Select genomic region:
Overview
1.1
2.1
2.2
3.1
3.2
3.3
5.1
5.2
5.3
5.4
5.5
5.6
5.7
6.1
6.2
6.3
7.1
7.2
7.3
7.4
7.5
7.6
7.7
8.1
8.2
8.3
9.1
9.2
9.3
11.1
13.1
14.1
14.2
14.3
15.1
18.1
18.2
21.1
22.1

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

NZ_ARPF01000001.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | RRE-containing | 331,760 | 352,053 |  |

NZ_ARPF01000002.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | betalactone | 350,780 | 378,595 |  |
Region 2.2 | butyrolactone,ectoine | 507,744 | 522,991 | Low | showdomycin | other:other

NZ_ARPF01000003.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | lanthipeptide-class-iii | 104,864 | 127,626 | High | AmfS | ribosomal:RiPP:Lanthipeptide
Region 3.2 | terpene-precursor | 248,498 | 269,541 |  |
Region 3.3 | terpene | 458,142 | 479,119 |

NZ_ARPF01000005.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | NRPS-like,arylpolyene | 10,656 | 53,804 |  |
Region 5.2 | butyrolactone | 63,056 | 73,925 | Low | coelimycin P1 | PKS:Type I
Region 5.3 | terpene | 102,028 | 124,241 | High | geosmin | terpene:Sesquiterpene
Region 5.4 | transAT-PKS,PKS-like,T1PKS,NRPS,NRP-metallophore,terpene | 126,483 | 262,111 | High | griseobactin | NRPS:Type I
Region 5.5 | NRP-metallophore,NRPS | 262,557 | 321,178 | High | coelichelin | NRPS:Type I
Region 5.6 | terpene,thioamide-NRP | 344,758 | 402,408 | Low | cadaside A/cadaside B | NRPS:Type I
Region 5.7 | T3PKS | 434,294 | 475,427 |  |

NZ_ARPF01000006.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 6.1 | NRPS | 51,919 | 106,339 |  |
Region 6.2 | t3nrps-iterative,RRE-containing,azole-containing-RiPP,ectoine | 317,833 | 386,679 |  |
Region 6.3 | thioamide-NRP,PKS-like,t3nrps-iterative,T1PKS | 442,974 | 509,947 | Low | enteromycin | PKS+NRPS:Type I

NZ_ARPF01000007.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 7.1 | NRPS,T1PKS,azole-containing-RiPP | 14,557 | 67,192 | Low | lactazole | ribosomal:RiPP:Thiopeptide
Region 7.2 | terpene | 76,244 | 104,633 | High | isorenieratene | terpene
Region 7.3 | T3PKS | 141,053 | 181,988 | Low | depsibosamycin B/depsibosamycin C/depsibosamycin D | NRPS:Type I
Region 7.4 | NRPS,T3PKS | 206,783 | 309,798 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 7.5 | terpene-precursor,melanin | 323,389 | 352,184 | High | melanin | other:other
Region 7.6 | RiPP-like,NRPS,T1PKS | 352,932 | 464,199 | High | valinomycin/montanastatin | saccharide:hybrid/tailoring+NRPS:Type I
Region 7.7 | NRPS | 464,910 | 501,280 |  |

NZ_ARPF01000008.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 8.1 | hydrogen-cyanide | 4,082 | 17,630 | Low | aborycin | ribosomal:RiPP
Region 8.2 | RiPP-like | 138,445 | 149,884 | Low | 14-hydroxyisochainin | PKS:Modular type I
Region 8.3 | NRPS-like,NRPS | 277,440 | 324,441 |  |

NZ_ARPF01000009.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 9.1 | NRPS-like | 126,562 | 170,554 | High | indigoidine | NRPS:Type I
Region 9.2 | NI-siderophore | 237,014 | 266,792 | High | desferrioxamin B | other:other
Region 9.3 | lanthipeptide-class-iii,lanthipeptide-class-ii | 329,118 | 360,527 |

NZ_ARPF01000012.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 11.1 | terpene | 275,528 | 302,101 | Medium | hopene | terpene

NZ_ARPF01000014.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 13.1 | NI-siderophore | 57,841 | 90,609 | Low | schizokinen | other:other

NZ_ARPF01000015.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 14.1 | T1PKS | 1 | 75,768 | High | bafilomycin B1 | PKS:Type I
Region 14.2 | t3nrps-iterative,NRPS,T1PKS,RiPP-like | 113,732 | 179,981 | High | 10-epi-HSAF/10-epi-3-deOH-HSAF/10-epi-maltophilin/10-epi-xanthobaccin C/10-epi-hydroxymaltophilin/10-epi-FI-2 | other:other+PKS
Region 14.3 | NRPS | 204,791 | 231,150 |  |

NZ_ARPF01000016.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 15.1 | ectoine | 125,000 | 135,398 | High | ectoine | other:other

NZ_ARPF01000020.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 18.1 | T2PKS | 1 | 42,234 | Low | prejadomycin/rabelomycin/gaudimycin C/gaudimycin D/UWM6/gaudimycin A | PKS:Type II+saccharide:hybrid/tailoring
Region 18.2 | lassopeptide | 81,005 | 103,798 | High | keywimysin | ribosomal:RiPP

NZ_ARPF01000023.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 21.1 | terpene | 67,387 | 88,481 | Low | steffimycin D | PKS:Type II+saccharide:hybrid/tailoring

NZ_ARPF01000024.1 (Streptomyces sp. SolWspMP-sol2th)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 22.1 | linaridin,T1PKS | 12,518 | 39,385 | Low | bafilomycin B1 | PKS:Type I

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | RRE-containing | 331,760 | 352,053 |  |
Region 2.1 | betalactone | 350,780 | 378,595 |  |
Region 2.2 | butyrolactone,ectoine | 507,744 | 522,991 | Low | showdomycin | other:other
Region 3.1 | lanthipeptide-class-iii | 104,864 | 127,626 | High | AmfS | ribosomal:RiPP:Lanthipeptide
Region 3.2 | terpene-precursor | 248,498 | 269,541 |  |
Region 3.3 | terpene | 458,142 | 479,119 |
Region 5.1 | NRPS-like,arylpolyene | 10,656 | 53,804 |  |
Region 5.2 | butyrolactone | 63,056 | 73,925 | Low | coelimycin P1 | PKS:Type I
Region 5.3 | terpene | 102,028 | 124,241 | High | geosmin | terpene:Sesquiterpene
Region 5.4 | transAT-PKS,PKS-like,T1PKS,NRPS,NRP-metallophore,terpene | 126,483 | 262,111 | High | griseobactin | NRPS:Type I
Region 5.5 | NRP-metallophore,NRPS | 262,557 | 321,178 | High | coelichelin | NRPS:Type I
Region 5.6 | terpene,thioamide-NRP | 344,758 | 402,408 | Low | cadaside A/cadaside B | NRPS:Type I
Region 5.7 | T3PKS | 434,294 | 475,427 |  |
Region 6.1 | NRPS | 51,919 | 106,339 |  |
Region 6.2 | t3nrps-iterative,RRE-containing,azole-containing-RiPP,ectoine | 317,833 | 386,679 |  |
Region 6.3 | thioamide-NRP,PKS-like,t3nrps-iterative,T1PKS | 442,974 | 509,947 | Low | enteromycin | PKS+NRPS:Type I
Region 7.1 | NRPS,T1PKS,azole-containing-RiPP | 14,557 | 67,192 | Low | lactazole | ribosomal:RiPP:Thiopeptide
Region 7.2 | terpene | 76,244 | 104,633 | High | isorenieratene | terpene
Region 7.3 | T3PKS | 141,053 | 181,988 | Low | depsibosamycin B/depsibosamycin C/depsibosamycin D | NRPS:Type I
Region 7.4 | NRPS,T3PKS | 206,783 | 309,798 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 7.5 | terpene-precursor,melanin | 323,389 | 352,184 | High | melanin | other:other
Region 7.6 | RiPP-like,NRPS,T1PKS | 352,932 | 464,199 | High | valinomycin/montanastatin | saccharide:hybrid/tailoring+NRPS:Type I
Region 7.7 | NRPS | 464,910 | 501,280 |  |
Region 8.1 | hydrogen-cyanide | 4,082 | 17,630 | Low | aborycin | ribosomal:RiPP
Region 8.2 | RiPP-like | 138,445 | 149,884 | Low | 14-hydroxyisochainin | PKS:Modular type I
Region 8.3 | NRPS-like,NRPS | 277,440 | 324,441 |  |
Region 9.1 | NRPS-like | 126,562 | 170,554 | High | indigoidine | NRPS:Type I
Region 9.2 | NI-siderophore | 237,014 | 266,792 | High | desferrioxamin B | other:other
Region 9.3 | lanthipeptide-class-iii,lanthipeptide-class-ii | 329,118 | 360,527 |
Region 11.1 | terpene | 275,528 | 302,101 | Medium | hopene | terpene
Region 13.1 | NI-siderophore | 57,841 | 90,609 | Low | schizokinen | other:other
Region 14.1 | T1PKS | 1 | 75,768 | High | bafilomycin B1 | PKS:Type I
Region 14.2 | t3nrps-iterative,NRPS,T1PKS,RiPP-like | 113,732 | 179,981 | High | 10-epi-HSAF/10-epi-3-deOH-HSAF/10-epi-maltophilin/10-epi-xanthobaccin C/10-epi-hydroxymaltophilin/10-epi-FI-2 | other:other+PKS
Region 14.3 | NRPS | 204,791 | 231,150 |  |
Region 15.1 | ectoine | 125,000 | 135,398 | High | ectoine | other:other
Region 18.1 | T2PKS | 1 | 42,234 | Low | prejadomycin/rabelomycin/gaudimycin C/gaudimycin D/UWM6/gaudimycin A | PKS:Type II+saccharide:hybrid/tailoring
Region 18.2 | lassopeptide | 81,005 | 103,798 | High | keywimysin | ribosomal:RiPP
Region 21.1 | terpene | 67,387 | 88,481 | Low | steffimycin D | PKS:Type II+saccharide:hybrid/tailoring
Region 22.1 | linaridin,T1PKS | 12,518 | 39,385 | Low | bafilomycin B1 | PKS:Type I

No secondary metabolite regions were found in these records:
  NZ_ARPF01000004.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_KK240935.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_ARPF01000013.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_ARPF01000017.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_KK240936.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_ARPF01000021.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_ARPF01000022.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_ARPF01000025.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_ARPF01000026.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_ARPF01000027.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_ARPF01000028.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_ARPF01000029.1 (Streptomyces sp. SolWspMP-sol2th)
  NZ_ARPF01000030.1 (Streptomyces sp. SolWspMP-sol2th)

Compact view
NZ_ARPF01000001.1 - Region 1 - RRE-containing
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 331,760 - 352,053 nt. (total: 20,294 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase transferase
B083_RS0101480: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

B083_RS1000000136060: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Ligases: ligase
B083_RS0101485: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001166.5 |  | 0.56 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001261.3 |  | 0.56 | NRPS | AM-toxin | Alternaria alternata
BGC0001250.4 |  | 0.56 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.56 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.56 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000595.3 |  | 0.50 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000903.3 |  | 0.49 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0000597.4 |  | 0.45 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000933.3 |  | 0.45 | other (other) | xiamenmycin A | Streptomyces xiamenensis
BGC0001137.5 |  | 0.45 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001166.5 |  | 0.56 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001261.3 |  | 0.56 | NRPS | AM-toxin | Alternaria alternata
BGC0001250.4 |  | 0.56 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.56 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.56 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000595.3 |  | 0.50 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000903.3 |  | 0.49 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0000597.4 |  | 0.45 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000933.3 |  | 0.45 | other (other) | xiamenmycin A | Streptomyces xiamenensis
BGC0001137.5 |  | 0.45 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans

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:
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.02 out of 28.19
Confidence: medium
Additional weak hits (10):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.85 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.09 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.40 out of 18.57
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.76 out of 27.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.66 out of 26.85
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.07 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.87 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.08 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.44 out of 24.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (331759...352053)
B083_RS01000000132765
  RRE type: PqqD_RRE
  Location: 11 - 93
  Score: 34.1
  RRE type: Stand_Alone_Lasso_RRE
  Location: 38 - 94
  Score: 31.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ZuR variant 1 | Zinc-responsive repressor

NZ_ARPF01000002.1 - Region 1 - betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 350,780 - 378,595 nt. (total: 27,816 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase phosphate reductase
B083_RS0105170: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

B083_RS0105195: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

B083_RS0105230: N-acetyl-gamma-glutamyl-phosphate reductase

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

B083_RS1000000137065: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase kinase
B083_RS0105205: aminotransferase

smcogs
  SMCOG1019: aminotransferase

B083_RS0105225: acetylglutamate kinase

smcogs
  SMCOG1174: acetylglutamate kinase

Ligases: ligase synthase
B083_RS0105210: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0105245: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate 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 | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000895.5 |  | 0.44 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0002282.2 |  | 0.41 | other (other) | formycin A | Streptomyces kaniharaensis
BGC0002040.3 |  | 0.41 | other (other) | coformycin, formycin A | Streptomyces kaniharaensis
BGC0001294.5 |  | 0.41 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002000.4 |  | 0.40 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0002047.2 |  | 0.39 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0001895.4 |  | 0.39 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0000904.5 |  | 0.39 | other (other) | FR-900098 | Streptomyces rubellomurinus
BGC0002514.3 |  | 0.39 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0001850.4 |  | 0.39 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000895.5 |  | 0.44 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0002282.2 |  | 0.41 | other (other) | formycin A | Streptomyces kaniharaensis
BGC0002040.3 |  | 0.41 | other (other) | coformycin, formycin A | Streptomyces kaniharaensis
BGC0001294.5 |  | 0.41 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002000.4 |  | 0.40 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0002047.2 |  | 0.39 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0001895.4 |  | 0.39 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0000904.5 |  | 0.39 | other (other) | FR-900098 | Streptomyces rubellomurinus
BGC0002514.3 |  | 0.39 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0001850.4 |  | 0.39 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.56 out of 26.85
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_ARPF01000002.1 - Region 2 - butyrolactone,ectoine
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: 507,744 - 522,991 nt. (total: 15,248 nt) Show pHMM detection rules used
butyrolactone: AfsA
ectoine: ectoine_synt

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase synthase
B083_RS0105845: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

B083_RS0105860: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B083_RS0105900: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: PPTase
B083_RS0105880: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: synthase
B083_RS0105845: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Ligases: ligase
B083_RS0105915: 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 | butyrolactone | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000848.5 |  |  | 0.96 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  |  | 0.73 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0001778.5 |  |  | 0.50 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000850.5 |  |  | 0.41 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  |  | 0.30 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000131.5 |  |  | 0.30 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000706.3 |  |  | 0.29 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001458.4 |  |  | 0.27 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0002276.2 |  |  | 0.25 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001464.3 |  |  | 0.25 | other (other) | tetrabromopyrrole | Pseudoalteromonas sp. PS5

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.78 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.77 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002276.2 |  | 0.61 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001778.5 |  | 0.57 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000850.5 |  | 0.55 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.49 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000131.5 |  | 0.46 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000706.3 |  | 0.44 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001458.4 |  | 0.44 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0002020.3 |  | 0.44 | NRPS, saccharide | photolose, oligosaccharide 1 (GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 2 (GlcNAc-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 3 (GlcNAc-β(1-4)-GlcNAc-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 4 (GlcN-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc), oligosaccharide 5 (6-phosphoGlcN-β(1-4)-GlcNAc-β(1-4)-1,6-anhydro-β-GlcNAc) | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
Additional weak hits (10):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.91 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.74 out of 20.01
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.22 out of 20.01
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.84 out of 29.38
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.07 out of 32.93
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.22 out of 20.01
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.74 out of 20.01
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.67 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.24 out of 28.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_ARPF01000003.1 - Region 1 - lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 104,864 - 127,626 nt. (total: 22,763 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase aminotransferase
B083_RS0107245: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

B083_RS0107290: 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 | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.86 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000553.3 |  | 0.67 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.60 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000518.3 |  | 0.55 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000501.3 |  | 0.53 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0001226.4 |  | 0.52 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000546.3 |  | 0.51 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.86 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000553.3 |  | 0.67 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.60 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000518.3 |  | 0.55 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000501.3 |  | 0.53 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0001226.4 |  | 0.52 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000546.3 |  | 0.51 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai

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

No significant matches found.

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

#### Lanthipeptide(s) for B083_RS0107250

B083_RS0107255
Leader:
MALLDLQAMETPAEESFGELAT
Core:
G S Q V S L L V C E Y S S L S V V L C T P
Core with dehydrations:
G Dha Q V Dha L L V Cys E Y Dha Dha L Dha V V L Cys Dhb P

#### antiSMASH-DB 4.0 matches for B083_RS0107255

100.0%
NC_010572.1 and 60 others:
NC_021177.1 Lanthipeptides: SFUL_RS24355_lanthipeptide NZ_AQRK01000102.1 Lanthipeptides: YUW_RS30025_lanthipeptide NZ_ARPF01000003.1 Lanthipeptides: B083_RS0107255_lanthipeptide NZ_BMRY01000001.1 Lanthipeptides: IE140_RS02070_lanthipeptide NZ_BMSP01000003.1 Lanthipeptides: IE150_RS06495_lanthipeptide NZ_BMSZ01000003.1 Lanthipeptides: IE135_RS07550_lanthipeptide NZ_BMTW01000017.1 Lanthipeptides: IE134_RS28550_lanthipeptide NZ_BMUG01000009.1 Lanthipeptides: IE264_RS25430_lanthipeptide NZ_BMVK01000002.1 Lanthipeptides: IE272_RS07115_lanthipeptide NZ_BNBJ01000002.1 Lanthipeptides: IE304_RS05195_lanthipeptide NZ_CM003601.1 Lanthipeptides: JI76_RS25200_lanthipeptide NZ_CP010833.1 Lanthipeptides: TK78_RS10875_lanthipeptide NZ_CP011522.1 Lanthipeptides: ABE83_RS11805_lanthipeptide NZ_CP013738.1 Lanthipeptides: WQO_RS23525_lanthipeptide NZ_CP015362.1 Lanthipeptides: A6E92_RS09975_lanthipeptide NZ_CP020563.1 Lanthipeptides: B7C62_RS24450_lanthipeptide NZ_CP020570.1 Lanthipeptides: B1H20_RS34690_lanthipeptide NZ_CP024957.1 Lanthipeptides: CVT27_RS22730_lanthipeptide NZ_CP029361.1 Lanthipeptides: DIJ69_RS10225_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS22865_lanthipeptide NZ_CP061072.1 Lanthipeptides: HYC88_RS10560_lanthipeptide NZ_CP079114.1 Lanthipeptides: KV381_RS24895_lanthipeptide NZ_CP084357.1 Lanthipeptides: LEL86_RS29435_lanthipeptide NZ_CP086102.1 Lanthipeptides: LK895_RS11660_lanthipeptide NZ_CP090837.1 Lanthipeptides: LZ559_RS24025_lanthipeptide NZ_CP096281.1 Lanthipeptides: MWG59_RS25685_lanthipeptide NZ_CP101397.1 Lanthipeptides: NLU04_RS06465_lanthipeptide NZ_CP110539.1 Lanthipeptides: OH133_RS12690_lanthipeptide NZ_CP112880.1 Lanthipeptides: N7925_RS11185_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS22935_lanthipeptide NZ_CP117709.1 Lanthipeptides: PSQ21_RS24530_lanthipeptide NZ_DS999644.1 Lanthipeptides: SSGG_RS09925_lanthipeptide NZ_GL877172.1 Lanthipeptides: SACT1_RS12960_lanthipeptide NZ_JAAWWP010000002.1 Lanthipeptides: HFV08_RS04115_lanthipeptide NZ_JAGGOV010000004.1 Lanthipeptides: J7E92_RS02930_lanthipeptide NZ_JAHHWT010000009.1 Lanthipeptides: KM153_RS24430_lanthipeptide NZ_JALDPQ010000064.1 Lanthipeptides: MQC87_RS23965_lanthipeptide NZ_JAMFLF010000002.1 Lanthipeptides: M1212_RS07295_lanthipeptide NZ_JANRMN010000004.1 Lanthipeptides: NW249_RS08610_lanthipeptide NZ_JNLT01000003.1 Lanthipeptides: CD02_RS0108685_lanthipeptide NZ_KB890925.1 Lanthipeptides: B053_RS0113845_lanthipeptide NZ_KL573549.1 Lanthipeptides: BG84_RS0119125_lanthipeptide NZ_KQ257779.1 Lanthipeptides: IQ60_RS22540_lanthipeptide NZ_KZ195572.1 Lanthipeptides: B9W61_RS11940_lanthipeptide NZ_KZ679082.1 Lanthipeptides: C6W96_RS24050_lanthipeptide NZ_KZ819154.1 Lanthipeptides: DBP12_RS10285_lanthipeptide NZ_KZ819178.1 Lanthipeptides: DBP20_RS23960_lanthipeptide NZ_KZ819182.1 Lanthipeptides: DBP21_RS24660_lanthipeptide NZ_LACR01000009.1 Lanthipeptides: YW5_RS12280_lanthipeptide NZ_LIPB01000001.1 Lanthipeptides: AMK17_RS03280_lanthipeptide NZ_LIPE01000001.1 Lanthipeptides: AMK12_RS03355_lanthipeptide NZ_LIVT01000001.1 Lanthipeptides: AMK24_RS01700_lanthipeptide NZ_LIVW01000001.1 Lanthipeptides: AMK28_RS03165_lanthipeptide NZ_LIXK01000001.1 Lanthipeptides: AMK23_RS04085_lanthipeptide NZ_LMEL01000012.1 Lanthipeptides: ASD29_RS10010_lanthipeptide NZ_LZRD01000054.1 Lanthipeptides: A3Q37_RS33745_lanthipeptide NZ_ML123117.1 Lanthipeptides: EES46_RS10300_lanthipeptide NZ_NNBN01000004.1 Lanthipeptides: CG717_RS12310_lanthipeptide NZ_VEHK01000004.1 Lanthipeptides: FS984_RS13530_lanthipeptide NZ_WWGD01000029.1 Lanthipeptides: GTY72_RS23245_lanthipeptide
Lanthipeptides: SGR_RS11800_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E Y S S L S V V L C T P
1
G S Q V S L L V C E Y S S L S V V L C T P
21
95.2%
NZ_BDHJ01000008.1 and 4 others:
NZ_CP032543.1 Lanthipeptides: D6270_RS22715_lanthipeptide NZ_CP076457.1 Lanthipeptides: KME66_RS09945_lanthipeptide NZ_CP077652.1 Lanthipeptides: KRR37_RS22855_lanthipeptide NZ_WUEJ01000001.1 Lanthipeptides: GRQ63_RS04560_lanthipeptide
Lanthipeptides: BHQ08_RS03045_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E Y S S L S V L C T P
1
G S Q V S L L V C E Y S S L S V T L C T P
21
95.2%
NZ_CP010519.1 and 1 other:
NZ_CP092644.1 Lanthipeptides: MID12_RS21330_lanthipeptide
Lanthipeptides: SLNWT_RS22370_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E Y S S L S V V L C+P
1
G S Q V S L L V C E Y S S L S V V L C S P
21
with 77 more sequence matches
Only the first 10 are displayed here.
95.2%
NZ_CP045178.1:
Lanthipeptides: GBW32_RS28450_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L+C E Y S S L S V V L C T P
1
G S Q V S L L I C E Y S S L S V V L C T P
21
95.2%
NZ_CP054926.1 and 11 others:
NZ_CP068598.1 Lanthipeptides: IFE09_RS23820_lanthipeptide NZ_CP071044.1 Lanthipeptides: JHY03_RS23495_lanthipeptide NZ_CP080029.1 Lanthipeptides: KZO11_RS24935_lanthipeptide NZ_JAJUKK010000008.1 Lanthipeptides: LXH09_RS27635_lanthipeptide NZ_JOJC01000009.1 Lanthipeptides: IO23_RS0108435_lanthipeptide NZ_KB891296.1 Lanthipeptides: B061_RS0103425_lanthipeptide NZ_KZ268499.1 Lanthipeptides: CE422_RS23450_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS22830_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS10975_lanthipeptide NZ_LZQS01000001.1 Lanthipeptides: STIB_RS05225_lanthipeptide NZ_RCOL01000001.1 Lanthipeptides: STAN_RS24840_lanthipeptide
Lanthipeptides: HUT09_RS23550_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E+S S L S V V L C T P
1
G S Q V S L L V C E F S S L S V V L C T P
21
95.2%
NZ_CP058556.1 and 5 others:
NZ_CP059898.1 Lanthipeptides: H3V39_RS22935_lanthipeptide NZ_CP070242.1 Lanthipeptides: I6J39_RS23755_lanthipeptide NZ_CP070260.1 Lanthipeptides: I6J40_RS10935_lanthipeptide NZ_JAJDST010000047.1 Lanthipeptides: LJC81_RS16960_lanthipeptide NZ_WWGL01000003.1 Lanthipeptides: GTY38_RS03410_lanthipeptide
Lanthipeptides: HXS80_RS11105_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S+L V C E Y S S L S V V L C T P
1
G S Q V S V L V C E Y S S L S V V L C T P
21
90.5%
NZ_CM001165.1 and 4 others:
NZ_CP021118.1 Lanthipeptides: CAC01_RS28155_lanthipeptide NZ_CP049945.1 Lanthipeptides: G9U55_RS17850_lanthipeptide NZ_CP119149.1 Lanthipeptides: P0D76_RS02270_lanthipeptide NZ_RWGV01000033.1 Lanthipeptides: EJA11_RS20985_lanthipeptide
Lanthipeptides: STTU_RS29395_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L+C E Y S S L S V L C T P
1
G S Q V S L L I C E Y S S L S V T L C T P
21
85.7%
NC_020990.1 and 26 others:
NZ_AMPN02000002.1 Lanthipeptides: SM8_RS12785_lanthipeptide NZ_AP025692.1 Lanthipeptides: MTP06_RS18190_lanthipeptide NZ_CM002273.1 Lanthipeptides: B590_RS12280_lanthipeptide NZ_CP009802.1 Lanthipeptides: SFR_RS12925_lanthipeptide NZ_CP014485.1 Lanthipeptides: Salbus254_RS12710_lanthipeptide NZ_CP016824.1 Lanthipeptides: BEN82_RS18165_lanthipeptide NZ_CP026490.1 Lanthipeptides: C3K23_RS19520_lanthipeptide NZ_CP031742.1 Lanthipeptides: D0C37_RS13445_lanthipeptide NZ_CP047147.1 Lanthipeptides: GR131_RS18520_lanthipeptide NZ_CP053539.1 Lanthipeptides: HN026_RS11800_lanthipeptide NZ_CP056773.1 Lanthipeptides: HWN34_RS12245_lanthipeptide NZ_CP063844.1 Lanthipeptides: IPZ55_RS12410_lanthipeptide NZ_CP064783.1 Lanthipeptides: IT782_RS12060_lanthipeptide NZ_CP076385.1 Lanthipeptides: KNZ81_RS12450_lanthipeptide NZ_CP079112.1 Lanthipeptides: STALF2_RS18135_lanthipeptide NZ_CP091820.1 Lanthipeptides: L2I08_RS02835_lanthipeptide NZ_CP106650.1 Lanthipeptides: B591_RS12385_lanthipeptide NZ_CP113103.1 Lanthipeptides: OSU72_RS17905_lanthipeptide NZ_JAHUVY010000001.1 Lanthipeptides: STALF3_RS17905_lanthipeptide NZ_JALLPQ010000001.1 Lanthipeptides: MWG58_RS12385_lanthipeptide NZ_KB890715.1 Lanthipeptides: B048_RS0115750_lanthipeptide NZ_KN549183.1 Lanthipeptides: D076_RS30740_lanthipeptide NZ_KZ195583.1 Lanthipeptides: B9W68_RS12440_lanthipeptide NZ_MNPQ01000004.1 Lanthipeptides: BGV78_RS11170_lanthipeptide NZ_OX371412.1 Lanthipeptides: OZE77_RS18215_lanthipeptide NZ_VOGX01000092.1 Lanthipeptides: FRZ02_RS31600_lanthipeptide
Lanthipeptides: XNR_RS11575_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q+S L L+C E Y S S L S V L C T P
1
G S Q I S L L I C E Y S S L S V T L C T P
21
85.7%
NZ_AQRJ01000051.1 and 1 other:
NZ_LFBV01000002.1 Lanthipeptides: AB852_RS09920_lanthipeptide
Lanthipeptides: YW7_RS14945_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L+V C E Y S S L S +L C T P
1
G S Q V S L I V C E Y S S L S A L L C T P
21
85.7%
NZ_CP045702.1:
Lanthipeptides: F0344_RS33200_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E+S S L S+ L C T P
1
G S Q V S L L V C E H S S L S L T L C T P
21
85.7%
NZ_ML123034.1:
Lanthipeptides: EES43_RS19795_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L+C E+S S L S V L C T P
1
G S Q V S L L I C E F S S L S V T L C T P
21
81.0%
NZ_LWLE01000019.1:
Lanthipeptides: A6A29_RS44250_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L+C E+S S L S+ L C T P
1
G S Q V S L L I C E H S S L S L T L C T P
21
61.9%
NZ_QGGR01000008.1:
Lanthipeptides: BC793_RS19230_lanthipeptide
1
G S Q V S L L V C E Y S S L S V V L C T
20
G S Q S L L+C S S L S V C
2
G S Q A S L L L C G D S S L S V T T C N
21

#### MIBiG 4.0 matches for B083_RS0107255

95.5%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
1
G S Q V S L L V C E Y S S L S V V L C T P
21
G S Q V S L L V C E Y S S L S V V L C T P
2
G S Q V S L L V C E Y S S L S V V L C T P
22

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (14):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.19 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.78 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.12 out of 28.14
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.97 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.32 out of 20.01
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.66 out of 29.51
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.15 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.56 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.90 out of 29.38
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.49 out of 39.62
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.65 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.91 out of 20.01
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.

B083_RS0107255 - Class III
  Cleavage pHMM score: 31.50
  RODEO score: 0
  Monoisotopic mass: 2075.1 Da
  Molecular weight: 2076.4 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2094.4 Da N = 1
    2112.4 Da N = 2
    2130.5 Da N = 3
    2148.5 Da N = 4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production

NZ_ARPF01000003.1 - Region 2 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 248,498 - 269,541 nt. (total: 21,044 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: dehydratase
B083_RS0107925: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthetase
B083_RS0107890: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000673.3 |  | 0.53 | terpene | pimara-8(14),15-diene | Aspergillus nidulans FGSC A4
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002578.2 |  | 0.38 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.36 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000678.5 |  | 0.35 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000644.3 |  | 0.35 | terpene | carotenoid | Dietzia sp. CQ4
BGC0000666.5 |  | 0.34 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001529.5 |  | 0.33 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000673.3 |  | 0.53 | terpene | pimara-8(14),15-diene | Aspergillus nidulans FGSC A4
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002578.2 |  | 0.38 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.36 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000678.5 |  | 0.35 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000644.3 |  | 0.35 | terpene | carotenoid | Dietzia sp. CQ4
BGC0000666.5 |  | 0.34 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001529.5 |  | 0.33 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18

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

No significant matches found.

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

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

Genes with terpene domains:
B083_RS0107890: PT_FPPS_like
Domain 1 (58 - 345): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.29 out of 23.43
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.11 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (10):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.21 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.07 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.52 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.03 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.86 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.78 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.13 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.82 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.83 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_ARPF01000003.1 - Region 3 - 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: 458,142 - 479,119 nt. (total: 20,978 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: deacetylase hydrolase
B083_RS0108730: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

B083_RS0108745: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: cyclase hydratase
B083_RS0108720: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

B083_RS0108755: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002196.2 |  | 0.30 | PKS | clavatol | Penicillium crustosum
BGC0002553.2 |  | 0.29 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0000913.3 |  | 0.29 | other (other) | MK-8 | Enterobacter cloacae
BGC0001866.4 |  | 0.28 | PKS | viriditoxin | Byssochlamys spectabilis
BGC0002034.3 |  | 0.28 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0000875.4 |  | 0.28 | other (nucleoside), saccharide | caprazamycin, caprazamycin aglycon | Streptomyces sp. MK730-62F2
BGC0000252.5 |  | 0.28 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0000518.3 |  | 0.28 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000243.4 |  | 0.27 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0000157.5 |  | 0.27 | PKS | tautomycetin | Streptomyces sp. CK4412

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002196.2 |  | 0.30 | PKS | clavatol | Penicillium crustosum
BGC0002553.2 |  | 0.29 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0000913.3 |  | 0.29 | other (other) | MK-8 | Enterobacter cloacae
BGC0001866.4 |  | 0.28 | PKS | viriditoxin | Byssochlamys spectabilis
BGC0002034.3 |  | 0.28 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0000875.4 |  | 0.28 | other (nucleoside), saccharide | caprazamycin, caprazamycin aglycon | Streptomyces sp. MK730-62F2
BGC0000252.5 |  | 0.28 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0000518.3 |  | 0.28 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000243.4 |  | 0.27 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0000157.5 |  | 0.27 | PKS | tautomycetin | Streptomyces sp. CK4412

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

No significant matches found.

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
B083_RS0108755: T1TS
Domain 1 (1 - 305): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
Additional weak hits (7):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.67 out of 25.88
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.36 out of 20.97
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.43 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.28 out of 28.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 23.43
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.94 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_ARPF01000005.1 - Region 1 - NRPS-like,arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 10,656 - 53,804 nt. (total: 43,149 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
B083_RS0112225: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B083_RS0112290: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: methyltransferase
B083_RS0112310: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase hydrolase
B083_RS0112185: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

B083_RS0112195: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

Ligases: ligase synthase
B083_RS0112200: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0112205: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0112210: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B083_RS0112215: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | NRPS-like | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001275.3 |  |  | 0.52 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.52 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002631.2 |  |  | 0.42 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000885.3 |  |  | 0.35 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0001374.5 |  |  | 0.34 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0000867.3 |  |  | 0.34 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002510.2 |  |  | 0.33 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0002127.3 |  |  | 0.33 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001075.5 |  |  | 0.33 | PKS, terpene | aurachin RE | Rhodococcus erythropolis
BGC0001197.5 |  |  | 0.32 | PKS | frankiamicin | Frankia sp. EAN1pec

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000885.3 |  | 0.49 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0001374.5 |  | 0.48 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0000867.3 |  | 0.48 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0002510.2 |  | 0.48 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001075.5 |  | 0.47 | PKS, terpene | aurachin RE | Rhodococcus erythropolis
BGC0001197.5 |  | 0.46 | PKS | frankiamicin | Frankia sp. EAN1pec

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 (12):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.60 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.02 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.21 out of 21.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.95 out of 32.93
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.91 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.12 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.89 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.25 out of 20.01
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.73 out of 25.75
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B083_RS0112200: X
AMP-binding (58..444): 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:
    GFRAHSSAIAFYLAVNLGD-----------HTTA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

B083_RS0112205: X
AMP-binding (183..574): 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:
    MGFAFGSSVLCDCSLTAGEMNCLGATEVMHVVVA
  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
--- | ---

NZ_ARPF01000005.1 - Region 2 - butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 63,056 - 73,925 nt. (total: 10,870 nt) Show pHMM detection rules used
butyrolactone: AfsA

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
B083_RS0112380: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

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

Reference | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.83 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.82 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.41 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000559.4 |  | 0.35 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000515.4 |  | 0.35 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.34 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0002673.2 |  | 0.33 | PKS, other (other) | iminimycin A, iminimycin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001789.3 |  | 0.33 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000537.3 |  | 0.33 | ribosomal | nisin U | Streptococcus uberis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.83 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.82 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.41 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000559.4 |  | 0.35 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000515.4 |  | 0.35 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.34 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0002673.2 |  | 0.33 | PKS, other (other) | iminimycin A, iminimycin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001789.3 |  | 0.33 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000537.3 |  | 0.33 | ribosomal | nisin U | Streptococcus uberis

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 (11):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.54 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.49 out of 19.26
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.74 out of 25.31
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.62 out of 32.93
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.32 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.68 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.64 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.86 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.42 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.51 out of 28.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_ARPF01000005.1 - Region 3 - 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: 102,028 - 124,241 nt. (total: 22,214 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase hydratase
B083_RS0112620: Terpene synthase/cyclase metal-binding domain protein

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

B083_RS0112650: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase
B083_RS0112655: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.55 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.55 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.55 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.55 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001844.4 |  | 0.41 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0000649.3 |  | 0.41 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000393.5 |  | 0.38 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.55 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.55 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.55 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.55 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001844.4 |  | 0.41 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0000649.3 |  | 0.41 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000393.5 |  | 0.38 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622

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

No significant matches found.

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

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

Genes with terpene domains:
B083_RS0112620: T1TS + T1TS
Domain 1 (2 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (336 - 697): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.10 out of 27.78
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.12 out of 23.79
Confidence: medium
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.90 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.65 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.70 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.75 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.75 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.29 out of 28.19
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
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
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_ARPF01000005.1 - Region 4 - NRP-metallophore,NRPS,PKS-like,T1PKS,terpene,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: 126,483 - 262,111 nt. (total: 135,629 nt) Show pHMM detection rules used
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))
PKS-like: (t2pks2 or ksIII)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
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
B083_RS0112710: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

B083_RS0112765: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B083_RS0112805: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

B083_RS0112810: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

B083_RS0112820: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

B083_RS0112950: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B083_RS0113045: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: acylase acyltransferase
B083_RS0112740: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B083_RS0112925: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: esterase hydrolase
B083_RS01000000133270: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

B083_RS0112705: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

B083_RS0112920: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

B083_RS0112940: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

B083_RS0112965: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
B083_RS0112955: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
B083_RS0112685: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0112695: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0112745: 3-oxoacyl-(acyl carrier protein) synthase III

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

B083_RS0112750: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B083_RS0112755: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B083_RS0112960: 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 | transAT-PKS | PKS-like | T1PKS | NRPS | NRP-metallophore | NRPS | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001845.2 |  |  |  |  |  |  |  | 2.06 | NRPS, PKS, other (aminocoumarin) | alpiniamide | Streptomyces sp. CBMAI 2042
BGC0002135.2 |  |  |  |  |  |  |  | 1.50 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  |  |  |  |  |  |  | 1.46 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000368.5 |  |  |  |  |  |  |  | 1.45 | NRPS | griseobactin | Streptomyces sp. ATCC 700974
BGC0001273.3 |  |  |  |  |  |  |  | 1.24 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  |  |  |  |  |  | 1.23 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001641.4 |  |  |  |  |  |  |  | 1.22 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001275.3 |  |  |  |  |  |  |  | 1.22 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  |  |  |  |  |  | 1.21 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002192.3 |  |  |  |  |  |  |  | 1.21 | PKS | FR901512 | fungal sp. No.14919

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000368.5 |  | 0.81 | NRPS | griseobactin | Streptomyces sp. ATCC 700974
BGC0001845.2 |  | 0.80 | NRPS, PKS, other (aminocoumarin) | alpiniamide | Streptomyces sp. CBMAI 2042
BGC0000343.5 |  | 0.68 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000401.5 |  | 0.68 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
No domains 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:
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 31.35 out of 32.93
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 31.91 out of 32.38
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.07 out of 36.53
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.85 out of 20.97
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.44 out of 23.79
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.57 out of 36.53
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.63 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.41 out of 27.04
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
Additional weak hits (41):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.52 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.99 out of 30.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.92 out of 25.88
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.15 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.71 out of 27.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.10 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.28 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.17 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.46 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.07 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.38 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.58 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.73 out of 29.65
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.45 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.29 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.48 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.45 out of 29.65
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 24.53 out of 32.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.23 out of 23.43
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.13 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.14 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.71 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.24 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.81 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.40 out of 36.53
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.14 out of 39.62
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.82 out of 36.53
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 26.85
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.72 out of 20.01
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.62 out of 25.75
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.16 out of 29.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.45 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.66 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 4, location 126482 - 262111:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (Me-mal) + (mal) + (Gly - Me-mal - Me-ccmal) + (Arg - Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 126482 - 192743:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - Me-mal - Me-ccmal) + (mal) + (Me-mal) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 184914 - 239887:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Arg - Thr)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B083_RS0112685: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (13..406): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    ESALAQMHVF-PFAYYGASYNCFGQSEIGPLATV
  Nearest Stachelhaus code(s):
    Abu DAWFYGAPLK (21% 8Å match)
  Stachelhaus code match:
    60% (weak)

B083_RS0112695: X
AMP-binding (7..410): 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:
    LSPA-------AHMIHGAAEEYYAASEGGGAFAT
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

B083_RS0112740: mal
PKS_AT (4..287): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 102.0
  Methoxymalonyl-CoA: 29.2
  inactive: 25.6
  Propionyl-CoA: 20.9
  Methylmalonyl-CoA: 17.5
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

B083_RS0112750: mmal
PKS_AT (537..834): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Malonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 187.1
  Ethylmalonyl-CoA: 183.3
  Methoxymalonyl-CoA: 151.8
  2-Methylbutyryl-CoA: 129.2
  Malonyl-CoA: 121.1
  Propionyl-CoA: 116.8
  trans-1,2-CPDA: 103.4
  CHC-CoA: 85.1
  Isobutyryl-CoA: 84.4
  Acetyl-CoA: 63.7
  Benzoyl-CoA: 63.4
  fatty_acid: 46.1
  inactive: 34.6
  3-Methylbutyryl-CoA: 27.2

B083_RS0112760: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (494..894): 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:
    FAMTFDIAALELQALCGGEWNLYGPTETTIWSAA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

B083_RS0112925: Arg - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (473..899): Arg
nrpys: Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGHAFDASWDPWDVVVGGEVNLYGPTETTVDAYY
  Nearest Stachelhaus code(s):
    Arg DADDVGLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1571..1979): 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:
    LATHFDFSVWEGNQVFGGEVNMYGITETTVHVSY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

B083_RS0112960: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (32..439): diOH-Bz
nrpys: diOH-Bz

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    SGSLFPLSSPGGGLLVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPGLGVVNK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
CsoR | Copper-responsive repressor
DasR | N-acetylglucosamine dependent repressor
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator
RicR | Copper-responsive regulator

NZ_ARPF01000005.1 - Region 5 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 262,557 - 321,178 nt. (total: 58,622 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
B083_RS0113120: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

B083_RS0113225: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: aminotransferase
B083_RS0113290: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase hydrolase
B083_RS0113185: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

B083_RS0113260: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Ligases: ligase
B083_RS0113195: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: transporter
B083_RS0113135: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000325.5 |  |  | 0.87 | NRPS | coelichelin | Streptomyces coelicolor A3(2)
BGC0000357.5 |  |  | 0.69 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001825.4 |  |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001240.4 |  |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000307.4 |  |  | 0.57 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  |  | 0.57 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002476.2 |  |  | 0.42 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0002494.3 |  |  | 0.39 | NRPS | vibriobactin | Vibrio cholerae
BGC0002073.3 |  |  | 0.37 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002680.2 |  |  | 0.37 | NRPS | viobactin | Chromobacterium violaceum ATCC 12472

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000325.5 |  | 0.74 | NRPS | coelichelin | Streptomyces coelicolor A3(2)
BGC0000357.5 |  | 0.68 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000307.4 |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.62 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002476.2 |  | 0.54 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0002494.3 |  | 0.52 | NRPS | vibriobactin | Vibrio cholerae
BGC0002073.3 |  | 0.51 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002680.2 |  | 0.50 | NRPS | viobactin | Chromobacterium violaceum ATCC 12472

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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.90 out of 30.12
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.68 out of 30.12
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.53 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.19 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.90 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.90 out of 36.53
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (25):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.65 out of 26.85
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.33 out of 29.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.46 out of 31.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.52 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.74 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.47 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.13 out of 29.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.76 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.64 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.94 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.49 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.82 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.38 out of 27.78
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.07 out of 33.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.63 out of 32.93
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.30 out of 36.53
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.00 out of 23.43
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.67 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.54 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.03 out of 26.06
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.74 out of 26.85
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
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 8, location 262556 - 321178:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Fo-OH-Orn - D-Thr - OH-Orn)

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).
B083_RS0113195: Fo-OH-Orn - Thr - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (145..543): Fo-OH-Orn
nrpys: Fo-OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWQAFDISLNELYLWCGGEYHGYGPAETTIGVSH
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DINYWGGIGK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1627..2040): Thr
nrpys: Thr

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

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

AMP-binding (3053..3451): OH-Orn
nrpys: OH-Orn

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

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

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
DmdR1 | Iron(II)-dependent repressor
OsdR | Development and stress management regulator

NZ_ARPF01000005.1 - Region 6 - terpene,thioamide-NRP
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: 344,758 - 402,408 nt. (total: 57,651 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)
thioamide-NRP: (ATP-grasp and AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
B083_RS0113450: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

B083_RS0113570: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B083_RS0113610: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B083_RS0113615: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B083_RS0113695: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: PPTase kinase
B083_RS0113665: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

B083_RS1000000135760: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Lyases: cyclase decarboxylase
B083_RS0113490: Terpene synthase/cyclase metal-binding domain protein

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

B083_RS0113590: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
B083_RS0113560: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B083_RS0113600: 3-oxoacyl-(acyl carrier protein) synthase III

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

B083_RS1000000136140: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
B083_RS0113685: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | terpene | thioamide-NRP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000674.5 |  |  | 0.34 | terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064
BGC0000357.5 |  |  | 0.32 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001135.5 |  |  | 0.32 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  |  | 0.29 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.29 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  | 0.29 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002277.2 |  |  | 0.29 | NRPS | atromentin | Suillus grevillei
BGC0001160.5 |  |  | 0.26 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.26 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000518.3 |  |  | 0.25 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000357.5 |  | 0.65 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002277.2 |  | 0.62 | NRPS | atromentin | Suillus grevillei
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002499.2 |  | 0.52 | NRPS, PKS | enteromycin | Streptomyces achromogenes subsp. streptozoticus
BGC0000674.5 |  | 0.48 | terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
B083_RS0113490: T1TS
Domain 1 (31 - 315): Type 1 terpene synthase
Subtype: unknown
B083_RS01000000133280: T2TS
Domain 1 (227 - 517): Type 2 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.63 out of 27.04
Confidence: medium
Additional weak hits (11):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.96 out of 36.54
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.88 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.10 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.81 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.47 out of 36.54
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.14 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.35 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.02 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.89 out of 32.93
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
Terpene
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B083_RS1000000136140: NH2
CAL_domain (39..487): NH2
minowa: NH2

Prediction, score:
  NH2: 132.2
  Acetyl-CoA: 48.4
  fatty_acid: 18.5
  AHBA: 8.0
  shikimic_acid: 4.1

Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
DasR | N-acetylglucosamine dependent repressor
OsdR | Development and stress management regulator

NZ_ARPF01000005.1 - Region 7 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 434,294 - 475,427 nt. (total: 41,134 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
B083_RS0113855: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B083_RS0113905: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

B083_RS0113935: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: kinase
B083_RS0113870: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: glucosidase protease
B083_RS0113925: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

B083_RS0113975: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Ligases: synthase
B083_RS0113860: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B083_RS0113865: 3-oxoacyl-(acyl carrier protein) synthase III

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

B083_RS0113930: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.83 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.71 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000280.5 |  | 0.53 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002711.2 |  | 0.52 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000281.3 |  | 0.52 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002476.2 |  | 0.51 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0000844.5 |  | 0.50 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002073.3 |  | 0.50 | NRPS | dehydroxynocardamine | Corynebacterium propinquum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.83 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.71 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000280.5 |  | 0.53 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002711.2 |  | 0.52 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000281.3 |  | 0.52 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0002476.2 |  | 0.51 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0000844.5 |  | 0.50 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002073.3 |  | 0.50 | NRPS | dehydroxynocardamine | Corynebacterium propinquum

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.21 out of 27.78
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.62 out of 36.53
Confidence: medium
Additional weak hits (14):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.84 out of 21.55
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.12 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.50 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.92 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.49 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.09 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.28 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.55 out of 27.78
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.54 out of 20.01
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.99 out of 25.88
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.48 out of 31.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.33 out of 30.97
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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
DmdR1 | Iron(II)-dependent repressor

NZ_ARPF01000006.1 - 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: 51,919 - 106,339 nt. (total: 54,421 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B083_RS0114690: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B083_RS0114700: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase aminotransferase
B083_RS0114550: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

B083_RS0114705: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: esterase
B083_RS1000000135165: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

Isomerases: mutase
B083_RS0114555: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase
B083_RS0114645: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0114650: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B083_RS0114655: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0114660: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B083_RS0114675: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B083_RS0114710: 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
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  | 0.69 | 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
BGC0001050.5 |  | 0.68 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis

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
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  | 0.69 | 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
BGC0001050.5 |  | 0.68 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.19 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.73 out of 36.53
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.69 out of 27.04
Confidence: medium
Additional weak hits (15):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.97 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.37 out of 39.62
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.41 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.85 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.86 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.29 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.30 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.67 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.89 out of 30.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.22 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.37 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.83 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.95 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.02 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 51918 - 106339:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Ser) + (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).
B083_RS0114645: X
AMP-binding (496..925): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMAFDTHAEEPDLILGADVNSYGPTETTIIATT
  Nearest Stachelhaus code(s):
    Lys DTEDIGSVIK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

B083_RS0114650: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (626..1020): 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:
    RWMTFDVSVWELHFVCSGEANLYGPTEAAVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

B083_RS0114655: X
AMP-binding (26..418): 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:
    GLDFTNAGQTMNFLGSTAAVNYYTSTEAAPAQVT
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

B083_RS0114660: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (445..836): 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:
    LTMTFDISTVELQAVAGGEVNVYGPTETTVWSTL
  Nearest Stachelhaus code(s):
    Gly DILQLGVVWK (76% 8Å match)
  Stachelhaus code match:
    80% (moderate)

B083_RS0114710: X
AMP-binding (56..511): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TATAFDRAAR-I--ICGGSFEGYGLTETTAAHTV
  Nearest Stachelhaus code(s):
    nDodec DVLFIGGVAK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
DasR | N-acetylglucosamine dependent repressor
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_ARPF01000006.1 - Region 2 - RRE-containing,azole-containing-RiPP,ectoine,t3nrps-iterative
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 317,833 - 386,679 nt. (total: 68,847 nt) Show pHMM detection rules used
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)
ectoine: ectoine_synt

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Azole RiPPs
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
B083_RS0115835: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B083_RS0115840: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: transferase
B083_RS0115735: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: hydrolase
B083_RS01000000133445: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

Lyases: decarboxylase dehydratase
B083_RS0115780: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

B083_RS0115905: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: ligase
B083_RS0115795: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | t3nrps-iterative | ectoine | RRE-containing | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002116.3 |  |  |  |  | 0.39 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0001146.5 |  |  |  |  | 0.37 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000603.5 |  |  |  |  | 0.37 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001660.3 |  |  |  |  | 0.36 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000857.3 |  |  |  |  | 0.36 | other (other) | ectoine | Methylophaga alcalica
BGC0000855.3 |  |  |  |  | 0.36 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000616.4 |  |  |  |  | 0.36 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000856.3 |  |  |  |  | 0.36 | other (other) | ectoine | Methylophaga thalassica
BGC0000853.3 |  |  |  |  | 0.35 | other (other) | ectoine | Streptomyces anulatus
BGC0002120.3 |  |  |  |  | 0.35 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.54 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.54 | other (ectoine) | ectoine | Streptomyces sp.
BGC0001860.4 |  | 0.53 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0000613.5 |  | 0.53 | ribosomal | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0000855.3 |  | 0.53 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.53 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.52 | other (other) | ectoine | Methylophaga alcalica
BGC0000603.5 |  | 0.51 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0000852.5 |  | 0.51 | other (other) | ectoine | Sporosarcina pasteurii
BGC0001146.5 |  | 0.50 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
Additional weak hits (13):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.91 out of 19.26
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.23 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.97 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.75 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.13 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.14 out of 30.22
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.57 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.31 out of 29.65
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.77 out of 32.38
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.26 out of 32.93
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
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
RREFinder
TFBS Finder
Azole RiPPs
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).
B083_RS0115795: X
AMP-binding (11..426): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAILFDYGLYQLASTNTGAQLMYGLTECKRTTIM
  Nearest Stachelhaus code(s):
    Asp DYYPTTMRAK (82% 8Å match)
  Stachelhaus code match:
    80% (moderate)

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (351643...373995)
B083_RS0115890
  RRE type: Thiopeptide_F_RRE
  Location: 37 - 116
  Score: 63.0
  RRE type: Heterocycloanthracin_C_RRE
  Location: 36 - 124
  Score: 43.7
azole-containing-RiPP protocluster (353984...386679)
B083_RS0115890
  RRE type: Thiopeptide_F_RRE
  Location: 37 - 116
  Score: 63.0
  RRE type: Heterocycloanthracin_C_RRE
  Location: 36 - 124
  Score: 43.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_ARPF01000006.1 - Region 3 - PKS-like,T1PKS,t3nrps-iterative,thioamide-NRP
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: 442,974 - 509,947 nt. (total: 66,974 nt) Show pHMM detection rules used
thioamide-NRP: (ATP-grasp and AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC))
PKS-like: (t2pks2 or ksIII)
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B083_RS0116295: nucleotide sugar dehydrogenase

smcogs
  SMCOG1152: nucleotide sugar dehydrogenase

B083_RS0116300: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: halogenase transferase
B083_RS01000000133480: halogenase

smcogs
  SMCOG1119: halogenase

B083_RS0116440: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Lyases: decarboxylase
B083_RS0116335: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
B083_RS0116305: 3-oxoacyl-(acyl carrier protein) synthase III

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

B083_RS0116325: 3-oxoacyl-(acyl carrier protein) synthase III

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

B083_RS0116330: 3-oxoacyl-(acyl carrier protein) synthase III

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

B083_RS0116370: 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 | thioamide-NRP | PKS-like | t3nrps-iterative | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000041.3 |  |  |  |  | 1.32 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001257.3 |  |  |  |  | 1.20 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  |  |  |  | 1.20 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001284.4 |  |  |  |  | 1.14 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001164.3 |  |  |  |  | 1.13 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  |  | 1.12 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001254.3 |  |  |  |  | 1.11 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  |  |  |  | 1.10 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  |  |  |  | 1.07 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001825.4 |  |  |  |  | 1.06 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000041.3 |  | 0.66 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.64 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  | 0.60 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001825.4 |  | 0.60 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.24 out of 19.26
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.08 out of 18.57
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
Additional weak hits (11):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.23 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.51 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.39 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.20 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.51 out of 29.65
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.03 out of 26.12
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.17 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.03 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.24 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.89 out of 33.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.62 out of 32.93
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 6, location 442973 - 509947:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B083_RS0116320: mal
PKS_AT (561..859): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 201.0
  inactive: 87.9
  Methoxymalonyl-CoA: 65.8
  Methylmalonyl-CoA: 54.4
  Acetyl-CoA: 34.4
  Propionyl-CoA: 28.4
  Isobutyryl-CoA: 28.3
  Benzoyl-CoA: 22.9
  Ethylmalonyl-CoA: 20.4
  trans-1,2-CPDA: 18.7
  CHC-CoA: 17.9
  2-Methylbutyryl-CoA: 12.9
  fatty_acid: 8.5
  3-Methylbutyryl-CoA: 0.0

B083_RS0116370: X
AMP-binding (11..408): 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:
    Unpolar aromatic ring (Phe, Trp)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAILFDYGLYQLAATNTGAQVMFGLTECKRATIM
  Nearest Stachelhaus code(s):
    Asp DYYPTTMRAK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_ARPF01000007.1 - Region 1 - NRPS,T1PKS,azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 14,557 - 67,192 nt. (total: 52,636 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Azole RiPPs
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
B083_RS0116805: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Hydrolases: hydrolase
B083_RS0116800: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: synthase
B083_RS01000000133575: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | NRPS | T1PKS | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000606.5 |  |  |  | 0.68 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0002135.2 |  |  |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  |  | 0.60 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001146.5 |  |  |  | 0.58 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0002311.3 |  |  |  | 0.57 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001160.5 |  |  |  | 0.54 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  | 0.53 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001145.5 |  |  |  | 0.51 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5 |  |  |  | 0.49 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001174.4 |  |  |  | 0.49 | ribosomal | corynazolicin | Corynebacterium urealyticum DSM 7111

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000606.5 |  | 0.56 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0001146.5 |  | 0.52 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0002311.3 |  | 0.51 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001145.5 |  | 0.49 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0002171.2 |  | 0.48 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger ATCC 1015
BGC0002275.2 |  | 0.48 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger CBS 101883

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 22.02 out of 23.79
Confidence: strong
Additional weak hits (23):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.24 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.91 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.02 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.12 out of 26.06
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.94 out of 33.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.20 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.66 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.38 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.62 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.51 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.77 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.29 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.54 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.36 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.71 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.66 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.55 out of 29.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.10 out of 25.88
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.03 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.42 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.75 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.38 out of 28.19
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
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
RREFinder
TFBS Finder
Azole RiPPs
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 14556 - 67192:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - ohmal - 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).
B083_RS01000000133575: NH2 - mal - X
CAL_domain (33..455): NH2
minowa: NH2

Prediction, score:
  NH2: 54.5
  fatty_acid: 44.2
  shikimic_acid: 0.0
  Acetyl-CoA: 0.0
  AHBA: 0.0

PKS_AT (1230..1524): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 66.7%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 110.5
  Methylmalonyl-CoA: 69.6
  Methoxymalonyl-CoA: 62.0
  inactive: 39.4
  Ethylmalonyl-CoA: 28.9
  Propionyl-CoA: 28.2
  Isobutyryl-CoA: 28.2
  fatty_acid: 27.3
  2-Methylbutyryl-CoA: 16.3
  trans-1,2-CPDA: 15.8
  Benzoyl-CoA: 13.4
  CHC-CoA: 13.1
  Acetyl-CoA: 9.8
  3-Methylbutyryl-CoA: 8.5

AMP-binding (2709..3130): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWAAFDASVRQASSHVGGEANLYGPTEATINTTC
  Nearest Stachelhaus code(s):
    Gln DACSTGVINK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (37866...66358)
B083_RS0116755
  RRE type: Thiopeptide_F_RRE
  Location: 21 - 107
  Score: 40.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_ARPF01000007.1 - 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: 76,244 - 104,633 nt. (total: 28,390 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B083_RS0116870: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

B083_RS0116875: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

B083_RS0116905: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
B083_RS0116925: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
B083_RS0116900: 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
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.86 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.78 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.76 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.71 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.71 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000645.3 |  | 0.55 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.53 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.51 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.50 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000639.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC260

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.86 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.78 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.76 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.71 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.71 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000645.3 |  | 0.55 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.53 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.51 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.50 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000639.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC260

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
B083_RS0116900: PT_FPPS_like
Domain 1 (74 - 372): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

B083_RS0116910: PT_phytoene_like
Domain 1 (16 - 315): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

B083_RS0116930: Lycopene_cycl
Domain 1 (5 - 380): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

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:
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 28.92 out of 32.38
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.61 out of 23.43
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.10 out of 23.43
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 31.03 out of 36.53
Confidence: medium
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 26.33 out of 32.38
Confidence: medium
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 29.28 out of 32.93
Confidence: medium
Additional weak hits (4):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.85 out of 20.01
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.27 out of 32.74
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
CsoR | Copper-responsive repressor
DmdR1 | Iron(II)-dependent repressor
RicR | Copper-responsive regulator

NZ_ARPF01000007.1 - Region 3 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 141,053 - 181,988 nt. (total: 40,936 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B083_RS0117170: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Hydrolases: hydrolase
B083_RS0117225: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

B083_RS0117330: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Lyases: decarboxylase
B083_RS01000000133610: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: synthase
B083_RS1000000134685: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.76 | other (other) | germicidin | Streptomyces argillaceus
BGC0001905.4 |  | 0.52 | PKS | violapyrone B | Streptomyces somaliensis
BGC0002073.3 |  | 0.44 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0001561.4 |  | 0.43 | NRPS | curacomycin | Streptomyces curacoi
BGC0002318.2 |  | 0.42 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0001526.4 |  | 0.40 | other (other) | bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K | Synechocystis salina LEGE 06099
BGC0001525.3 |  | 0.40 | other (other) | bartoloside B, bartoloside C, bartoloside D | Synechocystis salina LEGE 06155
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000548.4 |  | 0.40 | ribosomal | salivaricin A | Streptococcus salivarius
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.76 | other (other) | germicidin | Streptomyces argillaceus
BGC0001905.4 |  | 0.52 | PKS | violapyrone B | Streptomyces somaliensis
BGC0002073.3 |  | 0.44 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0001561.4 |  | 0.43 | NRPS | curacomycin | Streptomyces curacoi
BGC0002318.2 |  | 0.42 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0001526.4 |  | 0.40 | other (other) | bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K | Synechocystis salina LEGE 06099
BGC0001525.3 |  | 0.40 | other (other) | bartoloside B, bartoloside C, bartoloside D | Synechocystis salina LEGE 06155
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000548.4 |  | 0.40 | ribosomal | salivaricin A | Streptococcus salivarius
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.82 out of 23.79
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.54 out of 23.79
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.80 out of 23.79
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 26.21 out of 28.19
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.85 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.62 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.13 out of 20.47
Confidence: medium
Additional weak hits (10):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 30.11
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.05 out of 30.22
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.48 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.77 out of 29.38
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.21 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.05 out of 24.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.59 out of 27.04
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.58 out of 32.93
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_ARPF01000007.1 - Region 4 - NRPS,T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 206,783 - 309,798 nt. (total: 103,016 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
B083_RS0117500: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

B083_RS0117660: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

Transferases: methyltransferase
B083_RS0117665: Methylation

MITE
  MITE0000155Methylation (identity: 80.30%)
smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Hydrolases: hydrolase
B083_RS0117565: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
B083_RS0117580: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0117590: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0117625: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

B083_RS0117670: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | NRPS | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000282.3 |  |  | 1.27 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001831.3 |  |  | 0.45 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0002135.2 |  |  | 0.43 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002071.2 |  |  | 0.41 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001135.5 |  |  | 0.41 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  |  | 0.40 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  | 0.38 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  | 0.38 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  |  | 0.37 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  |  | 0.37 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.86 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002071.2 |  | 0.73 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  | 0.70 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.19 out of 30.11
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.73 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.19 out of 36.53
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.27 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.20 out of 23.79
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (16):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.78 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.15 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.45 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.52 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.21 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.79 out of 39.62
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.52 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.23 out of 27.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.53 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.40 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.97 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.75 out of 27.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.57 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 5, location 206782 - 309798:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - Gly - Thr - Ser - D-Leu) + (Thr - D-His - Val - D-X) + (D-X - Gly - D-Ser - OH-Orn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 206782 - 295191:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - Gly - Thr - Ser - D-Leu) + (Thr - D-His - Val - D-X) + (D-X - Gly - D-Ser - OH-Orn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 268745 - 309798:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - Gly - Thr - Ser - D-Leu)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B083_RS0117580: X - Gly - Ser - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (473..876): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWAAFDVTFCENVIIVGTEFNAYGPTEAVVNSAT
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DVWIIGAVNK (62% 8Å match)
    Trp or Pro DVMFIGAVNK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1996..2376): 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:
    LAITFDIAALEVQALSGGELNLYGPTETTIWSTV
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3042..3434): 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:
    RWMTFDVSVWELHFIASGEHNLYGPTEAAIDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHISLIDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4538..4977): OH-Orn
nrpys: OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSHWFDASWQPWEVGVGGEVNLYGPTEGTVDALV
  Nearest Stachelhaus code(s):
    OH-Orn DAQEGGLVDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

B083_RS0117585: Thr - His - Val - X
Search NORINE for peptide: strict or relaxed
AMP-binding (493..904): 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:
    LTTHFDFSVWEGNQVFGGEVNMYGITETTVHVTI
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1568..1963): His
nrpys: His

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTLAFDTSVWEMTVIVAGEFNSYGPTETTVDATL
  Nearest Stachelhaus code(s):
    His DTWTIASVDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3059..3458): 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:
    LDSSFDAATHEGWFWTGGDVNGYGPTETTTFATA
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4123..4518): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWTAFDVSVWEGHFFSGGEVNQYGPTEAAVDVTA
  Nearest Stachelhaus code(s):
    His DYWHFGAVDK (82% 8Å match)
    Ser DVWHFSLVDK (79% 8Å match)
  Stachelhaus code match:
    80% (moderate)

B083_RS0117590: Gly - Gly - Thr - Ser - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (468..866): 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:
    LAMTFDIAALEVQALSGGEVNLYGPTETTVWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLVWK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1553..1947): 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:
    FCLTFDIAVLELQALVGGEVNLYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2601..3011): 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:
    LATHFDFSVWEGNQVLGGEVNMYGITETTVHVTT
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3666..4063): 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:
    RWATFDVSVWEWHFLASGEHNLYGPTEAAVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4730..5113): Leu
nrpys: Leu

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

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

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CelR | Cellobiose uptake repressor
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism

NZ_ARPF01000007.1 - Region 5 - melanin,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 323,389 - 352,184 nt. (total: 28,796 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)
melanin: melC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
B083_RS0117955: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: glycosyltransferase
B083_RS0117900: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

B083_RS0117905: sugar transferase

smcogs
  SMCOG1146: sugar transferase

B083_RS0117925: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: hydrolase
B083_RS0117895: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Ligases: synthetase
B083_RS0117890: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000911.3 |  |  | 0.58 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  |  | 0.53 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  |  | 0.30 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  |  | 0.26 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000800.5 |  |  | 0.26 | saccharide | xanthan | Xanthomonas campestris
BGC0001529.5 |  |  | 0.20 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000908.3 |  |  | 0.17 | other (other) | melanin | Streptomyces avermitilis
BGC0000742.3 |  |  | 0.16 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000743.3 |  |  | 0.16 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0002397.2 |  |  | 0.16 | terpene | astallatene | Arabidopsis thaliana

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000911.3 |  | 0.83 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.80 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.64 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.53 | other (other) | melanin | Streptomyces avermitilis
BGC0002397.2 |  | 0.53 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.49 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000800.5 |  | 0.48 | saccharide | xanthan | Xanthomonas campestris
BGC0000677.5 |  | 0.48 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000742.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae

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

No significant matches found.

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

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

Genes with terpene domains:
B083_RS0117890: PT_FPPS_like
Domain 1 (58 - 341): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.58 out of 30.11
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
Additional weak hits (10):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 30.11
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.12 out of 32.93
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.71 out of 29.25
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.32 out of 20.01
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.30 out of 31.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_ARPF01000007.1 - Region 6 - NRPS,RiPP-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 352,932 - 464,199 nt. (total: 111,268 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))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
B083_RS01000000133680: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B083_RS0118135: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

B083_RS0118300: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase aminotransferase formyltransferase
B083_RS01000000133690: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

B083_RS0118320: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

B083_RS0118350: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: esterase
B083_RS0118090: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
B083_RS0118240: L-carnitine dehydratase/bile acid-inducible

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

Isomerases: mutase
B083_RS0118315: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase synthase
B083_RS0118055: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

B083_RS0118095: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B083_RS0118100: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B083_RS0118235: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0118270: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | RiPP-like | NRPS | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  |  |  | 0.96 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  |  |  |  | 0.91 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  |  |  | 0.90 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  |  |  | 0.90 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  |  |  |  | 0.89 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  |  |  |  | 0.89 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  |  |  | 0.89 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  |  | 0.88 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  |  |  |  | 0.88 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  |  |  |  | 0.88 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.82 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0001846.4 |  | 0.75 | NRPS, saccharide | valinomycin, montanastatin | Streptomyces sp. CBMAI 2042
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001825.4 |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000357.5 |  | 0.67 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001133.4 |  | 0.67 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.66 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.54 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.34 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.65 out of 28.19
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.74 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.57 out of 36.53
Confidence: medium
Additional weak hits (32):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.88 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.48 out of 21.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.54 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.35 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.70 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.10 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.99 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.29 out of 28.14
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.34 out of 26.12
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.56 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.33 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.70 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.64 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.18 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.90 out of 29.38
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.24 out of 25.88
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.58 out of 20.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.72 out of 32.74
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.23 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.54 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.28 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.23 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.85 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.60 out of 23.43
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.12 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 12, location 358732 - 464199:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Hiv - D-Val) + (shikimic_acid - Val) + (X) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 358732 - 416958:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Hiv - D-Val) + (shikimic_acid - Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 14, location 413472 - 464199:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (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).
B083_RS0118095: D-Hiv - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (14..452): D-Hiv
nrpys: D-Hiv

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:
    RGVMAGILMSHGWAINAGEAPVWGMAETCSGVFY
  Nearest Stachelhaus code(s):
    D-Hiv GISWIAVSGK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1838..2229): 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:
    LEPGFDASTLEGWMLVGGDINGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (100% 8Å match)
    bOH-Val DALWLGGTFK (71% 8Å match)
  Stachelhaus code match:
    100% (strong)

B083_RS0118100: shikimic_acid - Val
Search NORINE for peptide: strict or relaxed
CAL_domain (212..646): shikimic_acid
minowa: shikimic_acid

Prediction, score:
  shikimic_acid: 16.0
  AHBA: 15.7
  NH2: 10.0
  fatty_acid: 7.6
  Acetyl-CoA: 0.0

AMP-binding (1803..2194): 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:
    LEPGFDASTFEAWVVVGGDTNGYGPTENTTFSTT
  Nearest Stachelhaus code(s):
    Val DAFWVGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

B083_RS0118235: X
AMP-binding (40..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:
    GNFVSAFGSNGVLGVLGGAVNLYGSADGVNCHTG
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

B083_RS01000000133690: X
AMP-binding (1396..1798): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHCFDASLMEPVMLLGGELNVYGPTEATVLCVV
  Nearest Stachelhaus code(s):
    ndmHex DAMVLGVVAK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

B083_RS0118270: mal
PKS_AT (546..839): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 66.7%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 157.2
  inactive: 86.4
  Methylmalonyl-CoA: 76.2
  Methoxymalonyl-CoA: 64.0
  Ethylmalonyl-CoA: 50.3
  Propionyl-CoA: 46.2
  Isobutyryl-CoA: 35.3
  Acetyl-CoA: 28.1
  trans-1,2-CPDA: 27.3
  2-Methylbutyryl-CoA: 25.9
  fatty_acid: 16.4
  Benzoyl-CoA: 13.4
  3-Methylbutyryl-CoA: 12.5
  CHC-CoA: 11.4

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_ARPF01000007.1 - Region 7 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 464,910 - 501,280 nt. (total: 36,371 nt) Show pHMM detection rules used
Region on contig edge.
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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
B083_RS0118470: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Transferases: acyltransferase
B083_RS0118410: acyltransferase

smcogs
  SMCOG1141: acyltransferase

B083_RS0118475: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: deaminase
B083_RS0118445: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Ligases: ligase synthase
B083_RS0118440: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

B083_RS0118480: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
B083_RS0118420: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.71 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001133.4 |  | 0.70 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.71 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001133.4 |  | 0.70 | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
Additional weak hits (3):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.07 out of 27.04
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
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 15, location 464909 - 501280:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X) + (Ser - 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).
B083_RS0118475: X - X
AMP-binding (479..879): 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:
    RWSTFDASLWESQLSSAGESNTYGPTECSIDSTA
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIDK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1559..1958): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HVASFDVSMEQAETNLSSDVCCYGPTEATVTCLL
  Nearest Stachelhaus code(s):
    Arg DVEEIGAITK (44% 8Å match)
    Ahp DVENAGVVTK (41% 8Å match)
  Stachelhaus code match:
    60% (weak)

B083_RS0118480: Ser - X
Search NORINE for peptide: strict or relaxed
AMP-binding (508..903): 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:
    RWMTFDVSVWEWHFVCSGEHNLYGPTEAAVDVTH
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1560..1949): X
nrpys: Leu, 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:
    LDESFDASAFEGFLLTGGDSNMYGPTECTTFATG
  Nearest Stachelhaus code(s):
    Leu or Ile DAFFLGMTFK (71% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

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

NZ_ARPF01000008.1 - Region 1 - hydrogen-cyanide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,082 - 17,630 nt. (total: 13,549 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase reductase
B083_RS0118515: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

B083_RS1000000135260: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

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

Reference | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002285.2 |  | 0.26 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000883.5 |  | 0.20 | other (other) | arginomycin | Streptomyces arginensis
BGC0000595.3 |  | 0.20 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000135.5 |  | 0.20 | PKS | reveromycin A | Streptomyces sp. SN-593

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002285.2 |  | 0.26 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000883.5 |  | 0.20 | other (other) | arginomycin | Streptomyces arginensis
BGC0000595.3 |  | 0.20 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000135.5 |  | 0.20 | PKS | reveromycin A | Streptomyces sp. SN-593

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
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40
Confidence: strong
Additional weak hits (13):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.39 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.00 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.45 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.13 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.45 out of 30.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.31 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.36 out of 21.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.87 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.55 out of 18.57
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.15 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
HypR | L-hydroxyproline utilization repressor

NZ_ARPF01000008.1 - Region 2 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 138,445 - 149,884 nt. (total: 11,440 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002387.2 |  | 0.27 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0002788.2 |  | 0.27 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0001377.5 |  | 0.24 | PKS | uncialamycin | Streptomyces uncialis
BGC0000874.5 |  | 0.24 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0001060.5 |  | 0.22 | PKS | dynemicin A | Micromonospora chersina
BGC0001984.3 |  | 0.20 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0000241.5 |  | 0.19 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440
BGC0001693.3 |  | 0.18 | PKS | nenestatin | Micromonospora echinospora

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002387.2 |  | 0.27 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0002788.2 |  | 0.27 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0001377.5 |  | 0.24 | PKS | uncialamycin | Streptomyces uncialis
BGC0000874.5 |  | 0.24 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0001060.5 |  | 0.22 | PKS | dynemicin A | Micromonospora chersina
BGC0001984.3 |  | 0.20 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0000241.5 |  | 0.19 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440
BGC0001693.3 |  | 0.18 | PKS | nenestatin | Micromonospora echinospora

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (1):
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_ARPF01000008.1 - Region 3 - NRPS,NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 277,440 - 324,441 nt. (total: 47,002 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase
B083_RS0119650: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

B083_RS0119720: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: aminotransferase
B083_RS0119695: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Ligases: ligase
B083_RS0119625: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0119630: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0119680: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0119690: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: transporter
B083_RS0119750: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  | 0.83 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  |  | 0.75 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.70 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.08 out of 24.78
Confidence: medium
Additional weak hits (10):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.03 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.81 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.55 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.07 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.55 out of 30.25
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.89 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.86 out of 24.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.68 out of 27.04
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.67 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 3, location 277439 - 324441:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 277439 - 319824:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 281261 - 324441:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B083_RS0119625: X
AMP-binding (49..448): 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:
    GATSWAKHAWSACAVAAGERDGFGQTETAVQVAN
  Nearest Stachelhaus code(s):
    Phe or Tyr DAACVAGVAK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

B083_RS0119630: X
AMP-binding (31..444): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    NFVVFGMVMGNAYGIMAGSSICYGMTETSPVSTQ
  Nearest Stachelhaus code(s):
    Abu or Ival DMGFIAGVVK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

B083_RS0119680: X
AMP-binding (199..603): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  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:
    NDLSFDMSVYEGNSLLGGDVALGGATESSIHSTV
  Nearest Stachelhaus code(s):
    Lys DMYNFGLIHK (85% 8Å match)
    Ser DLYNLGLIHK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

B083_RS0119690: X
AMP-binding (476..871): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAYPFDMSQGEAGLMGGAEVNLYGPTEASIATTE
  Nearest Stachelhaus code(s):
    OH-Orn DMENMGLINK (44% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
LexA variant 2 | Repressor of DNA damage response
VqsM | Regulator of quorum-sensing signalling systems

NZ_ARPF01000009.1 - 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: 126,562 - 170,554 nt. (total: 43,993 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: reductase
B083_RS0120820: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

Transferases: phosphotransferase
B083_RS0120785: Glucose-specific phosphotransferase enzyme IIA

smcogs
  SMCOG1145: Glucose-specific phosphotransferase enzyme IIA

Hydrolases: hydrolase
B083_RS0120885: HAD-superfamily hydrolase, subfamily IA, variant

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

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
--- | --- | --- | --- | --- | ---
BGC0002295.3 |  | 0.69 | NRPS, saccharide | minimycin, indigoidine | Streptomyces hygroscopicus
BGC0001833.4 |  | 0.62 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.62 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.61 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000357.5 |  | 0.60 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002295.3 |  | 0.69 | NRPS, saccharide | minimycin, indigoidine | Streptomyces hygroscopicus
BGC0001833.4 |  | 0.62 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.62 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.61 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000357.5 |  | 0.60 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae

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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.09 out of 29.72
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.86 out of 27.04
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.95 out of 27.04
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.19 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.17 out of 27.04
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.68 out of 30.12
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.69 out of 30.11
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
Additional weak hits (13):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.33 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.51 out of 30.22
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.60 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.38 out of 27.04
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.20 out of 30.11
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.65 out of 26.12
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.89 out of 30.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.60 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 126561 - 170554:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gln)

Direct lookup in NORINE database: strict or relaxed
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).
B083_RS0120880: Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (31..473): Gln
nrpys: Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    QWLTFDAAQWEAQGFSGGEINLYGPTEATINATS
  Nearest Stachelhaus code(s):
    Gln DAWQFGLINK (85% 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
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_ARPF01000009.1 - Region 2 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 237,014 - 266,792 nt. (total: 29,779 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
B083_RS0121315: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Hydrolases: hydrolase
B083_RS0121290: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: decarboxylase
B083_RS0121320: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000941.3 |  | 0.87 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.78 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000940.5 |  | 0.71 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.71 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.61 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002690.2 |  | 0.59 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000941.3 |  | 0.87 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.78 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000940.5 |  | 0.71 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.71 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.61 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002690.2 |  | 0.59 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.52 out of 19.26
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.04 out of 27.04
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.62 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.77 out of 36.53
Confidence: medium
Additional weak hits (7):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.31 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.33 out of 30.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.84 out of 26.85
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.23 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.48 out of 27.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.91 out of 25.88
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.52 out of 20.97
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
DmdR1 | Iron(II)-dependent repressor

NZ_ARPF01000009.1 - Region 3 - lanthipeptide-class-ii,lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 329,118 - 360,527 nt. (total: 31,410 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
B083_RS0121685: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Hydrolases: protease
B083_RS0121620: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Lyases: cyclase
B083_RS0121675: 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-iii | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002700.2 |  |  | 0.38 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000551.5 |  |  | 0.37 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000525.5 |  |  | 0.36 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000519.4 |  |  | 0.35 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000501.3 |  |  | 0.35 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000518.3 |  |  | 0.35 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000513.3 |  |  | 0.32 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001229.4 |  |  | 0.30 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000517.4 |  |  | 0.29 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0000546.3 |  |  | 0.28 | ribosomal | SAL-2242 | Streptomyces albidoflavus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000551.5 |  | 0.50 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000519.4 |  | 0.49 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000501.3 |  | 0.49 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000518.3 |  | 0.49 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000513.3 |  | 0.47 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001407.5 |  | 0.45 | ribosomal | bicereucin | Bacillus cereus SJ1
BGC0001229.4 |  | 0.45 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000517.4 |  | 0.44 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125

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 B083_RS0121655

B083_RS1000000136445
Leader:
MSENTKPAADENNETETPEVEAHSVLDLQETPGVIDREIVPG
Core:
N C V S T V S L V L S
Core with dehydrations:
N Cys V Dha Dhb V Dha L V L Dha

#### antiSMASH-DB 4.0 matches for B083_RS1000000136445

100.0%
NZ_AQRK01000090.1 and 19 others:
NZ_AQRK01000090.1 Lanthipeptides: YUW_RS35860_lanthipeptide NZ_AQRK01000090.1 Lanthipeptides: YUW_RS35860_lanthipeptide NZ_AQRK01000090.1 Lanthipeptides: YUW_RS35860_lanthipeptide NZ_ARPF01000009.1 Lanthipeptides: B083_RS1000000136445_lanthipeptide NZ_BMSP01000007.1 Lanthipeptides: IE150_RS11895_lanthipeptide NZ_BMSP01000007.1 Lanthipeptides: IE150_RS11895_lanthipeptide NZ_BMSP01000007.1 Lanthipeptides: IE150_RS11895_lanthipeptide NZ_BMSP01000007.1 Lanthipeptides: IE150_RS11895_lanthipeptide NZ_CP015362.1 Lanthipeptides: A6E92_RS33505_lanthipeptide NZ_CP024957.1 Lanthipeptides: CVT27_RS32880_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS33175_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS33175_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS33175_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS33175_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS10800_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS10800_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS10800_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS10800_lanthipeptide NZ_KB890923.1 Lanthipeptides: B053_RS1000000137140_lanthipeptide
Lanthipeptides: YUW_RS35860_lanthipeptide
1
N C V S T V S L V L S
11
N C V S T V S L V L S
1
N C V S T V S L V L S
11
83.3%
NZ_LIXJ01000004.1:
Lanthipeptides: AMK22_RS39975_lanthipeptide
2
C V S T V S L V L S
11
C V S T V S L V L S
1
C V S T V S L V L S
10
72.7%
NZ_ML123034.1 and 3 others:
NZ_ML123034.1 Lanthipeptides: EES43_RS30570_lanthipeptide NZ_ML123034.1 Lanthipeptides: EES43_RS30570_lanthipeptide NZ_ML123034.1 Lanthipeptides: EES43_RS30570_lanthipeptide
Lanthipeptides: EES43_RS30570_lanthipeptide
2
C V S T V S L V L S
11
C V S T+S L V L
1
C V S T I S L V L E
10
with 2 more sequence matches
58.3%
NZ_CP119145.1:
Lanthipeptides: PZB75_RS01650_lanthipeptide
2
C V S T V S L V L S
11
C V S +S+V L S
1
C V S V I S V V L S
10
33.3%
NZ_BDHJ01000009.1 and 17 others:
NZ_CP076457.1 Lanthipeptides: KME66_RS23045_lanthipeptide NZ_KB891297.1 Lanthipeptides: B061_RS39730_lanthipeptide NZ_KB891297.1 Lanthipeptides: B061_RS39730_lanthipeptide NZ_KB891297.1 Lanthipeptides: B061_RS39730_lanthipeptide NZ_KB891297.1 Lanthipeptides: B061_RS39730_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS37365_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS37365_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS37365_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS37365_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS23845_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS23845_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS23845_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS23845_lanthipeptide NZ_LZQS01000002.1 Lanthipeptides: STIB_RS38140_lanthipeptide NZ_LZQS01000002.1 Lanthipeptides: STIB_RS38140_lanthipeptide NZ_RCOL01000001.1 Lanthipeptides: STAN_RS11445_lanthipeptide NZ_RCOL01000001.1 Lanthipeptides: STAN_RS11445_lanthipeptide
Lanthipeptides: BHQ08_RS34920_lanthipeptide
1
N C V S T V S L V L S
11
N C V S T V S L V L
20
N C V S T V S L V L G
30

#### Lanthipeptide(s) for B083_RS0121675

B083_RS1000000136445
Leader:
MSENTKPAADENNETETPEVEAHSVLDLQETPGVIDREIVPG
Core:
N C V S T V S L V L S
Core with dehydrations:
N Cys V Dha Dhb V Dha L V L Dha

#### antiSMASH-DB 4.0 matches for B083_RS1000000136445

100.0%
NZ_AQRK01000090.1 and 19 others:
NZ_AQRK01000090.1 Lanthipeptides: YUW_RS35860_lanthipeptide NZ_AQRK01000090.1 Lanthipeptides: YUW_RS35860_lanthipeptide NZ_AQRK01000090.1 Lanthipeptides: YUW_RS35860_lanthipeptide NZ_ARPF01000009.1 Lanthipeptides: B083_RS1000000136445_lanthipeptide NZ_BMSP01000007.1 Lanthipeptides: IE150_RS11895_lanthipeptide NZ_BMSP01000007.1 Lanthipeptides: IE150_RS11895_lanthipeptide NZ_BMSP01000007.1 Lanthipeptides: IE150_RS11895_lanthipeptide NZ_BMSP01000007.1 Lanthipeptides: IE150_RS11895_lanthipeptide NZ_CP015362.1 Lanthipeptides: A6E92_RS33505_lanthipeptide NZ_CP024957.1 Lanthipeptides: CVT27_RS32880_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS33175_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS33175_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS33175_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS33175_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS10800_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS10800_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS10800_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS10800_lanthipeptide NZ_KB890923.1 Lanthipeptides: B053_RS1000000137140_lanthipeptide
Lanthipeptides: YUW_RS35860_lanthipeptide
1
N C V S T V S L V L S
11
N C V S T V S L V L S
1
N C V S T V S L V L S
11
83.3%
NZ_LIXJ01000004.1:
Lanthipeptides: AMK22_RS39975_lanthipeptide
2
C V S T V S L V L S
11
C V S T V S L V L S
1
C V S T V S L V L S
10
72.7%
NZ_ML123034.1 and 3 others:
NZ_ML123034.1 Lanthipeptides: EES43_RS30570_lanthipeptide NZ_ML123034.1 Lanthipeptides: EES43_RS30570_lanthipeptide NZ_ML123034.1 Lanthipeptides: EES43_RS30570_lanthipeptide
Lanthipeptides: EES43_RS30570_lanthipeptide
2
C V S T V S L V L S
11
C V S T+S L V L
1
C V S T I S L V L E
10
with 2 more sequence matches
58.3%
NZ_CP119145.1:
Lanthipeptides: PZB75_RS01650_lanthipeptide
2
C V S T V S L V L S
11
C V S +S+V L S
1
C V S V I S V V L S
10
33.3%
NZ_BDHJ01000009.1 and 17 others:
NZ_CP076457.1 Lanthipeptides: KME66_RS23045_lanthipeptide NZ_KB891297.1 Lanthipeptides: B061_RS39730_lanthipeptide NZ_KB891297.1 Lanthipeptides: B061_RS39730_lanthipeptide NZ_KB891297.1 Lanthipeptides: B061_RS39730_lanthipeptide NZ_KB891297.1 Lanthipeptides: B061_RS39730_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS37365_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS37365_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS37365_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS37365_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS23845_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS23845_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS23845_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS23845_lanthipeptide NZ_LZQS01000002.1 Lanthipeptides: STIB_RS38140_lanthipeptide NZ_LZQS01000002.1 Lanthipeptides: STIB_RS38140_lanthipeptide NZ_RCOL01000001.1 Lanthipeptides: STAN_RS11445_lanthipeptide NZ_RCOL01000001.1 Lanthipeptides: STAN_RS11445_lanthipeptide
Lanthipeptides: BHQ08_RS34920_lanthipeptide
1
N C V S T V S L V L S
11
N C V S T V S L V L
20
N C V S T V S L V L G
30

#### 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.95 out of 23.79
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 26.03 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 30.11
Confidence: medium
Additional weak hits (4):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.95 out of 20.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.83 out of 20.97
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.75 out of 39.62
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.13 out of 27.18
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.

B083_RS1000000136445 - Class II
  Cleavage pHMM score: -6.60
  RODEO score: 0
  Monoisotopic mass: 1048.6 Da
  Molecular weight: 1049.2 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1067.2 Da N = 1
    1085.3 Da N = 2
    1103.3 Da N = 3
B083_RS1000000136445 - Class II
  Cleavage pHMM score: -6.60
  RODEO score: 0
  Monoisotopic mass: 1048.6 Da
  Molecular weight: 1049.2 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1067.2 Da N = 1
    1085.3 Da N = 2
    1103.3 Da N = 3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism

NZ_ARPF01000012.1 - 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: 275,528 - 302,101 nt. (total: 26,574 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B083_RS0122965: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

B083_RS0123000: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: aminotransferase transferase
B083_RS0122960: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

B083_RS0123025: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: dehydratase
B083_RS0122950: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthetase
B083_RS0123005: 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
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.69 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0001839.3 |  | 0.51 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.69 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0001839.3 |  | 0.51 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

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

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:
B083_RS0122990: PT_phytoene_like
Domain 1 (16 - 292): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

B083_RS0122995: PT_phytoene_like
Domain 1 (13 - 296): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

B083_RS0123005: PT_FPPS_like
Domain 1 (74 - 366): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

B083_RS0123010: T2TS
Domain 1 (23 - 652): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.09 out of 23.79
Confidence: medium
Additional weak hits (5):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.04 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.22 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.72 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.16 out of 22.40
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_ARPF01000014.1 - Region 1 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 57,841 - 90,609 nt. (total: 32,769 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
B083_RS0124945: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.52 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002692.2 |  | 0.52 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0001572.3 |  | 0.50 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000939.5 |  | 0.50 | other (other) | aerobactin | Grimontia hollisae
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0001499.5 |  | 0.49 | other (other) | aerobactin | Pantoea ananatis
BGC0002683.2 |  | 0.49 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.52 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002692.2 |  | 0.52 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0001572.3 |  | 0.50 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000939.5 |  | 0.50 | other (other) | aerobactin | Grimontia hollisae
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0001499.5 |  | 0.49 | other (other) | aerobactin | Pantoea ananatis
BGC0002683.2 |  | 0.49 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.79 out of 25.75
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.17 out of 27.18
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.80 out of 27.18
Confidence: medium
Additional weak hits (14):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.51 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.94 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.39 out of 30.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.40 out of 35.63
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.31 out of 27.04
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.84 out of 33.14
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.66 out of 27.04
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.64 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
LexA variant 2 | Repressor of DNA damage response
MatP | Cell cycle regulator
NrdR | Represses ribonucleotide reductase encoding genes

NZ_ARPF01000015.1 - Region 1 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 75,768 nt. (total: 75,768 nt) Show pHMM detection rules used
Region on contig edge.
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B083_RS0125550: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

B083_RS0125560: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: acylase
B083_RS01000000134050: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B083_RS0125590: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase phosphatase
B083_RS0125565: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

B083_RS0125580: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: synthase
B083_RS0125530: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B083_RS0125535: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

B083_RS0125540: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

B083_RS0125545: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000028.5 |  | 0.80 | PKS | bafilomycin B1 | Streptomyces lohii
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001348.5 |  | 0.69 | PKS | JBIR-100 | Streptomyces varsoviensis
BGC0000041.3 |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000113.5 |  | 0.65 | PKS | niddamycin | Streptomyces caelestis
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000028.5 |  | 0.80 | PKS | bafilomycin B1 | Streptomyces lohii
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001348.5 |  | 0.69 | PKS | JBIR-100 | Streptomyces varsoviensis
BGC0000041.3 |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000113.5 |  | 0.65 | PKS | niddamycin | Streptomyces caelestis
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.81 out of 23.79
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.08 out of 25.31
Confidence: medium
Additional weak hits (6):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.02 out of 28.14
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.58 out of 39.62
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.78 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.25 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.11 out of 30.25
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 - 75768:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ohmal - Me-mal) + (Me-ohmal - ohemal - ccmal) + (pk - Me-redmal) + (Me-ohmal - Me-ccmal) + (Me-ccmal)
Non-colinear ordering:
  B083_RS01000000134050 + B083_RS0125530 + B083_RS0125535 + B083_RS0125540 + B083_RS0125545

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).
B083_RS01000000134050: mal - mmal
PKS_AT (1391..1693): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 233.1
  inactive: 116.4
  Methoxymalonyl-CoA: 73.2
  Methylmalonyl-CoA: 59.7
  Propionyl-CoA: 46.9
  Isobutyryl-CoA: 37.0
  Benzoyl-CoA: 21.4
  Ethylmalonyl-CoA: 21.2
  2-Methylbutyryl-CoA: 20.1
  Acetyl-CoA: 17.2
  CHC-CoA: 12.1
  fatty_acid: 9.2
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3046..3342): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Malonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 196.4
  Ethylmalonyl-CoA: 195.2
  Methoxymalonyl-CoA: 162.9
  2-Methylbutyryl-CoA: 137.4
  trans-1,2-CPDA: 123.3
  Propionyl-CoA: 109.2
  CHC-CoA: 93.7
  Malonyl-CoA: 77.6
  Isobutyryl-CoA: 73.0
  Benzoyl-CoA: 64.3
  Acetyl-CoA: 41.7
  3-Methylbutyryl-CoA: 34.9
  fatty_acid: 34.0
  inactive: 24.7

B083_RS0125530: mmal - emal - mal
PKS_AT (577..877): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 218.3
  Ethylmalonyl-CoA: 215.2
  Methoxymalonyl-CoA: 175.1
  2-Methylbutyryl-CoA: 165.6
  trans-1,2-CPDA: 123.2
  Propionyl-CoA: 119.7
  CHC-CoA: 109.3
  Malonyl-CoA: 90.5
  Isobutyryl-CoA: 78.6
  Benzoyl-CoA: 78.3
  Acetyl-CoA: 67.3
  fatty_acid: 46.4
  3-Methylbutyryl-CoA: 44.2
  inactive: 27.3

PKS_AT (2155..2453): emal
ATSignature: Ethylmalonyl-CoA, Methylmalonyl-CoA, Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 221.8
  Methylmalonyl-CoA: 208.3
  Methoxymalonyl-CoA: 188.0
  2-Methylbutyryl-CoA: 143.5
  trans-1,2-CPDA: 139.1
  Malonyl-CoA: 102.5
  Propionyl-CoA: 102.2
  CHC-CoA: 97.6
  Isobutyryl-CoA: 70.6
  Benzoyl-CoA: 67.9
  Acetyl-CoA: 36.2
  inactive: 30.8
  3-Methylbutyryl-CoA: 30.5
  fatty_acid: 26.5

PKS_AT (3818..4108): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  2-Methylbutyryl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 213.6
  inactive: 100.6
  Methoxymalonyl-CoA: 63.3
  Methylmalonyl-CoA: 58.7
  Propionyl-CoA: 38.2
  Ethylmalonyl-CoA: 36.2
  Acetyl-CoA: 23.8
  Isobutyryl-CoA: 23.4
  CHC-CoA: 22.4
  2-Methylbutyryl-CoA: 19.4
  Benzoyl-CoA: 12.6
  trans-1,2-CPDA: 10.6
  fatty_acid: 8.8
  3-Methylbutyryl-CoA: 0.0

B083_RS0125535: pk - mmal
PKS_AT (607..905): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 233.4
  Methylmalonyl-CoA: 227.7
  Methoxymalonyl-CoA: 192.9
  2-Methylbutyryl-CoA: 178.2
  trans-1,2-CPDA: 155.7
  Propionyl-CoA: 123.5
  CHC-CoA: 121.8
  Malonyl-CoA: 119.3
  Benzoyl-CoA: 82.4
  Isobutyryl-CoA: 77.4
  3-Methylbutyryl-CoA: 44.2
  Acetyl-CoA: 40.9
  fatty_acid: 34.9
  inactive: 33.9

PKS_AT (2394..2688): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 199.6
  Ethylmalonyl-CoA: 189.9
  Methoxymalonyl-CoA: 161.5
  2-Methylbutyryl-CoA: 141.5
  trans-1,2-CPDA: 119.5
  Propionyl-CoA: 112.4
  CHC-CoA: 101.8
  Malonyl-CoA: 74.7
  Isobutyryl-CoA: 68.5
  Benzoyl-CoA: 61.6
  Acetyl-CoA: 48.8
  fatty_acid: 38.9
  3-Methylbutyryl-CoA: 28.3
  inactive: 19.3

B083_RS0125540: mmal - mmal
PKS_AT (680..979): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 216.6
  Ethylmalonyl-CoA: 216.6
  Methoxymalonyl-CoA: 182.4
  2-Methylbutyryl-CoA: 152.0
  trans-1,2-CPDA: 122.2
  CHC-CoA: 114.7
  Propionyl-CoA: 112.9
  Malonyl-CoA: 106.2
  Isobutyryl-CoA: 80.6
  Benzoyl-CoA: 74.4
  3-Methylbutyryl-CoA: 54.1
  Acetyl-CoA: 51.5
  inactive: 43.1
  fatty_acid: 41.2

PKS_AT (2267..2561): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 219.3
  Ethylmalonyl-CoA: 214.0
  Methoxymalonyl-CoA: 179.5
  2-Methylbutyryl-CoA: 162.3
  trans-1,2-CPDA: 130.4
  Propionyl-CoA: 123.4
  CHC-CoA: 114.3
  Malonyl-CoA: 95.0
  Isobutyryl-CoA: 85.8
  Benzoyl-CoA: 74.4
  Acetyl-CoA: 61.0
  fatty_acid: 51.0
  3-Methylbutyryl-CoA: 41.6
  inactive: 25.1

B083_RS0125545: mmal
PKS_AT (574..868): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 200.8
  Ethylmalonyl-CoA: 186.3
  Methoxymalonyl-CoA: 170.7
  2-Methylbutyryl-CoA: 153.0
  trans-1,2-CPDA: 128.8
  Propionyl-CoA: 113.1
  Malonyl-CoA: 104.7
  CHC-CoA: 100.0
  Isobutyryl-CoA: 71.1
  Benzoyl-CoA: 64.3
  fatty_acid: 60.3
  Acetyl-CoA: 32.5
  3-Methylbutyryl-CoA: 29.1
  inactive: 27.4

B083_RS0125590: pk
PKS_AT (16..277): pk
ATSignature: (unknown)
No matches above 50%
minowa: Isobutyryl-CoA

Prediction, score:
  Isobutyryl-CoA: 16.9
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Malonyl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_ARPF01000015.1 - Region 2 - NRPS,RiPP-like,T1PKS,t3nrps-iterative
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 113,732 - 179,981 nt. (total: 66,250 nt) Show pHMM detection rules used
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
B083_RS0125790: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

B083_RS0125865: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

B083_RS0125870: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

B083_RS0125875: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

B083_RS0125880: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B083_RS0125905: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

B083_RS0125950: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: aminotransferase
B083_RS0125850: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Lyases: decarboxylase
B083_RS0125935: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: synthase
B083_RS0125860: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transport transporter
B083_RS0125805: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

B083_RS0125995: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | t3nrps-iterative | NRPS | T1PKS | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002365.2 |  |  |  |  | 2.28 | PKS, other (other) | 10-epi-HSAF, 10-epi-3-deOH-HSAF, 10-epi-maltophilin, 10-epi-xanthobaccin C, 10-epi-hydroxymaltophilin, 10-epi-FI-2 | Streptomyces sp.
BGC0001043.4 |  |  |  |  | 1.93 | NRPS, PKS | SGR PTMs, SGR PTM Compound b, SGR PTM Compound c, SGR PTM Compound d | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001244.3 |  |  |  |  | 1.36 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  |  | 1.36 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  |  |  |  | 1.35 | PKS | asperlactone | Aspergillus ochraceus
BGC0000996.5 |  |  |  |  | 1.33 | NRPS, PKS | frontalamide B, frontalamide A | Streptomyces sp. SPB78
BGC0001726.4 |  |  |  |  | 1.12 | NRPS, PKS | pactamide A, pactamide B, pactamide C, pactamide D, pactamide E, pactamide F | Streptomyces pactum
BGC0002509.3 |  |  |  |  | 1.07 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0001833.4 |  |  |  |  | 1.02 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  |  |  | 1.02 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002365.2 |  | 0.91 | PKS, other (other) | 10-epi-HSAF, 10-epi-3-deOH-HSAF, 10-epi-maltophilin, 10-epi-xanthobaccin C, 10-epi-hydroxymaltophilin, 10-epi-FI-2 | Streptomyces sp.
BGC0001043.4 |  | 0.86 | NRPS, PKS | SGR PTMs, SGR PTM Compound b, SGR PTM Compound c, SGR PTM Compound d | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0000996.5 |  | 0.75 | NRPS, PKS | frontalamide B, frontalamide A | Streptomyces sp. SPB78
BGC0001726.4 |  | 0.70 | NRPS, PKS | pactamide A, pactamide B, pactamide C, pactamide D, pactamide E, pactamide F | Streptomyces pactum
BGC0002509.3 |  | 0.68 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0001556.5 |  | 0.68 | NRPS, PKS | combamide | Streptomyces sp.
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
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: 18.92 out of 20.47
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 30.11
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
Additional weak hits (17):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.96 out of 25.88
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.74 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.68 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.38 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.74 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.25 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.72 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.54 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.61 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.48 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.53 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.15 out of 33.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.85 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 113731 - 179981:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk - Orn)

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).
B083_RS0125860: pk - Orn
Search NORINE for peptide: strict or relaxed
PKS_AT (549..845): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  CE-Malonyl-CoA: 58.3%
  Acetyl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 124.8
  Methoxymalonyl-CoA: 115.8
  Malonyl-CoA: 113.5
  Ethylmalonyl-CoA: 108.0
  Isobutyryl-CoA: 89.4
  Propionyl-CoA: 74.6
  Acetyl-CoA: 72.8
  trans-1,2-CPDA: 70.9
  2-Methylbutyryl-CoA: 65.9
  Benzoyl-CoA: 61.1
  CHC-CoA: 51.0
  fatty_acid: 37.7
  inactive: 32.8
  3-Methylbutyryl-CoA: 31.3

AMP-binding (2301..2713): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAWAFDVFTGDREFVVGSDVNSYGLTEATIDSAC
  Nearest Stachelhaus code(s):
    Orn DVGEVGSIDK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CelR | Cellobiose uptake repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_ARPF01000015.1 - Region 3 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 204,791 - 231,150 nt. (total: 26,360 nt) Show pHMM detection rules used
Region on contig edge.
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase carbamoyltransferase
B083_RS0126240: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

B083_RS0126245: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

Hydrolases: deacetylase
B083_RS0126160: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

Lyases: cyclase
B083_RS0126205: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: ligase
B083_RS0126235: 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
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (4):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.65 out of 27.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.98 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 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 4, location 204790 - 231150:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).
B083_RS0126235: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (479..880): 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:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    gly (Gly)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAMTFDPSLMELQALSGGEWDLYGPTETTVWSTT
  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
--- | ---

NZ_ARPF01000016.1 - Region 1 - ectoine
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: 125,000 - 135,398 nt. (total: 10,399 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
B083_RS0126865: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: aminotransferase
B083_RS0126885: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

B083_RS0126895: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

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 | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.91 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.85 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.91 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.85 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.94 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (9):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.72 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.51 out of 27.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.04 out of 26.12
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.16 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.76 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.47 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.96 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.75 out of 21.55
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.46 out of 27.55
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism

NZ_ARPF01000020.1 - Region 1 - T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 42,234 nt. (total: 42,234 nt) Show pHMM detection rules used
Region on contig edge.
T2PKS: (t2ks and t2clf)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
B083_RS0128000: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

B083_RS0128025: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B083_RS0128035: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

B083_RS0128085: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: PPTase carboxylase glycosyltransferase transferase
B083_RS0127990: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

B083_RS0128045: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

B083_RS0128050: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

B083_RS0128125: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Lyases: cyclase
B083_RS0128005: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

B083_RS0128030: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Isomerases: mutase
B083_RS0128160: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: synthase
B083_RS0128010: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B083_RS0128015: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.84 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.83 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.78 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000235.5 |  | 0.64 | PKS | kiamycin | Streptomyces sp. W007
BGC0000253.4 |  | 0.63 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002477.3 |  | 0.62 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0000236.5 |  | 0.60 | PKS | kinamycin | Streptomyces murayamaensis
BGC0002047.2 |  | 0.60 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0001895.4 |  | 0.59 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0002672.2 |  | 0.59 | PKS | saccharothrixin D, saccharothrixin E, saccharothrixin F, saccharothrixin G, saccharothrixin H, saccharothrixin I, saccharothrixin J, saccharothrixin K, saccharothrixin L, saccharothrixin M | Saccharothrix sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.84 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.83 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.78 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000235.5 |  | 0.64 | PKS | kiamycin | Streptomyces sp. W007
BGC0000253.4 |  | 0.63 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002477.3 |  | 0.62 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0000236.5 |  | 0.60 | PKS | kinamycin | Streptomyces murayamaensis
BGC0002047.2 |  | 0.60 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0001895.4 |  | 0.59 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0002672.2 |  | 0.59 | PKS | saccharothrixin D, saccharothrixin E, saccharothrixin F, saccharothrixin G, saccharothrixin H, saccharothrixin I, saccharothrixin J, saccharothrixin K, saccharothrixin L, saccharothrixin M | Saccharothrix sp.

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05
Confidence: strong
Additional weak hits (14):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.68 out of 20.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.05 out of 27.55
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.88 out of 25.88
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.25 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.77 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.37 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.52 out of 20.01
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.53 out of 28.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.92 out of 23.43
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.52 out of 35.63
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.14 out of 20.01
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.90 out of 24.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.62 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  0 to 42234
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:
  8|9 (Score: 707.3; E-value: 1.1e-215)
Product class(es):
  angucycline
Product molecular weight(s):
  acetyl-CoA_8: 367 Da
  acetyl-CoA_9: 409 Da

B083_RS0128000
  OXY (Score: 598.2; E-value: 2.8e-182)
B083_RS0128005
  CYC C4-C17/C2-C19 (Score: 194.8; E-value: 3.1e-60)
B083_RS0128010
  KS (Score: 798.8; E-value: 2.3e-243)
B083_RS0128015
  CLF 8|9 (Score: 707.3; E-value: 1.1e-215)
B083_RS0128020
  ACP (Score: 130.6; E-value: 3.8e-41)
B083_RS0128025
  KR C9 (Score: 473.6; E-value: 3.4e-145)
B083_RS0128030
  CYC C7-C12 (Score: 493.9; E-value: 3.4e-151)
B083_RS0128035
  KR C15 (Score: 486.1; E-value: 5.1e-149)
B083_RS0128085
  OXY (Score: 12.7; E-value: 0.00012)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_ARPF01000020.1 - Region 2 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 81,005 - 103,798 nt. (total: 22,794 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
B083_RS0128435: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001634.3 |  | 0.86 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001507.3 |  | 0.67 | ribosomal | anantin C | Streptomyces olindensis
BGC0001548.4 |  | 0.65 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001550.3 |  | 0.63 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001549.3 |  | 0.63 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001645.3 |  | 0.61 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001551.4 |  | 0.61 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001493.5 |  | 0.60 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001539.4 |  | 0.59 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001506.5 |  | 0.59 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001634.3 |  | 0.86 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001507.3 |  | 0.67 | ribosomal | anantin C | Streptomyces olindensis
BGC0001548.4 |  | 0.65 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001550.3 |  | 0.63 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001549.3 |  | 0.63 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001645.3 |  | 0.61 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001551.4 |  | 0.61 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001493.5 |  | 0.60 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001539.4 |  | 0.59 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001506.5 |  | 0.59 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146

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.

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

#### Lassopeptide(s) for B083_RS1000000135975

B083_RS1000000135975
Leader:
MKQQQEKAKKAYMKPSLFKQGDFSKKTA
Full core:
G Y F Y G S Y K E Y W V R R I I
Putative macrolactam:
G Y F Y G S Y K E

#### antiSMASH-DB 4.0 matches for B083_RS1000000135975

100.0%
NZ_AQRK01000073.1 and 34 others:
NZ_ARPF01000020.1 Lassopeptides: B083_RS1000000135975_lassopeptide NZ_BMSP01000033.1 Lassopeptides: IE150_RS31095_lassopeptide NZ_BNBJ01000018.1 Lassopeptides: IE304_RS27885_lassopeptide NZ_CP011522.1 Lassopeptides: ABE83_RS36070_lassopeptide NZ_CP015362.1 Lassopeptides: A6E92_RS32825_lassopeptide NZ_CP020570.1 Lassopeptides: B1H20_RS34515_lassopeptide NZ_CP024957.1 Lassopeptides: CVT27_RS18750_lassopeptide NZ_CP030930.1 Lassopeptides: DTW94_RS18860_lassopeptide NZ_CP032543.1 Lassopeptides: D6270_RS18940_lassopeptide NZ_CP058556.1 Lassopeptides: HXS80_RS15025_lassopeptide NZ_CP059898.1 Lassopeptides: H3V39_RS14565_lassopeptide NZ_CP070242.1 Lassopeptides: I6J39_RS14950_lassopeptide NZ_CP070260.1 Lassopeptides: I6J40_RS19545_lassopeptide NZ_CP077652.1 Lassopeptides: KRR37_RS18710_lassopeptide NZ_CP079114.1 Lassopeptides: KV381_RS20695_lassopeptide NZ_CP101140.1 Lassopeptides: NF554_RS14180_lassopeptide NZ_CP101397.1 Lassopeptides: NLU04_RS02420_lassopeptide NZ_CP113262.1 Lassopeptides: OUQ49_RS18920_lassopeptide NZ_JAGGOV010000040.1 Lassopeptides: J7E92_RS24040_lassopeptide NZ_JAHHWT010000002.1 Lassopeptides: KM153_RS04955_lassopeptide NZ_JAJDST010000050.1 Lassopeptides: LJC81_RS32430_lassopeptide NZ_JALDPQ010000042.1 Lassopeptides: MQC87_RS04740_lassopeptide NZ_JAMFLF010000013.1 Lassopeptides: M1212_RS26530_lassopeptide NZ_JANRMN010000006.1 Lassopeptides: NW249_RS11850_lassopeptide NZ_KB890924.1 Lassopeptides: B053_RS1000000136555_lassopeptide NZ_KB891296.1 Lassopeptides: B061_RS39115_lassopeptide NZ_KL573564.1 Lassopeptides: BG84_RS1000000139430_lassopeptide NZ_KZ819159.1 Lassopeptides: DBP19_RS18270_lassopeptide NZ_LR881952.1 Lassopeptides: STRPST75_RS15280_lassopeptide NZ_LZQS01000001.1 Lassopeptides: STIB_RS37415_lassopeptide NZ_RCOL01000001.1 Lassopeptides: STAN_RS20170_lassopeptide NZ_VEHK01000003.1 Lassopeptides: FS984_RS09665_lassopeptide NZ_WUEJ01000001.1 Lassopeptides: GRQ63_RS00790_lassopeptide NZ_WWGL01000031.1 Lassopeptides: GTY38_RS20560_lassopeptide
Lassopeptides: YUW_RS35360_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F Y G S Y K E Y W V R R I I
1
G Y F Y G S Y K E Y W V R R I I
16
93.8%
NZ_CP110539.1 and 1 other:
NZ_CP112880.1 Lassopeptides: N7925_RS15605_lassopeptide
Lassopeptides: OH133_RS17115_lassopeptide
1
G Y F Y G S Y K E Y W V R R I
15
G Y F Y G S Y K E Y W V R R I
1
G Y F Y G S Y K E Y W V R R I
15
87.5%
NZ_BMRY01000001.1 and 14 others:
NZ_BMSZ01000030.1 Lassopeptides: IE135_RS32485_lassopeptide NZ_CP010833.1 Lassopeptides: TK78_RS35300_lassopeptide NZ_CP021707.1 Lassopeptides: CCZ36_RS19605_lassopeptide NZ_CP084357.1 Lassopeptides: LEL86_RS33655_lassopeptide NZ_DS999644.1 Lassopeptides: SSGG_RS36910_lassopeptide NZ_JNLT01000024.1 Lassopeptides: CD02_RS38355_lassopeptide NZ_KZ679082.1 Lassopeptides: C6W96_RS19995_lassopeptide NZ_KZ819154.1 Lassopeptides: DBP12_RS14735_lassopeptide NZ_KZ819178.1 Lassopeptides: DBP20_RS19850_lassopeptide NZ_KZ819182.1 Lassopeptides: DBP21_RS20195_lassopeptide NZ_LACR01000007.1 Lassopeptides: YW5_RS36195_lassopeptide NZ_LZRD01000023.1 Lassopeptides: A3Q37_RS36590_lassopeptide NZ_NNBN01000001.1 Lassopeptides: CG717_RS32755_lassopeptide NZ_WWGD01000017.1 Lassopeptides: GTY72_RS09250_lassopeptide
Lassopeptides: IE140_RS06105_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F G S Y K E Y W R R I I
1
G Y F V G S Y K E Y W S R R I I
16
with 12 more sequence matches
Only the first 10 are displayed here.
87.5%
NZ_CP013738.1 and 4 others:
NZ_CP029361.1 Lassopeptides: DIJ69_RS14415_lassopeptide NZ_CP090837.1 Lassopeptides: LZ559_RS19885_lassopeptide NZ_JAJUKK010000001.1 Lassopeptides: LXH09_RS00260_lassopeptide NZ_LIXK01000001.1 Lassopeptides: AMK23_RS36895_lassopeptide
Lassopeptides: WQO_RS35795_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F G S Y K E Y W R R I I
1
G Y F V G S Y K E Y W T R R I I
16
82.4%
NC_021177.1 and 5 others:
NZ_BMUG01000007.1 Lassopeptides: IE264_RS21365_lassopeptide NZ_CP054926.1 Lassopeptides: HUT09_RS19455_lassopeptide NZ_CP068598.1 Lassopeptides: IFE09_RS19740_lassopeptide NZ_CP071044.1 Lassopeptides: JHY03_RS19320_lassopeptide NZ_JOJC01000016.1 Lassopeptides: IO23_RS1000000136610_lassopeptide
Lassopeptides: SFUL_RS36235_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F G S Y K E Y W V R R I+
1
G Y F V G S Y K E Y W V R R I V
16
81.2%
NZ_BDHJ01000011.1 and 4 others:
NZ_BMTW01000001.1 Lassopeptides: IE134_RS04135_lassopeptide NZ_CP076457.1 Lassopeptides: KME66_RS14195_lassopeptide NZ_KZ268499.1 Lassopeptides: CE422_RS34520_lassopeptide NZ_ML123117.1 Lassopeptides: EES46_RS05210_lassopeptide
Lassopeptides: BHQ08_RS34645_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F G S Y K E Y W R R I+
1
G Y F V G S Y K E Y W T R R I V
16
81.2%
NZ_CP020563.1:
Lassopeptides: B7C62_RS35255_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F G S Y K E+W R R I I
1
G Y F I G S Y K E F W S R R I I
16
75.0%
NZ_KB891808.1:
Lassopeptides: B072_RS47760_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F G S Y K E+ V R R I+
1
G Y F V G S Y K E W I V R R I V
16
75.0%
NZ_PGGW01000069.1:
Lassopeptides: CUT44_RS32610_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F Y G S Y K E+ R R I+
1
G Y F Y G S Y K E F L S R R I V
16
68.8%
NZ_CP061281.1:
Lassopeptides: IAG42_RS10065_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F G Y K E+ V R R I+
1
G Y F V G P Y K E W I V R R I V
16
62.5%
NZ_FOET01000001.1:
Lassopeptides: BMY40_RS27365_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F G Y K E Y+ R R +
1
G Y F V G K Y K E Y F S R R F V
16
62.5%
NZ_FOSG01000008.1 and 1 other:
NZ_PDKQ02000012.1 Lassopeptides: BFM75_RS03245_lassopeptide
Lassopeptides: BM237_RS28735_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G Y F+G Y K E Y+ R R +
1
G Y F F G K Y K E Y F S R R F V
16
58.8%
NZ_JACHEM010000013.1:
Lassopeptides: HNQ79_RS23595_lassopeptide
1
G Y F Y G S Y K E Y W V R R I I
16
G F Y S K E Y W R R+
1
G M F Y A S C K E Y W S R R L C
16

#### 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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.07 out of 26.85
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 27.04
Confidence: medium
Additional weak hits (12):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.70 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.97 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.70 out of 29.38
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.90 out of 26.12
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.36 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.70 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.15 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.82 out of 24.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.78 out of 30.98
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.15 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.98 out of 28.14
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

B083_RS1000000135975 - Class II
  Cleavage pHMM score: 0.20
  RODEO score: 20
  Monoisotopic mass: 2081.0 Da
  Molecular weight: 2082.4 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (81004...103798)
B083_RS0128440
  RRE type: Stand_Alone_Lasso_RRE
  Location: 0 - 82
  Score: 87.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
DasR | N-acetylglucosamine dependent repressor
RutR | Regulator of the pyrimidine and purine metabolism

NZ_ARPF01000023.1 - 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: 67,387 - 88,481 nt. (total: 21,095 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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B083_RS0129740: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: formyltransferase
B083_RS0129770: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Lyases: cyclase hydratase
B083_RS0129730: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

B083_RS0129750: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002708.2 |  | 0.76 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0002707.2 |  | 0.47 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0000631.5 |  | 0.37 | terpene | Botrydial, 8,9-epibotrydial, 1-epibotrydial, Dihydrobotrydial, 10-Oxo-dihydrobotrydial, 10-dehydroxy dihydrobotrydialone, 10-epi-dihydrobotrydial, Botryendial, Botryenalol, Botrydienal, Norbotrydialone acetate, 10-Oxodihydrobotry-1(9),4(5)-diendial, 10-Oxodehydrodihydrobotrydial, Dehydrobotrydienol, 11-Hydroxydehydrobotrydienol, 12-hydroxydehydrobotrydienol, Secobotrytriendiol, Secobotrytriene-10,12,15-triol, Secobotrydiene-3,10,15-triol, Secobotrydiene-3,4,10,15-tetraol, 4β-Acetoxytetrahydrobotryslactone | Botrytis cinerea B05.10
BGC0002034.3 |  | 0.36 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0000879.5 |  | 0.35 | other (other) | toyocamycin, sangivamycin | Streptomyces rimosus
BGC0000881.3 |  | 0.33 | other (other) | toyocamycin | Streptomyces ahygroscopicus subsp. wuzhouensis
BGC0001808.5 |  | 0.33 | other (other) | toyocamycin | Streptomyces diastatochromogenes
BGC0000772.5 |  | 0.33 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0002255.3 |  | 0.33 | PKS | lijiquinone | Ascomycota sp. F53
BGC0001865.4 |  | 0.32 | PKS | elsinochrome C | Parastagonospora nodorum SN15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002708.2 |  | 0.76 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0002707.2 |  | 0.47 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0000631.5 |  | 0.37 | terpene | Botrydial, 8,9-epibotrydial, 1-epibotrydial, Dihydrobotrydial, 10-Oxo-dihydrobotrydial, 10-dehydroxy dihydrobotrydialone, 10-epi-dihydrobotrydial, Botryendial, Botryenalol, Botrydienal, Norbotrydialone acetate, 10-Oxodihydrobotry-1(9),4(5)-diendial, 10-Oxodehydrodihydrobotrydial, Dehydrobotrydienol, 11-Hydroxydehydrobotrydienol, 12-hydroxydehydrobotrydienol, Secobotrytriendiol, Secobotrytriene-10,12,15-triol, Secobotrydiene-3,10,15-triol, Secobotrydiene-3,4,10,15-tetraol, 4β-Acetoxytetrahydrobotryslactone | Botrytis cinerea B05.10
BGC0002034.3 |  | 0.36 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0000879.5 |  | 0.35 | other (other) | toyocamycin, sangivamycin | Streptomyces rimosus
BGC0000881.3 |  | 0.33 | other (other) | toyocamycin | Streptomyces ahygroscopicus subsp. wuzhouensis
BGC0001808.5 |  | 0.33 | other (other) | toyocamycin | Streptomyces diastatochromogenes
BGC0000772.5 |  | 0.33 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0002255.3 |  | 0.33 | PKS | lijiquinone | Ascomycota sp. F53
BGC0001865.4 |  | 0.32 | PKS | elsinochrome C | Parastagonospora nodorum SN15

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
monoterpene |  |  | C10 | C1-C10 | none
sesquiterpene |  |  | C15 | C1-C10 | none

Genes with terpene domains:
B083_RS0129750: T1TS
Domain 1 (4 - 315): Type 1 terpene synthase
Subtype: Germacrene A synthase type

Reactions:
  GPP → monoterpene_C1-C10
  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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.10 out of 23.79
Confidence: medium
Additional weak hits (16):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.94 out of 23.43
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.44 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.28 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.79 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.15 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.76 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.18 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.15 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.70 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.65 out of 26.12
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.43 out of 39.62
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.11 out of 25.88
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.97 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.72 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GPP | Geranyl diphoshate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_ARPF01000024.1 - Region 1 - T1PKS,linaridin
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 12,518 - 39,385 nt. (total: 26,868 nt) Show pHMM detection rules used
Region on contig edge.
linaridin: (cypemycin or cypI)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
B083_RS0129935: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Ligases: ligase synthase
B083_RS01000000134275: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

B083_RS0129965: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0129970: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B083_RS0129975: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate 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 | linaridin | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002193.2 |  |  | 0.54 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001641.4 |  |  | 0.51 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000357.5 |  |  | 0.48 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001164.3 |  |  | 0.47 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.47 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001735.5 |  |  | 0.40 | other (other) | pentostatine, vidarabine | Streptomyces antibioticus
BGC0001050.5 |  |  | 0.35 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0001188.3 |  |  | 0.31 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0002150.2 |  |  | 0.28 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0002151.2 |  |  | 0.28 | ribosomal | alboverticillin | Streptomyces griseocarneus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002193.2 |  | 0.62 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002191.2 |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000037.4 |  | 0.60 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000357.5 |  | 0.59 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  | 0.59 | PKS | FR901512 | fungal sp. No.14919
BGC0001050.5 |  | 0.59 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0000948.5 |  | 0.57 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (3):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.52 out of 24.78
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
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 12517 - 39385:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 15050 - 39385:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B083_RS0129965: X
AMP-binding (10..416): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    NTTLHTFGICGTMGFSGGALEGYGLTETSPVVAY
  Nearest Stachelhaus code(s):
    nLev GFCMYGGCSK (74% 8Å match)
  Stachelhaus code match:
    60% (weak)

B083_RS0129970: X
AMP-binding (15..418): 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:
    -ARLHSSGATADLLTYVGCIQVYATSEAGFVSML
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

B083_RS01000000134275: mmal - mmal
PKS_AT (111..410): mmal
ATSignature: Isobutyryl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 158.9
  Ethylmalonyl-CoA: 153.4
  2-Methylbutyryl-CoA: 150.0
  Methoxymalonyl-CoA: 133.8
  Propionyl-CoA: 129.7
  CHC-CoA: 96.9
  Isobutyryl-CoA: 88.0
  Malonyl-CoA: 82.4
  trans-1,2-CPDA: 80.2
  Benzoyl-CoA: 49.0
  Acetyl-CoA: 33.2
  3-Methylbutyryl-CoA: 29.6
  inactive: 22.5
  fatty_acid: 15.4

PKS_AT (1126..1420): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 214.6
  Ethylmalonyl-CoA: 211.8
  Methoxymalonyl-CoA: 176.9
  2-Methylbutyryl-CoA: 153.3
  trans-1,2-CPDA: 133.8
  CHC-CoA: 119.3
  Propionyl-CoA: 118.1
  Malonyl-CoA: 95.3
  Benzoyl-CoA: 83.9
  Isobutyryl-CoA: 77.3
  Acetyl-CoA: 54.1
  fatty_acid: 40.9
  3-Methylbutyryl-CoA: 28.1
  inactive: 25.3

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

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