Select genomic region:
Overview
1.1
3.1
3.2
5.1
6.1
6.2
7.1
8.1
8.2
9.1
10.1
12.1
12.2
13.1
13.2
18.1
23.1
23.2
24.1
27.1
28.1
34.1
34.2
45.1
45.2
45.3
45.4
50.1
50.2
50.3
51.1
51.2
51.3
52.1
52.2
52.3
53.1

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

NZ_VYTZ01000001.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | PKS-like,NRPS | 60,728 | 122,824 | Low | naphthyridinomycin | NRPS:Type I

NZ_VYTZ01000011.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | T1PKS | 1 | 44,091 | Low | X-14547 | PKS
Region 3.2 | T1PKS | 89,280 | 142,221 | Low | Legonmycin A/Legonmycin B/Legonindolizine A/Legonindolizine B | NRPS:Type I+other:other

NZ_VYTZ01000013.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | NI-siderophore | 135,429 | 166,764 |  |

NZ_VYTZ01000014.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 6.1 | NRPS,t3nrps-iterative,blactam,PKS-like,NRPS-like,butyrolactone | 1 | 95,858 | Low | pyridomycin | NRPS:Type I+PKS
Region 6.2 | lanthipeptide-class-i | 158,029 | 183,229 |

NZ_VYTZ01000015.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 7.1 | terpene | 90,304 | 111,236 | Low | isorenieratene | terpene

NZ_VYTZ01000016.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 8.1 | terpene | 84,536 | 107,068 |  |
Region 8.2 | T3PKS,NRPS | 119,457 | 194,694 | Medium | feglymycin | NRPS:Type I

NZ_VYTZ01000017.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 9.1 | phenazine | 59,463 | 79,951 | Medium | phenazine SA/phenazine SB/phenazine SC | other:other

NZ_VYTZ01000018.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 10.1 | lanthipeptide-class-iv | 6,440 | 29,223 | Low | labyrinthopeptin A2/labyrinthopeptin A1/labyrinthopeptin A3 | ribosomal:RiPP:Lanthipeptide

NZ_VYTZ01000002.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 12.1 | lanthipeptide-class-ii | 515,290 | 538,166 |  |
Region 12.2 | terpene | 565,166 | 586,134 |  |

NZ_VYTZ01000020.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 13.1 | redox-cofactor | 34,034 | 56,882 |
Region 13.2 | T1PKS | 58,958 | 120,244 | Medium | salinilactam | PKS

NZ_VYTZ01000025.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 18.1 | terpene-precursor,T1PKS,NRPS,NRPS-like | 1 | 73,029 | Low | aurachin C/aurachin D/aurachin SS | PKS+terpene

NZ_VYTZ01000003.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 23.1 | lanthipeptide-class-i | 63,778 | 87,925 |
Region 23.2 | terpene-precursor | 286,940 | 308,007 |

NZ_VYTZ01000030.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 24.1 | T1PKS | 1 | 10,302 | Low | desulfoclethramycin/clethramycin | other:other

NZ_VYTZ01000033.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 27.1 | T1PKS | 1 | 8,331 |  |

NZ_VYTZ01000034.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 28.1 | NRPS | 1 | 7,501 |  |

NZ_VYTZ01000004.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 34.1 | NI-siderophore | 325,848 | 356,196 | Low | FW0622 | other:other
Region 34.2 | RRE-containing | 631,467 | 652,591 |  |

NZ_VYTZ01000005.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 45.1 | T1PKS | 1 | 29,272 |  |
Region 45.2 | terpene | 436,503 | 461,760 | Low | hopene | terpene
Region 45.3 | terpene-precursor | 462,361 | 483,428 |  |
Region 45.4 | azole-containing-RiPP,thioamitides | 600,749 | 630,916 |

NZ_VYTZ01000006.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 50.1 | T3PKS,lanthipeptide-class-iii | 109,423 | 150,511 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 50.2 | T1PKS,other | 236,548 | 327,175 | Medium | maduropeptin | PKS:Iterative type I
Region 50.3 | NRPS | 410,391 | 468,763 |  |

NZ_VYTZ01000007.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 51.1 | terpene | 128,328 | 153,210 | High | geosmin | terpene:Sesquiterpene
Region 51.2 | NAPAA | 156,414 | 190,478 |  |
Region 51.3 | NRPS | 301,558 | 347,092 |

NZ_VYTZ01000008.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 52.1 | lanthipeptide-class-i | 33,423 | 58,545 | Low | tobramycin | saccharide
Region 52.2 | RiPP-like | 177,179 | 187,448 |
Region 52.3 | RRE-containing | 224,420 | 245,541 |

NZ_VYTZ01000009.1 (Microbispora cellulosiformans)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 53.1 | T1PKS | 131,384 | 179,195 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | PKS-like,NRPS | 60,728 | 122,824 | Low | naphthyridinomycin | NRPS:Type I
Region 3.1 | T1PKS | 1 | 44,091 | Low | X-14547 | PKS
Region 3.2 | T1PKS | 89,280 | 142,221 | Low | Legonmycin A/Legonmycin B/Legonindolizine A/Legonindolizine B | NRPS:Type I+other:other
Region 5.1 | NI-siderophore | 135,429 | 166,764 |  |
Region 6.1 | NRPS,t3nrps-iterative,blactam,PKS-like,NRPS-like,butyrolactone | 1 | 95,858 | Low | pyridomycin | NRPS:Type I+PKS
Region 6.2 | lanthipeptide-class-i | 158,029 | 183,229 |
Region 7.1 | terpene | 90,304 | 111,236 | Low | isorenieratene | terpene
Region 8.1 | terpene | 84,536 | 107,068 |  |
Region 8.2 | T3PKS,NRPS | 119,457 | 194,694 | Medium | feglymycin | NRPS:Type I
Region 9.1 | phenazine | 59,463 | 79,951 | Medium | phenazine SA/phenazine SB/phenazine SC | other:other
Region 10.1 | lanthipeptide-class-iv | 6,440 | 29,223 | Low | labyrinthopeptin A2/labyrinthopeptin A1/labyrinthopeptin A3 | ribosomal:RiPP:Lanthipeptide
Region 12.1 | lanthipeptide-class-ii | 515,290 | 538,166 |  |
Region 12.2 | terpene | 565,166 | 586,134 |  |
Region 13.1 | redox-cofactor | 34,034 | 56,882 |
Region 13.2 | T1PKS | 58,958 | 120,244 | Medium | salinilactam | PKS
Region 18.1 | terpene-precursor,T1PKS,NRPS,NRPS-like | 1 | 73,029 | Low | aurachin C/aurachin D/aurachin SS | PKS+terpene
Region 23.1 | lanthipeptide-class-i | 63,778 | 87,925 |
Region 23.2 | terpene-precursor | 286,940 | 308,007 |
Region 24.1 | T1PKS | 1 | 10,302 | Low | desulfoclethramycin/clethramycin | other:other
Region 27.1 | T1PKS | 1 | 8,331 |  |
Region 28.1 | NRPS | 1 | 7,501 |  |
Region 34.1 | NI-siderophore | 325,848 | 356,196 | Low | FW0622 | other:other
Region 34.2 | RRE-containing | 631,467 | 652,591 |  |
Region 45.1 | T1PKS | 1 | 29,272 |  |
Region 45.2 | terpene | 436,503 | 461,760 | Low | hopene | terpene
Region 45.3 | terpene-precursor | 462,361 | 483,428 |  |
Region 45.4 | azole-containing-RiPP,thioamitides | 600,749 | 630,916 |
Region 50.1 | T3PKS,lanthipeptide-class-iii | 109,423 | 150,511 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 50.2 | T1PKS,other | 236,548 | 327,175 | Medium | maduropeptin | PKS:Iterative type I
Region 50.3 | NRPS | 410,391 | 468,763 |  |
Region 51.1 | terpene | 128,328 | 153,210 | High | geosmin | terpene:Sesquiterpene
Region 51.2 | NAPAA | 156,414 | 190,478 |  |
Region 51.3 | NRPS | 301,558 | 347,092 |
Region 52.1 | lanthipeptide-class-i | 33,423 | 58,545 | Low | tobramycin | saccharide
Region 52.2 | RiPP-like | 177,179 | 187,448 |
Region 52.3 | RRE-containing | 224,420 | 245,541 |
Region 53.1 | T1PKS | 131,384 | 179,195 |

No secondary metabolite regions were found in these records:
  NZ_VYTZ01000010.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000012.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000019.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000021.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000022.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000023.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000024.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000026.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000027.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000028.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000029.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000031.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000032.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000035.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000036.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000037.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000038.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000039.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000040.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000041.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000042.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000043.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000044.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000045.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000046.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000047.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000048.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000049.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000050.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000051.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000052.1 (Microbispora cellulosiformans)
  NZ_VYTZ01000053.1 (Microbispora cellulosiformans)

Compact view
NZ_VYTZ01000001.1 - Region 1 - NRPS,PKS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 60,728 - 122,824 nt. (total: 62,097 nt) Show pHMM detection rules used
PKS-like: (t2pks2 or ksIII)
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: oxidase oxygenase
F5972_RS00220: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

F5972_RS00250: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

F5972_RS00330: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

F5972_RS00335: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

Transferases: aminotransferase methyltransferase transketolase
F5972_RS00255: methyltransferase

smcogs
  SMCOG1248: methyltransferase

F5972_RS00370: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

F5972_RS00375: transketolase

smcogs
  SMCOG1204: transketolase

Hydrolases: esterase
F5972_RS00295: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
F5972_RS00355: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Isomerases: isomerase
F5972_RS00230: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
F5972_RS00275: 1-deoxy-D-xylulose-5-phosphate synthase

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

F5972_RS00280: 3-oxoacyl-(acyl carrier protein) synthase III

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

F5972_RS00285: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F5972_RS00290: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS00300: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS00310: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS00320: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS00380: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | PKS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.93 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.88 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  |  | 0.87 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  | 0.84 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  |  | 0.83 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  |  | 0.83 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.82 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  | 0.81 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  |  | 0.80 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001240.4 |  |  | 0.78 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.74 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001240.4 |  | 0.72 | 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.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 21.84 out of 21.84
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.25 out of 29.72
Confidence: medium
Additional weak hits (15):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.48 out of 26.85
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.70 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.98 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.77 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.96 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.60 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.16 out of 27.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.42 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.72 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.16 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 out of 29.65
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.09 out of 26.06
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.78 out of 20.01
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 60727 - 122824:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ala - Ala - Ala) + (NH2) + (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 60727 - 101738:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ala - Ala - Ala) + (NH2) + (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 61866 - 122824:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ala - Ala - Ala) + (NH2) + (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).
F5972_RS00285: Ala - Ala - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (520..942): 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:
    MWATFDLSVFEANTNLAGENNLYGPTEDTTYSTH
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1639..2078): 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:
    MWATFDLSVFEANTNLAGENNLYGPTEDTTYSTH
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2794..3193): 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:
    MWATFDLSVFEANTNLAGENNLYGPTEDTTYSTH
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

F5972_RS00290: NH2
CAL_domain (150..445): NH2
minowa: NH2

Prediction, score:
  NH2: 127.2
  Acetyl-CoA: 38.6
  fatty_acid: 36.1
  AHBA: 10.3
  shikimic_acid: 0.0

F5972_RS00300: X
AMP-binding (487..802): 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:
    AAVSGPAHLADAVACVG----------NTVFVGR
  Nearest Stachelhaus code(s):
    6-clTrp DAAMCGGVAK (21% 8Å match)
  Stachelhaus code match:
    60% (weak)

F5972_RS00310: X
AMP-binding (494..891): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AARAFDAAGGGWDGVVAGEFNEYGPTEATVWASV
  Nearest Stachelhaus code(s):
    4,5-dhArg DAGDIAEVWK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

F5972_RS00320: X
AMP-binding (263..650): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    SARMFDGAAGGWHSSVGGELNDYGPTECAVWATA
  Nearest Stachelhaus code(s):
    dohmTyr DGGHAGDVWK (85% 8Å match)
    mTyr or ohdmTyr DGSHSGDVWK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
MexT | Global virulence regulator
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_VYTZ01000011.1 - 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 - 44,091 nt. (total: 44,091 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: oxidoreductase oxygenase
F5972_RS26945: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

F5972_RS26955: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

F5972_RS27010: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: PPTase acylase
F5972_RS26925: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

F5972_RS26930: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

F5972_RS26960: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Ligases: synthase
F5972_RS37495: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
F5972_RS26995: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.65 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0000067.5 |  | 0.62 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0002192.3 |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.65 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0000067.5 |  | 0.62 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0002192.3 |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

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 (13):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.10 out of 25.88
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.48 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.21 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.60 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.30 out of 18.57
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.74 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.85 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.27 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 0 - 44091:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk - mal) + (ohmal) + (ccmal - ccmal)
Non-colinear ordering:
  F5972_RS37495 + F5972_RS26930 + F5972_RS26925

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).
F5972_RS26925: mal - mal
PKS_AT (561..849): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.9
  inactive: 118.9
  Methoxymalonyl-CoA: 60.8
  Methylmalonyl-CoA: 58.1
  Isobutyryl-CoA: 26.3
  Propionyl-CoA: 26.0
  Ethylmalonyl-CoA: 21.5
  trans-1,2-CPDA: 21.2
  fatty_acid: 20.9
  Benzoyl-CoA: 20.7
  Acetyl-CoA: 18.5
  CHC-CoA: 16.0
  2-Methylbutyryl-CoA: 10.0
  3-Methylbutyryl-CoA: 3.7

PKS_AT (2251..2538): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.7
  inactive: 102.9
  Methoxymalonyl-CoA: 59.9
  Methylmalonyl-CoA: 54.2
  Acetyl-CoA: 22.7
  Propionyl-CoA: 22.5
  Isobutyryl-CoA: 22.1
  fatty_acid: 20.0
  Ethylmalonyl-CoA: 18.3
  Benzoyl-CoA: 17.9
  trans-1,2-CPDA: 17.5
  CHC-CoA: 13.9
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -2.5

F5972_RS26930: mal
PKS_AT (559..849): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 83.3%
  Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 200.3
  inactive: 97.7
  Methoxymalonyl-CoA: 72.9
  Methylmalonyl-CoA: 63.7
  Isobutyryl-CoA: 41.1
  Propionyl-CoA: 31.4
  Ethylmalonyl-CoA: 30.5
  2-Methylbutyryl-CoA: 27.1
  Acetyl-CoA: 21.9
  trans-1,2-CPDA: 17.3
  Benzoyl-CoA: 16.7
  fatty_acid: 14.8
  3-Methylbutyryl-CoA: 2.8
  CHC-CoA: 2.1

F5972_RS37495: pk - mal
PKS_AT (563..860): 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: 228.1
  Methylmalonyl-CoA: 227.0
  Methoxymalonyl-CoA: 186.7
  2-Methylbutyryl-CoA: 160.0
  trans-1,2-CPDA: 144.1
  Propionyl-CoA: 116.3
  CHC-CoA: 106.1
  Malonyl-CoA: 103.2
  Isobutyryl-CoA: 93.0
  Benzoyl-CoA: 70.0
  Acetyl-CoA: 65.7
  fatty_acid: 51.7
  3-Methylbutyryl-CoA: 39.9
  inactive: 30.2

PKS_AT (2324..2614): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 209.2
  inactive: 99.4
  Methoxymalonyl-CoA: 56.5
  Methylmalonyl-CoA: 53.1
  Acetyl-CoA: 24.4
  Propionyl-CoA: 22.1
  Isobutyryl-CoA: 18.9
  Ethylmalonyl-CoA: 18.0
  Benzoyl-CoA: 16.6
  fatty_acid: 16.4
  trans-1,2-CPDA: 13.3
  CHC-CoA: 10.3
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -2.5

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

Regulator | Description
--- | ---

NZ_VYTZ01000011.1 - 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: 89,280 - 142,221 nt. (total: 52,942 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer
F5972_RS27275: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

F5972_RS27345: flavodoxin

smcogs
  SMCOG1134: flavodoxin

Lyases: decarboxylase
F5972_RS27295: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
F5972_RS27305: 3-oxoacyl-(acyl carrier protein) synthase III

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

F5972_RS27310: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F5972_RS27315: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
F5972_RS27365: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001276.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002499.2 |  | 0.54 | NRPS, PKS | enteromycin | Streptomyces achromogenes subsp. streptozoticus
BGC0001137.5 |  | 0.50 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000056.3 |  | 0.48 | PKS | esperamicin | Actinomadura verrucosospora
BGC0001868.4 |  | 0.45 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0002294.3 |  | 0.45 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000043.5 |  | 0.44 | PKS | curacin A | Moorea producens 19L
BGC0000207.5 |  | 0.44 | PKS | chartreusin | Streptomyces chartreusis
BGC0002666.2 |  | 0.43 | NRPS, other (other) | Legonmycin A, Legonmycin B, Legonindolizine A, Legonindolizine B | Streptomyces sp. MA37

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001276.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002499.2 |  | 0.54 | NRPS, PKS | enteromycin | Streptomyces achromogenes subsp. streptozoticus
BGC0001137.5 |  | 0.50 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000056.3 |  | 0.48 | PKS | esperamicin | Actinomadura verrucosospora
BGC0001868.4 |  | 0.45 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0002294.3 |  | 0.45 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000043.5 |  | 0.44 | PKS | curacin A | Moorea producens 19L
BGC0000207.5 |  | 0.44 | PKS | chartreusin | Streptomyces chartreusis
BGC0002666.2 |  | 0.43 | NRPS, other (other) | Legonmycin A, Legonmycin B, Legonindolizine A, Legonindolizine B | Streptomyces sp. MA37

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.67 out of 20.97
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.96 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.27 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.47 out of 26.06
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.94 out of 27.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.13 out of 23.43
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.57 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 89279 - 142221:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ohmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
F5972_RS27315: mal
PKS_AT (1487..1791): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 210.6
  inactive: 114.3
  Methoxymalonyl-CoA: 78.9
  Methylmalonyl-CoA: 57.0
  Propionyl-CoA: 42.1
  Isobutyryl-CoA: 36.2
  Benzoyl-CoA: 28.6
  Acetyl-CoA: 27.9
  Ethylmalonyl-CoA: 27.1
  fatty_acid: 9.7
  trans-1,2-CPDA: 9.0
  2-Methylbutyryl-CoA: 8.0
  CHC-CoA: 6.9
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
CelR | Cellobiose uptake repressor

NZ_VYTZ01000013.1 - Region 1 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 135,429 - 166,764 nt. (total: 31,336 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
F5972_RS29375: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: decarboxylase
F5972_RS29350: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.52 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0001408.5 |  | 0.49 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002527.2 |  | 0.48 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000947.5 |  | 0.43 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000943.5 |  | 0.38 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002138.2 |  | 0.37 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670
BGC0002313.3 |  | 0.33 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000121.3 |  | 0.31 | PKS | Pestheic Acid, RES-1214-2 | Pestalotiopsis fici
BGC0002466.3 |  | 0.30 | NRPS | peucechelin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000069.5 |  | 0.26 | PKS | gephyronic acid | Archangium violaceum Cb vi76

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.52 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0001408.5 |  | 0.49 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002527.2 |  | 0.48 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000947.5 |  | 0.43 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000943.5 |  | 0.38 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002138.2 |  | 0.37 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670
BGC0002313.3 |  | 0.33 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000121.3 |  | 0.31 | PKS | Pestheic Acid, RES-1214-2 | Pestalotiopsis fici
BGC0002466.3 |  | 0.30 | NRPS | peucechelin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000069.5 |  | 0.26 | PKS | gephyronic acid | Archangium violaceum Cb vi76

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 22.22 out of 23.05
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.52 out of 19.26
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.86 out of 36.53
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.17 out of 25.31
Confidence: medium
Additional weak hits (7):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.39 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.77 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.70 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.41 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.95 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.98 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
DmdR1 | Iron(II)-dependent repressor
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_VYTZ01000014.1 - Region 1 - NRPS,NRPS-like,PKS-like,blactam,butyrolactone,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: 1 - 95,858 nt. (total: 95,858 nt) Show pHMM detection rules used
Region on contig edge.
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
blactam: (BLS or CAS or tabtoxin)
PKS-like: (t2pks2 or ksIII)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
butyrolactone: AfsA

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
F5972_RS29640: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

F5972_RS29665: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

F5972_RS29710: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F5972_RS29770: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F5972_RS29790: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F5972_RS29800: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

F5972_RS29805: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

F5972_RS29820: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F5972_RS29860: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

F5972_RS29875: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: aminotransferase transferase
F5972_RS29620: aminotransferase

smcogs
  SMCOG1019: aminotransferase

F5972_RS29625: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

F5972_RS29700: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: hydrolase
F5972_RS29660: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: decarboxylase hydratase lyase
F5972_RS29635: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

F5972_RS29655: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

F5972_RS29675: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

F5972_RS29690: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

F5972_RS29775: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
F5972_RS29565: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS29745: 3-oxoacyl-(acyl carrier protein) synthase III

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

F5972_RS29750: 3-oxoacyl-(acyl carrier protein) synthase III

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

F5972_RS29780: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS29845: 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 | t3nrps-iterative | blactam | PKS-like | NRPS-like | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000848.5 |  |  |  |  |  |  | 1.37 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  |  |  |  |  |  | 1.35 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0002276.2 |  |  |  |  |  |  | 1.09 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000850.5 |  |  |  |  |  |  | 0.95 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000846.5 |  |  |  |  |  |  | 0.84 | other (other) | tabtoxin | Pseudomonas syringae
BGC0001223.5 |  |  |  |  |  |  | 0.68 | other (other) | hydroxysporine | uncultured bacterium
BGC0000894.4 |  |  |  |  |  |  | 0.68 | other (other) | citrinin | Monascus aurantiacus
BGC0002081.3 |  |  |  |  |  |  | 0.66 | PKS | streptoketide A, streptoketide B, streptoketide C, S2502, S2507, UWM5 | Streptomyces sp. Tue6314
BGC0001909.3 |  |  |  |  |  |  | 0.64 | PKS | strobilurin A | Strobilurus tenacellus
BGC0001622.5 |  |  |  |  |  |  | 0.63 | PKS | isatropolone A, isotropolone B, isotropolone C | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.75 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002276.2 |  | 0.73 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.83 out of 20.97
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 23.04 out of 27.55
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
Additional weak hits (34):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.27 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.30 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.56 out of 20.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.42 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.12 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.67 out of 30.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.04 out of 29.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.33 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.99 out of 27.78
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
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.51 out of 20.97
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.56 out of 39.62
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.18 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.96 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.82 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.67 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.58 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.82 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.39 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.51 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.09 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.96 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.93 out of 21.55
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.13 out of 36.53
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.48 out of 27.04
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.45 out of 36.54
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.54 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.22 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.77 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.86 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.16 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 95858:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Phe)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 24632:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 15151 - 95858:
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).
F5972_RS29565: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (723..1138): 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:
    LDQAFDASVWEMTVVVAGEVNAYGPTEVTVCATM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

F5972_RS29780: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (50..453): Ala
nrpys: Ala

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

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

F5972_RS29845: X
AMP-binding (89..512): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MPPLHLVARRLKAMVLGGAFDSYGTTETGLVMLD
  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
CcpA | Catabolite control protein A
GnfM | Regulator of nitrogen-fixation genes
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_VYTZ01000014.1 - Region 2 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 158,029 - 183,229 nt. (total: 25,201 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
F5972_RS30185: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

F5972_RS30190: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000544.4 |  | 0.43 | ribosomal | planosporicin | Planomonospora alba
BGC0001727.3 |  | 0.43 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000506.4 |  | 0.41 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000559.4 |  | 0.40 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0002294.3 |  | 0.35 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0002509.3 |  | 0.34 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0000213.4 |  | 0.26 | PKS | colabomycin E | Streptomyces aureus
BGC0000360.5 |  | 0.24 | NRPS | GE81112 | Streptomyces sp. L-49973
BGC0000907.5 |  | 0.24 | other (other) | lincomycin | Streptomyces lincolnensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000544.4 |  | 0.43 | ribosomal | planosporicin | Planomonospora alba
BGC0001727.3 |  | 0.43 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000506.4 |  | 0.41 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000559.4 |  | 0.40 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0002294.3 |  | 0.35 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0002509.3 |  | 0.34 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0000213.4 |  | 0.26 | PKS | colabomycin E | Streptomyces aureus
BGC0000360.5 |  | 0.24 | NRPS | GE81112 | Streptomyces sp. L-49973
BGC0000907.5 |  | 0.24 | other (other) | lincomycin | Streptomyces lincolnensis

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

No significant matches found.

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

No significant matches found.

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 F5972_RS30190

F5972_RS30195
Leader:
MSTQTITRSAEPRQHASDEADDPFQLDITFIENTPATE
Core:
T V L L C S T G D N C G S S C P S A C T T S
Core with dehydrations:
Dhb V L L Cys Dha Dhb G D N Cys G Dha Dha Cys P Dha A Cys Dhb Dhb Dha

#### antiSMASH-DB 4.0 matches for F5972_RS30195

100.0%
NZ_KI866523.1 and 2 others:
NZ_VYTZ01000014.1 Lanthipeptides: F5972_RS30195_lanthipeptide NZ_VYTZ01000014.1 Lanthipeptides: F5972_RS30195_lanthipeptide
Lanthipeptides: MPTA5024_RS18085_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L L C S T G D N C G S S C P S A C T T S
1
T V L L C S T G D N C G S S C P S A C T T S
22
95.5%
NZ_CP029042.1:
Lanthipeptides: DDE74_RS17120_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L+C S T G D N C G S S C P S A C T T S
1
T V L M C S T G D N C G S S C P S A C T T S
22
95.5%
NZ_CP036455.1:
Lanthipeptides: EKD16_RS21370_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T L L C S T G D N C G S S C P S A C T T S
1
T E L L C S T G D N C G S S C P S A C T T S
22
with 173 more sequence matches
Only the first 10 are displayed here.
90.9%
NZ_BBYG01000011.1 and 23 others:
NZ_BBZE01000004.1 Lanthipeptides: AOQ56_RS00075_lanthipeptide NZ_BMUG01000008.1 Lanthipeptides: IE264_RS24565_lanthipeptide NZ_CP013219.1 Lanthipeptides: SHL15_RS30830_lanthipeptide NZ_CP021978.1 Lanthipeptides: CEB94_RS33350_lanthipeptide NZ_CP029342.1 Lanthipeptides: B9S64_RS02555_lanthipeptide NZ_CP030073.1 Lanthipeptides: DN051_RS07240_lanthipeptide NZ_CP041610.2 Lanthipeptides: FNV62_RS40125_lanthipeptide NZ_CP041613.2 Lanthipeptides: FNV68_RS42745_lanthipeptide NZ_CP051006.1 Lanthipeptides: HEP81_RS07390_lanthipeptide NZ_CP074102.1 Lanthipeptides: SMIR_RS04425_lanthipeptide NZ_CP101397.1 Lanthipeptides: NLU04_RS20150_lanthipeptide NZ_CP113910.1 Lanthipeptides: HUV60_RS04250_lanthipeptide NZ_FKJI03000004.1 Lanthipeptides: A7P67_RS09720_lanthipeptide NZ_JACHCX010000047.1 Lanthipeptides: HDC93_RS37275_lanthipeptide NZ_KQ948477.1 Lanthipeptides: AQJ27_RS43755_lanthipeptide NZ_KQ948550.1 Lanthipeptides: AQJ30_RS07460_lanthipeptide NZ_LIVY01000006.1 Lanthipeptides: AMK30_RS21645_lanthipeptide NZ_LMDL01000002.1 Lanthipeptides: ASD08_RS03885_lanthipeptide NZ_RAII01000001.1 Lanthipeptides: EBH12_RS06225_lanthipeptide NZ_SHKS01000004.1 Lanthipeptides: EV567_RS16240_lanthipeptide NZ_SHKU01000001.1 Lanthipeptides: EV284_RS02155_lanthipeptide NZ_SZNQ01000001.1 Lanthipeptides: E4U91_RS28815_lanthipeptide NZ_VIUV01000003.1 Lanthipeptides: FB570_RS08885_lanthipeptide
Lanthipeptides: AOQ37_RS11080_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L+C S T G D C G S S C P S A C T T S
1
T V L M C S T G D T C G S S C P S A C T T S
22
90.9%
NZ_CP045178.1:
Lanthipeptides: GBW32_RS14380_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T+L+C S T G D N C G S S C P S A C T T S
1
T M L M C S T G D N C G S S C P S A C T T S
22
90.9%
NZ_ML123117.1:
Lanthipeptides: EES46_RS09865_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L+C T G D N C G S S C P S A C T T S
1
T V L M C G T G D N C G S S C P S A C T T S
22
86.4%
NZ_BMVW01000003.1 and 2 others:
NZ_CP011799.1 Lanthipeptides: QR97_RS02045_lanthipeptide NZ_JAEVFI010000002.1 Lanthipeptides: JJV70_RS02680_lanthipeptide
Lanthipeptides: IE242_RS12765_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L+C S T G D C G S S C P S A C T S
1
T V L M C S T G D T C G S S C P S A C V T S
22
86.4%
NZ_CP050976.1:
Lanthipeptides: HEP86_RS36805_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L+C+T G D C G S S C P S A C T T S
1
T V L M C T T G D T C G S S C P S A C T T S
22
86.4%
NZ_JAHLXF010000013.1:
Lanthipeptides: KQY13_RS21225_lanthipeptide
3
L L C S T G D N C G S S C P S A C T T S
22
L+C S T G D N C G S S C P S A C T T S
1
L M C S T G D N C G S S C P S A C T T S
20
81.8%
NZ_BMSO01000039.1 and 5 others:
NZ_BMTU01000002.1 Lanthipeptides: IE118_RS05930_lanthipeptide NZ_BMUK01000002.1 Lanthipeptides: IE276_RS05195_lanthipeptide NZ_CP036534.1 Lanthipeptides: EZV63_RS30040_lanthipeptide NZ_KB907208.1 Lanthipeptides: G339_RS0101560_lanthipeptide NZ_KB907208.1 Lanthipeptides: G339_RS0101560_lanthipeptide
Lanthipeptides: IE184_RS41715_lanthipeptide
3
L L C S T G D N C G S S C P S A C T T S
22
L+C S T G D C G S S C P S A C T T S
1
L M C S T G D T C G S S C P S A C T T S
20
81.8%
NZ_CP070379.1:
Lanthipeptides: JVE63_RS10125_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L C+T G D C G S S C P S A C T S
1
T V L T C T T G D T C G S S C P S A C V T S
22
81.8%
NZ_FOQY01000053.1:
Lanthipeptides: BM085_RS43985_lanthipeptide
3
L L C S T G D N C G S S C P S A C T T S
22
L+C S T G D N C G+S C P S A C T T S
1
L M C S T G D N C G T S C P S A C T T S
20
79.2%
NZ_BNBV01000037.1:
Lanthipeptides: IE286_RS24415_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L C S T G D N C G S S C P S A C+ S
1
T V L T C S T G D N C G S S C P S A C S G S
22

#### Lanthipeptide(s) for F5972_RS30220

F5972_RS30195
Leader:
MSTQTITRSAEPRQHASDEADDPFQLDITFIENTPATE
Core:
T V L L C S T G D N C G S S C P S A C T T S
Core with dehydrations:
Dhb V L L Cys Dha Dhb G D N Cys G Dha Dha Cys P Dha A Cys Dhb Dhb Dha

#### antiSMASH-DB 4.0 matches for F5972_RS30195

100.0%
NZ_KI866523.1 and 2 others:
NZ_VYTZ01000014.1 Lanthipeptides: F5972_RS30195_lanthipeptide NZ_VYTZ01000014.1 Lanthipeptides: F5972_RS30195_lanthipeptide
Lanthipeptides: MPTA5024_RS18085_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L L C S T G D N C G S S C P S A C T T S
1
T V L L C S T G D N C G S S C P S A C T T S
22
95.5%
NZ_CP029042.1:
Lanthipeptides: DDE74_RS17120_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L+C S T G D N C G S S C P S A C T T S
1
T V L M C S T G D N C G S S C P S A C T T S
22
95.5%
NZ_CP036455.1:
Lanthipeptides: EKD16_RS21370_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T L L C S T G D N C G S S C P S A C T T S
1
T E L L C S T G D N C G S S C P S A C T T S
22
with 173 more sequence matches
Only the first 10 are displayed here.
90.9%
NZ_BBYG01000011.1 and 23 others:
NZ_BBZE01000004.1 Lanthipeptides: AOQ56_RS00075_lanthipeptide NZ_BMUG01000008.1 Lanthipeptides: IE264_RS24565_lanthipeptide NZ_CP013219.1 Lanthipeptides: SHL15_RS30830_lanthipeptide NZ_CP021978.1 Lanthipeptides: CEB94_RS33350_lanthipeptide NZ_CP029342.1 Lanthipeptides: B9S64_RS02555_lanthipeptide NZ_CP030073.1 Lanthipeptides: DN051_RS07240_lanthipeptide NZ_CP041610.2 Lanthipeptides: FNV62_RS40125_lanthipeptide NZ_CP041613.2 Lanthipeptides: FNV68_RS42745_lanthipeptide NZ_CP051006.1 Lanthipeptides: HEP81_RS07390_lanthipeptide NZ_CP074102.1 Lanthipeptides: SMIR_RS04425_lanthipeptide NZ_CP101397.1 Lanthipeptides: NLU04_RS20150_lanthipeptide NZ_CP113910.1 Lanthipeptides: HUV60_RS04250_lanthipeptide NZ_FKJI03000004.1 Lanthipeptides: A7P67_RS09720_lanthipeptide NZ_JACHCX010000047.1 Lanthipeptides: HDC93_RS37275_lanthipeptide NZ_KQ948477.1 Lanthipeptides: AQJ27_RS43755_lanthipeptide NZ_KQ948550.1 Lanthipeptides: AQJ30_RS07460_lanthipeptide NZ_LIVY01000006.1 Lanthipeptides: AMK30_RS21645_lanthipeptide NZ_LMDL01000002.1 Lanthipeptides: ASD08_RS03885_lanthipeptide NZ_RAII01000001.1 Lanthipeptides: EBH12_RS06225_lanthipeptide NZ_SHKS01000004.1 Lanthipeptides: EV567_RS16240_lanthipeptide NZ_SHKU01000001.1 Lanthipeptides: EV284_RS02155_lanthipeptide NZ_SZNQ01000001.1 Lanthipeptides: E4U91_RS28815_lanthipeptide NZ_VIUV01000003.1 Lanthipeptides: FB570_RS08885_lanthipeptide
Lanthipeptides: AOQ37_RS11080_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L+C S T G D C G S S C P S A C T T S
1
T V L M C S T G D T C G S S C P S A C T T S
22
90.9%
NZ_CP045178.1:
Lanthipeptides: GBW32_RS14380_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T+L+C S T G D N C G S S C P S A C T T S
1
T M L M C S T G D N C G S S C P S A C T T S
22
90.9%
NZ_ML123117.1:
Lanthipeptides: EES46_RS09865_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L+C T G D N C G S S C P S A C T T S
1
T V L M C G T G D N C G S S C P S A C T T S
22
86.4%
NZ_BMVW01000003.1 and 2 others:
NZ_CP011799.1 Lanthipeptides: QR97_RS02045_lanthipeptide NZ_JAEVFI010000002.1 Lanthipeptides: JJV70_RS02680_lanthipeptide
Lanthipeptides: IE242_RS12765_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L+C S T G D C G S S C P S A C T S
1
T V L M C S T G D T C G S S C P S A C V T S
22
86.4%
NZ_CP050976.1:
Lanthipeptides: HEP86_RS36805_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L+C+T G D C G S S C P S A C T T S
1
T V L M C T T G D T C G S S C P S A C T T S
22
86.4%
NZ_JAHLXF010000013.1:
Lanthipeptides: KQY13_RS21225_lanthipeptide
3
L L C S T G D N C G S S C P S A C T T S
22
L+C S T G D N C G S S C P S A C T T S
1
L M C S T G D N C G S S C P S A C T T S
20
81.8%
NZ_BMSO01000039.1 and 5 others:
NZ_BMTU01000002.1 Lanthipeptides: IE118_RS05930_lanthipeptide NZ_BMUK01000002.1 Lanthipeptides: IE276_RS05195_lanthipeptide NZ_CP036534.1 Lanthipeptides: EZV63_RS30040_lanthipeptide NZ_KB907208.1 Lanthipeptides: G339_RS0101560_lanthipeptide NZ_KB907208.1 Lanthipeptides: G339_RS0101560_lanthipeptide
Lanthipeptides: IE184_RS41715_lanthipeptide
3
L L C S T G D N C G S S C P S A C T T S
22
L+C S T G D C G S S C P S A C T T S
1
L M C S T G D T C G S S C P S A C T T S
20
81.8%
NZ_CP070379.1:
Lanthipeptides: JVE63_RS10125_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L C+T G D C G S S C P S A C T S
1
T V L T C T T G D T C G S S C P S A C V T S
22
81.8%
NZ_FOQY01000053.1:
Lanthipeptides: BM085_RS43985_lanthipeptide
3
L L C S T G D N C G S S C P S A C T T S
22
L+C S T G D N C G+S C P S A C T T S
1
L M C S T G D N C G T S C P S A C T T S
20
79.2%
NZ_BNBV01000037.1:
Lanthipeptides: IE286_RS24415_lanthipeptide
1
T V L L C S T G D N C G S S C P S A C T T S
22
T V L C S T G D N C G S S C P S A C+ S
1
T V L T C S T G D N C G S S C P S A C S G S
22

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.97 out of 30.22
Confidence: medium
Additional weak hits (3):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.75 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

F5972_RS30195 - Class I
  Cleavage pHMM score: -5.30
  RODEO score: 23
  Monoisotopic mass: 1943.8 Da
  Molecular weight: 1945.1 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1963.2 Da N = 1
    1981.2 Da N = 2
    1999.2 Da N = 3
    2017.2 Da N = 4
    2035.2 Da N = 5
F5972_RS30195 - Class I
  Cleavage pHMM score: -5.30
  RODEO score: 23
  Monoisotopic mass: 1943.8 Da
  Molecular weight: 1945.1 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1963.2 Da N = 1
    1981.2 Da N = 2
    1999.2 Da N = 3
    2017.2 Da N = 4
    2035.2 Da N = 5

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (158028...183229)
F5972_RS30190
  RRE type: Lanthipeptide_LanB_RRE
  Location: 156 - 240
  Score: 63.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
ClgR | Caseinolytic protease gene regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_VYTZ01000015.1 - 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: 90,304 - 111,236 nt. (total: 20,933 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
F5972_RS30690: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

F5972_RS30720: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Ligases: synthase
F5972_RS30695: 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.53 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.53 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001227.3 |  | 0.51 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000633.3 |  | 0.51 | terpene | carotenoid | Streptomyces avermitilis
BGC0000649.3 |  | 0.48 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000645.3 |  | 0.46 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000650.3 |  | 0.45 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000648.3 |  | 0.43 | terpene | carotenoid | Myxococcus xanthus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.53 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.53 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001227.3 |  | 0.51 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000633.3 |  | 0.51 | terpene | carotenoid | Streptomyces avermitilis
BGC0000649.3 |  | 0.48 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000645.3 |  | 0.46 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000650.3 |  | 0.45 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000648.3 |  | 0.43 | terpene | carotenoid | 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.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

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

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

Genes with terpene domains:
F5972_RS30715: PT_phytoene_like
Domain 1 (16 - 305): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (12):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.61 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.04 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.15 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.50 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.34 out of 20.97
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.65 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.67 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.34 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.58 out of 35.63
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.08 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.10 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.08 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_VYTZ01000016.1 - 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: 84,536 - 107,068 nt. (total: 22,533 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
F5972_RS31540: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F5972_RS31555: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Translocases: transporter
F5972_RS31590: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0001910.4 |  | 0.51 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.51 | terpene | raimonol | Streptomyces anulatus
BGC0001197.5 |  | 0.44 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000286.3 |  | 0.42 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0001483.4 |  | 0.42 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001840.2 |  | 0.39 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325
BGC0001315.3 |  | 0.37 | terpene | cucurbitacin C | Cucumis sativus
BGC0000188.5 |  | 0.36 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0001910.4 |  | 0.51 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.51 | terpene | raimonol | Streptomyces anulatus
BGC0001197.5 |  | 0.44 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000286.3 |  | 0.42 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0001483.4 |  | 0.42 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001840.2 |  | 0.39 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325
BGC0001315.3 |  | 0.37 | terpene | cucurbitacin C | Cucumis sativus
BGC0000188.5 |  | 0.36 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3

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

No significant matches found.

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

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

Genes with terpene domains:
F5972_RS31565: T2TS
Domain 1 (3 - 490): Type 2 terpene synthase
Subtype: Diterpene synthase

Reactions:
  GGPP → diterpene_C6-C11/C10-C15_PP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (7):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.66 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.06 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.79 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.24 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.95 out of 29.65
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.04 out of 30.98
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.87 out of 36.53
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_VYTZ01000016.1 - Region 2 - NRPS,T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 119,457 - 194,694 nt. (total: 75,238 nt) Show pHMM detection rules used
Region on contig edge.
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: halogenase methyltransferase
F5972_RS31685: methyltransferase

smcogs
  SMCOG1089: methyltransferase

F5972_RS31695: methyltransferase

smcogs
  SMCOG1089: methyltransferase

F5972_RS31795: flavin-dependent tyrosine-like hpg halogenase

halogenases
  flavin-dependent tyrosine-like hpg halogenase
MITE
  MITE0000040Halogenation (identity: 69.10%)
smcogs
  SMCOG1119: halogenase

Hydrolases: hydrolase
F5972_RS31800: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: hydratase
F5972_RS31790: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
F5972_RS31730: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS31780: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

F5972_RS31825: 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 | T3PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002341.2 |  |  | 0.94 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002608.2 |  |  | 0.91 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0001166.5 |  |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001261.3 |  |  | 0.59 | NRPS | AM-toxin | Alternaria alternata
BGC0001641.4 |  |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000357.5 |  |  | 0.51 | 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
BGC0002071.2 |  |  | 0.51 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0002135.2 |  |  | 0.44 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.42 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  |  | 0.41 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002608.2 |  | 0.76 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002071.2 |  | 0.73 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.71 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 22.47 out of 25.31
Confidence: strong
Additional weak hits (15):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.31 out of 21.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.12 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.86 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.14 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.56 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.43 out of 20.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.05 out of 27.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.74 out of 29.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.99 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.38 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.33 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.35 out of 20.97
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.18 out of 27.18
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.00 out of 32.93
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 119456 - 194694:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Dhpg - D-Dhpg - Phe - D-Dhpg) + (Tyr - Pro - Dhpg - X - Tyr - Pro - Dhpg - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 119456 - 160566:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Dhpg - D-Dhpg - Phe - D-Dhpg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 130142 - 194694:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Dhpg - D-Dhpg - Phe - D-Dhpg) + (Tyr - Pro - Dhpg - X - Tyr - Pro - Dhpg - 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).
F5972_RS31730: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (6..375): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    NALH---LILGGFGVSGSALNRYGMTETLVTLSG
  Nearest Stachelhaus code(s):
    Leu DALFVGAVAK (35% 8Å match)
    Val DALFVGLVAK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

F5972_RS31825: Dhpg - Dhpg - Phe - Dhpg
Search NORINE for peptide: strict or relaxed
AMP-binding (118..553): Dhpg
nrpys: Dhpg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMAFDAAVLDVSVVLGAEWNTYGPTEASVITTA
  Nearest Stachelhaus code(s):
    Dhpg DALSVGTVIK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1759..2174): Dhpg
nrpys: Dhpg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMAFDAAVLDVSVVLGAEWNTYGPTEASVITTA
  Nearest Stachelhaus code(s):
    Dhpg DALSVGTVIK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3388..3789): 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:
    LVHSFDASVWEMTVVVAGEVNAYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4459..4852): Dhpg
nrpys: Dhpg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMAFDAAVLDVSVVLGAEWNTYGPTEASVITTA
  Nearest Stachelhaus code(s):
    Dhpg DALSVGTVIK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

F5972_RS31830: Tyr - Pro - Dhpg - X - Tyr - Pro - Dhpg - X
Search NORINE for peptide: strict or relaxed
AMP-binding (464..863): Tyr
nrpys: Tyr

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

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

AMP-binding (1529..1925): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAHTFDVAFAETMTSVAGEVNAYGPTEATVIATM
  Nearest Stachelhaus code(s):
    Trp DVAMVGAVCK (68% 8Å match)
    Ala DVWIYAAVIK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (2590..3003): Dhpg
nrpys: Dhpg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMAFDAAVLDVSVVLGAEWNTYGPTEASVITTA
  Nearest Stachelhaus code(s):
    Dhpg DALSVGTVIK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3692..4090): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMAFDAAVLDVSVVVGAEWVAYGPTEASVIATS
  Nearest Stachelhaus code(s):
    Dhpg DALSVGTVIK (82% 8Å match)
    Hpg DALSIGAVIK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4786..5189): Tyr
nrpys: Tyr

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

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

AMP-binding (5854..6250): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAHTFDVAFAETMMSVAGEVNAYGPTEATVIATM
  Nearest Stachelhaus code(s):
    Trp DVAMVGAVCK (68% 8Å match)
    Ala DVWIYAAVIK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (6914..7326): Dhpg
nrpys: Dhpg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMAFDAAVLDVSVVLGAEWNTYGPTEASVITTA
  Nearest Stachelhaus code(s):
    Dhpg DALSVGTVIK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (8036..8429): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMAFDAAVLDVSVVVGAEWVAYGPTEASVIATT
  Nearest Stachelhaus code(s):
    Dhpg DALSVGTVIK (82% 8Å match)
    Hpg DALSIGAVIK (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
--- | ---
CatR | H2O2-responsive repressor

NZ_VYTZ01000017.1 - Region 1 - phenazine
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 59,463 - 79,951 nt. (total: 20,489 nt) Show pHMM detection rules used
phenazine: phzB

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
F5972_RS32175: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
F5972_RS32180: isochorismate synthase

smcogs
  SMCOG1018: isochorismate 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 | phenazine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000936.5 |  | 0.66 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1
BGC0002561.3 |  | 0.60 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0001221.5 |  | 0.50 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0000934.4 |  | 0.48 | other (phenazine) | 5-acetyl-5,10-dihydrophenazine-1-carboxylic acid, 5-(2-hydroxyacetyl)-5,10-dihydrophenazine-1-carboxylic acid, endophenazine A1, endophenazine F, endophenazine G | Kitasatospora sp. HKI 714
BGC0001868.4 |  | 0.46 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0001080.5 |  | 0.45 | other (phenazine) | endophenazine A, endophenazine B | Streptomyces anulatus
BGC0001302.5 |  | 0.45 | other (other) | lomofungin | Streptomyces lomondensis
BGC0000343.5 |  | 0.44 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0002557.2 |  | 0.43 | terpene | penifulvin A | Penicillium griseofulvum
BGC0002439.3 |  | 0.41 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000936.5 |  | 0.66 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1
BGC0002561.3 |  | 0.60 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0001221.5 |  | 0.50 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0000934.4 |  | 0.48 | other (phenazine) | 5-acetyl-5,10-dihydrophenazine-1-carboxylic acid, 5-(2-hydroxyacetyl)-5,10-dihydrophenazine-1-carboxylic acid, endophenazine A1, endophenazine F, endophenazine G | Kitasatospora sp. HKI 714
BGC0001868.4 |  | 0.46 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0001080.5 |  | 0.45 | other (phenazine) | endophenazine A, endophenazine B | Streptomyces anulatus
BGC0001302.5 |  | 0.45 | other (other) | lomofungin | Streptomyces lomondensis
BGC0000343.5 |  | 0.44 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0002557.2 |  | 0.43 | terpene | penifulvin A | Penicillium griseofulvum
BGC0002439.3 |  | 0.41 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.12 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.84 out of 30.12
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.90 out of 30.12
Confidence: medium
Additional weak hits (10):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.56 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.76 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.60 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.95 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.93 out of 28.14
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.08 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 22.78 out of 36.54
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.09 out of 24.78
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_VYTZ01000018.1 - Region 1 - lanthipeptide-class-iv
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,440 - 29,223 nt. (total: 22,784 nt) Show pHMM detection rules used
Region on contig edge.
lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
F5972_RS32745: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

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

Reference | lanthipeptide-class-iv | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.60 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002337.2 |  | 0.57 | ribosomal | class IV lanthipeptide, SflA | Streptomyces sp. NRRL S-1022
BGC0000513.3 |  | 0.56 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.56 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000496.5 |  | 0.56 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001226.4 |  | 0.54 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0002276.2 |  | 0.53 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000563.4 |  | 0.53 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000553.3 |  | 0.46 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.60 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002337.2 |  | 0.57 | ribosomal | class IV lanthipeptide, SflA | Streptomyces sp. NRRL S-1022
BGC0000513.3 |  | 0.56 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.56 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000496.5 |  | 0.56 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001226.4 |  | 0.54 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0002276.2 |  | 0.53 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000563.4 |  | 0.53 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000553.3 |  | 0.46 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.36 out of 25.31
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (12):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.17 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.18 out of 36.54
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.81 out of 26.85
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.13 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.02 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.32 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.95 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.81 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.35 out of 24.78
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.23 out of 26.85
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_VYTZ01000002.1 - Region 1 - 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: 515,290 - 538,166 nt. (total: 22,877 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
F5972_RS06295: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

F5972_RS06345: 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
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.52 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000500.5 |  | 0.47 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002704.2 |  | 0.46 | ribosomal | archalan β | Halorussus salinus
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0001576.3 |  | 0.46 | ribosomal | divamide A | Prochloron didemni
BGC0002700.2 |  | 0.45 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000503.5 |  | 0.45 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001789.3 |  | 0.44 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000536.3 |  | 0.44 | ribosomal | nisin Q | Lactococcus lactis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000528.5 |  | 0.52 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000500.5 |  | 0.47 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002704.2 |  | 0.46 | ribosomal | archalan β | Halorussus salinus
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0001576.3 |  | 0.46 | ribosomal | divamide A | Prochloron didemni
BGC0002700.2 |  | 0.45 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000503.5 |  | 0.45 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001789.3 |  | 0.44 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000536.3 |  | 0.44 | ribosomal | nisin Q | Lactococcus lactis

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 F5972_RS06345

F5972_RS06335
Leader:
MPVTLDRSEEIVSAWRSGADVEGWDSPAG
Core:
P L F I G E Y A E S E I T L T A L D T R R P S S C T G A N T I P C C
Core with dehydrations:
P L F I G E Y A E Dha E I Dhb L Dhb A L D Dhb R R P Dha Dha Cys Dhb G A N Dhb I P Cys Cys

#### antiSMASH-DB 4.0 matches for F5972_RS06335

70.6%
NZ_JABBWY010000002.1 and 3 others:
NZ_JABBWZ010000011.1 Lanthipeptides: HHX40_RS26720_lanthipeptide NZ_VANP01000002.1 Lanthipeptides: FED44_RS05225_lanthipeptide NZ_VYTZ01000002.1 Lanthipeptides: F5972_RS06340_lanthipeptide
Lanthipeptides: HHX37_RS08025_lanthipeptide
1
P L F I G E Y A E S E I T L T A L D T R R P S S C T
26
P L F I G E Y A E S E I T L T A L D T R S S C T
1
P L F I G E Y A E S E I T L T A L D T R L A S S C T
26
69.4%
NZ_JABBWY010000002.1 and 3 others:
NZ_JABBWZ010000011.1 Lanthipeptides: HHX40_RS26715_lanthipeptide NZ_VANP01000002.1 Lanthipeptides: FED44_RS05230_lanthipeptide NZ_VYTZ01000002.1 Lanthipeptides: F5972_RS06335_lanthipeptide
Lanthipeptides: HHX37_RS08020_lanthipeptide
1
P L F I G E Y A E S E I T L T A L D T R R P S S C T G A N T I P C C
34
P L F I G E Y A E S E I T L T A L D T R R P S S C T G A N T I P C C
16
P L F I G E Y A E S E I T L T A L D T R R P S S C T G A N T I P C C
49
48.9%
NZ_BMQJ01000023.1:
Lanthipeptides: IEZ10_RS33030_lanthipeptide
1
P L F I G E Y A E S E I T L T A L D T R R P S S C T
26
P L F I G+Y A E S E I T L T A L D T R S S C T
16
P L F I G D Y A E S E I T L T A L D T R L A S S C T
41
with 39 more sequence matches
Only the first 10 are displayed here.
48.6%
NZ_JANZKX010000002.1:
Lanthipeptides: O9Y01_RS08280_lanthipeptide
1
P L F I-G E Y A E S E I T L-T A L D T R R P-S S C T G A N T I P C C
34
P L F G Y+E+E I + +T R+ S S C+G+ T I C C
1
P L F S S G V Y S E A E I A G D V S R E T R Q G C S S C S G S R T I M C C
37
47.2%
NZ_JALPRT010000019.1 and 1 other:
NZ_KB895919.1 Lanthipeptides: C570_RS1000000130195_lanthipeptide
Lanthipeptides: M0M45_RS13255_lanthipeptide
1
P L F I G-E Y A E S E I T L T A L D-T R R P S S C T G A N T I P C C
34
P L F G Y E I T T + S S C T G+ I C C
1
P L F T G G R Y V V Q E I T S T W G G C S T V C S S C T G S V P I Q C C
36
44.4%
NZ_AZWQ01000024.1:
Lanthipeptides: B116_RS0113780_lanthipeptide
1
P L F I G-E Y A E S E I T L T A L D-T R R P S S C T G A N T I P C C
34
P L F G +Y E I T T + S S C T G+ + C C
1
P L F T G G K Y V V Q E I T S T W G G C S T V C S S C T G S Q R V S C C
36
41.5%
NZ_CP079946.1:
Lanthipeptides: KYK13_RS20175_lanthipeptide
1
P L F I G----E Y A E S E I T L T A L D T R R P S S C T G A N T I P C C
34
P+F+G E A +E L A D T S S C T + T C C
6
P V F V G G T S T E K A L T E S N L V A-D T G C-S S C T A S T T A F C C
41
40.0%
NZ_FWXV01000001.1:
Lanthipeptides: B9C43_RS03005_lanthipeptide
1
P L F I-G E Y A E S E I T L T A L D T R R P S S C T G A N T I P C C
34
P+F G E+A E +I R S S C T + + C C
1
P I F A S G E F A E G D I V A C N P P G S R C S S C T A S R P V F C C
35
40.0%
NZ_JANYMP010000013.1:
Lanthipeptides: NZH93_RS25860_lanthipeptide
1
P L F I-G E Y A E S E I T L T A L D T R R P S S C T G A N T I P C C
34
P L F G E+A E +I R S+C T + + C C
1
P L F A S G E F A E G D I V A C N P P G S R C S A C T A S R P V V C C
35
39.5%
NZ_CP064030.1:
Lanthipeptides: ISN74_RS08625_lanthipeptide
1
P L F I-G E Y A E S E I-------T L T A L D T R R-P S S C T G A N T I P C C
34
P L F+ G++A E S+I T L A+ + R S+C+G+ C C
1
P L F V S G Q F A E S D I V S S T N V L T L G A V C S G R C G S A C S G S A H A E C C
43
37.8%
NZ_AZVD01000036.1 and 1 other:
NZ_KB913036.1 Lanthipeptides: A39M_RS0105590_lanthipeptide
Lanthipeptides: K389_RS0119060_lanthipeptide
1
P L F I G-E Y A E S E I T L T A L-D T R R P S S C T G A N
29
P L F G Y E I T T A+ + S+C T G+
1
P L F T G G R Y V V Q E I T A T A V A N W T Y C S A C T G S G
31
37.5%
NZ_CP072597.1:
Lanthipeptides: J5226_RS01600_lanthipeptide
1
P L F I-G E Y A E S E I T L-T A L D T R R P S S C T G A N T I P C C
34
P L F I G E+A E++I + +R S+C T G T I C C
13
P L F I S G E F A E A D I A G D N E I I S R N T S A C T G C G T I Q C C
48
37.5%
NZ_FOZI01000001.1:
Lanthipeptides: BM338_RS00935_lanthipeptide
1
P L F I G-E Y A E S E I T L T A L D T R R----P S S C T G A N T I P C C
34
P L F G ++A E+E I A ++C T G++T C C
2
P L F T G G Q F A E A E I I S E A S S L T T F G G C G T A C T G S H T R Y C C
40
F5972_RS06340
Leader:
MPLTLDRSEEIVSAWRSGADVEGWDSPAG
Core:
P L F I G E Y A E S E I T L T A L D T R L A S S C T C S R F C C
Core with dehydrations:
P L F I G E Y A E Dha E I Dhb L Dhb A L D Dhb R L A Dha Dha Cys Dhb Cys Dha R F Cys Cys

#### antiSMASH-DB 4.0 matches for F5972_RS06340

100.0%
NZ_JABBWY010000002.1 and 3 others:
NZ_JABBWZ010000011.1 Lanthipeptides: HHX40_RS26720_lanthipeptide NZ_VANP01000002.1 Lanthipeptides: FED44_RS05225_lanthipeptide NZ_VYTZ01000002.1 Lanthipeptides: F5972_RS06340_lanthipeptide
Lanthipeptides: HHX37_RS08025_lanthipeptide
1
P L F I G E Y A E S E I T L T A L D T R L A S S C T C S R F C C
32
P L F I G E Y A E S E I T L T A L D T R L A S S C T C S R F C C
1
P L F I G E Y A E S E I T L T A L D T R L A S S C T C S R F C C
32
66.0%
NZ_BMQJ01000023.1:
Lanthipeptides: IEZ10_RS33030_lanthipeptide
1
P L F I G E Y A E S E I T L T A L D T R L A S S C T C S R F C C
32
P L F I G+Y A E S E I T L T A L D T R L A S S C T C S R F C C
16
P L F I G D Y A E S E I T L T A L D T R L A S S C T C S R F C C
47
49.0%
NZ_JABBWY010000002.1 and 3 others:
NZ_JABBWZ010000011.1 Lanthipeptides: HHX40_RS26715_lanthipeptide NZ_VANP01000002.1 Lanthipeptides: FED44_RS05230_lanthipeptide NZ_VYTZ01000002.1 Lanthipeptides: F5972_RS06335_lanthipeptide
Lanthipeptides: HHX37_RS08020_lanthipeptide
1
P L F I G E Y A E S E I T L T A L D T R L A S S C T
26
P L F I G E Y A E S E I T L T A L D T R S S C T
16
P L F I G E Y A E S E I T L T A L D T R R P S S C T
41
with 26 more sequence matches
Only the first 10 are displayed here.
45.7%
NZ_FWXV01000001.1:
Lanthipeptides: B9C43_RS03005_lanthipeptide
1
P L F I-G E Y A E S E I T L T A L D T R L A S S C T C S R--F C C
32
P+F G E+A E +I S S C T S R F C C
1
P I F A S G E F A E G D I V A C N P P G S R C S S C T A S R P V F C C
35
40.5%
NZ_CP048405.1:
Lanthipeptides: GXW83_RS14070_lanthipeptide
1
P L F I-G E Y A E S E I T L T A L D T R L A S S C T C S----R F C C
32
P L F G Y A E S E+T + + C S R C C
1
P L F T S G A Y A E S E L T A S G A V R T I Q C G T A C S Y S A G R E C C
37
40.0%
NZ_FOZI01000001.1:
Lanthipeptides: BM338_RS00935_lanthipeptide
1
P L F I G-E Y A E S E I-----T L T A L D T R L A S S C T C S--R F C C
32
P L F G ++A E+E I +L T ++C T S R+C C
2
P L F T G G Q F A E A E I I S E A S S L T T F G-G C G T A C T G S H T R Y C C
40
38.9%
NZ_AZWQ01000024.1:
Lanthipeptides: B116_RS0113780_lanthipeptide
1
P L F I G-E Y A E S E I T L T A L D-T R L A S S C T C S R
29
P L F G +Y E I T T + + S S C T S+
1
P L F T G G K Y V V Q E I T S T W G G C S T V C S S C T G S Q
31
37.8%
NZ_AZVD01000036.1 and 1 other:
NZ_KB913036.1 Lanthipeptides: A39M_RS0105590_lanthipeptide
Lanthipeptides: K389_RS0119060_lanthipeptide
1
P L F I G-E Y A E S E I T L T A L-D T R L A S S C T C S
28
P L F G Y E I T T A+ + S+C T S
1
P L F T G G R Y V V Q E I T A T A V A N W T Y C S A C T G S
30
37.1%
NZ_JANYMP010000013.1:
Lanthipeptides: NZH93_RS25860_lanthipeptide
1
P L F I-G E Y A E S E I T L T A L D T R L A S S C T C S R
29
P L F G E+A E +I S+C T S R
1
P L F A S G E F A E G D I V A C N P P G S R C S A C T A S R
30
37.0%
NZ_QFWW01000008.1:
Lanthipeptides: DI276_RS14925_lanthipeptide
1
P L F I-G E Y A E S E I T L T A L D T R L A S S C T C S--R F C C
32
P L F G E Y A E E+T+T + + C T S R C C
12
P L F P S G E Y A E H E L T M T G H S G K C G T V C T Y S Q G R Q C C
46
36.1%
NZ_JALPRT010000019.1 and 1 other:
NZ_KB895919.1 Lanthipeptides: C570_RS1000000130195_lanthipeptide
Lanthipeptides: M0M45_RS13255_lanthipeptide
1
P L F I G-E Y A E S E I T L T A L D-T R L A S S C T
26
P L F G Y E I T T + + S S C T
1
P L F T G G R Y V V Q E I T S T W G G C S T V C S S C T
28
35.3%
NZ_CP034550.1:
Lanthipeptides: EKG83_RS30035_lanthipeptide
5
G E Y A E S E I T L T A L D T R L A S S C T C S R--F C C
32
G E+A E +I S S C T S +C C
5
G E F A E G D I V A C N P P G S R C S S C T A S A H V Y C C
34
34.7%
NZ_QOIL01000017.1:
Lanthipeptides: DQ384_RS40545_lanthipeptide
1
P L F I G E Y A E S E I T L T A L D T R L A S S C T C-S R F C C
32
P I G E Y E E I T++ ++T+ S S C T F C C
17
P P L I G E Y T E E E I T M S L I E T K R P S S C T A G G G F C C
49
allorf_519450_519632
Leader:
MATGRRRGRASRRDAGAGPRAWSGPGTRRDETGA
Core:
R C F R R H R V T L S I E L G D S G R G K S I S W G
Core with dehydrations:
R Cys F R R H R V Dhb L Dha I E L G D Dha G R G K Dha I Dha W G

#### antiSMASH-DB 4.0 matches for allorf_519450_519632

100.0%
NZ_VYTZ01000002.1:
Lanthipeptides: allorf_519450_519632_lanthipeptide
1
R C F R R H R V T L S I E L G D S G R G K S I S W G
26
R C F R R H R V T L S I E L G D S G R G K S I S W G
1
R C F R R H R V T L S I E L G D S G R G K S I S W G
26
73.1%
NZ_JABBWY010000002.1 and 1 other:
NZ_JABBWZ010000011.1 Lanthipeptides: allorf_012175_012357_lanthipeptide
Lanthipeptides: allorf_683196_683378_lanthipeptide
1
R C F R R H R V T L S I E L G D S G R G K S I S W
25
R C F H R +L +E L G D S G R G K S I S W
1
R C F P P H R A S L L M E L G D S G R G K S I S W
25
73.1%
NZ_VANP01000002.1:
Lanthipeptides: allorf_020225_020401_lanthipeptide
1
R C F R R H R V T L S I E L G D S G R G K S I S
24
R C F H R T L +E L G D S G R G K S I S
1
R C F P P H R A T L L M E L G D S G R G K S I S
24
with 3 more sequence matches
30.8%
NZ_CP007153.1:
Lanthipeptides: allorf_02389419_02389625_lanthipeptide
9
T L S I E L G D S G R G K S I S W G
26
T L S I E G + +W G
5
T L S I E A P C P G W P S T F T W G
22
21.2%
NZ_KL997439.1 and 1 other:
NZ_KL997439.1 Lanthipeptides: IQ62_RS47105_lanthipeptide
Lanthipeptides: IQ62_RS47105_lanthipeptide
9
T L S I E L G D S G
18
T L S +L G D G
10
T L S A Q L G D K G
19
20.6%
NZ_SLWA01000002.1:
Lanthipeptides: EV142_RS05900_lanthipeptide
1
R C F R R H R V T L S I E L G D S G R G
20
+C+ V T L S D G+
15
K C W N E K T V T L S C S S C D F G Q A
34

#### MIBiG 4.0 matches for allorf_519450_519632

19.2%
BGC0002150.2 (MBO0654592.1):
Lasso peptide: triculamin
13
E L G D S G R G K S I
23
+ G D R G K +
5
K P G D G I R G K G V
15
allorf_524647_524781
Leader:
MEGGRSRSRVPDIPSASRQAPSQSTAAFA
Core:
I S A E C R Q V Y V S L A M Y
Core with dehydrations:
I Dha A E Cys R Q V Y V Dha L A M Y

#### antiSMASH-DB 4.0 matches for allorf_524647_524781

100.0%
NZ_VYTZ01000002.1:
Lanthipeptides: allorf_524647_524781_lanthipeptide
1
I S A E C R Q V Y V S L A M Y
15
I S A E C R Q V Y V S L A M Y
1
I S A E C R Q V Y V S L A M Y
15
32.5%
NZ_JABBWY010000002.1 and 1 other:
NZ_JABBWZ010000011.1 Lanthipeptides: allorf_016510_016680_lanthipeptide
Lanthipeptides: allorf_687494_687664_lanthipeptide
1
I S A E C R Q V Y V S L A M Y
15
I S A E C R Q V Y+S A M Y
26
I S A E C R Q V Y I S P A M Y
40
25.0%
NC_012470.1 and 50 others:
NZ_ALSD01000046.1 Lanthipeptides: SAG0161_RS1000000124770_lanthipeptide NZ_CAAHGW010000010.1 Lanthipeptides: E9435_RS08895_lanthipeptide NZ_CAAHHE010000002.1 Lanthipeptides: E9499_RS02930_lanthipeptide NZ_CAAHHF010000009.1 Lanthipeptides: E9478_RS08675_lanthipeptide NZ_CAAHHN010000003.1 Lanthipeptides: E9502_RS05705_lanthipeptide NZ_CAAHHU010000009.1 Lanthipeptides: E9510_RS08735_lanthipeptide NZ_CAAHHW010000012.1 Lanthipeptides: E9525_RS08985_lanthipeptide NZ_CAAHIB010000001.1 Lanthipeptides: E9539_RS01075_lanthipeptide NZ_CAAHIV010000024.1 Lanthipeptides: E9612_RS09255_lanthipeptide NZ_CAAHKK010000019.1 Lanthipeptides: E9649_RS08770_lanthipeptide NZ_CAAHKP010000014.1 Lanthipeptides: E9652_RS08920_lanthipeptide NZ_CAAHKQ010000003.1 Lanthipeptides: E9664_RS02160_lanthipeptide NZ_CAAHKY010000014.1 Lanthipeptides: E9668_RS09650_lanthipeptide NZ_CAAHLP010000002.1 Lanthipeptides: E9684_RS03445_lanthipeptide NZ_CAAHQE010000012.1 Lanthipeptides: E9931_RS08815_lanthipeptide NZ_CAAHRY010000002.1 Lanthipeptides: E9986_RS03175_lanthipeptide NZ_CAAIES010000002.1 Lanthipeptides: FAH15_RS02475_lanthipeptide NZ_CAAIIA010000012.1 Lanthipeptides: FAH55_RS08475_lanthipeptide NZ_CAAIJM010000015.1 Lanthipeptides: FAI23_RS09585_lanthipeptide NZ_CAAINV010000013.1 Lanthipeptides: FAI86_RS09025_lanthipeptide NZ_CAAIRS010000012.1 Lanthipeptides: FAK24_RS08485_lanthipeptide NZ_CAAJFI010000013.1 Lanthipeptides: FAP60_RS08495_lanthipeptide NZ_CABY01000005.1 Lanthipeptides: SZBHS5_RS10120_lanthipeptide NZ_CAJHJS010000009.1 Lanthipeptides: JMX87_RS06795_lanthipeptide NZ_CM001076.1 Lanthipeptides: SDD27957_RS10995_lanthipeptide NZ_CP018188.1 Lanthipeptides: BSR19_RS11185_lanthipeptide NZ_CP029398.1 Lanthipeptides: DF184_RS05190_lanthipeptide NZ_CP035426.1 Lanthipeptides: ETT73_RS02600_lanthipeptide NZ_CP035428.1 Lanthipeptides: ETT71_RS02820_lanthipeptide NZ_CP035437.1 Lanthipeptides: ETT62_RS06670_lanthipeptide NZ_CP035443.1 Lanthipeptides: ETT56_RS07260_lanthipeptide NZ_CP060646.1 Lanthipeptides: H7789_RS06840_lanthipeptide NZ_CP066093.1 Lanthipeptides: I6I02_RS07305_lanthipeptide NZ_CP078012.1 Lanthipeptides: KV238_RS09825_lanthipeptide NZ_GL636070.1 Lanthipeptides: HMPREF9171_RS1000000113590_lanthipeptide NZ_JAFLMI010000009.1 Lanthipeptides: J0638_RS05340_lanthipeptide NZ_JALDUD010000010.1 Lanthipeptides: M1G10_RS09695_lanthipeptide NZ_JAQDVH010000019.1 Lanthipeptides: PGU04_RS09305_lanthipeptide NZ_JAQDVH010000019.1 Lanthipeptides: PGU04_RS09305_lanthipeptide NZ_JAQMJT010000006.1 Lanthipeptides: PNU26_RS06590_lanthipeptide NZ_JAQMJT010000006.1 Lanthipeptides: PNU26_RS06590_lanthipeptide NZ_KV832031.1 Lanthipeptides: HMPREF2637_RS10860_lanthipeptide NZ_LR738724.1 Lanthipeptides: GPW69_RS05070_lanthipeptide NZ_LR793258.1 Lanthipeptides: HV369_RS03150_lanthipeptide NZ_LS483425.1 Lanthipeptides: DQN36_RS06745_lanthipeptide NZ_LT545678.1 Lanthipeptides: BJR96_RS11590_lanthipeptide NZ_NWMU01000024.1 Lanthipeptides: CO197_RS09155_lanthipeptide NZ_PKIA01000004.1 Lanthipeptides: CYK22_RS04325_lanthipeptide NZ_VMMF01000004.1 Lanthipeptides: HT717_RS01580_lanthipeptide NZ_VZNS01000007.1 Lanthipeptides: F6P79_RS05570_lanthipeptide
Lanthipeptides: SZO_RS10260_lanthipeptide
1
I S A E C R
6
I S A E C R
8
I S A E C R
13
allorf_533472_533681
Leader:
MPGNGAGADRLTFTVDEPAG
Core:
R P R Q G L A P C R G R S G L H R A G W S V T P T R G D P R D S A T E N R P P L L G G K G E T V V
Core with dehydrations:
R P R Q G L A P Cys R G R Dha G L H R A G W Dha V Dhb P Dhb R G D P R D Dha A Dhb E N R P P L L G G K G E Dhb V V

#### antiSMASH-DB 4.0 matches for allorf_533472_533681

100.0%
NZ_VYTZ01000002.1:
Lanthipeptides: allorf_533472_533681_lanthipeptide
1
R P R Q G L A P C R G R S G L H R A G W S V T P T R G D P R D S A T E N R P P L L G G K G E T V V
49
R P R Q G L A P C R G R S G L H R A G W S V T P T R G D P R D S A T E N R P P L L G G K G E T V V
1
R P R Q G L A P C R G R S G L H R A G W S V T P T R G D P R D S A T E N R P P L L G G K G E T V V
49
95.9%
NZ_JABBWY010000002.1:
Lanthipeptides: allorf_693655_693864_lanthipeptide
1
R P R Q G L A P C R G R S G L H R A G W S V T P T R G D P R D S A T E N R P P L L G G K G E T V V
49
R P R Q G L A P C R G R S G L H R A G W S V T P T R G D P R D S A T E N R P P L G K G E T V V
1
R P R Q G L A P C R G R S G L H R A G W S V T P T R G D P R D S A T E N R P P L P R G K G E T V V
49
18.0%
NZ_BNCA01000011.1 and 1 other:
NZ_BNCA01000011.1 Lanthipeptides: allorf_141930_142139_lanthipeptide
Lanthipeptides: allorf_141930_142139_lanthipeptide
6
L A P C R G R S G L H R A G W S V T
23
+A P C R R L A W V
25
I A P C R W R R D L R Y A R W W V A
42
with 2 more sequence matches
16.3%
NZ_JAKRKC020000002.1:
Lanthipeptides: allorf_0822210_0822440_lanthipeptide
2
P R Q G L A P C R G R S
13
P R G P C R R S
17
P R D G T R P C R D R S
28
10.2%
NZ_CP066762.1:
Lanthipeptides: allorf_2733265_2733486_lanthipeptide
19
G W S V T P T R G D
28
G+S+ P T R D
8
G Y S I C P T R H D
17

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.25 out of 29.72
Confidence: medium
Additional weak hits (10):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.25 out of 26.85
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.47 out of 27.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.07 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.08 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.08 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.08 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.26 out of 18.57
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.50 out of 30.22
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
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.

F5972_RS06335 - Class II
  Cleavage pHMM score: -5.00
  RODEO score: 0
  Monoisotopic mass: 3484.7 Da
  Molecular weight: 3486.9 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3504.9 Da N = 1
    3523.0 Da N = 2
    3541.0 Da N = 3
    3559.0 Da N = 4
    3577.0 Da N = 5
F5972_RS06340 - Class II
  Cleavage pHMM score: -5.00
  RODEO score: 0
  Monoisotopic mass: 3355.6 Da
  Molecular weight: 3357.8 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3375.8 Da N = 1
    3393.9 Da N = 2
    3411.9 Da N = 3
    3429.9 Da N = 4
allorf_519450_519632 - Class II
  Cleavage pHMM score: -4.50
  RODEO score: 0
  Monoisotopic mass: 2882.6 Da
  Molecular weight: 2884.3 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2902.3 Da N = 1
    2920.3 Da N = 2
    2938.3 Da N = 3
    2956.3 Da N = 4
allorf_524647_524781 - Class II
  Cleavage pHMM score: -6.30
  RODEO score: 0
  Monoisotopic mass: 1695.8 Da
  Molecular weight: 1697.0 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1715.0 Da N = 1
allorf_533472_533681 - Class II
  Cleavage pHMM score: -6.10
  RODEO score: 0
  Monoisotopic mass: 5091.7 Da
  Molecular weight: 5094.7 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    5112.7 Da N = 1
    5130.7 Da N = 2
    5148.7 Da N = 3
    5166.7 Da N = 4
    5184.8 Da N = 5
    5202.8 Da N = 6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_VYTZ01000002.1 - Region 2 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 565,166 - 586,134 nt. (total: 20,969 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
F5972_RS06575: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Hydrolases: hydrolase
F5972_RS06605: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: cyclase
F5972_RS06565: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001746.3 |  | 0.76 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0001201.3 |  | 0.51 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0000675.5 |  | 0.45 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0001387.5 |  | 0.41 | other (other) | nucleocidin | Streptomyces calvus
BGC0001294.5 |  | 0.40 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002318.2 |  | 0.39 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000528.5 |  | 0.36 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002316.2 |  | 0.36 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002509.3 |  | 0.35 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0001972.4 |  | 0.35 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001746.3 |  | 0.76 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0001201.3 |  | 0.51 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0000675.5 |  | 0.45 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0001387.5 |  | 0.41 | other (other) | nucleocidin | Streptomyces calvus
BGC0001294.5 |  | 0.40 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002318.2 |  | 0.39 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000528.5 |  | 0.36 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002316.2 |  | 0.36 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002509.3 |  | 0.35 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0001972.4 |  | 0.35 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis

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:
F5972_RS06565: T1TS
Domain 1 (11 - 317): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 25.31
Confidence: medium
Additional weak hits (4):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.42 out of 20.97
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.96 out of 27.18
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.82 out of 25.88
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_VYTZ01000020.1 - Region 1 - 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: 34,034 - 56,882 nt. (total: 22,849 nt) Show pHMM detection rules used
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
F5972_RS34045: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: transferase
F5972_RS34060: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

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
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002116.3 |  | 0.46 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0000623.3 |  | 0.42 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0002493.3 |  | 0.41 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001221.5 |  | 0.40 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0002698.2 |  | 0.39 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0002218.2 |  | 0.39 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0000527.5 |  | 0.39 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0002470.2 |  | 0.38 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0002284.3 |  | 0.37 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002116.3 |  | 0.46 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0000623.3 |  | 0.42 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0002493.3 |  | 0.41 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001221.5 |  | 0.40 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0002698.2 |  | 0.39 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0002218.2 |  | 0.39 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0000527.5 |  | 0.39 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0002470.2 |  | 0.38 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0002284.3 |  | 0.37 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f

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 (8):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.88 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.10 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.13 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.73 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.88 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.95 out of 28.19
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (34033...56882)
F5972_RS34030
  RRE type: Mycofactocin_RRE
  Location: 5 - 85
  Score: 93.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_VYTZ01000020.1 - 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: 58,958 - 120,244 nt. (total: 61,287 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
F5972_RS34135: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase aminotransferase
F5972_RS34175: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

F5972_RS34185: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase hydrolase
F5972_RS34115: thioesterase

smcogs
  SMCOG1004: thioesterase

F5972_RS34195: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
F5972_RS34150: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F5972_RS34160: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS34165: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS34200: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F5972_RS39095: 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
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  | 0.69 | PKS | oronofacic acid | Pseudomonas syringae
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
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002175.3 |  | 0.63 | PKS | YWA1 | Aspergillus oryzae RIB40

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0000041.3 |  | 0.69 | PKS | oronofacic acid | Pseudomonas syringae
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
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002175.3 |  | 0.63 | PKS | YWA1 | Aspergillus oryzae RIB40

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

No significant matches found.

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 (33):
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.60 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.91 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.39 out of 30.97
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.10 out of 29.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.92 out of 30.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.79 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.20 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.53 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.30 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.64 out of 30.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.67 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.59 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.06 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.66 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.35 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.08 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.76 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.56 out of 36.53
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.20 out of 26.06
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
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: 19.90 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.91 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.78 out of 28.14
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.34 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.61 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.21 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.47 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.68 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.50 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.31 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 2, location 58957 - 120244:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ccmal) + (ccmal - ccmal - ccmal) + (ccmal - ccmal)
Non-colinear ordering:
  F5972_RS34150 + F5972_RS39095 + F5972_RS34200

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).
F5972_RS34150: mal
PKS_AT (554..843): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 187.2
  inactive: 88.4
  Methoxymalonyl-CoA: 58.8
  Methylmalonyl-CoA: 50.2
  Propionyl-CoA: 23.6
  Isobutyryl-CoA: 22.9
  Acetyl-CoA: 22.3
  Ethylmalonyl-CoA: 19.4
  Benzoyl-CoA: 14.6
  CHC-CoA: 10.7
  fatty_acid: 10.1
  trans-1,2-CPDA: 3.4
  2-Methylbutyryl-CoA: 2.1
  3-Methylbutyryl-CoA: -0.8

F5972_RS39095: mal - mal - mal
PKS_AT (706..1004): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 213.5
  inactive: 113.6
  Methoxymalonyl-CoA: 65.8
  Methylmalonyl-CoA: 54.2
  Propionyl-CoA: 28.7
  Isobutyryl-CoA: 23.4
  Acetyl-CoA: 20.3
  fatty_acid: 17.7
  Ethylmalonyl-CoA: 14.9
  Benzoyl-CoA: 11.7
  CHC-CoA: 8.4
  trans-1,2-CPDA: 7.3
  2-Methylbutyryl-CoA: 6.3
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2443..2731): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 213.8
  inactive: 106.0
  Methylmalonyl-CoA: 60.0
  Methoxymalonyl-CoA: 59.8
  Propionyl-CoA: 36.4
  Isobutyryl-CoA: 33.6
  Acetyl-CoA: 25.8
  2-Methylbutyryl-CoA: 13.7
  CHC-CoA: 12.8
  fatty_acid: 12.6
  Benzoyl-CoA: 12.4
  trans-1,2-CPDA: 8.0
  3-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -4.5

PKS_AT (4206..4497): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.4
  inactive: 102.7
  Methoxymalonyl-CoA: 62.8
  Methylmalonyl-CoA: 55.8
  Isobutyryl-CoA: 32.2
  Propionyl-CoA: 18.1
  Ethylmalonyl-CoA: 16.9
  Acetyl-CoA: 15.8
  Benzoyl-CoA: 12.5
  fatty_acid: 8.1
  CHC-CoA: 6.6
  2-Methylbutyryl-CoA: 4.4
  trans-1,2-CPDA: 4.2
  3-Methylbutyryl-CoA: 0.0

F5972_RS34160: X
AMP-binding (2..411): X
nrpys: Val, Leu, Ile, Abu, Ival

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

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

F5972_RS34165: X
AMP-binding (18..410): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YLMFFDCAMFDCFSLFAGEENIYGPTELTITVTG
  Nearest Stachelhaus code(s):
    bMe-Asp DCFFFALITK (82% 8Å match)
    Ala DCFFFALITK (79% 8Å match)
  Stachelhaus code match:
    80% (moderate)

F5972_RS34175: mmal
PKS_AT (40..278): mmal
ATSignature: (unknown)
No matches above 50%
minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 13.5
  CHC-CoA: 13.1
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Malonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

F5972_RS34200: mal - mal
PKS_AT (301..591): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 200.0
  inactive: 112.7
  Methoxymalonyl-CoA: 56.6
  Methylmalonyl-CoA: 53.6
  Isobutyryl-CoA: 33.0
  Propionyl-CoA: 25.8
  Acetyl-CoA: 22.7
  fatty_acid: 18.4
  Ethylmalonyl-CoA: 16.2
  Benzoyl-CoA: 15.5
  CHC-CoA: 13.1
  trans-1,2-CPDA: 9.9
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -2.5

PKS_AT (2085..2375): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 213.5
  inactive: 117.1
  Methoxymalonyl-CoA: 56.5
  Methylmalonyl-CoA: 54.1
  Acetyl-CoA: 24.5
  Propionyl-CoA: 24.1
  Isobutyryl-CoA: 20.9
  Ethylmalonyl-CoA: 16.5
  Benzoyl-CoA: 16.5
  fatty_acid: 15.2
  trans-1,2-CPDA: 13.5
  CHC-CoA: 10.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -2.3

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

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

NZ_VYTZ01000025.1 - Region 1 - NRPS,NRPS-like,T1PKS,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 73,029 nt. (total: 73,029 nt) Show pHMM detection rules used
Region on contig edge.
terpene-precursor: (PT_FPPS_like and not PT_HPP)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
F5972_RS35790: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

F5972_RS35850: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F5972_RS35855: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

F5972_RS35860: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

F5972_RS35900: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

F5972_RS35910: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

F5972_RS35960: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F5972_RS35975: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: acylase aminotransferase sulfhydrylase
F5972_RS35825: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

F5972_RS35830: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

F5972_RS35890: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

F5972_RS35945: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

F5972_RS35985: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

Hydrolases: amidase deacetylase esterase
F5972_RS35800: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

F5972_RS35865: amidase

smcogs
  SMCOG1105: amidase

F5972_RS35935: thioesterase

smcogs
  SMCOG1004: thioesterase

F5972_RS35940: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: lyase
F5972_RS35950: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Isomerases: isomerase
F5972_RS35920: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase synthetase
F5972_RS35780: 1-deoxy-D-xylulose-5-phosphate synthase

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

F5972_RS35815: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

F5972_RS35845: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS35875: 1-deoxy-D-xylulose-5-phosphate synthase

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

F5972_RS35885: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS35970: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS35990: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport
F5972_RS35995: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | terpene-precursor | T1PKS | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  |  |  | 0.88 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000357.5 |  |  |  |  | 0.85 | 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
BGC0001268.4 |  |  |  |  | 0.78 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001132.4 |  |  |  |  | 0.77 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  |  |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  |  |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  |  |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  |  |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  |  |  |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.67 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | 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.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene 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:
F5972_RS35815: PT_FPPS_like
Domain 1 (51 - 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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.79 out of 21.84
Confidence: medium
Additional weak hits (19):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.21 out of 36.54
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.25 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.67 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 21.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.25 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.60 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.75 out of 27.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.41 out of 33.73
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.70 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.72 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.04 out of 21.84
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.13 out of 27.18
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.57 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.60 out of 35.63
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.44 out of 28.14
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.79 out of 20.01
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.04 out of 29.65
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
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 73029:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (D-Tyr - X) + (mal - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 5970 - 49327:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - mal) + (D-Tyr - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 25850 - 72801:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (D-Tyr - X) + (mal - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 36633 - 73029:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (D-Tyr - 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).
F5972_RS35845: X
AMP-binding (36..433): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

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

F5972_RS35885: X
AMP-binding (15..416): 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:
    ATTTHTVGPMAAFWLYGGTVQTYGTTETWEIGTM
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

F5972_RS35890: mal
PKS_AT (5..283): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 79.5
  Methoxymalonyl-CoA: 40.6
  Methylmalonyl-CoA: 33.3
  inactive: 20.4
  Isobutyryl-CoA: 16.0
  Benzoyl-CoA: 13.0
  trans-1,2-CPDA: 11.7
  Ethylmalonyl-CoA: 11.6
  fatty_acid: 10.7
  2-Methylbutyryl-CoA: 9.0
  Propionyl-CoA: 1.2
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

F5972_RS35970: Tyr - X
Search NORINE for peptide: strict or relaxed
AMP-binding (22..411): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LEQAFDASVSEVTLIVAGEINAYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Tyr DASTIAAVCK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1546..1942): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPRGDSLAFEIWVWTGGDVNGYGSSETAVFTTR
  Nearest Stachelhaus code(s):
    Ile or aIle DAFWWGGVFK (62% 8Å match)
  Stachelhaus code match:
    90% (moderate)

F5972_RS35990: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (24..416): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDGCFDPSAFEGWMLGGGEVNGYGPTEDTCFTSC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MexT | Global virulence regulator

NZ_VYTZ01000003.1 - Region 1 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 63,778 - 87,925 nt. (total: 24,148 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
F5972_RS08255: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

F5972_RS08260: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: 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-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.52 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000544.4 |  | 0.41 | ribosomal | planosporicin | Planomonospora alba
BGC0000506.4 |  | 0.40 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000559.4 |  | 0.39 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0001727.3 |  | 0.39 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0001701.4 |  | 0.36 | ribosomal | nisin O | Blautia obeum
BGC0000511.5 |  | 0.36 | ribosomal | ericin S | Bacillus subtilis
BGC0002120.3 |  | 0.36 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000529.5 |  | 0.35 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0002359.3 |  | 0.30 | NRPS | dudomycin A | Streptomyces albus subsp. chlorinus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.52 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000544.4 |  | 0.41 | ribosomal | planosporicin | Planomonospora alba
BGC0000506.4 |  | 0.40 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000559.4 |  | 0.39 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0001727.3 |  | 0.39 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0001701.4 |  | 0.36 | ribosomal | nisin O | Blautia obeum
BGC0000511.5 |  | 0.36 | ribosomal | ericin S | Bacillus subtilis
BGC0002120.3 |  | 0.36 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000529.5 |  | 0.35 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0002359.3 |  | 0.30 | NRPS | dudomycin A | Streptomyces albus subsp. chlorinus

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

No significant matches found.

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.16 out of 25.88
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.77 out of 23.79
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 24.66 out of 29.65
Confidence: medium
Additional weak hits (9):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.37 out of 30.22
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
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 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.03 out of 24.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.86 out of 24.78
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.81 out of 20.01
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.93 out of 26.06
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (63777...87925)
F5972_RS08255
  RRE type: Lanthipeptide_LanB_RRE
  Location: 126 - 215
  Score: 28.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism
LexA variant 1 | Repressor of DNA damage response
PsrA | Oleic acid responsive regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_VYTZ01000003.1 - Region 2 - 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: 286,940 - 308,007 nt. (total: 21,068 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
F5972_RS09380: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

F5972_RS09385: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: carbamoyltransferase phosphorylase
F5972_RS09395: thiamine-phosphate pyrophosphorylase

smcogs
  SMCOG1280: thiamine-phosphate pyrophosphorylase

F5972_RS09445: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

Ligases: synthetase
F5972_RS09400: 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 |  | 0.43 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001521.3 |  | 0.43 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001456.3 |  | 0.41 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000664.5 |  | 0.41 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.40 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.40 | terpene | carotenoid | Streptomyces avermitilis
BGC0001529.5 |  | 0.40 | 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
BGC0002345.2 |  | 0.40 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0000678.5 |  | 0.39 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.43 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001521.3 |  | 0.43 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001456.3 |  | 0.41 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000664.5 |  | 0.41 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.40 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.40 | terpene | carotenoid | Streptomyces avermitilis
BGC0001529.5 |  | 0.40 | 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
BGC0002345.2 |  | 0.40 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0000678.5 |  | 0.39 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

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:
F5972_RS09400: PT_FPPS_like
Domain 1 (47 - 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.86 out of 21.84
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.27 out of 24.78
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 25.49 out of 29.65
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.00 out of 24.78
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.29 out of 26.85
Confidence: medium
Additional weak hits (2):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.87 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.39 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
--- | ---
CRP | Cyclic AMP receptor protein
LexA variant 1 | Repressor of DNA damage response
LexA variant 2 | Repressor of DNA damage response
MexT | Global virulence regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_VYTZ01000030.1 - 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 - 10,302 nt. (total: 10,302 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
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: synthase
F5972_RS36540: 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
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.64 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.63 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000037.4 |  | 0.60 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.64 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.63 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000037.4 |  | 0.60 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

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.

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 - 10302:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - ccmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
F5972_RS36540: mal - mal
PKS_AT (191..481): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 214.2
  inactive: 107.9
  Methoxymalonyl-CoA: 57.3
  Methylmalonyl-CoA: 53.8
  Acetyl-CoA: 23.9
  Propionyl-CoA: 21.9
  Isobutyryl-CoA: 17.5
  fatty_acid: 17.3
  Benzoyl-CoA: 16.6
  trans-1,2-CPDA: 13.6
  Ethylmalonyl-CoA: 13.2
  CHC-CoA: 10.3
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -2.5

PKS_AT (1996..2283): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 204.9
  inactive: 109.8
  Methoxymalonyl-CoA: 55.4
  Methylmalonyl-CoA: 52.5
  Isobutyryl-CoA: 25.9
  Ethylmalonyl-CoA: 22.9
  Acetyl-CoA: 22.8
  Propionyl-CoA: 21.3
  trans-1,2-CPDA: 18.5
  Benzoyl-CoA: 17.1
  fatty_acid: 16.1
  CHC-CoA: 13.3
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -2.4

Link to PARAS substrate predictor
NZ_VYTZ01000033.1 - 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 - 8,331 nt. (total: 8,331 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
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
F5972_RS36635: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: synthase
F5972_RS36630: 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
--- | --- | --- | --- | --- | ---
BGC0002191.2 |  | 0.66 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002192.3 |  | 0.63 | PKS | FR901512 | fungal sp. No.14919
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000037.4 |  | 0.62 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002191.2 |  | 0.66 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002192.3 |  | 0.63 | PKS | FR901512 | fungal sp. No.14919
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000037.4 |  | 0.62 | PKS | cichorine | Aspergillus nidulans FGSC A4
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.

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 - 8331:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - Me-mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
F5972_RS36635: mal - mmal
PKS_AT (144..453): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 159.8
  Methoxymalonyl-CoA: 61.6
  inactive: 50.3
  Methylmalonyl-CoA: 49.7
  Propionyl-CoA: 38.3
  Isobutyryl-CoA: 23.4
  fatty_acid: 19.1
  Ethylmalonyl-CoA: 16.9
  2-Methylbutyryl-CoA: 13.2
  CHC-CoA: 12.9
  trans-1,2-CPDA: 8.9
  Benzoyl-CoA: 8.9
  3-Methylbutyryl-CoA: 0.0
  Acetyl-CoA: -3.0

PKS_AT (1947..2245): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 214.7
  Ethylmalonyl-CoA: 206.0
  Methoxymalonyl-CoA: 177.1
  2-Methylbutyryl-CoA: 146.3
  trans-1,2-CPDA: 128.4
  Malonyl-CoA: 109.7
  Propionyl-CoA: 101.7
  CHC-CoA: 84.4
  Isobutyryl-CoA: 83.5
  Benzoyl-CoA: 66.2
  Acetyl-CoA: 38.7
  inactive: 37.9
  3-Methylbutyryl-CoA: 36.6
  fatty_acid: 30.1

Link to PARAS substrate predictor
NZ_VYTZ01000034.1 - 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 - 7,501 nt. (total: 7,501 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
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
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
F5972_RS36640: 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
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  | 0.63 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000342.4 |  | 0.63 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  | 0.62 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001249.5 |  | 0.62 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001166.5 |  | 0.62 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001758.4 |  | 0.62 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  | 0.63 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000342.4 |  | 0.63 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  | 0.62 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001249.5 |  | 0.62 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001166.5 |  | 0.62 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001758.4 |  | 0.62 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

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 - 7501:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Dhpg)

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).
F5972_RS36645: Dhpg
Search NORINE for peptide: strict or relaxed
AMP-binding (770..1196): Dhpg
nrpys: Dhpg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMAFDAAVLDVSVVLGAEWNTYGPTEASVITTA
  Nearest Stachelhaus code(s):
    Dhpg DALSVGTVIK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
NZ_VYTZ01000004.1 - Region 1 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 325,848 - 356,196 nt. (total: 30,349 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
F5972_RS12690: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

F5972_RS12715: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: protease
F5972_RS12730: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Lyases: decarboxylase
F5972_RS12685: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001572.3 |  | 0.73 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002073.3 |  | 0.70 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0001478.5 |  | 0.68 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.65 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  | 0.64 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0002690.2 |  | 0.60 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002305.2 |  | 0.58 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002464.3 |  | 0.58 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0001453.5 |  | 0.57 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000244.4 |  | 0.55 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001572.3 |  | 0.73 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002073.3 |  | 0.70 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0001478.5 |  | 0.68 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.65 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  | 0.64 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0002690.2 |  | 0.60 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002305.2 |  | 0.58 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002464.3 |  | 0.58 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0001453.5 |  | 0.57 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000244.4 |  | 0.55 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.57 out of 36.53
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.06 out of 20.01
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.57 out of 36.53
Confidence: medium
Additional weak hits (9):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.91 out of 21.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.03 out of 26.85
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.33 out of 20.01
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.41 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.31 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.01 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.68 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes
DmdR1 | Iron(II)-dependent repressor

NZ_VYTZ01000004.1 - Region 2 - RRE-containing
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 631,467 - 652,591 nt. (total: 21,125 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
F5972_RS14170: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

F5972_RS14195: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Ligases: ligase
F5972_RS14155: 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 | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.56 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002276.2 |  | 0.54 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002391.2 |  | 0.52 | terpene | zealexin B3, zealexin C2 | Zea mays
BGC0000812.3 |  | 0.49 | other (other) | huperzine A | Shiraia sp. slf14
BGC0000585.5 |  | 0.47 | ribosomal | microcin C7 | Escherichia coli
BGC0001137.5 |  | 0.44 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001668.4 |  | 0.41 | NRPS | microperfuranone | Aspergillus nidulans FGSC A4
BGC0000595.3 |  | 0.41 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000131.5 |  | 0.40 | PKS | pyrrolomycin | Streptomyces sp. UC 11065

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.56 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002276.2 |  | 0.54 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002391.2 |  | 0.52 | terpene | zealexin B3, zealexin C2 | Zea mays
BGC0000812.3 |  | 0.49 | other (other) | huperzine A | Shiraia sp. slf14
BGC0000585.5 |  | 0.47 | ribosomal | microcin C7 | Escherichia coli
BGC0001137.5 |  | 0.44 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001668.4 |  | 0.41 | NRPS | microperfuranone | Aspergillus nidulans FGSC A4
BGC0000595.3 |  | 0.41 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000131.5 |  | 0.40 | PKS | pyrrolomycin | Streptomyces sp. UC 11065

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: 18.07 out of 20.47
Confidence: medium
Additional weak hits (9):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.19 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.59 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.10 out of 27.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.72 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.51 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.30 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.16 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.51 out of 26.06
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.32 out of 32.93
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (631466...652591)
F5972_RS14190
  RRE type: Pantocin_Microcin_RRE
  Location: 1 - 85
  Score: 43.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_VYTZ01000005.1 - 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 - 29,272 nt. (total: 29,272 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
Transferases: transferase
F5972_RS14255: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Ligases: synthase
F5972_RS14245: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

F5972_RS14250: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001284.4 |  | 0.64 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001244.3 |  | 0.63 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002192.3 |  | 0.63 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000037.4 |  | 0.62 | PKS | cichorine | Aspergillus nidulans FGSC A4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001284.4 |  | 0.64 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001244.3 |  | 0.63 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002192.3 |  | 0.63 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000037.4 |  | 0.62 | PKS | cichorine | Aspergillus nidulans FGSC A4

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (25):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.83 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.46 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.89 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.20 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.51 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.08 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.06 out of 27.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.61 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.03 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.00 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.59 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.73 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.82 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.21 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.93 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.54 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.17 out of 27.78
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.18 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.86 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.77 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.26 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 29272:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mxmal - ohmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
F5972_RS14250: mxmal - mal
PKS_AT (570..798): mxmal
ATSignature: Malonyl-CoA, Methylmalonyl-CoA, Methoxymalonyl-CoA, Ethylmalonyl-CoA

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

minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 89.1
  Methylmalonyl-CoA: 71.1
  Ethylmalonyl-CoA: 64.1
  trans-1,2-CPDA: 58.9
  Malonyl-CoA: 57.6
  CHC-CoA: 42.5
  2-Methylbutyryl-CoA: 41.3
  Propionyl-CoA: 30.8
  Benzoyl-CoA: 17.0
  Isobutyryl-CoA: 16.2
  inactive: 11.8
  Acetyl-CoA: 6.3
  3-Methylbutyryl-CoA: 4.9
  fatty_acid: 4.1

PKS_AT (1666..1963): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 171.8
  Methoxymalonyl-CoA: 69.3
  inactive: 61.1
  Methylmalonyl-CoA: 56.4
  Propionyl-CoA: 46.3
  Isobutyryl-CoA: 23.4
  Acetyl-CoA: 20.0
  Ethylmalonyl-CoA: 19.2
  fatty_acid: 15.1
  CHC-CoA: 14.4
  trans-1,2-CPDA: 10.6
  2-Methylbutyryl-CoA: 9.0
  Benzoyl-CoA: 8.6
  3-Methylbutyryl-CoA: 8.3

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

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

NZ_VYTZ01000005.1 - Region 2 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 436,503 - 461,760 nt. (total: 25,258 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
F5972_RS16310: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: deacetylase
F5972_RS16275: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

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
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000663.5 |  | 0.55 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0002276.2 |  | 0.53 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000646.5 |  | 0.46 | terpene | β-carotein | uncultured bacterium
BGC0001456.3 |  | 0.45 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001227.3 |  | 0.44 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000633.3 |  | 0.44 | terpene | carotenoid | Streptomyces avermitilis
BGC0000648.3 |  | 0.43 | terpene | carotenoid | Myxococcus xanthus
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000663.5 |  | 0.55 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0002276.2 |  | 0.53 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000646.5 |  | 0.46 | terpene | β-carotein | uncultured bacterium
BGC0001456.3 |  | 0.45 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001227.3 |  | 0.44 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000633.3 |  | 0.44 | terpene | carotenoid | Streptomyces avermitilis
BGC0000648.3 |  | 0.43 | terpene | carotenoid | Myxococcus xanthus
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338

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

No significant matches found.

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

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

Genes with terpene domains:
F5972_RS16280: PT_phytoene_like
Domain 1 (10 - 254): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

F5972_RS16285: PT_phytoene_like
Domain 1 (54 - 372): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

F5972_RS16295: T2TS
Domain 1 (7 - 620): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (8):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.84 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.68 out of 27.04
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.21 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.36 out of 29.38
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.70 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.54 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.73 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.68 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
MexT | Global virulence regulator

NZ_VYTZ01000005.1 - Region 3 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 462,361 - 483,428 nt. (total: 21,068 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
F5972_RS16370: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

F5972_RS16375: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

F5972_RS16410: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

F5972_RS16420: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: hydrolase
F5972_RS16450: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Ligases: synthetase
F5972_RS16415: 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
--- | --- | --- | --- | --- | ---
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000706.3 |  | 0.46 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000249.5 |  | 0.42 | PKS | nogalamycin | Streptomyces nogalater
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000665.5 |  | 0.41 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000679.5 |  | 0.40 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0000905.5 |  | 0.40 | other (other) | heme D1 | Heliobacillus mobilis
BGC0001529.5 |  | 0.39 | 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
BGC0001374.5 |  | 0.39 | other (other) | thienodolin | Streptomyces albogriseolus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000706.3 |  | 0.46 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000249.5 |  | 0.42 | PKS | nogalamycin | Streptomyces nogalater
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000665.5 |  | 0.41 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000679.5 |  | 0.40 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0000905.5 |  | 0.40 | other (other) | heme D1 | Heliobacillus mobilis
BGC0001529.5 |  | 0.39 | 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
BGC0001374.5 |  | 0.39 | other (other) | thienodolin | Streptomyces albogriseolus

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

No significant matches found.

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:
F5972_RS16415: PT_FPPS_like
Domain 1 (64 - 353): 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.
No hits above weak threshold.
Weak hits (5):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.47 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.67 out of 20.01
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.19 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.71 out of 31.73
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.19 out of 29.51
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
--- | ---

NZ_VYTZ01000005.1 - Region 4 - azole-containing-RiPP,thioamitides
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 600,749 - 630,916 nt. (total: 30,168 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)
thioamitides: ((YcaO or TIGR03604) and TfuA)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
F5972_RS17045: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F5972_RS17055: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F5972_RS37290: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

Transferases: methyltransferase
F5972_RS17050: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

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

Reference | azole-containing-RiPP | thioamitides | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002084.4 |  |  | 0.48 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  |  | 0.48 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0001849.4 |  |  | 0.46 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0001201.3 |  |  | 0.40 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002560.3 |  |  | 0.38 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0000844.5 |  |  | 0.37 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002127.3 |  |  | 0.33 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001802.5 |  |  | 0.32 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0001696.5 |  |  | 0.32 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0000625.5 |  |  | 0.32 | ribosomal | thioviridamide | Streptomyces olivoviridis

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
BGC0001849.4 |  | 0.56 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0001201.3 |  | 0.52 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002560.3 |  | 0.51 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0000844.5 |  | 0.50 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002127.3 |  | 0.48 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001802.5 |  | 0.47 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0001696.5 |  | 0.47 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0000625.5 |  | 0.47 | ribosomal | thioviridamide | Streptomyces olivoviridis

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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (13):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.88 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.65 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.31 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.77 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.09 out of 28.14
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.82 out of 21.55
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.30 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.31 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.89 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.87 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.03 out of 29.65
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (600748...630916)
F5972_RS37285
  RRE type: Stand_Alone_Lasso_RRE
  Location: 1 - 89
  Score: 46.6
thioamitides protocluster (608362...630916)
F5972_RS37285
  RRE type: Stand_Alone_Lasso_RRE
  Location: 1 - 89
  Score: 46.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
MexT | Global virulence regulator

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_VYTZ01000006.1 - Region 1 - T3PKS,lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 109,423 - 150,511 nt. (total: 41,089 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
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
F5972_RS17740: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

F5972_RS17785: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

F5972_RS17840: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F5972_RS17845: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F5972_RS17855: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: methyltransferase
F5972_RS17745: Methylation

MITE
  MITE0000155Methylation (identity: 68.40%)
smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Ligases: ligase synthase
F5972_RS17680: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS17750: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

F5972_RS17770: 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 | T3PKS | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000282.3 |  |  | 1.14 | 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
BGC0000551.5 |  |  | 0.64 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000496.5 |  |  | 0.59 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3 |  |  | 0.55 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  |  | 0.54 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  |  | 0.53 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0001831.3 |  |  | 0.45 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000518.3 |  |  | 0.45 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000553.3 |  |  | 0.43 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002700.2 |  |  | 0.38 | ribosomal | bacinapeptin | Bacillus nakamurai

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.82 | 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
BGC0000551.5 |  | 0.65 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000496.5 |  | 0.63 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.61 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000518.3 |  | 0.56 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0001831.3 |  | 0.56 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000553.3 |  | 0.55 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998

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 F5972_RS17730

F5972_RS17715
Leader:
MALLDLQTLEAPTGGGGGT
F5972_RS17720
Leader:
MALLDLQTLEAPTGGGGT
Shared core:
T G S N L S L L G C T P H E N S S L S I I C G
Core with dehydrations:
Dhb G Dha N L Dha L L G Cys Dhb P H E N Dha Dha L Dha I I Cys G

#### antiSMASH-DB 4.0 matches for F5972_RS17715

100.0%
NZ_VYTZ01000006.1 and 1 other:
NZ_VYTZ01000006.1 Lanthipeptides: F5972_RS17715_lanthipeptide
Lanthipeptides: F5972_RS17720_lanthipeptide
1
T G S N L S L L G C T P H E N S S L S I I C G
23
T G S N L S L L G C T P H E N S S L S I I C G
1
T G S N L S L L G C T P H E N S S L S I I C G
23
95.7%
NZ_BMMN01000011.1 and 4 others:
NZ_FTNI01000016.1 Lanthipeptides: BXA11_RS42310_lanthipeptide NZ_JABBWY010000006.1 Lanthipeptides: HHX37_RS18535_lanthipeptide NZ_JABBWZ010000004.1 Lanthipeptides: HHX40_RS12965_lanthipeptide NZ_VANP01000005.1 Lanthipeptides: FED44_RS16255_lanthipeptide
Lanthipeptides: IEY80_RS26010_lanthipeptide
2
G S N L S L L G C T P H E N S S L S I I C G
23
G S N L S L L G C T P H E N S S L S I I C G
1
G S N L S L L G C T P H E N S S L S I I C G
22
91.3%
NZ_QOIL01000022.1 and 1 other:
NZ_QOIL01000022.1 Lanthipeptides: DQ384_RS31185_lanthipeptide
Lanthipeptides: DQ384_RS31190_lanthipeptide
2
G S N L S L L G C T P H E N S S L S I I C G
23
G S N L S L L G C T P H E N S S L S I+C G
1
G S N L S L L G C T P H E N S S L S I L C G
22
with 29 more sequence matches
Only the first 10 are displayed here.
87.5%
NZ_JABBWU010000019.1 and 5 others:
NZ_JABBWU010000019.1 Lanthipeptides: HHX30_RS29850_lanthipeptide NZ_JABBWV010000002.1 Lanthipeptides: HHX31_RS05735_lanthipeptide NZ_JABBWX010000013.1 Lanthipeptides: HHX35_RS30145_lanthipeptide NZ_JABBXA010000003.1 Lanthipeptides: HHX41_RS08060_lanthipeptide NZ_JABBXA010000003.1 Lanthipeptides: HHX41_RS08055_lanthipeptide
Lanthipeptides: HHX30_RS29860_lanthipeptide
2
G S N L S L L G C T P H E N S S L S I I C G
23
G S N L S L L G C T P H E N S S L S+I C G
3
G S N L S L L G C T P H E N S S L S L I C G
24
87.0%
NZ_BMMN01000011.1 and 1 other:
NZ_FTNI01000016.1 Lanthipeptides: BXA11_RS42315_lanthipeptide
Lanthipeptides: IEY80_RS26005_lanthipeptide
2
G S N L S L L G C T P H E N S S L S I I C G
23
G S N L S L L C T P H E N S S L S+I C G
1
G S N L S L L A C T P H E N S S L S L I C G
22
87.0%
NZ_KI866522.1:
Lanthipeptides: MPTA5024_RS40525_lanthipeptide
2
G S N L S L L G C T P H E N S S L S I I C G
23
G S N L S L L G C T P H E N S S L S++C G
1
G S N L S L L G C T P H E N S S L S V L C G
22
82.6%
NZ_JABBWU010000019.1:
Lanthipeptides: HHX30_RS29855_lanthipeptide
4
N L S L L G C T P H E N S S L S I I C G
23
N+S L L G C T P H E N S S L S I I C G
1
N V S L L G C T P H E N S S L S I I C G
20
82.6%
NZ_JABBWX010000013.1:
Lanthipeptides: HHX35_RS30140_lanthipeptide
4
N L S L L G C T P H E N S S L S I I C G
23
N L S L L G C T P H E N S S L S I+C G
1
N L S L L G C T P H E N S S L S I V C G
20
82.6%
NZ_JABBXA010000003.1:
Lanthipeptides: HHX41_RS08065_lanthipeptide
4
N L S L L G C T P H E N S S L S I I C G
23
N L S L L G C T P H E N S S L S+I C G
1
N L S L L G C T P H E N S S L S L I C G
20
78.3%
NZ_BCBX01000043.1 and 1 other:
NZ_BCBX01000043.1 Lanthipeptides: AP234_RS36585_lanthipeptide
Lanthipeptides: AP234_RS36580_lanthipeptide
2
G S N L S L L G C T P H E N S S L S I I C G
23
G S N L S L L C P H E N S S L S++C G
1
G S N L S L L A C V P H E N S S L S L L C G
22
78.3%
NZ_JABBWV010000002.1:
Lanthipeptides: HHX31_RS05740_lanthipeptide
4
N L S L L G C T P H E N S S L S I I C G
23
N L S L L G C T P H E N S S L S++C G
1
N L S L L G C T P H E N S S L S L V C G
20
73.9%
NZ_JABBWY010000006.1 and 3 others:
NZ_JABBWZ010000004.1 Lanthipeptides: HHX40_RS12960_lanthipeptide NZ_VANP01000005.1 Lanthipeptides: FED44_RS16250_lanthipeptide NZ_VYTZ01000006.1 Lanthipeptides: F5972_RS17725_lanthipeptide
Lanthipeptides: HHX37_RS18530_lanthipeptide
5
L S L L G C T P H E N S S L S I I C G
23
L S L L C T P H E N S S L S+I C G
1
L S L L A C T P H E N S S L S L I C G
19
52.2%
NZ_BIFH01000016.1:
Lanthipeptides: EMA17_RS12985_lanthipeptide
2
G S N L S L L G C T P H E N S S L S I I
21
G S N+S L L C N S S L S++
3
G S N V S L L L C G---N S S L S L L
19

#### MIBiG 4.0 matches for F5972_RS17715

52.2%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
1
T G S N L S L L G C T P H E N S S L S I I
21
T G S +S L L C E S S L S++
1
T G S Q V S L L V C---E Y S S L S V V
18
F5972_RS17725
Leader:
MALLDLQTLEAPGGHGGGGGSN
Core:
L S L L A C T P H E N S S L S L I C G
Core with dehydrations:
L Dha L L A Cys Dhb P H E N Dha Dha L Dha L I Cys G

#### antiSMASH-DB 4.0 matches for F5972_RS17725

86.4%
NZ_BMMN01000011.1 and 5 others:
NZ_FTNI01000016.1 Lanthipeptides: BXA11_RS42315_lanthipeptide NZ_JABBWY010000006.1 Lanthipeptides: HHX37_RS18530_lanthipeptide NZ_JABBWZ010000004.1 Lanthipeptides: HHX40_RS12960_lanthipeptide NZ_VANP01000005.1 Lanthipeptides: FED44_RS16250_lanthipeptide NZ_VYTZ01000006.1 Lanthipeptides: F5972_RS17725_lanthipeptide
Lanthipeptides: IEY80_RS26005_lanthipeptide
1
L S L L A C T P H E N S S L S L I C G
19
L S L L A C T P H E N S S L S L I C G
4
L S L L A C T P H E N S S L S L I C G
22
85.0%
NZ_JABBWV010000002.1:
Lanthipeptides: HHX31_RS05740_lanthipeptide
1
L S L L A C T P H E N S S L S L I C G
19
L S L L C T P H E N S S L S L+C G
2
L S L L G C T P H E N S S L S L V C G
20
80.0%
NZ_JABBWU010000019.1:
Lanthipeptides: HHX30_RS29855_lanthipeptide
1
L S L L A C T P H E N S S L S L I C G
19
+S L L C T P H E N S S L S+I C G
2
V S L L G C T P H E N S S L S I I C G
20
with 16 more sequence matches
Only the first 10 are displayed here.
80.0%
NZ_JABBWX010000013.1:
Lanthipeptides: HHX35_RS30140_lanthipeptide
1
L S L L A C T P H E N S S L S L I C G
19
L S L L C T P H E N S S L S++C G
2
L S L L G C T P H E N S S L S I V C G
20
77.3%
NZ_BCBX01000043.1 and 1 other:
NZ_BCBX01000043.1 Lanthipeptides: AP234_RS36585_lanthipeptide
Lanthipeptides: AP234_RS36580_lanthipeptide
1
L S L L A C T P H E N S S L S L I C G
19
L S L L A C P H E N S S L S L+C G
4
L S L L A C V P H E N S S L S L L C G
22
77.3%
NZ_BMMN01000011.1 and 6 others:
NZ_FTNI01000016.1 Lanthipeptides: BXA11_RS42310_lanthipeptide NZ_JABBWY010000006.1 Lanthipeptides: HHX37_RS18535_lanthipeptide NZ_JABBWZ010000004.1 Lanthipeptides: HHX40_RS12965_lanthipeptide NZ_VANP01000005.1 Lanthipeptides: FED44_RS16255_lanthipeptide NZ_VYTZ01000006.1 Lanthipeptides: F5972_RS17720_lanthipeptide NZ_VYTZ01000006.1 Lanthipeptides: F5972_RS17715_lanthipeptide
Lanthipeptides: IEY80_RS26010_lanthipeptide
1
L S L L A C T P H E N S S L S L I C G
19
L S L L C T P H E N S S L S+I C G
4
L S L L G C T P H E N S S L S I I C G
22
75.0%
NZ_JABBWU010000019.1 and 6 others:
NZ_JABBWU010000019.1 Lanthipeptides: HHX30_RS29850_lanthipeptide NZ_JABBWV010000002.1 Lanthipeptides: HHX31_RS05735_lanthipeptide NZ_JABBWX010000013.1 Lanthipeptides: HHX35_RS30145_lanthipeptide NZ_JABBXA010000003.1 Lanthipeptides: HHX41_RS08060_lanthipeptide NZ_JABBXA010000003.1 Lanthipeptides: HHX41_RS08055_lanthipeptide NZ_JABBXA010000003.1 Lanthipeptides: HHX41_RS08065_lanthipeptide
Lanthipeptides: HHX30_RS29860_lanthipeptide
1
L S L L A C T P H E N S S L S L I C G
19
L S L L C T P H E N S S L S L I C G
6
L S L L G C T P H E N S S L S L I C G
24
69.6%
NZ_KI866522.1:
Lanthipeptides: MPTA5024_RS40525_lanthipeptide
1
L S L L A C T P H E N S S L S L I C G
19
L S L L C T P H E N S S L S++C G
4
L S L L G C T P H E N S S L S V L C G
22
69.6%
NZ_QOIL01000022.1 and 1 other:
NZ_QOIL01000022.1 Lanthipeptides: DQ384_RS31185_lanthipeptide
Lanthipeptides: DQ384_RS31190_lanthipeptide
1
L S L L A C T P H E N S S L S L I C G
19
L S L L C T P H E N S S L S++C G
4
L S L L G C T P H E N S S L S I L C G
22
50.0%
NZ_AUBE01000003.1:
Lanthipeptides: G412_RS38950_lanthipeptide
1
L S L L A C T P H E N S S L S L I C
18
L S L L A C H ++S L+C
3
L S L L A C D K H S S N S F-L L C
19
45.5%
NZ_CM000913.1 and 1 other:
NZ_CP016559.1 Lanthipeptides: BB341_RS04185_lanthipeptide
Lanthipeptides: SCLAV_RS23790_lanthipeptide
2
S L L A C T P H E N S S L S L I C
18
S L L C P H + S L L+C
6
S L L V C G P H S S Q S L-L L C
21
42.9%
NZ_CP042266.1:
Lanthipeptides: FQU76_RS00910_lanthipeptide
1
L S L L A C T P H E N S S L
14
L S L L+C H N S L
5
L S L L S C G H H S N L S L
18
38.1%
NZ_BMQJ01000002.1:
Lanthipeptides: IEZ10_RS04315_lanthipeptide
1
L S L L A C T P H E N S S L S L I
17
L++L C H S+L S L+
2
L T V L G C E S H T P S N L S L L
18

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (24):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.00 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.42 out of 20.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.97 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.28 out of 21.55
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.43 out of 36.54
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.35 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.87 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.66 out of 29.65
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.65 out of 32.93
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.26 out of 29.65
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.14 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.53 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.35 out of 25.88
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.22 out of 29.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.52 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.48 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Lanthipeptides
NRPS/PKS substrates
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.

F5972_RS17715 - Class III
  Cleavage pHMM score: 10.40
  RODEO score: 0
  Monoisotopic mass: 2210.1 Da
  Molecular weight: 2211.4 Da
  Number of bridges: 2
  Additional modifications: Cl
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2229.4 Da N = 1
    2247.5 Da N = 2
    2265.5 Da N = 3
    2283.5 Da N = 4
    2301.5 Da N = 5
F5972_RS17720 - Class III
  Cleavage pHMM score: 11.00
  RODEO score: 0
  Monoisotopic mass: 2210.1 Da
  Molecular weight: 2211.4 Da
  Number of bridges: 2
  Additional modifications: Cl
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2229.4 Da N = 1
    2247.5 Da N = 2
    2265.5 Da N = 3
    2283.5 Da N = 4
    2301.5 Da N = 5
F5972_RS17725 - Class III
  Cleavage pHMM score: 14.60
  RODEO score: 0
  Monoisotopic mass: 1901.0 Da
  Molecular weight: 1902.2 Da
  Number of bridges: 2
  Additional modifications: Cl
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1920.2 Da N = 1
    1938.2 Da N = 2
    1956.2 Da N = 3

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).
F5972_RS17680: X
AMP-binding (24..487): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    EATLHIARALSLFGMAAGEIDVYGMTETTGAFTV
  Nearest Stachelhaus code(s):
    Trp GALFFAAGVK (41% 8Å match)
    Ile DALFMGVVFK (35% 8Å match)
    Leu DALFMGAVAK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---

NZ_VYTZ01000006.1 - Region 2 - T1PKS,other
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: 236,548 - 327,175 nt. (total: 90,628 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))
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
F5972_RS18285: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F5972_RS18295: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F5972_RS18335: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

F5972_RS18385: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

F5972_RS18390: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

F5972_RS18400: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

F5972_RS18440: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

F5972_RS18480: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

F5972_RS18485: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

F5972_RS18525: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

F5972_RS18530: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

Transferases: acylase aminotransferase glycosyltransferase transferase
F5972_RS18290: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

F5972_RS18305: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

F5972_RS18340: aminotransferase

smcogs
  SMCOG1019: aminotransferase

F5972_RS18395: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

F5972_RS18405: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

F5972_RS18430: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

F5972_RS18470: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

F5972_RS18545: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Hydrolases: peptidase
F5972_RS18360: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: dehydratase
F5972_RS18315: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

F5972_RS18420: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
F5972_RS18300: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS18310: 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 | other | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001817.5 |  |  |  | 0.83 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0001160.5 |  |  |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001254.3 |  |  |  | 0.53 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000056.3 |  |  |  | 0.53 | PKS | esperamicin | Actinomadura verrucosospora
BGC0000827.3 |  |  |  | 0.50 | other (other) | staurosporine | Salinispora arenicola CNS-205
BGC0002154.2 |  |  |  | 0.49 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001258.3 |  |  |  | 0.49 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001257.3 |  |  |  | 0.49 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002047.2 |  |  |  | 0.48 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000813.3 |  |  |  | 0.47 | other (other) | K-252a | Nonomuraea longicatena

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000056.3 |  | 0.70 | PKS | esperamicin | Actinomadura verrucosospora
BGC0001164.3 |  | 0.69 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.68 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001817.5 |  | 0.65 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0001254.3 |  | 0.64 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (25):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.44 out of 25.88
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.66 out of 21.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.22 out of 26.85
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.93 out of 20.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.12 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.62 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.46 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.99 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.46 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.49 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.19 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.89 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.39 out of 20.01
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.72 out of 32.74
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.71 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 25.75
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.68 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.68 out of 28.19
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 21.93 out of 30.11
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.70 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.90 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 3, location 236547 - 327175:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 236547 - 281794:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-ohmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
F5972_RS18300: NH2
CAL_domain (40..486): NH2
minowa: NH2

Prediction, score:
  NH2: 100.0
  AHBA: 13.3
  shikimic_acid: 6.1
  Acetyl-CoA: 2.7
  fatty_acid: -2.1

F5972_RS18305: mmal
PKS_AT (660..945): mmal
ATSignature: Ethylmalonyl-CoA, Methylmalonyl-CoA

Top 3 matches:
  Ethylmalonyl-CoA: 66.7%
  Methylmalonyl-CoA: 66.7%
  Methoxymalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 118.9
  Methoxymalonyl-CoA: 113.0
  Ethylmalonyl-CoA: 112.3
  Malonyl-CoA: 92.2
  2-Methylbutyryl-CoA: 66.9
  trans-1,2-CPDA: 65.2
  Isobutyryl-CoA: 64.3
  Benzoyl-CoA: 58.7
  Propionyl-CoA: 57.4
  fatty_acid: 47.6
  Acetyl-CoA: 43.3
  CHC-CoA: 40.6
  inactive: 22.5
  3-Methylbutyryl-CoA: 19.5

F5972_RS18470: mal
PKS_AT (623..850): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 62.5%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 92.7
  Methoxymalonyl-CoA: 53.1
  Methylmalonyl-CoA: 45.5
  inactive: 33.5
  Propionyl-CoA: 25.0
  Ethylmalonyl-CoA: 23.0
  fatty_acid: 14.3
  Isobutyryl-CoA: 14.3
  2-Methylbutyryl-CoA: 10.1
  trans-1,2-CPDA: 9.9
  CHC-CoA: 9.0
  Benzoyl-CoA: 8.8
  Acetyl-CoA: 4.1
  3-Methylbutyryl-CoA: 0.0

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

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

NZ_VYTZ01000006.1 - Region 3 - 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: 410,391 - 468,763 nt. (total: 58,373 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
F5972_RS18995: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

F5972_RS19110: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: hydrolase
F5972_RS19140: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase synthase
F5972_RS19020: 1-deoxy-D-xylulose-5-phosphate synthase

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

F5972_RS19030: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F5972_RS19035: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS19040: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F5972_RS19050: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F5972_RS19060: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F5972_RS19065: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS19070: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
F5972_RS19095: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001050.5 |  | 0.71 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001050.5 |  | 0.71 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.08 out of 18.57
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.19 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.39 out of 30.11
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.20 out of 23.43
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (14):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.71 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.05 out of 27.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.88 out of 33.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.86 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.73 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.88 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.07 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.09 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.20 out of 27.78
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.41 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.57 out of 24.78
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.94 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 7, location 410390 - 468763:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Gly) + (Asp)

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).
F5972_RS19030: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (517..939): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YGVQFDFGVTVLKILLGGEVNHYGPTEATVGVTT
  Nearest Stachelhaus code(s):
    Asp DLTKIGHVGK (74% 8Å match)
    Asn DLTKLGEVGK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

F5972_RS19035: X
AMP-binding (21..420): 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:
    CQPFTNAGQTMNFLGSAAATNYYTSTEAAPAQTI
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

F5972_RS19065: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (29..426): Gly
nrpys: Gly

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

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

F5972_RS19070: X
AMP-binding (460..891): 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:
    RWMAFDTHVEEPDLIIGGELNTYGPTEAAVIATW
  Nearest Stachelhaus code(s):
    Lys DTCDIGTVIK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AbrC3 | Antibiotic production activator
BldD | Development and antibiotic global regulator
CelR | Cellobiose uptake repressor
ToxT | Regulator of MSHA biosynthesis

NZ_VYTZ01000007.1 - 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: 128,328 - 153,210 nt. (total: 24,883 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase sulfotransferase
F5972_RS20430: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

F5972_RS20495: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase
F5972_RS20450: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthetase
F5972_RS20460: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.80 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002708.2 |  | 0.75 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0000657.5 |  | 0.57 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000677.5 |  | 0.50 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002309.2 |  | 0.47 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000675.5 |  | 0.45 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0001911.3 |  | 0.45 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.43 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000496.5 |  | 0.41 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000927.3 |  | 0.41 | other (flavin) | roseoflavin | Streptomyces davaonensis JCM 4913

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.80 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002708.2 |  | 0.75 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0000657.5 |  | 0.57 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000677.5 |  | 0.50 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002309.2 |  | 0.47 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000675.5 |  | 0.45 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0001911.3 |  | 0.45 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.43 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000496.5 |  | 0.41 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000927.3 |  | 0.41 | other (flavin) | roseoflavin | Streptomyces davaonensis JCM 4913

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

No significant matches found.

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

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

Genes with terpene domains:
F5972_RS20450: T1TS + T1TS
Domain 1 (2 - 321): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (340 - 685): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

F5972_RS20460: PT_FPPS_like
Domain 1 (52 - 356): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.22 out of 30.22
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.45 out of 25.75
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.74 out of 29.72
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.31 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.90 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.70 out of 29.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.19 out of 20.97
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_VYTZ01000007.1 - Region 2 - 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: 156,414 - 190,478 nt. (total: 34,065 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
F5972_RS20625: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: hydrolase
F5972_RS20540: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Ligases: ligase
F5972_RS20600: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
F5972_RS20635: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.62 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000357.5 |  | 0.60 | 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 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001833.4 |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.62 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000357.5 |  | 0.60 | 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 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001833.4 |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | 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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (12):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.09 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.23 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.88 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.08 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.33 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.99 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.79 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.79 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.37 out of 21.55
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.61 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.41 out of 30.11
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.15 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 2, location 156413 - 190478:
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).
F5972_RS20600: X
AMP-binding (28..423): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FVVMFDFSVEEPYCLVGGELNTYGPTEATVTATC
  Nearest Stachelhaus code(s):
    Lys DIESIGTVTK (62% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

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

NZ_VYTZ01000007.1 - Region 3 - 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: 301,558 - 347,092 nt. (total: 45,535 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
F5972_RS21220: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

F5972_RS21225: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F5972_RS21240: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

F5972_RS21295: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F5972_RS21330: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

F5972_RS21335: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

F5972_RS21340: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: glycosyltransferase
F5972_RS21230: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

Hydrolases: hydrolase phosphatase
F5972_RS21215: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

F5972_RS21235: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Ligases: ligase
F5972_RS21245: 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
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.52 out of 27.55
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.37 out of 26.85
Confidence: medium
Additional weak hits (26):
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.17 out of 29.51
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.34 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.23 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.32 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.79 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.13 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.38 out of 28.14
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.53 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.55 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.44 out of 36.54
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.69 out of 21.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.81 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.98 out of 30.22
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.32 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.49 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.65 out of 21.55
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.05 out of 27.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.33 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.90 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.83 out of 25.88
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.51 out of 26.85
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 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 3, location 301557 - 347092:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Asn)

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).
F5972_RS21245: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (508..906): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWAGFDLVVPNAKCVVAGEVNEYGPTEASVGTCI
  Nearest Stachelhaus code(s):
    D-Ala DLTKVNEVGK (71% 8Å match)
    Asn DLTKVGEVGK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CelR | Cellobiose uptake repressor
GnfM | Regulator of nitrogen-fixation genes
RutR | Regulator of the pyrimidine and purine metabolism

NZ_VYTZ01000008.1 - Region 1 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 33,423 - 58,545 nt. (total: 25,123 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
F5972_RS22695: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

F5972_RS22700: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.44 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0001727.3 |  | 0.40 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000721.4 |  | 0.39 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000529.5 |  | 0.37 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000288.5 |  | 0.25 | NRPS | A-503083 A, A-503083 B, A-503083 E, A-503083 F | Streptomyces sp. SANK 62799

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.44 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0001727.3 |  | 0.40 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000721.4 |  | 0.39 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000529.5 |  | 0.37 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000288.5 |  | 0.25 | NRPS | A-503083 A, A-503083 B, A-503083 E, A-503083 F | Streptomyces sp. SANK 62799

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 F5972_RS22690

F5972_RS22705
Leader:
MSIQIENAPATQAGEEDFGEWDLDVSIVESGPAAD
Core:
K L I R M T D D G C G T S C Q S A C P A T C P
Core with dehydrations:
K L I R M Dhb D D G Cys G Dhb Dha Cys Q Dha A Cys P A Dhb Cys P

#### antiSMASH-DB 4.0 matches for F5972_RS22705

100.0%
NZ_JABBWZ010000004.1 and 4 others:
NZ_JABBWZ010000004.1 Lanthipeptides: HHX40_RS10860_lanthipeptide NZ_JABBWZ010000004.1 Lanthipeptides: HHX40_RS10860_lanthipeptide NZ_VYTZ01000008.1 Lanthipeptides: F5972_RS22705_lanthipeptide NZ_VYTZ01000008.1 Lanthipeptides: F5972_RS22705_lanthipeptide
Lanthipeptides: HHX40_RS10860_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
K L I R M T D D G C G T S C Q S A C P A T C P
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
87.0%
NZ_BMMN01000001.1 and 1 other:
NZ_BMMN01000001.1 Lanthipeptides: IEY80_RS02165_lanthipeptide
Lanthipeptides: IEY80_RS02165_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
K L I R M T D D G C G T+C Q S A C T C P
1
K L I R M T D D G C G T T C Q S A C S T T C P
23
78.3%
NZ_CP047146.1 and 1 other:
NZ_CP047146.1 Lanthipeptides: GR130_RS38445_lanthipeptide
Lanthipeptides: GR130_RS38445_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G +C+S A C A T C P
1
R L I R M T D D G C G Q T C E S A C S A T C P
23
with 180 more sequence matches
Only the first 10 are displayed here.
78.3%
NZ_CP054916.1 and 1 other:
NZ_CP054916.1 Lanthipeptides: HUT19_RS32830_lanthipeptide
Lanthipeptides: HUT19_RS32830_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G +C Q S A C T C P
1
R L I R M T D D G C G Q T C Q S A C S T T C P
23
78.3%
NZ_WBMT01000015.1 and 1 other:
NZ_WBMT01000015.1 Lanthipeptides: F8566_RS30065_lanthipeptide
Lanthipeptides: F8566_RS30065_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C
22
+L I R M T D D G C G +C Q S A C P T C
1
R L I R M T D D G C G K T C Q S A C P N T C
22
73.9%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G T+C++A C T C P
1
R L I R M T D D G C G T T C E T A C S T T C P
23
73.9%
NZ_CM000913.1 and 7 others:
NZ_CM000913.1 Lanthipeptides: SCLAV_RS11700_lanthipeptide NZ_CP016559.1 Lanthipeptides: BB341_RS16135_lanthipeptide NZ_CP016559.1 Lanthipeptides: BB341_RS16135_lanthipeptide NZ_CP042266.1 Lanthipeptides: FQU76_RS24360_lanthipeptide NZ_CP042266.1 Lanthipeptides: FQU76_RS24360_lanthipeptide NZ_CP070379.1 Lanthipeptides: JVE63_RS07215_lanthipeptide NZ_CP070379.1 Lanthipeptides: JVE63_RS07215_lanthipeptide
Lanthipeptides: SCLAV_RS11700_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G +C+S A C T C P
1
R L I R M T D D G C G V T C E S A C S T T C P
23
73.9%
NZ_CP048875.1 and 1 other:
NZ_CP048875.1 Lanthipeptides: G3260_RS00640_lanthipeptide
Lanthipeptides: G3260_RS00640_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I+M T D D G C G +C+S A C A T C P
1
R L I Q M T D D G C G Q T C E S A C S A T C P
23
73.9%
NZ_CP119145.1 and 1 other:
NZ_CP119145.1 Lanthipeptides: PZB75_RS00285_lanthipeptide
Lanthipeptides: PZB75_RS00285_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I+M T D D G C G++C Q S A C T C P
1
R L I Q M T D D G C G S T C Q S A C S T T C P
23
73.9%
NZ_FOLM01000022.1 and 1 other:
NZ_FOLM01000022.1 Lanthipeptides: BM242_RS25935_lanthipeptide
Lanthipeptides: BM242_RS25935_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G +C+S A C T C P
1
R L I R M T D D G C G E T C E S A C S T T C P
23
71.4%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS09160_lanthipeptide
Lanthipeptides: FRANCCI3_RS09160_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G T+C Q S A C P T C P
4
E L I R M T D D G C G T T C Q S A C P N T C P
26
69.6%
NZ_JACHGT010000013.1 and 1 other:
NZ_JACHGT010000013.1 Lanthipeptides: HNR73_RS27205_lanthipeptide
Lanthipeptides: HNR73_RS27205_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I M T+D G C G +C Q S A C T C P
1
R L I H M T N D G C G Q T C Q S A C S T T C P
23
69.6%
NZ_JAFIQY010000004.1 and 1 other:
NZ_JAFIQY010000004.1 Lanthipeptides: JXZ78_RS08025_lanthipeptide
Lanthipeptides: JXZ78_RS08025_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I+M T D D G C G +C+S A C T C P
1
R L I Q M T D D G C G E T C E S A C S T T C P
23

#### MIBiG 4.0 matches for F5972_RS22705

15.4%
BGC0002110.3 (QKV49894.1):
Lanthipeptide: birimositide
12
T S C Q S A C
18
T C S C
20
T K C T S K C
26
10.8%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
12
T S C Q S A C
18
T C S C
31
T K C T S R C
37

#### Lanthipeptide(s) for F5972_RS22700

F5972_RS22705
Leader:
MSIQIENAPATQAGEEDFGEWDLDVSIVESGPAAD
Core:
K L I R M T D D G C G T S C Q S A C P A T C P
Core with dehydrations:
K L I R M Dhb D D G Cys G Dhb Dha Cys Q Dha A Cys P A Dhb Cys P

#### antiSMASH-DB 4.0 matches for F5972_RS22705

100.0%
NZ_JABBWZ010000004.1 and 4 others:
NZ_JABBWZ010000004.1 Lanthipeptides: HHX40_RS10860_lanthipeptide NZ_JABBWZ010000004.1 Lanthipeptides: HHX40_RS10860_lanthipeptide NZ_VYTZ01000008.1 Lanthipeptides: F5972_RS22705_lanthipeptide NZ_VYTZ01000008.1 Lanthipeptides: F5972_RS22705_lanthipeptide
Lanthipeptides: HHX40_RS10860_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
K L I R M T D D G C G T S C Q S A C P A T C P
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
87.0%
NZ_BMMN01000001.1 and 1 other:
NZ_BMMN01000001.1 Lanthipeptides: IEY80_RS02165_lanthipeptide
Lanthipeptides: IEY80_RS02165_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
K L I R M T D D G C G T+C Q S A C T C P
1
K L I R M T D D G C G T T C Q S A C S T T C P
23
78.3%
NZ_CP047146.1 and 1 other:
NZ_CP047146.1 Lanthipeptides: GR130_RS38445_lanthipeptide
Lanthipeptides: GR130_RS38445_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G +C+S A C A T C P
1
R L I R M T D D G C G Q T C E S A C S A T C P
23
with 180 more sequence matches
Only the first 10 are displayed here.
78.3%
NZ_CP054916.1 and 1 other:
NZ_CP054916.1 Lanthipeptides: HUT19_RS32830_lanthipeptide
Lanthipeptides: HUT19_RS32830_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G +C Q S A C T C P
1
R L I R M T D D G C G Q T C Q S A C S T T C P
23
78.3%
NZ_WBMT01000015.1 and 1 other:
NZ_WBMT01000015.1 Lanthipeptides: F8566_RS30065_lanthipeptide
Lanthipeptides: F8566_RS30065_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C
22
+L I R M T D D G C G +C Q S A C P T C
1
R L I R M T D D G C G K T C Q S A C P N T C
22
73.9%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G T+C++A C T C P
1
R L I R M T D D G C G T T C E T A C S T T C P
23
73.9%
NZ_CM000913.1 and 7 others:
NZ_CM000913.1 Lanthipeptides: SCLAV_RS11700_lanthipeptide NZ_CP016559.1 Lanthipeptides: BB341_RS16135_lanthipeptide NZ_CP016559.1 Lanthipeptides: BB341_RS16135_lanthipeptide NZ_CP042266.1 Lanthipeptides: FQU76_RS24360_lanthipeptide NZ_CP042266.1 Lanthipeptides: FQU76_RS24360_lanthipeptide NZ_CP070379.1 Lanthipeptides: JVE63_RS07215_lanthipeptide NZ_CP070379.1 Lanthipeptides: JVE63_RS07215_lanthipeptide
Lanthipeptides: SCLAV_RS11700_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G +C+S A C T C P
1
R L I R M T D D G C G V T C E S A C S T T C P
23
73.9%
NZ_CP048875.1 and 1 other:
NZ_CP048875.1 Lanthipeptides: G3260_RS00640_lanthipeptide
Lanthipeptides: G3260_RS00640_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I+M T D D G C G +C+S A C A T C P
1
R L I Q M T D D G C G Q T C E S A C S A T C P
23
73.9%
NZ_CP119145.1 and 1 other:
NZ_CP119145.1 Lanthipeptides: PZB75_RS00285_lanthipeptide
Lanthipeptides: PZB75_RS00285_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I+M T D D G C G++C Q S A C T C P
1
R L I Q M T D D G C G S T C Q S A C S T T C P
23
73.9%
NZ_FOLM01000022.1 and 1 other:
NZ_FOLM01000022.1 Lanthipeptides: BM242_RS25935_lanthipeptide
Lanthipeptides: BM242_RS25935_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G +C+S A C T C P
1
R L I R M T D D G C G E T C E S A C S T T C P
23
71.4%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS09160_lanthipeptide
Lanthipeptides: FRANCCI3_RS09160_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I R M T D D G C G T+C Q S A C P T C P
4
E L I R M T D D G C G T T C Q S A C P N T C P
26
69.6%
NZ_JACHGT010000013.1 and 1 other:
NZ_JACHGT010000013.1 Lanthipeptides: HNR73_RS27205_lanthipeptide
Lanthipeptides: HNR73_RS27205_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I M T+D G C G +C Q S A C T C P
1
R L I H M T N D G C G Q T C Q S A C S T T C P
23
69.6%
NZ_JAFIQY010000004.1 and 1 other:
NZ_JAFIQY010000004.1 Lanthipeptides: JXZ78_RS08025_lanthipeptide
Lanthipeptides: JXZ78_RS08025_lanthipeptide
1
K L I R M T D D G C G T S C Q S A C P A T C P
23
+L I+M T D D G C G +C+S A C T C P
1
R L I Q M T D D G C G E T C E S A C S T T C P
23

#### MIBiG 4.0 matches for F5972_RS22705

15.4%
BGC0002110.3 (QKV49894.1):
Lanthipeptide: birimositide
12
T S C Q S A C
18
T C S C
20
T K C T S K C
26
10.8%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
12
T S C Q S A C
18
T C S C
31
T K C T S R C
37

#### 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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.61 out of 30.11
Confidence: medium
Additional weak hits (8):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.98 out of 29.25
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.13 out of 29.51
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.54 out of 39.62
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.04 out of 19.26
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.20 out of 21.55
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.41 out of 30.11
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

F5972_RS22705 - Class I
  Cleavage pHMM score: -4.70
  RODEO score: 19
  Monoisotopic mass: 2267.0 Da
  Molecular weight: 2268.6 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2286.6 Da N = 1
F5972_RS22705 - Class I
  Cleavage pHMM score: -4.70
  RODEO score: 19
  Monoisotopic mass: 2267.0 Da
  Molecular weight: 2268.6 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2286.6 Da N = 1

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (33422...58545)
F5972_RS22700
  RRE type: Lanthipeptide_LanB_RRE
  Location: 152 - 243
  Score: 71.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CelR | Cellobiose uptake repressor

NZ_VYTZ01000008.1 - 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: 177,179 - 187,448 nt. (total: 10,270 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
F5972_RS23380: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001652.5 |  | 0.19 | NRPS | limazepine C, limazepine D, limazepine E, limazepine F, limazepine A | Streptomyces sp. ICBB 8177

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001652.5 |  | 0.19 | NRPS | limazepine C, limazepine D, limazepine E, limazepine F, limazepine A | Streptomyces sp. ICBB 8177

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: 17.80 out of 20.47
Confidence: medium
Additional weak hits (3):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.88 out of 25.88
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.65 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.88 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_VYTZ01000008.1 - Region 3 - RRE-containing
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 224,420 - 245,541 nt. (total: 21,122 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
F5972_RS23670: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

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

Reference | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002317.2 |  | 0.45 | ribosomal | herbicolin O, mcceh252, pantocin A | Pantoea agglomerans
BGC0000585.5 |  | 0.44 | ribosomal | microcin C7 | Escherichia coli
BGC0001633.3 |  | 0.36 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000812.3 |  | 0.35 | other (other) | huperzine A | Shiraia sp. slf14
BGC0001187.4 |  | 0.34 | NRPS, PKS | xenolozoyenone | Glarea lozoyensis
BGC0000041.3 |  | 0.33 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001858.2 |  | 0.32 | PKS | alternapyrone B, alternapyrone C, alternapyrone D, alternapyrone E, alternapyrone F | Parastagonospora nodorum SN15
BGC0000353.5 |  | 0.31 | NRPS | tacrolimus | Streptomyces sp. MA6548
BGC0001221.5 |  | 0.30 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0000925.5 |  | 0.29 | other (other) | quinolobactin | Pseudomonas fluorescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002317.2 |  | 0.45 | ribosomal | herbicolin O, mcceh252, pantocin A | Pantoea agglomerans
BGC0000585.5 |  | 0.44 | ribosomal | microcin C7 | Escherichia coli
BGC0001633.3 |  | 0.36 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000812.3 |  | 0.35 | other (other) | huperzine A | Shiraia sp. slf14
BGC0001187.4 |  | 0.34 | NRPS, PKS | xenolozoyenone | Glarea lozoyensis
BGC0000041.3 |  | 0.33 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001858.2 |  | 0.32 | PKS | alternapyrone B, alternapyrone C, alternapyrone D, alternapyrone E, alternapyrone F | Parastagonospora nodorum SN15
BGC0000353.5 |  | 0.31 | NRPS | tacrolimus | Streptomyces sp. MA6548
BGC0001221.5 |  | 0.30 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0000925.5 |  | 0.29 | other (other) | quinolobactin | Pseudomonas fluorescens

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 (9):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.08 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.59 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.27 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.28 out of 27.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.31 out of 25.88
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.00 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.85 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.89 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.21 out of 33.14
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (224419...245541)
F5972_RS23695
  RRE type: Pantocin_Microcin_RRE
  Location: 0 - 94
  Score: 61.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_VYTZ01000009.1 - 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: 131,384 - 179,195 nt. (total: 47,812 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: dehalogenase protease
F5972_RS25215: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

F5972_RS25220: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: dehydratase
F5972_RS25225: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
F5972_RS25230: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F5972_RS25235: 3-oxoacyl-(acyl carrier protein) synthase III

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

F5972_RS25240: 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
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001268.4 |  | 0.62 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001268.4 |  | 0.62 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919

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: 19.75 out of 23.05
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.52 out of 30.11
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.38 out of 23.79
Confidence: medium
Additional weak hits (12):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.85 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.82 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.13 out of 26.33
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.04 out of 30.11
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.44 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.79 out of 27.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.65 out of 26.12
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.72 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.74 out of 31.73
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.36 out of 31.73
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 131383 - 179195:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-pk)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
F5972_RS25230: X
AMP-binding (24..443): 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:
    QLLF-----PFGFAVSAGALSVYGATECMPVAAI
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

F5972_RS25240: pk
PKS_AT (572..867): pk
ATSignature: Malonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 109.5
  Methoxymalonyl-CoA: 95.3
  Malonyl-CoA: 90.6
  Isobutyryl-CoA: 69.4
  Ethylmalonyl-CoA: 67.5
  CHC-CoA: 56.5
  trans-1,2-CPDA: 42.1
  Propionyl-CoA: 39.4
  Benzoyl-CoA: 29.2
  2-Methylbutyryl-CoA: 25.9
  inactive: 25.3
  fatty_acid: 21.4
  Acetyl-CoA: 10.1
  3-Methylbutyryl-CoA: 8.1

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems