Select genomic region:
Overview
1.1
2.1
5.1
5.2
11.1
12.1
12.2
12.3
19.1
26.1
29.1
32.1
34.1
48.1
51.1
54.1
55.1
56.1
67.1
67.2

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

NZ_RYYV01000001.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | RiPP-like | 377,967 | 388,812 |

NZ_RYYV01000010.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | NRPS | 78,376 | 122,374 |  |

NZ_RYYV01000013.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | terpene | 40,889 | 61,755 |
Region 5.2 | arylpolyene | 77,803 | 125,463 | Low | aryl polyenes | other:other

NZ_RYYV01000019.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 11.1 | indole | 38,887 | 60,878 |

NZ_RYYV01000002.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 12.1 | NRPS | 15,441 | 62,595 | High | rhizomide A/rhizomide B/rhizomide C | NRPS:Type I
Region 12.2 | lanthipeptide-class-ii | 160,886 | 183,753 |
Region 12.3 | NRPS,transAT-PKS | 185,121 | 273,093 | Low | FR900359 | NRPS:Type I

NZ_RYYV01000026.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 19.1 | terpene | 33,377 | 52,734 |

NZ_RYYV01000032.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 26.1 | NRPS | 1 | 32,883 |  |

NZ_RYYV01000035.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 29.1 | NRPS-like | 1 | 21,480 | Low | FR900359 | NRPS:Type I

NZ_RYYV01000038.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 32.1 | NRPS | 1 | 20,574 | Low | sarpeptin A/sarpeptin B | NRPS:Type I

NZ_RYYV01000004.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 34.1 | lanthipeptide-class-ii | 98,541 | 121,363 |

NZ_RYYV01000052.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 48.1 | NRPS | 1 | 5,727 |

NZ_RYYV01000055.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 51.1 | transAT-PKS-like | 1 | 4,467 |

NZ_RYYV01000058.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 54.1 | NRPS | 1 | 2,825 | Low | tasikamide A/tasikamide B/tasikamide C | NRPS:Type I

NZ_RYYV01000059.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 55.1 | NRPS | 1 | 2,774 | Medium | FR900359 | NRPS:Type I

NZ_RYYV01000006.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 56.1 | arylpolyene | 142,314 | 183,519 | Low | xanthomonadin I | other:other

NZ_RYYV01000008.1 (Dyella choica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 67.1 | RiPP-like | 14,573 | 25,430 |
Region 67.2 | terpene | 42,421 | 69,536 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | RiPP-like | 377,967 | 388,812 |
Region 2.1 | NRPS | 78,376 | 122,374 |  |
Region 5.1 | terpene | 40,889 | 61,755 |
Region 5.2 | arylpolyene | 77,803 | 125,463 | Low | aryl polyenes | other:other
Region 11.1 | indole | 38,887 | 60,878 |
Region 12.1 | NRPS | 15,441 | 62,595 | High | rhizomide A/rhizomide B/rhizomide C | NRPS:Type I
Region 12.2 | lanthipeptide-class-ii | 160,886 | 183,753 |
Region 12.3 | NRPS,transAT-PKS | 185,121 | 273,093 | Low | FR900359 | NRPS:Type I
Region 19.1 | terpene | 33,377 | 52,734 |
Region 26.1 | NRPS | 1 | 32,883 |  |
Region 29.1 | NRPS-like | 1 | 21,480 | Low | FR900359 | NRPS:Type I
Region 32.1 | NRPS | 1 | 20,574 | Low | sarpeptin A/sarpeptin B | NRPS:Type I
Region 34.1 | lanthipeptide-class-ii | 98,541 | 121,363 |
Region 48.1 | NRPS | 1 | 5,727 |
Region 51.1 | transAT-PKS-like | 1 | 4,467 |
Region 54.1 | NRPS | 1 | 2,825 | Low | tasikamide A/tasikamide B/tasikamide C | NRPS:Type I
Region 55.1 | NRPS | 1 | 2,774 | Medium | FR900359 | NRPS:Type I
Region 56.1 | arylpolyene | 142,314 | 183,519 | Low | xanthomonadin I | other:other
Region 67.1 | RiPP-like | 14,573 | 25,430 |
Region 67.2 | terpene | 42,421 | 69,536 |

No secondary metabolite regions were found in these records:
  NZ_RYYV01000011.1 (Dyella choica)
  NZ_RYYV01000012.1 (Dyella choica)
  NZ_RYYV01000014.1 (Dyella choica)
  NZ_RYYV01000015.1 (Dyella choica)
  NZ_RYYV01000016.1 (Dyella choica)
  NZ_RYYV01000017.1 (Dyella choica)
  NZ_RYYV01000018.1 (Dyella choica)
  NZ_RYYV01000020.1 (Dyella choica)
  NZ_RYYV01000021.1 (Dyella choica)
  NZ_RYYV01000022.1 (Dyella choica)
  NZ_RYYV01000023.1 (Dyella choica)
  NZ_RYYV01000024.1 (Dyella choica)
  NZ_RYYV01000025.1 (Dyella choica)
  NZ_RYYV01000027.1 (Dyella choica)
  NZ_RYYV01000028.1 (Dyella choica)
  NZ_RYYV01000029.1 (Dyella choica)
  NZ_RYYV01000003.1 (Dyella choica)
  NZ_RYYV01000030.1 (Dyella choica)
  NZ_RYYV01000031.1 (Dyella choica)
  NZ_RYYV01000033.1 (Dyella choica)
  NZ_RYYV01000034.1 (Dyella choica)
  NZ_RYYV01000036.1 (Dyella choica)
  NZ_RYYV01000037.1 (Dyella choica)
  NZ_RYYV01000039.1 (Dyella choica)
  NZ_RYYV01000040.1 (Dyella choica)
  NZ_RYYV01000041.1 (Dyella choica)
  NZ_RYYV01000042.1 (Dyella choica)
  NZ_RYYV01000043.1 (Dyella choica)
  NZ_RYYV01000044.1 (Dyella choica)
  NZ_RYYV01000045.1 (Dyella choica)
  NZ_RYYV01000046.1 (Dyella choica)
  NZ_RYYV01000047.1 (Dyella choica)
  NZ_RYYV01000048.1 (Dyella choica)
  NZ_RYYV01000049.1 (Dyella choica)
  NZ_RYYV01000005.1 (Dyella choica)
  NZ_RYYV01000050.1 (Dyella choica)
  NZ_RYYV01000051.1 (Dyella choica)
  NZ_RYYV01000053.1 (Dyella choica)
  NZ_RYYV01000054.1 (Dyella choica)
  NZ_RYYV01000056.1 (Dyella choica)
  NZ_RYYV01000057.1 (Dyella choica)
  NZ_RYYV01000060.1 (Dyella choica)
  NZ_RYYV01000061.1 (Dyella choica)
  NZ_RYYV01000062.1 (Dyella choica)
  NZ_RYYV01000063.1 (Dyella choica)
  NZ_RYYV01000064.1 (Dyella choica)
  NZ_RYYV01000065.1 (Dyella choica)
  NZ_RYYV01000066.1 (Dyella choica)
  NZ_RYYV01000067.1 (Dyella choica)
  NZ_RYYV01000068.1 (Dyella choica)
  NZ_RYYV01000007.1 (Dyella choica)
  NZ_RYYV01000009.1 (Dyella choica)

Compact view
NZ_RYYV01000001.1 - Region 1 - 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: 377,967 - 388,812 nt. (total: 10,846 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: sulfotransferase
EKH80_RS01865: glutathione S-transferase

smcogs
  SMCOG1193: glutathione S-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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002133.3 |  | 0.36 | ribosomal | group 1 methanobactin | Methylosinus sp. LW3
BGC0000404.4 |  | 0.35 | NRPS | penicillin | Penicillium chrysogenum
BGC0001484.3 |  | 0.31 | other (other) | 2'-chloropentostatin, 2'-amino-2'-deoxyadenosine | Actinomadura sp. ATCC 39365
BGC0001285.5 |  | 0.31 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001369.3 |  | 0.23 | PKS | metatricycloene | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002133.3 |  | 0.36 | ribosomal | group 1 methanobactin | Methylosinus sp. LW3
BGC0000404.4 |  | 0.35 | NRPS | penicillin | Penicillium chrysogenum
BGC0001484.3 |  | 0.31 | other (other) | 2'-chloropentostatin, 2'-amino-2'-deoxyadenosine | Actinomadura sp. ATCC 39365
BGC0001285.5 |  | 0.31 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001369.3 |  | 0.23 | PKS | metatricycloene | uncultured bacterium

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.71 out of 26.33
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.59 out of 24.78
Confidence: medium
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
LexA variant 2 | Repressor of DNA damage response

NZ_RYYV01000010.1 - 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: 78,376 - 122,374 nt. (total: 43,999 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase aminotransferase glycosyltransferase transferase
EKH80_RS14305: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

EKH80_RS14345: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

EKH80_RS14385: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

EKH80_RS14415: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

EKH80_RS14445: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: deacetylase
EKH80_RS14460: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Ligases: ligase
EKH80_RS14380: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 20.76 out of 21.84
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.31 out of 18.57
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 22.87 out of 26.33
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.94 out of 20.97
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.95 out of 27.78
Confidence: medium
Additional weak hits (6):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.48 out of 27.78
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.64 out of 20.01
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.46 out of 20.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.35 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.22 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.42 out of 26.06
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 78375 - 122374:
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).
EKH80_RS14380: X
AMP-binding (459..851): 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:
    LGMAFDIALLELWALVGGETQLYGPTETTVLSTS
  Nearest Stachelhaus code(s):
    Gly DILQLGLVWK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MexT | Global virulence regulator
ToxT | Regulator of MSHA biosynthesis

NZ_RYYV01000013.1 - 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: 40,889 - 61,755 nt. (total: 20,867 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: carbamoyltransferase methyltransferase
EKH80_RS16305: methyltransferase

smcogs
  SMCOG1089: methyltransferase

EKH80_RS16375: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

Hydrolases: hydrolase
EKH80_RS16310: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: cyclase
EKH80_RS16280: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001444.5 |  | 0.35 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0001985.4 |  | 0.35 | other (other) | Pyrazofurin | Streptomyces candidus
BGC0002657.2 |  | 0.32 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0000874.5 |  | 0.32 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0002443.3 |  | 0.32 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0002571.2 |  | 0.30 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0002661.2 |  | 0.29 | NRPS | tasikamide A, tasikamide B, tasikamide C | Streptomyces tasikensis
BGC0002491.3 |  | 0.28 | NRPS | myxochelin B, myxochelin A, pseudochelin A | Pseudoalteromonas piscicida
BGC0000981.3 |  | 0.28 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E6
BGC0002713.2 |  | 0.28 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001444.5 |  | 0.35 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0001985.4 |  | 0.35 | other (other) | Pyrazofurin | Streptomyces candidus
BGC0002657.2 |  | 0.32 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0000874.5 |  | 0.32 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0002443.3 |  | 0.32 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0002571.2 |  | 0.30 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0002661.2 |  | 0.29 | NRPS | tasikamide A, tasikamide B, tasikamide C | Streptomyces tasikensis
BGC0002491.3 |  | 0.28 | NRPS | myxochelin B, myxochelin A, pseudochelin A | Pseudoalteromonas piscicida
BGC0000981.3 |  | 0.28 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E6
BGC0002713.2 |  | 0.28 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
EKH80_RS16315: PT_phytoene_like
Domain 1 (61 - 214): Prenyltransferase; Phytoene synthase like
Subtype: unknown

Reactions:
  FPP → squalene
  FPP → diapophytoene
  FPP → PSPP
  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.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
Additional weak hits (7):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.96 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.78 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.44 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.43 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.12 out of 30.98
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
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_RYYV01000013.1 - Region 2 - arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 77,803 - 125,463 nt. (total: 47,661 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS 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
EKH80_RS16530: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EKH80_RS16540: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase acyltransferase carboxylase methyltransferase transferase
EKH80_RS16475: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

EKH80_RS16510: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

EKH80_RS16520: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

EKH80_RS16555: methyltransferase

smcogs
  SMCOG1089: methyltransferase

EKH80_RS16585: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Hydrolases: protease
EKH80_RS16525: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Lyases: hydratase
EKH80_RS16485: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: synthase
EKH80_RS16470: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

EKH80_RS16550: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EKH80_RS16595: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

EKH80_RS16610: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

Translocases: transport
EKH80_RS16600: 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 | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000866.5 |  | 0.55 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.52 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0000234.5 |  | 0.50 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001987.2 |  | 0.48 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0001197.5 |  | 0.47 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002477.3 |  | 0.47 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0000231.5 |  | 0.47 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001917.4 |  | 0.47 | PKS | 5aTHQ-9i, 5aTHQ-9n, 5aTHQ-10a, STAMs-9i, STAMs-9n | Streptomyces nigrescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000866.5 |  | 0.55 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.52 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0000234.5 |  | 0.50 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001987.2 |  | 0.48 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0001197.5 |  | 0.47 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002477.3 |  | 0.47 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0000231.5 |  | 0.47 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001917.4 |  | 0.47 | PKS | 5aTHQ-9i, 5aTHQ-9n, 5aTHQ-10a, STAMs-9i, STAMs-9n | Streptomyces nigrescens

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.45 out of 26.06
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.45 out of 25.31
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.80 out of 20.97
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.02 out of 20.01
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.81 out of 18.57
Confidence: medium
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 24.14 out of 26.12
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.81 out of 18.57
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.79 out of 20.97
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 24.24 out of 30.25
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
Additional weak hits (17):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.85 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.73 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.93 out of 32.74
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.82 out of 20.01
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.78 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.39 out of 28.14
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.32 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.65 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.59 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.31 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.65 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.92 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.97 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.94 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.43 out of 28.14
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.85 out of 20.01
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.56 out of 39.62
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A
ColR | Phenol-responsive regulator
LuxO | Repressor of luminescence
MexT | Global virulence regulator
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_RYYV01000019.1 - Region 1 - indole
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: 38,887 - 60,878 nt. (total: 21,992 nt) Show pHMM detection rules used
indole: (indsynth or dmat or indole_PTase)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
EKH80_RS19290: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: cyclase
EKH80_RS19240: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

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

Reference | indole | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001197.5 |  | 0.41 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001810.3 |  | 0.39 | PKS | trehangelin | Polymorphospora rubra
BGC0000204.5 |  | 0.38 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0000218.5 |  | 0.38 | PKS | doxorubicin | Streptomyces peucetius
BGC0002138.2 |  | 0.38 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670
BGC0001782.3 |  | 0.38 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0000384.6 |  | 0.36 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0002746.3 |  | 0.36 | ribosomal | dendrothelin A | Dendrothele bispora CBS 962.96
BGC0001987.2 |  | 0.35 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0001768.4 |  | 0.35 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001197.5 |  | 0.41 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001810.3 |  | 0.39 | PKS | trehangelin | Polymorphospora rubra
BGC0000204.5 |  | 0.38 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0000218.5 |  | 0.38 | PKS | doxorubicin | Streptomyces peucetius
BGC0002138.2 |  | 0.38 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670
BGC0001782.3 |  | 0.38 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0000384.6 |  | 0.36 | NRPS | lyngbyatoxin | Lyngbya majuscula
BGC0002746.3 |  | 0.36 | ribosomal | dendrothelin A | Dendrothele bispora CBS 962.96
BGC0001987.2 |  | 0.35 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0001768.4 |  | 0.35 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4

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: 19.59 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.15 out of 23.79
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.74 out of 29.72
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.53 out of 28.19
Confidence: medium
Additional weak hits (9):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 27.09 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.47 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.96 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.62 out of 29.38
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.40 out of 26.12
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.66 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.36 out of 29.65
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
ZuR variant 1 | Zinc-responsive repressor

NZ_RYYV01000002.1 - 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: 15,441 - 62,595 nt. (total: 47,155 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
EKH80_RS02930: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

EKH80_RS02960: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

EKH80_RS02980: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase aminotransferase methyltransferase
EKH80_RS02915: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

EKH80_RS02935: methyltransferase

smcogs
  SMCOG1089: methyltransferase

EKH80_RS02945: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Ligases: ligase synthase
EKH80_RS02955: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EKH80_RS02990: Pseudouridine synthase

smcogs
  SMCOG1154: Pseudouridine synthase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
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: 20.54 out of 26.33
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.49 out of 23.43
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
Additional weak hits (19):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.30 out of 36.54
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.21 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.75 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.90 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.79 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.64 out of 29.65
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.63 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.69 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.62 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.54 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.25 out of 28.14
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.50 out of 39.62
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.69 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.54 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.93 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.97 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
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 15440 - 62595:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Cys)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
EKH80_RS02945: X - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (474..872): 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:
    pro (Pro)
  Single AA prediction:
    pro (Pro)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQAFDVSFQEAFLITAGEYNQYGPTETHLASEL
  Nearest Stachelhaus code(s):
    4Me-Pro DVQFIAHLAK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1528..1934): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWITFDLSVYDGDSFFSGDIGLGGATEASVWSNY
  Nearest Stachelhaus code(s):
    Cys DLFDFSLVWK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

EKH80_RS02955: X
AMP-binding (32..446): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    IAVPMIGFLYNVYAVTGSAQALWGMTEIGGATFT
  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
--- | ---
ANR | Anaerobic transcriptional regulator
AbrC3 | Antibiotic production activator
BldD | Development and antibiotic global regulator
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis

NZ_RYYV01000002.1 - Region 2 - 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: 160,886 - 183,753 nt. (total: 22,868 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
EKH80_RS03415: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

EKH80_RS03425: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: dehalogenase
EKH80_RS03480: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: cyclase hydratase
EKH80_RS03450: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

EKH80_RS03470: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

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
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001928.2 |  | 0.48 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000528.5 |  | 0.48 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000894.4 |  | 0.45 | other (other) | citrinin | Monascus aurantiacus
BGC0000243.4 |  | 0.43 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0000503.5 |  | 0.43 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0002698.2 |  | 0.43 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001364.3 |  | 0.43 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001928.2 |  | 0.48 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000528.5 |  | 0.48 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000894.4 |  | 0.45 | other (other) | citrinin | Monascus aurantiacus
BGC0000243.4 |  | 0.43 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0000503.5 |  | 0.43 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0002698.2 |  | 0.43 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001364.3 |  | 0.43 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919

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 EKH80_RS03450

EKH80_RS03455
Leader:
MDTVLEGEALVAQWRASADVDSPAG
Core:
P L F I G G K Y A K A D I V N S A E S I T T N F L C T C G T A I H D N C C N
Core with dehydrations:
P L F I G G K Y A K A D I V N Dha A E Dha I Dhb Dhb N F L Cys Dhb Cys G Dhb A I H D N Cys Cys N

#### antiSMASH-DB 4.0 matches for EKH80_RS03455

100.0%
NZ_RYYV01000002.1:
Lanthipeptides: EKH80_RS03455_lanthipeptide
1
P L F I G G K Y A K A D I V N S A E S I T T N F L C T C G T A I H D N C C N
38
P L F I G G K Y A K A D I V N S A E S I T T N F L C T C G T A I H D N C C N
1
P L F I G G K Y A K A D I V N S A E S I T T N F L C T C G T A I H D N C C N
38
40.0%
NZ_FOZI01000001.1:
Lanthipeptides: BM338_RS00935_lanthipeptide
1
P L F I G G K Y A K A D I V N S A E S I T T N F L C T C G T A
31
P L F G G++A+A+I++ A S+T T C G T A
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
30
39.6%
NZ_FNOG01000007.1:
Lanthipeptides: BLU84_RS27270_lanthipeptide
1
P L F I G G K Y A K A D I V N S A E S I T--T N F L C T C G T A I H D N C C
37
P L F I G G++A+A D I +E+++ T+ C G T I H C C
13
P L F I G G E F A E A D I A G D S E A V S M I T S V C T G C G T-I H--C C
48
with 53 more sequence matches
Only the first 10 are displayed here.
39.5%
NZ_CP064030.1:
Lanthipeptides: ISN74_RS08625_lanthipeptide
1
P L F I G G K Y A K A D I V N S A E S I T T N F L C T--C G T A----I H D N C C
37
P L F+ G++A++D I V+S +T +C+ C G+A H 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
39.5%
NZ_JADIKF010000040.1:
Lanthipeptides: ISS99_RS17245_lanthipeptide
1
P L F I G G K Y A K A D I V N S A E S I T T N F L C T--C G T----A I H D N C C
37
P L F+ G++A++D I V+S +T +C+ C G T + H C C
1
P L F V S G R F A E S D I V S S T N I V T A Y A V C S G R C G T I C S G S S H A E C C
43
35.4%
NZ_CP072597.1:
Lanthipeptides: J5226_RS01600_lanthipeptide
1
P L F I G G K Y A K A D I V N S A E S I T T N-F L C T-C G T
30
P L F I G++A+A D I E I+ N C T C G T
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
44
35.2%
NZ_CP076103.1:
Lanthipeptides: KME82_RS02870_lanthipeptide
1
P L F I G G K Y A K A D I V N S-A E S I T T N F L C T C G T A I H D N C C
37
P L F I G G+Y ++D I+ A +I T L C T +I N C C
18
P L F I G G E Y V E S D I I G E V A P A I T G C S L C T--G S I R I N C C
53
34.2%
NZ_CP041730.1:
Lanthipeptides: FNU76_RS16940_lanthipeptide
2
L F I G G K Y A K A D I V N S A E S I T T N F L C T C G T A
31
L++ G+Y A+A D I S +T C G T A
1
L Y V S G E Y A E A D I A M S I R P L T W G---G C G T A
27
34.1%
NZ_RYYV01000004.1:
Lanthipeptides: allorf_108254_108448_lanthipeptide
1
P L F I G G K Y A K A D I V N-S A E S I T T N F L C T C G T A I H D N C C
37
P L F+ G K S A E I T F T A +C C
7
P L F V D G S T E K K M T T R A S A E R I D T M F R T T Q S C A S G C S C C
44
34.0%
NZ_CP040709.1:
Lanthipeptides: FF090_RS18940_lanthipeptide
1
P L F I G G K Y A K A D I V N S A E S I T T N F L C T C G T A
31
P L F I G G+Y A+A D I+ S I+ C G T A
14
P L F I G G E Y A E A D I I G D T T S I S G K----C G T A
40
33.3%
NZ_AP014940.1:
Lanthipeptides: LEN_RS25395_lanthipeptide
1
P L F I G G K Y A K A D I V N S A E S I T--T N F L C T C G T
30
P L F I G G++A+A D I +E+I+ T+ C G T
13
P L F I G G E F A E A D I A G D S E A I S M I T S V C T G C G T
44
33.3%
NZ_CP011130.1 and 4 others:
NZ_CP023465.1 Lanthipeptides: CNO08_RS25510_lanthipeptide NZ_CP094357.1 Lanthipeptides: IEQ11_RS02795_lanthipeptide NZ_KQ061218.1 Lanthipeptides: WN54_RS23295_lanthipeptide NZ_LMHM01000017.1 Lanthipeptides: ASD86_RS21560_lanthipeptide
Lanthipeptides: LC55x_RS02840_lanthipeptide
1
P L F I G G K Y A K A D I V N S-A E S I T T N F L C T C G T A I H D N C C
37
P L F I G G+Y ++D I+ A +I T L C T ++ N C C
18
P L F I G G E Y V E S D I I G E V A P A I T G C S L C T--G S M R I N C C
53
32.1%
NZ_JAIQCM010000003.1:
Lanthipeptides: K9V56_RS08295_lanthipeptide
1
P L F I G G K Y A K A D I V N S A E S I T T N F L C T C G T A
31
P L F I G G+Y A+A D I V +I+ C G T A
17
P L F I G G E Y A E A D I V G D T S T I S G K----C G T A
43

#### MIBiG 4.0 matches for EKH80_RS03455

10.5%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
27
T C G T A I H
33
T C +I H
25
T C H C S I H
31
10.3%
BGC0001229.4 (SBI_06990):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
26
C T C G T A I H D N C
36
C T N C
28
C T L S K E C Q P N C
38
allorf_163957_164115
Leader:
MRRSGAMRKRTSQSEMTQRVGCIWCAEDLRAA
Core:
N R R N Y E T R L M H C A S T R C V K E
Core with dehydrations:
N R R N Y E Dhb R L M H Cys A Dha Dhb R Cys V K E

#### antiSMASH-DB 4.0 matches for allorf_163957_164115

100.0%
NZ_RYYV01000002.1:
Lanthipeptides: allorf_163957_164115_lanthipeptide
1
N R R N Y E T R L M H C A S T R C V K E
20
N R R N Y E T R L M H C A S T R C V K E
1
N R R N Y E T R L M H C A S T R C V K E
20
allorf_175843_175911
Leader:
MSPQNALGQAAMARA
Core:
Y T C L R G T
Core with dehydrations:
Y Dhb Cys L R G Dhb

#### antiSMASH-DB 4.0 matches for allorf_175843_175911

100.0%
NZ_RYYV01000002.1:
Lanthipeptides: allorf_175843_175911_lanthipeptide
1
Y T C L R G T
7
Y T C L R G T
1
Y T C L R G T
7
allorf_183483_183668
Leader:
MMLGVIRPSSLLHRRGEGRFSHGG
Core:
C M S Q A M Q P S T K C R N S T R A K G P L G F A P N G V F L S V H L D A
Core with dehydrations:
Cys M Dha Q A M Q P Dha Dhb K Cys R N Dha Dhb R A K G P L G F A P N G V F L Dha V H L D A

#### antiSMASH-DB 4.0 matches for allorf_183483_183668

100.0%
NZ_RYYV01000002.1:
Lanthipeptides: allorf_183483_183668_lanthipeptide
1
C M S Q A M Q P S T K C R N S T R A K G P L G F A P N G V F L S V H L D A
37
C M S Q A M Q P S T K C R N S T R A K G P L G F A P N G V F L S V H L D A
1
C M S Q A M Q P S T K C R N S T R A K G P L G F A P N G V F L S V H L D A
37
24.3%
NZ_CP040417.1 and 7 others:
NZ_CP040417.1 Lanthipeptides: FE328_RS09035_lanthipeptide NZ_CP040419.1 Lanthipeptides: FE326_RS02890_lanthipeptide NZ_CP040419.1 Lanthipeptides: FE326_RS02890_lanthipeptide NZ_CP040421.1 Lanthipeptides: FE324_RS02830_lanthipeptide NZ_CP040421.1 Lanthipeptides: FE324_RS02830_lanthipeptide NZ_CP040422.1 Lanthipeptides: FE323_RS02865_lanthipeptide NZ_CP040422.1 Lanthipeptides: FE323_RS02865_lanthipeptide
Lanthipeptides: FE328_RS09035_lanthipeptide
2
M S Q A M Q P S T K C R N S T R
17
+S A+ P S T K C + T R
9
I S L A I C P S T K C A S I T R
24
24.3%
NZ_KV815277.1:
Lanthipeptides: allorf_240001_240225_lanthipeptide
1
C M S Q A M Q P S T K C R N S T R A K G P L G F A P N G
28
C+S A P S T R + +P+G
2
C L S G A A S P S T P T R E C S E C S R S Y T D S P S G
29
with 3 more sequence matches
18.9%
NZ_KZ819159.1 and 2 others:
NZ_KZ819159.1 Lanthipeptides: allorf_2152839_2153060_lanthipeptide NZ_KZ819159.1 Lanthipeptides: allorf_2152839_2153060_lanthipeptide
Lanthipeptides: allorf_2152839_2153060_lanthipeptide
17
R A K G P L G F A P N
27
R A+G P G F P+
5
R A E G P G G F L P S
15
16.3%
NZ_BNBV01000031.1 and 3 others:
NZ_BNBV01000031.1 Lanthipeptides: IE286_RS22985_lanthipeptide NZ_BNBV01000031.1 Lanthipeptides: IE286_RS22990_lanthipeptide NZ_BNBV01000031.1 Lanthipeptides: IE286_RS22985_lanthipeptide
Lanthipeptides: IE286_RS22990_lanthipeptide
3
S Q A M Q P S T K C R N
14
S A P+T K C N
30
S A A F C P T T K C T N
41
16.3%
NZ_CP107567.1 and 3 others:
NZ_CP107567.1 Lanthipeptides: OGH68_RS19755_lanthipeptide NZ_CP107567.1 Lanthipeptides: OGH68_RS19755_lanthipeptide NZ_CP107567.1 Lanthipeptides: OGH68_RS19755_lanthipeptide
Lanthipeptides: OGH68_RS19755_lanthipeptide
2
M S Q A M Q P S T K C R N S
15
+S A M P+T K C ++
29
V S A A M C P T T K C T S A
42

#### MIBiG 4.0 matches for allorf_183483_183668

16.2%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
2
M S Q A M Q P S T K C R N
14
+S A P+T K C +
23
V S A A F C P T T K C T S
35
13.5%
BGC0001639.3 (OUH62395.1):
Lasso peptide: klebsidin
24
F A P N G V
29
F P N G V
10
F N P N G V
15
10.8%
BGC0002110.3 (QKV49894.1):
Lanthipeptide: birimositide
8
P S T K C R N
14
P+T K C +
18
P T T K C T S
24
allorf_183661_183744
Leader:
MLDVIPVG
Core:
G Q V D G A S K R A T R L S T C H S G
Core with dehydrations:
G Q V D G A Dha K R A Dhb R L Dha Dhb Cys H Dha G

#### antiSMASH-DB 4.0 matches for allorf_183661_183744

100.0%
NZ_RYYV01000002.1:
Lanthipeptides: allorf_183661_183744_lanthipeptide
1
G Q V D G A S K R A T R L S T C H S G
19
G Q V D G A S K R A T R L S T C H S G
1
G Q V D G A S K R A T R L S T C H S G
19
26.3%
NZ_CP029194.1:
Lanthipeptides: allorf_0972442_0972567_lanthipeptide
10
A T R L S T C H S
18
A T+ +T C H
3
A T K W T T C H E
11
21.4%
NZ_LIWB01000026.1:
Lanthipeptides: AMK33_RS42645_lanthipeptide
3
V D G A S K R A T R L S T C H S
18
D G + +S+C H S
7
F D G C Q W W S L T V S S C H S
22
with 2 more sequence matches
19.4%
NZ_CP073766.1:
Lanthipeptides: KD145_RS08730_lanthipeptide
3
V D G A S K R A T R L S T C H S
18
V+G + T R T C S
5
V E G G A I P V T R F I T C L S
20
18.5%
NZ_CP059991.1:
Lanthipeptides: allorf_7879374_7879520_lanthipeptide
10
A T R L S T C H S
18
A T+ +T C H+
12
A T K W T T C H T
20

#### 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 (2):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.01 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.86 out of 26.06
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.

EKH80_RS03455 - Class II
  Cleavage pHMM score: -4.60
  RODEO score: 0
  Monoisotopic mass: 3895.9 Da
  Molecular weight: 3898.4 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3916.4 Da N = 1
    3934.4 Da N = 2
allorf_163957_164115 - Class II
  Cleavage pHMM score: -6.40
  RODEO score: 0
  Monoisotopic mass: 2412.2 Da
  Molecular weight: 2413.7 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2431.8 Da N = 1
allorf_175843_175911 - Class II
  Cleavage pHMM score: -6.90
  RODEO score: 0
  Monoisotopic mass: 776.4 Da
  Molecular weight: 776.9 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    794.9 Da N = 1
allorf_183483_183668 - Class II
  Cleavage pHMM score: -3.00
  RODEO score: 0
  Monoisotopic mass: 3810.9 Da
  Molecular weight: 3813.4 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3831.4 Da N = 1
    3849.4 Da N = 2
    3867.4 Da N = 3
    3885.5 Da N = 4
allorf_183661_183744 - Class II
  Cleavage pHMM score: -6.00
  RODEO score: 0
  Monoisotopic mass: 1839.9 Da
  Molecular weight: 1841.0 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1859.0 Da N = 1
    1877.0 Da N = 2
    1895.1 Da N = 3
    1913.1 Da N = 4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_RYYV01000002.1 - Region 3 - NRPS,transAT-PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 185,121 - 273,093 nt. (total: 87,973 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase synthase
EKH80_RS03560: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

EKH80_RS03630: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: acylase aminotransferase
EKH80_RS03525: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

EKH80_RS03640: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase synthase
EKH80_RS03560: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

EKH80_RS03590: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: ligase synthase
EKH80_RS03595: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

EKH80_RS03600: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EKH80_RS03635: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: permease
EKH80_RS03540: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | NRPS | transAT-PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  | 0.92 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  |  | 0.92 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  |  | 0.90 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  |  | 0.88 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.86 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  |  | 0.86 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  | 0.85 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.84 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  |  | 0.83 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001050.5 |  |  | 0.80 | 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 |  | 0.76 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.75 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001133.4 |  | 0.72 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.79 out of 21.84
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.13 out of 20.47
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.86 out of 18.57
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.69 out of 30.25
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.28 out of 23.43
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.25 out of 20.01
Confidence: medium
Additional weak hits (12):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.69 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.63 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.78 out of 20.01
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.29 out of 25.75
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.26 out of 32.74
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.41 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.53 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.10 out of 30.98
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.40 out of 23.43
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.84 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.32 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 3, location 185120 - 273093:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe - Phe - NMe-X) + (Ile) + (NMe-X) + (ccmal - ccmal - mal - Thr - Ala - Ala)

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).
EKH80_RS03595: Phe - Phe - X
Search NORINE for peptide: strict or relaxed
AMP-binding (475..865): 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:
    LCQAFDAAFWEMAMVVAGEFNSYGPTEGTVGATL
  Nearest Stachelhaus code(s):
    Trp DGWAVASVCK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1521..1909): 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:
    LSQAFDASVWEAVMATGGEVNAYGPTESSVCASI
  Nearest Stachelhaus code(s):
    Leu DAWLLGAVCK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2572..2969): X
nrpys: Ile, 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:
    LDRSFDASTYEVFLWTGGEMHVYGPTESTTFATA
  Nearest Stachelhaus code(s):
    Ile or Val DAYFWGVTFK (91% 8Å match)
    Val DAYFWGVTFK (85% 8Å match)
    Ile DAYFWGVTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

EKH80_RS03600: Ile
Search NORINE for peptide: strict or relaxed
AMP-binding (470..866): Ile
nrpys: Ile

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:
    LNRSFDACTYEVFLWSGGEVNVYGPTETTTFATC
  Nearest Stachelhaus code(s):
    Ile DAYFWGVTFK (91% 8Å match)
    Ile or Val DAYFWGVTFK (88% 8Å match)
    Leu DAYFWGVTFK (85% 8Å match)
    Val DAYFWGVTFK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

EKH80_RS03605: X
AMP-binding (30..424): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSYAFDASFAEMALVVGGEINAYGPTEITVDALI
  Nearest Stachelhaus code(s):
    Arg DAESVGAVDK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

EKH80_RS03635: Thr - Ala - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (4163..4578): Thr
nrpys: Thr

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

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

AMP-binding (5260..5654): 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:
    FWATFDLSIFEVNTNLAGEYNLYGPSEDTTYSTF
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6315..6709): 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:
    FWATFDLSIFEVNTNLAGEYNLYGPSEDTTYSTF
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

EKH80_RS03640: mal
PKS_AT (8..288): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 75.5
  inactive: 51.8
  Methoxymalonyl-CoA: 22.3
  Methylmalonyl-CoA: 21.3
  Isobutyryl-CoA: 15.3
  Propionyl-CoA: 12.6
  fatty_acid: 10.8
  trans-1,2-CPDA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes
BldD | Development and antibiotic global regulator
ColR | Phenol-responsive regulator
MexT | Global virulence regulator
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_RYYV01000026.1 - 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: 33,377 - 52,734 nt. (total: 19,358 nt) Show pHMM detection rules used
Region on contig edge.
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: glucosidase
EKH80_RS21185: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

EKH80_RS21195: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Lyases: cyclase
EKH80_RS21200: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase
EKH80_RS21205: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001642.3 |  | 0.74 | terpene | koraiol | Fusarium fujikuroi IMI 58289
BGC0002285.2 |  | 0.47 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000550.3 |  | 0.38 | ribosomal | salivaricin G32 | Streptococcus salivarius
BGC0000545.5 |  | 0.38 | ribosomal | ruminococcin A | [Ruminococcus] gnavus E1
BGC0001788.3 |  | 0.37 | ribosomal | suicin 65 | Streptococcus suis
BGC0000557.5 |  | 0.37 | ribosomal | streptococcin A-FF22 | Streptococcus pyogenes
BGC0000527.5 |  | 0.37 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000547.5 |  | 0.36 | ribosomal | salivaricin 9 | Streptococcus salivarius
BGC0000188.5 |  | 0.36 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0000506.4 |  | 0.35 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001642.3 |  | 0.74 | terpene | koraiol | Fusarium fujikuroi IMI 58289
BGC0002285.2 |  | 0.47 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000550.3 |  | 0.38 | ribosomal | salivaricin G32 | Streptococcus salivarius
BGC0000545.5 |  | 0.38 | ribosomal | ruminococcin A | [Ruminococcus] gnavus E1
BGC0001788.3 |  | 0.37 | ribosomal | suicin 65 | Streptococcus suis
BGC0000557.5 |  | 0.37 | ribosomal | streptococcin A-FF22 | Streptococcus pyogenes
BGC0000527.5 |  | 0.37 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000547.5 |  | 0.36 | ribosomal | salivaricin 9 | Streptococcus salivarius
BGC0000188.5 |  | 0.36 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0000506.4 |  | 0.35 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii

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 |  |  | C15 | C1-C10 | none

Genes with terpene domains:
EKH80_RS21200: T1TS
Domain 1 (22 - 325): Type 1 terpene synthase
Subtype: Corvol ether A and B synthase type

Reactions:
  FPP → sesquiterpene_C1-C10

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 23.45 out of 27.55
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.31 out of 20.97
Confidence: medium
Additional weak hits (4):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.94 out of 20.01
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.94 out of 20.01
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.94 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.75 out of 27.78
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
GnfM | Regulator of nitrogen-fixation genes

NZ_RYYV01000032.1 - 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 - 32,883 nt. (total: 32,883 nt) Show pHMM detection rules used
Region on contig edge.
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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
EKH80_RS22220: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: esterase
EKH80_RS22285: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase
EKH80_RS22300: 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
--- | --- | --- | --- | --- | ---
BGC0000465.4 |  | 0.68 | NRPS | xenortide A, xenortide B, xenortide C, xenortide D | Xenorhabdus nematophila ATCC 19061
BGC0000426.5 |  | 0.67 | NRPS | sevadicin | Paenibacillus larvae
BGC0001133.4 |  | 0.65 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  | 0.65 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000465.4 |  | 0.68 | NRPS | xenortide A, xenortide B, xenortide C, xenortide D | Xenorhabdus nematophila ATCC 19061
BGC0000426.5 |  | 0.67 | NRPS | sevadicin | Paenibacillus larvae
BGC0001133.4 |  | 0.65 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  | 0.65 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (5):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.20 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.51 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.34 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.94 out of 30.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.66 out of 25.75
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 - 32883:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-Ser - D-Gly) + (D-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).
EKH80_RS22295: Ser - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (471..876): Ser
nrpys: Ser

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

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

AMP-binding (1948..2357): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    KAVSFDISLLELHALTGGDIELYGPTEAAIICAH
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (59% 8Å match)
  Stachelhaus code match:
    80% (moderate)

EKH80_RS22300: Asp - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (463..861): 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:
    asn (Asn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWDFFDAGVTTGKLMCGGEINHFGPTETTVGCAT
  Nearest Stachelhaus code(s):
    Asp DATKMGHVGK (71% 8Å match)
    CysA DATKMGHVGK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1984..2293): Thr
nrpys: Thr

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

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

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

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

NZ_RYYV01000035.1 - Region 1 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 21,480 nt. (total: 21,480 nt) Show pHMM detection rules used
Region on contig edge.
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
EKH80_RS22615: aminotransferase

smcogs
  SMCOG1019: aminotransferase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.62 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.62 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 24.28 out of 27.78
Confidence: strong
Additional weak hits (2):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.73 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.83 out of 26.12
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RYYV01000038.1 - 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 - 20,574 nt. (total: 20,574 nt) Show pHMM detection rules used
Region on contig edge.
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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
Ligases: ligase
EKH80_RS22930: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.69 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.69 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (1):
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.19 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 20574:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe - Ile) + (D-Asp - X - Gly)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
EKH80_RS22930: Phe - Ile
Search NORINE for peptide: strict or relaxed
AMP-binding (714..1104): 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:
    LSQAFDAAFWEMTLIVAGEFNAYGPTEATVCATV
  Nearest Stachelhaus code(s):
    Phe DAWTIAAVCK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1769..2158): Ile
nrpys: Ile

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:
    LNNGFDISTLEAHLLVGGDLHCYGPTESTTFATT
  Nearest Stachelhaus code(s):
    Ile DALFLGCTFK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

EKH80_RS22935: Asp - X - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (462..860): 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:
    asn (Asn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWDFFDAGVTTGKLMCGGEINHFGPTETTVGCAT
  Nearest Stachelhaus code(s):
    Asp DATKMGHVGK (71% 8Å match)
    CysA DATKMGHVGK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1984..2577): X
nrpys: OH-Asn, Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWATFDATVTSLKLVVGGEINEYGPTETVVGCVA
  Nearest Stachelhaus code(s):
    OH-Asn or Asn DATKVGEVGK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3233..3633): 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:
    FSMTFDIAGLELQALTGGEVNLYGPTETTVWSSL
  Nearest Stachelhaus code(s):
    Gly DILQLGLVWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---

NZ_RYYV01000004.1 - 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: 98,541 - 121,363 nt. (total: 22,823 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: electron transfer oxidoreductase
EKH80_RS06625: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

EKH80_RS06650: flavodoxin

smcogs
  SMCOG1134: flavodoxin

Transferases: sulfotransferase
EKH80_RS06615: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

Hydrolases: dehalogenase hydrolase peptidase
EKH80_RS06635: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

EKH80_RS06640: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

EKH80_RS06680: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: cyclase
EKH80_RS06645: 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
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000528.5 |  | 0.45 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001579.4 |  | 0.43 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0001660.3 |  | 0.43 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0001576.3 |  | 0.43 | ribosomal | divamide A | Prochloron didemni
BGC0000503.5 |  | 0.42 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000554.4 |  | 0.42 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002346.3 |  | 0.40 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0001210.5 |  | 0.39 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000528.5 |  | 0.45 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001579.4 |  | 0.43 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0001660.3 |  | 0.43 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0001576.3 |  | 0.43 | ribosomal | divamide A | Prochloron didemni
BGC0000503.5 |  | 0.42 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000554.4 |  | 0.42 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002346.3 |  | 0.40 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0001210.5 |  | 0.39 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442

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

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 EKH80_RS06645

allorf_104369_104572
Leader:
MRIALFGKDRVGWGHHKCDKSGLSSLVIRRRHSAVTAM
Core:
P A W Y R N T L R S R S T A G K G R N T C L R R Q V H A C
Core with dehydrations:
P A W Y R N Dhb L R Dha R Dha Dhb A G K G R N Dhb Cys L R R Q V H A Cys

#### antiSMASH-DB 4.0 matches for allorf_104369_104572

100.0%
NZ_RYYV01000004.1:
Lanthipeptides: allorf_104369_104572_lanthipeptide
1
P A W Y R N T L R S R S T A G K G R N T C L R R Q V H A C
29
P A W Y R N T L R S R S T A G K G R N T C L R R Q V H A C
1
P A W Y R N T L R S R S T A G K G R N T C L R R Q V H A C
29
30.6%
NZ_CABWKH010000001.1 and 1 other:
NZ_CP010411.1 Lanthipeptides: allorf_1259634_1259786_lanthipeptide
Lanthipeptides: allorf_022146_022298_lanthipeptide
3
W Y R N T L R S R S T-A G K G R N T C L R R Q V H A C
29
W+R L R T G G R+ C R +C
6
W H R A G L A V R E T R M G D G R S A C P R V A A G S C
33
27.6%
NC_019673.1:
Lanthipeptides: allorf_4537901_4538068_lanthipeptide
10
S R S T A G K G R N T C L R R Q V H A C
29
S R G G R +R + A C
2
S R G P P G P G R T N T V R P R N A A C
21
with 1 more sequence matches
21.7%
NZ_LR881952.1 and 4 others:
NZ_LR881952.1 Lanthipeptides: allorf_5341425_5341625_lanthipeptide NZ_LR881952.1 Lanthipeptides: allorf_5341425_5341625_lanthipeptide NZ_LR881952.1 Lanthipeptides: allorf_5341425_5341625_lanthipeptide NZ_LZQS01000002.1 Lanthipeptides: allorf_595585_595785_lanthipeptide
Lanthipeptides: allorf_5341425_5341625_lanthipeptide
1
P A W Y R N T L R S R S T A G K G
17
P A W T L R R A G G
12
P A W--E T L R L R Y G A G M G
26
allorf_104699_104878
Leader:
MGAHRKQDAAARTGIGASWSSCLIPEEHRSRGA
Core:
A R C L R T A H D P S I G H K G T P A P R Y A S A P
Core with dehydrations:
A R Cys L R Dhb A H D P Dha I G H K G Dhb P A P R Y A Dha A P

#### antiSMASH-DB 4.0 matches for allorf_104699_104878

100.0%
NZ_RYYV01000004.1:
Lanthipeptides: allorf_104699_104878_lanthipeptide
1
A R C L R T A H D P S I G H K G T P A P R Y A S A P
26
A R C L R T A H D P S I G H K G T P A P R Y A S A P
1
A R C L R T A H D P S I G H K G T P A P R Y A S A P
26
26.3%
NZ_FMXV01000009.1:
Lanthipeptides: allorf_148352_148558_lanthipeptide
3
C L R T A---H D P S I G H K G T P A P
20
C L R T H P S G H P
14
C L R T V G I G H C P S A G H N A R R L P
34
21.9%
NZ_CP015405.2:
Lanthipeptides: allorf_4801575_4801745_lanthipeptide
1
A R C L R T A H D P S I G H K
15
R C T A H P G +
8
C R C A D T A H F P E A G K E
22
with 1 more sequence matches
12.3%
NZ_LMEI01000006.1:
Lanthipeptides: allorf_386141_386362_lanthipeptide
3
C L R T A H D P S I G H
14
C L R T H D P+
27
C L R T V H D P A T A Q
38
allorf_107615_107755
Leader:
MRHGANQVQAG
Core:
A G M T A W L S V V P S D R H W K P A G R T D I Q P P C A K W S R F G
Core with dehydrations:
A G M Dhb A W L Dha V V P Dha D R H W K P A G R Dhb D I Q P P Cys A K W Dha R F G

#### antiSMASH-DB 4.0 matches for allorf_107615_107755

100.0%
NZ_RYYV01000004.1:
Lanthipeptides: allorf_107615_107755_lanthipeptide
1
A G M T A W L S V V P S D R H W K P A G R T D I Q P P C A K W S R F G
35
A G M T A W L S V V P S D R H W K P A G R T D I Q P P C A K W S R F G
1
A G M T A W L S V V P S D R H W K P A G R T D I Q P P C A K W S R F G
35
16.2%
NZ_CP023465.1 and 1 other:
NZ_KQ061218.1 Lanthipeptides: allorf_237147_237311_lanthipeptide
Lanthipeptides: allorf_0704938_0705102_lanthipeptide
20
G R T D I Q P P C A K W S R F
34
G R + P C++ +R F
14
G R N L L L P S C S R S A R F
28
14.3%
NZ_CP102384.1 and 1 other:
NZ_JAATIT010000001.1 Lassopeptides: allorf_0891587_0891718_lassopeptide
Lassopeptides: NP825_RS15870_lassopeptide
18
P A G R T D I Q P
26
P+G+ D+Q P
4
P S G Q Q D V Q P
12
with 2 more sequence matches
14.3%
NZ_QLLX01000002.1 and 1 other:
NZ_QLLX01000002.1 Lanthipeptides: allorf_335018_335257_lanthipeptide
Lanthipeptides: allorf_335018_335257_lanthipeptide
19
A G R T D I Q P P C A K W S R F G
35
A R T D +P P S R G
16
A P R T D R R P P A M S R S R T G
32
11.9%
NZ_CP072384.1:
Lanthipeptides: allorf_0337653_0337835_lanthipeptide
21
R T D I Q P P C A K W S R
33
R+D+ P C++++R
1
R S D M S G P C S R F A R
13
allorf_108229_108468
Leader:
MLASVENQQQLQPEAQDCVVLNMVSILSA
Core:
L A R V V I F F S V E P S T K S G P A G L P K P L M L S A P S S Q A E T T L S F C C I A E L L R R S
Core with dehydrations:
L A R V V I F F Dha V E P Dha Dhb K Dha G P A G L P K P L M L Dha A P Dha Dha Q A E Dhb Dhb L Dha F Cys Cys I A E L L R R Dha

#### antiSMASH-DB 4.0 matches for allorf_108229_108468

100.0%
NZ_RYYV01000004.1:
Lanthipeptides: allorf_108229_108468_lanthipeptide
1
L A R V V I F F S V E P S T K S G P A G L P K P L M L S A P S S Q A E T T L S F C C I A E L L R R S
50
L A R V V I F F S V E P S T K S G P A G L P K P L M L S A P S S Q A E T T L S F C C I A E L L R R S
1
L A R V V I F F S V E P S T K S G P A G L P K P L M L S A P S S Q A E T T L S F C C I A E L L R R S
50
23.2%
NZ_FOGI01000013.1:
Lanthipeptides: allorf_142264_142503_lanthipeptide
7
F F S V E P S T K S G-P A G L P K P L M L S A--P S S Q A E T T L S F C C I A E L L R R S
50
F S + T S P A G P P L + A P +++ C A L R+
16
F A S P D R K T N S H L P A G S P P P L A V E A C S P G G R S D W K E W I T C K A R L W W R A
62
allorf_108254_108448
Leader:
MQQNDNVVSAWLEGADSISG
Core:
L G N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R T T Q S C A S G C S C C
Core with dehydrations:
L G N P A G P L F V D G Dha Dhb E K K M Dhb Dhb R A Dha A E R I D Dhb M F R Dhb Dhb Q Dha Cys A Dha G Cys Dha Cys Cys

#### antiSMASH-DB 4.0 matches for allorf_108254_108448

100.0%
NZ_RYYV01000004.1:
Lanthipeptides: allorf_108254_108448_lanthipeptide
1
L G N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R T T Q S C A S G C S C C
44
L G N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R T T Q S C A S G C S C C
1
L G N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R T T Q S C A S G C S C C
44
36.4%
NZ_CP023690.1 and 1 other:
NZ_CP030771.1 Lanthipeptides: C9F11_RS41405_lanthipeptide
Lanthipeptides: CP982_RS40715_lanthipeptide
3
N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R--T T Q S C A S G C S C C
44
N P A G P L+V G S + T S D+++ ++ S + G C C
3
N P A G P L Y V G G S A A E A A L T D P S----D S L Y G F C S S P S G S H G S W C C
42
34.1%
NZ_BMNG01000007.1:
Lanthipeptides: IEY91_RS17560_lanthipeptide
3
N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R T T Q S C A S G C S C C
44
N P A G P L+V G+ + T A+ F ++ S + G C C
3
N P A G P L Y V G G T V G E A A L T D A T D S L Y G--F C S S P S G S L G S W C C
42
with 47 more sequence matches
Only the first 10 are displayed here.
34.1%
NZ_BMUQ01000012.1 and 11 others:
NZ_CP041604.2 Lanthipeptides: FNV64_RS07000_lanthipeptide NZ_CP041610.2 Lanthipeptides: FNV62_RS03705_lanthipeptide NZ_CP041611.1 Lanthipeptides: FNV63_RS03970_lanthipeptide NZ_CP041613.2 Lanthipeptides: FNV68_RS05855_lanthipeptide NZ_CP041650.2 Lanthipeptides: FNV59_RS05275_lanthipeptide NZ_CP050974.1 Lanthipeptides: HEP84_RS02235_lanthipeptide NZ_CP051010.1 Lanthipeptides: HEP87_RS03725_lanthipeptide NZ_FONR01000009.1 Lanthipeptides: BM303_RS25620_lanthipeptide NZ_KQ948493.1 Lanthipeptides: AQJ27_RS49365_lanthipeptide NZ_VISR01000021.1 Lanthipeptides: FB157_RS31330_lanthipeptide NZ_VISR01000021.1 Lanthipeptides: FB157_RS31330_lanthipeptide
Lanthipeptides: IE289_RS27575_lanthipeptide
3
N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R--T T Q S C A S G C S C C
44
N P A G P L+V G+ + T S D+++ ++ S + G C C
3
N P A G P L Y V G G A A A E A A L T D P S----D S L Y G F C S S P S G S H G S W C C
42
34.1%
NZ_BMUU01000006.1 and 2 others:
NZ_BMUZ01000004.1 Lanthipeptides: IE267_RS12185_lanthipeptide NZ_CP070373.1 Lanthipeptides: GWQ54_RS15625_lanthipeptide
Lanthipeptides: IE233_RS19480_lanthipeptide
3
N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R--T T Q S C A S G C S C C
44
N P A G P L+V G+ + T +S D+++ ++ S + G C C
3
N P A G P L Y V G G A A A E A A L T D S S----D S L Y G F C S S P S G S H G S W C C
42
34.1%
NZ_BMVR01000007.1 and 3 others:
NZ_CP040916.1 Lanthipeptides: FH965_RS39150_lanthipeptide NZ_MQUS01000030.1 Lanthipeptides: AV521_RS36555_lanthipeptide NZ_RHGC01000002.1 Lanthipeptides: EJ355_RS11575_lanthipeptide
Lanthipeptides: IE274_RS20785_lanthipeptide
3
N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R--T T Q S C A S G C S C C
44
N P A G P L+V G+ + T S D+++ ++ S + G C C
3
N P A G P L Y V G G T A A E A A L T D P S----D S L Y G F C S S P S G S H G S W C C
42
34.1%
NZ_CP016279.1 and 1 other:
NZ_CP016279.1 Lanthipeptides: AVL59_RS19575_lanthipeptide
Lanthipeptides: AVL59_RS19575_lanthipeptide
3
N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R T T Q S C A S G C S C C
44
N P A G P L+V G + T S F ++ S + G C C
3
N P A G P L Y V G G R A A E A A L T D P S D A L Y G--F C S S P S G S H G S W C C
42
34.1%
NZ_CP029194.1 and 1 other:
NZ_CP059991.1 Lanthipeptides: H4W23_RS35675_lanthipeptide
Lanthipeptides: DEJ46_RS04155_lanthipeptide
3
N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R T T Q S C A S G C S C C
44
N P A G P L+V G+ + T A T++ +G C S C
2
N P A G P L Y V G G A A G E A A L T D A-----------T E A L L T G C S S C
32
34.1%
NZ_CP032698.1 and 4 others:
NZ_CP106795.1 Lanthipeptides: N8I86_RS02690_lanthipeptide NZ_CP106795.1 Lanthipeptides: N8I86_RS02690_lanthipeptide NZ_LIWA01000005.1 Lanthipeptides: AMK32_RS23965_lanthipeptide NZ_LIWA01000005.1 Lanthipeptides: AMK32_RS23965_lanthipeptide
Lanthipeptides: DWB77_RS04745_lanthipeptide
3
N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R--T T Q S C A S G C S C C
44
N P A G P L+V G+ + T S D+++ ++ S + G C C
3
N P A G P L Y V G G T A A E A A L T D P S----D S L Y G F C S S P S G S R G S W C C
42
34.1%
NZ_CP098485.1 and 4 others:
NZ_CP098485.1 Lanthipeptides: NAT22_RS36135_lanthipeptide NZ_CP106798.1 Lanthipeptides: N8I87_RS37365_lanthipeptide NZ_JACHJK010000003.1 Lanthipeptides: FHS34_RS11895_lanthipeptide NZ_JACHJK010000003.1 Lanthipeptides: FHS34_RS11895_lanthipeptide
Lanthipeptides: NAT22_RS36135_lanthipeptide
3
N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R--T T Q S C A S G C S C C
44
N P A G P L+V G+ + T S D+++ ++ S + G C C
3
N P A G P L Y V G G A A A E A A L T D P S----D S L Y G F C S S P S G S R G S W C C
42
34.1%
NZ_NNBJ01000008.1:
Lanthipeptides: CG740_RS17895_lanthipeptide
3
N P A G P L F V D G S T E K K M T T R A S A E R I D T M F R--T T Q S C A S G C S C C
44
N P A G P L+V G+ + T +S D+++ ++ S + G C C
3
N P A G P L Y V G G A A A E A G L T D S S----D S L Y G F C S S P S G S H G S W C C
42
34.1%
NZ_RYYV01000002.1:
Lanthipeptides: EKH80_RS03455_lanthipeptide
7
P L F V D G S T E K K M T T R A S A E R I D T M F R T T Q S C A S G C S C C
44
P L F+ G K S A E I T F T A +C C
1
P L F I G G K Y A K A D I V N-S A E S I T T N F L C T C G T A I H D N C C
37
32.7%
NZ_CP089414.1:
Lanthipeptides: DYST_RS04430_lanthipeptide
3
N P A G P L F V D--G S T E K K M T T R A S A E R I D T M F R T T------Q S C A S G C S C C
44
N P A G P L++ G+T E +T+ + + + T T T + G C+C C
3
N P A G P L Y I Q G A G A T E A A L T S D K T V K S M L T S V G T T C S T C S I H T S G G G C A C C
52

#### MIBiG 4.0 matches for allorf_108254_108448

9.1%
BGC0000480.5 (ACA04484.1 (core 1)):
Cyanobactin: tenuecyclamide A or tenuecyclamide C
38
A S G C S C
43
A+G C C
1
A T G C M C
6
allorf_108405_108521
Leader:
MMRRGDMEKA
Core:
N T R P D S A V C W P R W K I S N N C S R K R R T A L S
Core with dehydrations:
N Dhb R P D Dha A V Cys W P R W K I Dha N N Cys Dha R K R R Dhb A L Dha

#### antiSMASH-DB 4.0 matches for allorf_108405_108521

100.0%
NZ_RYYV01000004.1:
Lanthipeptides: allorf_108405_108521_lanthipeptide
1
N T R P D S A V C W P R W K I S N N C S R K R R T A L S
28
N T R P D S A V C W P R W K I S N N C S R K R R T A L S
1
N T R P D S A V C W P R W K I S N N C S R K R R T A L S
28
22.2%
NC_017299.1 and 1 other:
NC_017299.1 Lanthipeptides: H04402_RS03105_lanthipeptide
Lanthipeptides: H04402_RS03105_lanthipeptide
5
D S A V C W P R W K I S N N C S R K R
23
D V C + N N C S K+
18
D G K V C T W T V E C Q N N C S H K K
36
21.4%
NZ_CP068102.1 and 1 other:
NZ_CP068102.1 Lanthipeptides: allorf_1176509_1176580_lanthipeptide
Lanthipeptides: allorf_1176509_1176580_lanthipeptide
11
P R W K I S N N C S R K
22
P++ N C S R K
2
P K Y S A I K N C S R K
13
with 2 more sequence matches
15.2%
NZ_JANTYU010000003.1:
Lanthipeptides: allorf_298984_299208_lanthipeptide
12
R W K I S N N C S R K R R T A
26
R W++S +C+ R R A
4
R W R M S I D C A V G R R G A
18
13.8%
NZ_RJUP01000016.1:
Lanthipeptides: allorf_085018_085254_lanthipeptide
6
S A V C W P R W K I S N N C S R K R R T A L S
28
S V C W +S N C + +S
30
S T V C D S D W C L S F N C D S E G T F C I S
52

#### MIBiG 4.0 matches for allorf_108405_108521

8.8%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
7
A V C W P R W K
14
++C P K
5
S L C T P G C K
12
allorf_118876_118977
Leader:
MLRLSGASSIFAA
Core:
A G R Y P V K C P V L V M R V S S T V M
Core with dehydrations:
A G R Y P V K Cys P V L V M R V Dha Dha Dhb V M

#### antiSMASH-DB 4.0 matches for allorf_118876_118977

100.0%
NZ_RYYV01000004.1:
Lanthipeptides: allorf_118876_118977_lanthipeptide
1
A G R Y P V K C P V L V M R V S S T V M
20
A G R Y P V K C P V L V M R V S S T V M
1
A G R Y P V K C P V L V M R V S S T V M
20

#### 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26
Confidence: medium
Additional weak hits (4):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.93 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.66 out of 27.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.67 out of 26.06
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

allorf_104369_104572 - Class II
  Cleavage pHMM score: -6.30
  RODEO score: 0
  Monoisotopic mass: 3267.7 Da
  Molecular weight: 3269.7 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3287.7 Da N = 1
    3305.7 Da N = 2
    3323.8 Da N = 3
allorf_104699_104878 - Class II
  Cleavage pHMM score: -2.90
  RODEO score: 0
  Monoisotopic mass: 2657.4 Da
  Molecular weight: 2659.0 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2677.0 Da N = 1
    2695.0 Da N = 2
    2713.0 Da N = 3
allorf_107615_107755 - Class II
  Cleavage pHMM score: -3.00
  RODEO score: 0
  Monoisotopic mass: 3818.0 Da
  Molecular weight: 3820.3 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3838.4 Da N = 1
    3856.4 Da N = 2
    3874.4 Da N = 3
    3892.4 Da N = 4
allorf_108229_108468 - Class II
  Cleavage pHMM score: -5.60
  RODEO score: 0
  Monoisotopic mass: 5106.8 Da
  Molecular weight: 5110.0 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    5128.0 Da N = 1
    5146.0 Da N = 2
    5164.0 Da N = 3
    5182.1 Da N = 4
    5200.1 Da N = 5
    5218.1 Da N = 6
    5236.1 Da N = 7
    5254.1 Da N = 8
    5272.2 Da N = 9
allorf_108254_108448 - Class II
  Cleavage pHMM score: -5.20
  RODEO score: 0
  Monoisotopic mass: 4429.1 Da
  Molecular weight: 4432.0 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4450.0 Da N = 1
    4468.0 Da N = 2
    4486.1 Da N = 3
    4504.1 Da N = 4
    4522.1 Da N = 5
    4540.1 Da N = 6
    4558.1 Da N = 7
allorf_108405_108521 - Class II
  Cleavage pHMM score: -6.80
  RODEO score: 0
  Monoisotopic mass: 3193.7 Da
  Molecular weight: 3195.6 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3213.6 Da N = 1
    3231.7 Da N = 2
    3249.7 Da N = 3
    3267.7 Da N = 4
allorf_118876_118977 - Class II
  Cleavage pHMM score: -2.80
  RODEO score: 0
  Monoisotopic mass: 2138.2 Da
  Molecular weight: 2139.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2157.7 Da N = 1
    2175.7 Da N = 2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RYYV01000052.1 - 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 - 5,727 nt. (total: 5,727 nt) Show pHMM detection rules used
Region on contig edge.
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  | 0.65 | 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.

No significant matches found.

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

No significant matches found.

Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 5727:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
EKH80_RS23515: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (719..1117): 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:
    LHRSFDASTYEVWLIAGGDVNGYGPTETTTFATN
  Nearest Stachelhaus code(s):
    Val DAYWVGGTFK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

Link to PARAS substrate predictor
NZ_RYYV01000055.1 - Region 1 - transAT-PKS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 4,467 nt. (total: 4,467 nt) Show pHMM detection rules used
Region on contig edge.
transAT-PKS-like: cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS) and not PKS_AT)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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
EKH80_RS23565: 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 | transAT-PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000180.5 |  | 0.45 | PKS | legioliulin | Legionella parisiensis
BGC0001050.5 |  | 0.42 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0000353.5 |  | 0.41 | NRPS | tacrolimus | Streptomyces sp. MA6548
BGC0001109.4 |  | 0.39 | NRPS, PKS | pederin | unidentified unclassified sequences.
BGC0001235.4 |  | 0.38 | NRPS, PKS | antalid | Polyangium spumosum
BGC0000067.5 |  | 0.37 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000185.5 |  | 0.37 | PKS | tartrolon D, tartrolon E | Teredinibacter turnerae T7901
BGC0001795.3 |  | 0.36 | PKS | swinholide A | Nostoc sp. UHCC 0450
BGC0001876.2 |  | 0.36 | NRPS | thalassospiramide A | Thalassospira sp. CNJ-328
BGC0001301.5 |  | 0.36 | PKS | anthracimycin | Streptomyces sp. T676

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000180.5 |  | 0.45 | PKS | legioliulin | Legionella parisiensis
BGC0001050.5 |  | 0.42 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0000353.5 |  | 0.41 | NRPS | tacrolimus | Streptomyces sp. MA6548
BGC0001109.4 |  | 0.39 | NRPS, PKS | pederin | unidentified unclassified sequences.
BGC0001235.4 |  | 0.38 | NRPS, PKS | antalid | Polyangium spumosum
BGC0000067.5 |  | 0.37 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000185.5 |  | 0.37 | PKS | tartrolon D, tartrolon E | Teredinibacter turnerae T7901
BGC0001795.3 |  | 0.36 | PKS | swinholide A | Nostoc sp. UHCC 0450
BGC0001876.2 |  | 0.36 | NRPS | thalassospiramide A | Thalassospira sp. CNJ-328
BGC0001301.5 |  | 0.36 | PKS | anthracimycin | Streptomyces sp. T676

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 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
NZ_RYYV01000058.1 - 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 - 2,825 nt. (total: 2,825 nt) Show pHMM detection rules used
Region on contig edge.
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
NRPS/PKS 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
EKH80_RS23635: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

EKH80_RS23920: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000342.4 |  | 0.64 | NRPS | enniatin | Fusarium equiseti
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000342.4 |  | 0.64 | NRPS | enniatin | Fusarium equiseti
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae

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

No significant matches found.

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
NZ_RYYV01000059.1 - 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 - 2,774 nt. (total: 2,774 nt) Show pHMM detection rules used
Region on contig edge.
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
NRPS/PKS 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
EKH80_RS23645: 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 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

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

No significant matches found.

Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
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).
EKH80_RS23645: X
AMP-binding (422..669): 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:
    QWFSFDAAVWELQW--------------------
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

Link to PARAS substrate predictor
NZ_RYYV01000006.1 - Region 1 - arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 142,314 - 183,519 nt. (total: 41,206 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS 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
EKH80_RS09910: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: acyltransferase transferase
EKH80_RS09975: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

EKH80_RS10115: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Hydrolases: dehalogenase
EKH80_RS10070: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Isomerases: mutase
EKH80_RS10035: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: synthase
EKH80_RS10010: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

EKH80_RS10020: 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 | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002191.2 |  | 0.56 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001217.5 |  | 0.50 | other (other) | PreQ0 Base | Streptomyces qinglanensis
BGC0000840.5 |  | 0.48 | other (other) | xanthomonadin I | Xanthomonas oryzae pv. oryzae
BGC0000255.5 |  | 0.44 | PKS | pederin | Uncultured bacterium
BGC0002008.3 |  | 0.44 | other (other) | aryl polyenes | Xenorhabdus doucetiae
BGC0001285.5 |  | 0.43 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0000836.5 |  | 0.43 | other (other) | APE Ec | Escherichia coli CFT073
BGC0001400.3 |  | 0.43 | PKS | citreoviridin | Aspergillus terreus NIH2624
BGC0000837.4 |  | 0.42 | other (other) | APE Vf | Aliivibrio fischeri ES114
BGC0001987.2 |  | 0.42 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002191.2 |  | 0.56 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001217.5 |  | 0.50 | other (other) | PreQ0 Base | Streptomyces qinglanensis
BGC0000840.5 |  | 0.48 | other (other) | xanthomonadin I | Xanthomonas oryzae pv. oryzae
BGC0000255.5 |  | 0.44 | PKS | pederin | Uncultured bacterium
BGC0002008.3 |  | 0.44 | other (other) | aryl polyenes | Xenorhabdus doucetiae
BGC0001285.5 |  | 0.43 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0000836.5 |  | 0.43 | other (other) | APE Ec | Escherichia coli CFT073
BGC0001400.3 |  | 0.43 | PKS | citreoviridin | Aspergillus terreus NIH2624
BGC0000837.4 |  | 0.42 | other (other) | APE Vf | Aliivibrio fischeri ES114
BGC0001987.2 |  | 0.42 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis

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

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: 18.92 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05
Confidence: medium
Additional weak hits (19):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.20 out of 26.12
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.96 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.19 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.99 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.55 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.12 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.57 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.58 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.35 out of 31.73
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.04 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.33 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.93 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.53 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.43 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.78 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.35 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.96 out of 35.63
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.27 out of 20.01
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.88 out of 30.98
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
VqsM | Regulator of quorum-sensing signalling systems

NZ_RYYV01000008.1 - Region 1 - 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: 14,573 - 25,430 nt. (total: 10,858 nt) Show pHMM detection rules used
Region on contig edge.
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001047.4 |  | 0.28 | NRPS, PKS | syringolin A | Pseudomonas syringae
BGC0000495.5 |  | 0.23 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0000807.3 |  | 0.20 | saccharide | phosphonoglycans | Stackebrandtia nassauensis DSM 44728
BGC0001106.6 |  | 0.19 | NRPS, PKS | oxazolomycin | Streptomyces albus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001047.4 |  | 0.28 | NRPS, PKS | syringolin A | Pseudomonas syringae
BGC0000495.5 |  | 0.23 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0000807.3 |  | 0.20 | saccharide | phosphonoglycans | Stackebrandtia nassauensis DSM 44728
BGC0001106.6 |  | 0.19 | NRPS, PKS | oxazolomycin | Streptomyces albus

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
Additional weak hits (2):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.45 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.10 out of 29.38
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RYYV01000008.1 - 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: 42,421 - 69,536 nt. (total: 27,116 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: dehydratase
EKH80_RS12240: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthetase
EKH80_RS12270: 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
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.53 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.50 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000640.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002398.2 |  | 0.48 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000639.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000641.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0002173.2 |  | 0.47 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000642.3 |  | 0.47 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000630.3 |  | 0.47 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000638.3 |  | 0.47 | terpene | carotenoid | Pantoea ananatis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.53 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.50 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000640.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002398.2 |  | 0.48 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000639.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000641.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0002173.2 |  | 0.47 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000642.3 |  | 0.47 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000630.3 |  | 0.47 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000638.3 |  | 0.47 | terpene | carotenoid | Pantoea ananatis

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
EKH80_RS12245: PT_phytoene_like
Domain 1 (24 - 280): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

EKH80_RS12250: T2TS
Domain 1 (18 - 655): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

EKH80_RS12270: PT_FPPS_like
Domain 1 (40 - 300): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  IPP, DMAPP → FPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.70 out of 27.55
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.79 out of 20.97
Confidence: medium
Additional weak hits (5):
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 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.19 out of 32.74
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.97 out of 30.22
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.09 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
GnfM | Regulator of nitrogen-fixation genes