454_lanthipeptide
1
S R R H C Y R L V S I R L D V E R V I P E E R E T C R A C P Y H Q P G K H S G
39
S R R H C Y R L V S I R L D V E R V I P E E R E T C R A C P Y H Q P G K H S G
1
S R R H C Y R L V S I R L D V E R V I P E E R E T C R A C P Y H Q P G K H S G
39
94.9%
NZ_JACKVL010000013.1:
Lanthipeptides: allorf_1201393_1201533_lanthipeptide
1
S R R H C Y R L V S I R L D V E R V I P E E R E T C R A C P Y H Q P G K H S G
39
S R H C Y R L V S I R L D V E R V I P+E R E T C R A C P Y H Q P G K H S G
1
S G R H C Y R L V S I R L D V E R V I P K E R E T C R A C P Y H Q P G K H S G
39
17.9%
NZ_JPLW01000002.1:
Lanthipeptides: allorf_1062224_1062367_lanthipeptide
23
R E T C R A C P Y H Q P G K
36
R E T R H Q G+
2
R E T V R L V D V H Q I G E
15
with 2 more sequence matches
12.8%
NZ_CP036053.1 and 7 others:
NZ_JAOPRA010000024.1 Lanthipeptides: OCE16_RS27090_lanthipeptide NZ_KB976667.1 Lanthipeptides: IG5_RS06165_lanthipeptide NZ_LDKD02000003.1 Lanthipeptides: ABH17_RS27060_lanthipeptide NZ_NUAO01000019.1 Lanthipeptides: CN544_RS19345_lanthipeptide NZ_NVFH01000027.1 Lanthipeptides: COL40_RS24675_lanthipeptide NZ_NVHY01000021.1 Lanthipeptides: COM05_RS26660_lanthipeptide NZ_NVOV01000033.1 Lanthipeptides: CON78_RS26470_lanthipeptide
Lanthipeptides: EXW64_RS27135_lanthipeptide
27
R A C P Y H Q P G
35
+ C P+ Q P G
11
K D C P W K Q P G
19
12.8%
NZ_JVXR01000038.1 and 2 others:
NZ_KV815277.1 Lanthipeptides: allorf_235630_235746_lanthipeptide NZ_KV820076.1 Lanthipeptides: allorf_135222_135338_lanthipeptide
Lanthipeptides: allorf_10948_11064_lanthipeptide
18
V I P E E R E T C R A C
29
+ P+E+E C+ C
2
L T P Q E K E V C K I C
13
allorf_0596542_0596658
Leader:
MCVPAEYADADPSQVLAG
Core:
N C A T P T T L K P L T I A A V I S V P
Core with dehydrations:
N Cys A Dhb P Dhb Dhb L K P L Dhb I A A V I Dha V P

#### antiSMASH-DB 4.0 matches for allorf_0596542_0596658

100.0%
NZ_BFCH01000018.1:
Lanthipeptides: allorf_0596542_0596658_lanthipeptide
1
N C A T P T T L K P L T I A A V I S V P
20
N C A T P T T L K P L T I A A V I S V P
1
N C A T P T T L K P L T I A A V I S V P
20
90.0%
NZ_JACKVL010000013.1:
Lanthipeptides: allorf_1201621_1201737_lanthipeptide
1
N C A T P T T L K P L T I A A V I S V P
20
N C T P T T L K P L T I A A V I S P
1
N C V T P T T L K P L T I A A V I S A P
20
14.3%
NZ_FUWS01000010.1:
Lanthipeptides: B5D66_RS17810_lanthipeptide
2
C A T P T T L K P L T I A
14
C A+ + P T I A
24
C A S T C S F G P F T I A
36

#### 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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.13 out of 29.72
Confidence: medium
Additional weak hits (3):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.71 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.89 out of 25.75
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.52 out of 33.14
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

allorf_0576386_0576550 - Class II
  Cleavage pHMM score: -4.40
  RODEO score: 0
  Monoisotopic mass: 4117.0 Da
  Molecular weight: 4119.6 Da
  Number of bridges: 3
  Additional modifications: OH
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4137.6 Da N = 1
    4155.7 Da N = 2
    4173.7 Da N = 3
    4191.7 Da N = 4
allorf_0578448_0578525 - Class II
  Cleavage pHMM score: -6.20
  RODEO score: 0
  Monoisotopic mass: 1187.6 Da
  Molecular weight: 1188.4 Da
  Number of bridges: 1
  Additional modifications: OH
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1206.4 Da N = 1
allorf_0580148_0580336 - Class II
  Cleavage pHMM score: -4.70
  RODEO score: 0
  Monoisotopic mass: 5327.8 Da
  Molecular weight: 5331.0 Da
  Number of bridges: 1
  Additional modifications: OH
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    5349.0 Da N = 1
    5367.1 Da N = 2
    5385.1 Da N = 3
    5403.1 Da N = 4
    5421.1 Da N = 5
    5439.1 Da N = 6
    5457.2 Da N = 7
    5475.2 Da N = 8
    5493.2 Da N = 9
    5511.2 Da N = 10
    5529.2 Da N = 11
    5547.3 Da N = 12
allorf_0587891_0587971 - Class II
  Cleavage pHMM score: -6.70
  RODEO score: 0
  Monoisotopic mass: 1926.9 Da
  Molecular weight: 1928.1 Da
  Number of bridges: 1
  Additional modifications: OH
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1946.2 Da N = 1
    1964.2 Da N = 2
    1982.2 Da N = 3
allorf_0593429_0593524 - Class II
  Cleavage pHMM score: -6.60
  RODEO score: 0
  Monoisotopic mass: 1874.9 Da
  Molecular weight: 1876.2 Da
  Number of bridges: 2
  Additional modifications: OH
allorf_0596314_0596454 - Class II
  Cleavage pHMM score: -6.90
  RODEO score: 0
  Monoisotopic mass: 4576.3 Da
  Molecular weight: 4579.2 Da
  Number of bridges: 3
  Additional modifications: OH
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4597.2 Da N = 1
allorf_0596542_0596658 - Class II
  Cleavage pHMM score: -7.10
  RODEO score: 0
  Monoisotopic mass: 1935.1 Da
  Molecular weight: 1936.3 Da
  Number of bridges: 1
  Additional modifications: OH
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1954.3 Da N = 1
    1972.3 Da N = 2
    1990.4 Da N = 3
    2008.4 Da N = 4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_BFCH01000018.1 - Region 5 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 615,161 - 658,670 nt. (total: 43,510 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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 synthase
DB708_RS15395: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

DB708_RS15400: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

DB708_RS15425: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

DB708_RS15435: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

DB708_RS15440: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

DB708_RS15480: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS15500: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

DB708_RS15510: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS15515: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase methyltransferase
DB708_RS15465: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

DB708_RS15470: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: dehalogenase synthase
DB708_RS15395: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

DB708_RS15525: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: ligase
DB708_RS15430: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001757.3 |  | 0.47 | other (other) | rhabduscin | Xenorhabdus nematophila ATCC 19061
BGC0002474.2 |  | 0.46 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0001904.2 |  | 0.45 | PKS | fluostatin L, fluostatin D, difluostatin A, fluostatin C, fluostatin F, fluostatin G/H, fluostatin J, fluostatin K, rabelomycin | Micromonospora rosaria
BGC0001868.4 |  | 0.45 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0001625.5 |  | 0.44 | PKS | Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F | Streptomyces sp. CB01883
BGC0000219.4 |  | 0.44 | PKS, saccharide | elloramycin | Streptomyces olivaceus
BGC0001334.5 |  | 0.43 | other (other) | caldoniamide A, cladoniamide B, cladoniamide C7, cladoniamide D, cladoniamide E, cladoniamide F, cladoniamide G | Streptomyces uncialis
BGC0001386.5 |  | 0.43 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77
BGC0001369.3 |  | 0.43 | PKS | metatricycloene | uncultured bacterium
BGC0001987.2 |  | 0.43 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001757.3 |  | 0.47 | other (other) | rhabduscin | Xenorhabdus nematophila ATCC 19061
BGC0002474.2 |  | 0.46 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0001904.2 |  | 0.45 | PKS | fluostatin L, fluostatin D, difluostatin A, fluostatin C, fluostatin F, fluostatin G/H, fluostatin J, fluostatin K, rabelomycin | Micromonospora rosaria
BGC0001868.4 |  | 0.45 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0001625.5 |  | 0.44 | PKS | Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F | Streptomyces sp. CB01883
BGC0000219.4 |  | 0.44 | PKS, saccharide | elloramycin | Streptomyces olivaceus
BGC0001334.5 |  | 0.43 | other (other) | caldoniamide A, cladoniamide B, cladoniamide C7, cladoniamide D, cladoniamide E, cladoniamide F, cladoniamide G | Streptomyces uncialis
BGC0001386.5 |  | 0.43 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77
BGC0001369.3 |  | 0.43 | PKS | metatricycloene | uncultured bacterium
BGC0001987.2 |  | 0.43 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis

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

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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (6):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.06 out of 21.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.56 out of 32.74
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.58 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.14 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 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 5, location 615160 - 658670:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
DB708_RS15430: X
AMP-binding (80..511): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VSGMHLGGRLPSGVFVGSAVDGYGLTETGILARD
  Nearest Stachelhaus code(s):
    Ser DFDTFGGILK (26% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production

NZ_BFCH01000018.1 - Region 6 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 688,306 - 731,809 nt. (total: 43,504 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
DB708_RS15685: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

DB708_RS15690: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

DB708_RS15710: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

DB708_RS15715: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS15730: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS15765: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS15770: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

DB708_RS15795: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
DB708_RS15815: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: peptidase
DB708_RS15745: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

DB708_RS15750: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: hydratase
DB708_RS15720: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase
DB708_RS15760: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.74 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000894.4 |  | 0.50 | other (other) | citrinin | Monascus aurantiacus
BGC0002372.3 |  | 0.48 | PKS, other (other), terpene | marinoterpin B, marinoterpin A, marinoterpin C | Streptomyces sp.
BGC0000844.5 |  | 0.48 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001219.3 |  | 0.47 | PKS | shanorellin | Chaetomium globosum CBS 148.51
BGC0001605.3 |  | 0.46 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002347.3 |  | 0.46 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6
BGC0001224.5 |  | 0.46 | other (other) | reductasporine | uncultured bacterium
BGC0001335.5 |  | 0.46 | other (other) | borregomycin A, borregomycin B, borregomycin C, borregomycin D | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.74 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000894.4 |  | 0.50 | other (other) | citrinin | Monascus aurantiacus
BGC0002372.3 |  | 0.48 | PKS, other (other), terpene | marinoterpin B, marinoterpin A, marinoterpin C | Streptomyces sp.
BGC0000844.5 |  | 0.48 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001219.3 |  | 0.47 | PKS | shanorellin | Chaetomium globosum CBS 148.51
BGC0001605.3 |  | 0.46 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002347.3 |  | 0.46 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6
BGC0001224.5 |  | 0.46 | other (other) | reductasporine | uncultured bacterium
BGC0001335.5 |  | 0.46 | other (other) | borregomycin A, borregomycin B, borregomycin C, borregomycin D | uncultured bacterium

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.73 out of 18.46
Confidence: medium
Additional weak hits (4):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.78 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.99 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.09 out of 31.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 21.07 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 6, location 688305 - 731809:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
DB708_RS15760: X
AMP-binding (95..524): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAQMHLIGYGYLSLPGGGGRVL------AVGCGS
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

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

NZ_BFCH01000018.1 - Region 7 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,148,667 - 1,201,152 nt. (total: 52,486 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
DB708_RS17910: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

DB708_RS17920: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS17930: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS17980: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

DB708_RS17985: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

DB708_RS18070: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: sulfotransferase
DB708_RS18060: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

Lyases: dehydratase
DB708_RS17990: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
DB708_RS17995: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

DB708_RS18015: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

DB708_RS18075: cobaltochelatase subunit CobN

smcogs
  SMCOG1263: cobaltochelatase subunit CobN

DB708_RS28325: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001201.3 |  | 0.51 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0001310.5 |  | 0.50 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001605.3 |  | 0.48 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001504.4 |  | 0.47 | PKS | amycomicin | Amycolatopsis sp. AA4
BGC0000867.3 |  | 0.47 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002234.3 |  | 0.47 | PKS | flavoglaucin | Aspergillus ruber CBS 135680
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000041.3 |  | 0.47 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001529.5 |  | 0.46 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0001987.2 |  | 0.45 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001201.3 |  | 0.51 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0001310.5 |  | 0.50 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001605.3 |  | 0.48 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001504.4 |  | 0.47 | PKS | amycomicin | Amycolatopsis sp. AA4
BGC0000867.3 |  | 0.47 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002234.3 |  | 0.47 | PKS | flavoglaucin | Aspergillus ruber CBS 135680
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000041.3 |  | 0.47 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001529.5 |  | 0.46 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0001987.2 |  | 0.45 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (4):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.33 out of 21.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.31 out of 32.74
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.51 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.94 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 7, location 1148666 - 1201152:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk - redmal)

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).
DB708_RS17995: pk - mal
PKS_AT (556..855): pk
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 225.7
  Methylmalonyl-CoA: 223.3
  Methoxymalonyl-CoA: 182.1
  2-Methylbutyryl-CoA: 154.8
  trans-1,2-CPDA: 128.2
  Malonyl-CoA: 124.9
  Propionyl-CoA: 105.0
  Isobutyryl-CoA: 94.0
  CHC-CoA: 86.2
  Benzoyl-CoA: 73.1
  Acetyl-CoA: 47.5
  inactive: 41.1
  3-Methylbutyryl-CoA: 38.1
  fatty_acid: 35.7

PKS_AT (2583..2876): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 180.5
  inactive: 83.2
  Methoxymalonyl-CoA: 65.7
  Methylmalonyl-CoA: 51.6
  Propionyl-CoA: 44.0
  Acetyl-CoA: 22.8
  2-Methylbutyryl-CoA: 22.7
  Benzoyl-CoA: 19.7
  CHC-CoA: 18.7
  Isobutyryl-CoA: 13.8
  Ethylmalonyl-CoA: 13.8
  fatty_acid: 10.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---

NZ_BFCH01000019.1 - Region 1 - 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: 157,223 - 198,323 nt. (total: 41,101 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
DB708_RS19020: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS19045: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS19050: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

DB708_RS19055: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

DB708_RS19095: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

DB708_RS19135: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase methyltransferase
DB708_RS19085: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

DB708_RS19100: Methylation

MITE
  MITE0000155Methylation (identity: 61.30%)
smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

DB708_RS19150: methyltransferase

smcogs
  SMCOG1089: methyltransferase

DB708_RS19220: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: amidase
DB708_RS19080: amidase

smcogs
  SMCOG1105: amidase

Lyases: dehydratase hydratase
DB708_RS19090: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

DB708_RS19125: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

DB708_RS19130: L-carnitine dehydratase/bile acid-inducible

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

Ligases: synthase
DB708_RS19105: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

Translocases: transport
DB708_RS19145: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.80 | 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
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.56 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0001924.3 |  | 0.54 | terpene | ascofuranone | Acremonium egyptiacum
BGC0001831.3 |  | 0.53 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000902.4 |  | 0.52 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.49 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000866.5 |  | 0.47 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0001262.3 |  | 0.46 | PKS | AK-toxin I | Alternaria alternata
BGC0002103.2 |  | 0.46 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.80 | 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
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.56 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0001924.3 |  | 0.54 | terpene | ascofuranone | Acremonium egyptiacum
BGC0001831.3 |  | 0.53 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000902.4 |  | 0.52 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.49 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000866.5 |  | 0.47 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0001262.3 |  | 0.46 | PKS | AK-toxin I | Alternaria alternata
BGC0002103.2 |  | 0.46 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.44 out of 23.79
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.45 out of 25.31
Confidence: medium
Additional weak hits (8):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.81 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.12 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.02 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.52 out of 27.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.32 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.29 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.04 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.35 out of 30.98
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
IolR | Regulator of the inositol catabolism

NZ_BFCH01000021.1 - Region 1 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 222,378 - 243,037 nt. (total: 20,660 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: dehydrogenase
DB708_RS20805: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS20810: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
DB708_RS20835: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: decarboxylase dehydratase
DB708_RS20750: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

DB708_RS20815: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
DB708_RS20740: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000883.5 |  | 0.50 | other (other) | arginomycin | Streptomyces arginensis
BGC0000674.5 |  | 0.42 | terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064
BGC0001778.5 |  | 0.41 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000866.5 |  | 0.41 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000671.3 |  | 0.41 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0002474.2 |  | 0.40 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0000204.5 |  | 0.38 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0001850.4 |  | 0.37 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0001797.3 |  | 0.37 | ribosomal | telomestatin | Streptomyces anulatus
BGC0000253.4 |  | 0.36 | PKS | oviedomycin | Streptomyces antibioticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000883.5 |  | 0.50 | other (other) | arginomycin | Streptomyces arginensis
BGC0000674.5 |  | 0.42 | terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064
BGC0001778.5 |  | 0.41 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000866.5 |  | 0.41 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000671.3 |  | 0.41 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0002474.2 |  | 0.40 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0000204.5 |  | 0.38 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0001850.4 |  | 0.37 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0001797.3 |  | 0.37 | ribosomal | telomestatin | Streptomyces anulatus
BGC0000253.4 |  | 0.36 | PKS | oviedomycin | Streptomyces antibioticus

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
DB708_RS20785: TS_Pyr4
Domain 1 (3 - 207): Pyr4 type terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.08 out of 18.57
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.47 out of 26.85
Confidence: medium
Additional weak hits (4):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.13 out of 20.01
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 24.35 out of 33.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.21 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
RutR | Regulator of the pyrimidine and purine metabolism
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_BFCH01000023.1 - Region 1 - NRP-metallophore,NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 123,211 nt. (total: 123,211 nt) Show pHMM detection rules used
Region on contig edge.
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase
DB708_RS21180: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

DB708_RS21200: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

DB708_RS21230: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS21315: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

DB708_RS21385: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

DB708_RS21390: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

DB708_RS21470: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: acylase acyltransferase
DB708_RS21155: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

DB708_RS21400: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: amidase back translocase esterase hydrolase
DB708_RS21060: amidase

smcogs
  SMCOG1105: amidase

DB708_RS21165: thioesterase

smcogs
  SMCOG1004: thioesterase

DB708_RS21225: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

DB708_RS21330: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Lyases: decarboxylase
DB708_RS21115: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

Isomerases: isomerase mutase
DB708_RS21250: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

DB708_RS21445: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase synthase
DB708_RS21040: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

DB708_RS21145: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

DB708_RS21150: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

DB708_RS21160: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

DB708_RS21170: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

DB708_RS21175: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

DB708_RS21395: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

DB708_RS21415: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport
DB708_RS21195: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

DB708_RS21405: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

DB708_RS21430: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | NRP-metallophore | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002286.3 |  |  |  | 1.06 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  |  |  | 0.87 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  | 0.87 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002135.2 |  |  |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  | 0.76 | NRPS | AM-toxin | Alternaria alternata
BGC0001021.5 |  |  |  | 0.75 | NRPS, PKS | mycobactin | Mycobacterium tuberculosis H37Rv
BGC0001833.4 |  |  |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  |  |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.73 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001021.5 |  | 0.72 | NRPS, PKS | mycobactin | Mycobacterium tuberculosis H37Rv
BGC0001825.4 |  | 0.71 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.65 out of 18.46
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.44 out of 20.97
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (14):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.99 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.14 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.48 out of 27.78
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.07 out of 39.62
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.42 out of 29.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.16 out of 20.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.10 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.95 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.80 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.89 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.27 out of 36.53
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.86 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 123211:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ohmal - redmal) + (X) + (Me-ohmal) + (Lys - X) + (D-Lys) + (D-Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 82047:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Me-ohmal) + (Lys - X) + (D-Lys) + (D-Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 72150 - 123211:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ohmal - redmal)

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).
DB708_RS21040: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (464..864): 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:
    LSLHFDFSVWEGSQVFGGEINMYGITETTVHASF
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

DB708_RS21145: Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (473..857): Lys
nrpys: Lys

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:
    lys (Lys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YDHWFDAAWQPADTALGGEYNCYGPTETTVEAVV
  Nearest Stachelhaus code(s):
    Lys DAQDAGCVEK (97% 8Å match)
    N6-ohLys DAQDAGCVEK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

DB708_RS21150: Lys - X
Search NORINE for peptide: strict or relaxed
AMP-binding (502..882): Lys
nrpys: Lys

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:
    asp,asn (Asp, Asn)
  Single AA prediction:
    lys (Lys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWFAFDVSMGEGHFPIGGEYNFYGPTETVVNCTS
  Nearest Stachelhaus code(s):
    Lys DVAHPGFINK (79% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1574..1969): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  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:
    RWQAFLEGGMEATAVCGGELNNIGSTETSGAVSR
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

DB708_RS21155: mmal
PKS_AT (102..393): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 75.0%
  CE-Malonyl-CoA: 66.7%
  Malonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 119.9
  Methoxymalonyl-CoA: 118.3
  Ethylmalonyl-CoA: 103.2
  Malonyl-CoA: 72.6
  2-Methylbutyryl-CoA: 65.9
  Propionyl-CoA: 62.1
  Isobutyryl-CoA: 61.5
  trans-1,2-CPDA: 60.1
  Benzoyl-CoA: 55.4
  CHC-CoA: 55.0
  Acetyl-CoA: 40.5
  3-Methylbutyryl-CoA: 32.0
  inactive: 28.2
  fatty_acid: 13.9

DB708_RS21170: X
AMP-binding (560..955): 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:
    TFISGDISVMDVHFPTGGDAGLGGATETPVHNTI
  Nearest Stachelhaus code(s):
    Gly DIYHLGLVWK (32% 8Å match)
  Stachelhaus code match:
    70% (weak)

DB708_RS21175: X
AMP-binding (39..446): X
nrpys: Sal

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:
    NASLFPLACPGGALQVGGAQQVFGMAEGLLNYTR
  Nearest Stachelhaus code(s):
    Sal PLPAQGVLNK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

DB708_RS21395: mal - mal
PKS_AT (549..848): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 188.1
  inactive: 119.1
  Methylmalonyl-CoA: 72.0
  Methoxymalonyl-CoA: 60.5
  Propionyl-CoA: 47.9
  Isobutyryl-CoA: 40.2
  fatty_acid: 26.1
  Acetyl-CoA: 24.1
  2-Methylbutyryl-CoA: 23.6
  Benzoyl-CoA: 19.0
  Ethylmalonyl-CoA: 18.0
  CHC-CoA: 16.3
  trans-1,2-CPDA: 11.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2108..2409): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 186.2
  inactive: 114.5
  Methylmalonyl-CoA: 83.4
  Methoxymalonyl-CoA: 68.0
  Propionyl-CoA: 63.7
  2-Methylbutyryl-CoA: 40.3
  fatty_acid: 39.7
  Acetyl-CoA: 30.4
  Isobutyryl-CoA: 29.6
  trans-1,2-CPDA: 27.8
  Benzoyl-CoA: 27.8
  CHC-CoA: 26.3
  Ethylmalonyl-CoA: 25.2
  3-Methylbutyryl-CoA: 9.4

DB708_RS21415: Acetyl-CoA
CAL_domain (39..481): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 38.0
  fatty_acid: 20.9
  NH2: 12.6
  shikimic_acid: 0.0
  AHBA: 0.0

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_BFCH01000024.1 - Region 1 - 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 - 6,792 nt. (total: 6,792 nt) Show pHMM detection rules used
Region on contig edge.
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
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
Ligases: ligase
DB708_RS21545: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.65 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002071.2 |  | 0.64 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.65 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002071.2 |  | 0.64 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001240.4 |  | 0.64 | 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.

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
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 6792:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
DB708_RS21545: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (459..846): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDTAFDVSMLEGFMLTGGDQNGYGPTEATIFTTY
  Nearest Stachelhaus code(s):
    Val DALFLGGTFK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

Link to PARAS substrate predictor
NZ_BFCH01000036.1 - Region 1 - CDPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 198,776 - 220,704 nt. (total: 21,929 nt) Show pHMM detection rules used
CDPS: CDPS

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
DB708_RS24780: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acyltransferase
DB708_RS24745: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Lyases: dehydratase
DB708_RS24740: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

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

Reference | CDPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0001948.3 |  | 0.50 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000870.5 |  | 0.41 | other (other) | mycolic acid | Mycobacterium tuberculosis H37Rv
BGC0000871.4 |  | 0.36 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
BGC0001483.4 |  | 0.34 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000430.5 |  | 0.33 | NRPS, PKS | spumigin E, Spumigin E | Nodularia spumigena CCY9414
BGC0002591.2 |  | 0.30 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0001504.4 |  | 0.30 | PKS | amycomicin | Amycolatopsis sp. AA4
BGC0000322.3 |  | 0.29 | NRPS | chloroeremomycin | Amycolatopsis orientalis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0001948.3 |  | 0.50 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000870.5 |  | 0.41 | other (other) | mycolic acid | Mycobacterium tuberculosis H37Rv
BGC0000871.4 |  | 0.36 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
BGC0001483.4 |  | 0.34 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000430.5 |  | 0.33 | NRPS, PKS | spumigin E, Spumigin E | Nodularia spumigena CCY9414
BGC0002591.2 |  | 0.30 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0001504.4 |  | 0.30 | PKS | amycomicin | Amycolatopsis sp. AA4
BGC0000322.3 |  | 0.29 | NRPS | chloroeremomycin | Amycolatopsis orientalis

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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 25.31
Confidence: medium
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.74 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.98 out of 28.14
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.70 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.57 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.72 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.87 out of 27.04
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.66 out of 28.14
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CatR | H2O2-responsive repressor

NZ_BFCH01000036.1 - Region 2 - redox-cofactor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 391,093 - 413,802 nt. (total: 22,710 nt) Show pHMM detection rules used
Region on contig edge.
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
DB708_RS25665: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

DB708_RS25670: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

DB708_RS25675: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

DB708_RS25685: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

DB708_RS25755: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: glycosyltransferase
DB708_RS25745: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

Hydrolases: phosphatase
DB708_RS25680: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

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 | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002103.2 |  | 0.46 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0000769.3 |  | 0.45 | saccharide | glycopeptidolipid | Mycobacterium avium subsp. hominissuis A5
BGC0000894.4 |  | 0.45 | other (other) | citrinin | Monascus aurantiacus
BGC0001485.4 |  | 0.45 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000905.5 |  | 0.43 | other (other) | heme D1 | Heliobacillus mobilis
BGC0001928.2 |  | 0.43 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000906.3 |  | 0.43 | other (other) | heme D1 | Heliophilum fasciatum
BGC0001605.3 |  | 0.43 | terpene | gibberellin | Sinorhizobium fredii NGR234

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002103.2 |  | 0.46 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0000769.3 |  | 0.45 | saccharide | glycopeptidolipid | Mycobacterium avium subsp. hominissuis A5
BGC0000894.4 |  | 0.45 | other (other) | citrinin | Monascus aurantiacus
BGC0001485.4 |  | 0.45 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000905.5 |  | 0.43 | other (other) | heme D1 | Heliobacillus mobilis
BGC0001928.2 |  | 0.43 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000906.3 |  | 0.43 | other (other) | heme D1 | Heliophilum fasciatum
BGC0001605.3 |  | 0.43 | terpene | gibberellin | Sinorhizobium fredii NGR234

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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (5):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.05 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.69 out of 21.55
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: 18.98 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.24 out of 35.63
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (391092...413802)
DB708_RS25715
  RRE type: Mycofactocin_RRE
  Location: 22 - 102
  Score: 101.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_BFCH01000048.1 - Region 1 - NAPAA
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 28,051 nt. (total: 28,051 nt) Show pHMM detection rules used
Region on contig edge.
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
DB708_RS25875: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

DB708_RS25895: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

DB708_RS25945: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase sulfotransferase
DB708_RS25910: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

DB708_RS25940: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Lyases: dehydratase hydratase
DB708_RS25870: L-carnitine dehydratase/bile acid-inducible

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

DB708_RS25960: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase
DB708_RS25885: 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 | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.66 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001268.4 |  | 0.58 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002518.3 |  | 0.46 | NRPS | syringafactin A, syringafactin C | Pseudomonas sp. SZ57
BGC0000252.5 |  | 0.45 | PKS | nonactin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.66 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001268.4 |  | 0.58 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002518.3 |  | 0.46 | NRPS | syringafactin A, syringafactin C | Pseudomonas sp. SZ57
BGC0000252.5 |  | 0.45 | PKS | nonactin | Streptomyces griseus subsp. griseus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
Additional weak hits (3):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.65 out of 28.14
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.70 out of 20.01
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.90 out of 26.12
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 1, location 0 - 28051:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
DB708_RS25885: X
AMP-binding (34..406): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAELFDASCEELSTIFGGEWNTYGPTEATVVACA
  Nearest Stachelhaus code(s):
    Lys DAEDIGTVVK (71% 8Å match)
    Gln or Tyr DAESVGTVVK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

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

NZ_BFCH01000048.1 - Region 2 - T1PKS,t3nrps-iterative
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 78,066 - 140,662 nt. (total: 62,597 nt) Show pHMM detection rules used
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
DB708_RS26320: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

DB708_RS26460: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: acyltransferase transferase
DB708_RS26335: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

DB708_RS26430: acyltransferase

smcogs
  SMCOG1141: acyltransferase

DB708_RS26435: acyltransferase

smcogs
  SMCOG1141: acyltransferase

DB708_RS26440: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Hydrolases: esterase hydrolase
DB708_RS26355: putative esterase

smcogs
  SMCOG1104: putative esterase

DB708_RS26360: putative esterase

smcogs
  SMCOG1104: putative esterase

DB708_RS26425: hydrolase

smcogs
  SMCOG1179: hydrolase

Lyases: decarboxylase
DB708_RS28125: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Isomerases: mutase
DB708_RS26495: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase synthase
DB708_RS26340: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

DB708_RS26345: 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 | t3nrps-iterative | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.61 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.61 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001161.5 |  |  | 0.57 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0001160.5 |  |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001162.3 |  |  | 0.57 | PKS | 1-heptadecene | Moorea producens JHB
BGC0001163.3 |  |  | 0.57 | PKS | 1-heptadecene | Moorea producens 3L
BGC0001164.3 |  |  | 0.54 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002192.3 |  |  | 0.50 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  |  | 0.48 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002171.2 |  |  | 0.33 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger ATCC 1015

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001161.5 |  | 0.62 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001162.3 |  | 0.62 | PKS | 1-heptadecene | Moorea producens JHB
BGC0001163.3 |  | 0.62 | PKS | 1-heptadecene | Moorea producens 3L
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002192.3 |  | 0.59 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  | 0.57 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002171.2 |  | 0.48 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger ATCC 1015

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47
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
Additional weak hits (16):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
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
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.17 out of 29.51
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 out of 26.12
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.63 out of 32.74
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.76 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.09 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.16 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.64 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.66 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.37 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.63 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.14 out of 27.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.25 out of 30.98
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.79 out of 33.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.40 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 2, location 78065 - 140662:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
DB708_RS26340: pk
PKS_AT (700..1003): pk
ATSignature: Malonyl-CoA, Methylmalonyl-CoA

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

minowa: fatty_acid

Prediction, score:
  fatty_acid: 143.9
  Methylmalonyl-CoA: 65.6
  Methoxymalonyl-CoA: 59.4
  Malonyl-CoA: 43.5
  Ethylmalonyl-CoA: 36.0
  Isobutyryl-CoA: 35.2
  Propionyl-CoA: 28.2
  trans-1,2-CPDA: 28.0
  inactive: 24.2
  CHC-CoA: 20.2
  2-Methylbutyryl-CoA: 20.2
  Benzoyl-CoA: 10.6
  Acetyl-CoA: 9.2
  3-Methylbutyryl-CoA: 0.0

DB708_RS26345: Acetyl-CoA
CAL_domain (58..511): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 36.7
  fatty_acid: 24.5
  AHBA: 13.4
  NH2: 0.7
  shikimic_acid: 0.0

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
VqsM | Regulator of quorum-sensing signalling systems