Select genomic region:
Overview
3.1
29.1
29.2
29.3
40.1
40.2
88.1

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

NZ_JZOJ01000007.1 (Escherichia coli)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | RiPP-like | 2,542 | 11,415 | Low | microcin L | ribosomal:RiPP:Microcin

NZ_JZOJ01000072.1 (Escherichia coli)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 29.1 | azole-containing-RiPP | 103,213 | 129,505 |  |
Region 29.2 | NRP-metallophore,NRPS | 429,040 | 483,994 | High | enterobactin | NRPS:Type I
Region 29.3 | terpene-precursor | 596,430 | 617,329 |

NZ_JZOJ01000078.1 (Escherichia coli)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 40.1 | NRP-metallophore,NRPS,T1PKS,butyrolactone | 444,371 | 512,382 | Low | yersiniabactin | NRPS:Type I+PKS
Region 40.2 | NRPS,T1PKS | 517,864 | 589,026 | High | N-myristoyl-D-asparagine/cis-7-tetradecenoyl-D-asparagine/(R)-N1-((S)-5-oxohexan-2-yl)-2-tetradecanamidosuccinamide/colibactin/precolibactin 1489 | NRPS:Type I+PKS:Type I

NZ_JZOJ01000049.1 (Escherichia coli)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 88.1 | lassopeptide | 1 | 6,012 | High | microcin J25 | ribosomal:RiPP:Lasso peptide

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | RiPP-like | 2,542 | 11,415 | Low | microcin L | ribosomal:RiPP:Microcin
Region 29.1 | azole-containing-RiPP | 103,213 | 129,505 |  |
Region 29.2 | NRP-metallophore,NRPS | 429,040 | 483,994 | High | enterobactin | NRPS:Type I
Region 29.3 | terpene-precursor | 596,430 | 617,329 |
Region 40.1 | NRP-metallophore,NRPS,T1PKS,butyrolactone | 444,371 | 512,382 | Low | yersiniabactin | NRPS:Type I+PKS
Region 40.2 | NRPS,T1PKS | 517,864 | 589,026 | High | N-myristoyl-D-asparagine/cis-7-tetradecenoyl-D-asparagine/(R)-N1-((S)-5-oxohexan-2-yl)-2-tetradecanamidosuccinamide/colibactin/precolibactin 1489 | NRPS:Type I+PKS:Type I
Region 88.1 | lassopeptide | 1 | 6,012 | High | microcin J25 | ribosomal:RiPP:Lasso peptide

No secondary metabolite regions were found in these records:
  NZ_JZOJ01000050.1 (Escherichia coli)
  NZ_JZOJ01000051.1 (Escherichia coli)
  NZ_JZOJ01000052.1 (Escherichia coli)
  NZ_JZOJ01000053.1 (Escherichia coli)
  NZ_JZOJ01000054.1 (Escherichia coli)
  NZ_JZOJ01000008.1 (Escherichia coli)
  NZ_JZOJ01000055.1 (Escherichia coli)
  NZ_JZOJ01000056.1 (Escherichia coli)
  NZ_JZOJ01000057.1 (Escherichia coli)
  NZ_JZOJ01000058.1 (Escherichia coli)
  NZ_JZOJ01000059.1 (Escherichia coli)
  NZ_JZOJ01000060.1 (Escherichia coli)
  NZ_JZOJ01000061.1 (Escherichia coli)
  NZ_JZOJ01000062.1 (Escherichia coli)
  NZ_JZOJ01000063.1 (Escherichia coli)
  NZ_JZOJ01000009.1 (Escherichia coli)
  NZ_JZOJ01000064.1 (Escherichia coli)
  NZ_JZOJ01000065.1 (Escherichia coli)
  NZ_JZOJ01000010.1 (Escherichia coli)
  NZ_JZOJ01000066.1 (Escherichia coli)
  NZ_JZOJ01000067.1 (Escherichia coli)
  NZ_JZOJ01000068.1 (Escherichia coli)
  NZ_JZOJ01000069.1 (Escherichia coli)
  NZ_JZOJ01000001.1 (Escherichia coli)
  NZ_JZOJ01000070.1 (Escherichia coli)
  NZ_JZOJ01000071.1 (Escherichia coli)
  NZ_JZOJ01000011.1 (Escherichia coli)
  NZ_JZOJ01000012.1 (Escherichia coli)
  NZ_JZOJ01000013.1 (Escherichia coli)
  NZ_JZOJ01000073.1 (Escherichia coli)
  NZ_JZOJ01000014.1 (Escherichia coli)
  NZ_JZOJ01000074.1 (Escherichia coli)
  NZ_JZOJ01000015.1 (Escherichia coli)
  NZ_JZOJ01000075.1 (Escherichia coli)
  NZ_JZOJ01000016.1 (Escherichia coli)
  NZ_JZOJ01000076.1 (Escherichia coli)
  NZ_JZOJ01000077.1 (Escherichia coli)
  NZ_JZOJ01000002.1 (Escherichia coli)
  NZ_JZOJ01000079.1 (Escherichia coli)
  NZ_JZOJ01000080.1 (Escherichia coli)
  NZ_JZOJ01000017.1 (Escherichia coli)
  NZ_JZOJ01000081.1 (Escherichia coli)
  NZ_JZOJ01000082.1 (Escherichia coli)
  NZ_JZOJ01000018.1 (Escherichia coli)
  NZ_JZOJ01000019.1 (Escherichia coli)
  NZ_JZOJ01000083.1 (Escherichia coli)
  NZ_JZOJ01000084.1 (Escherichia coli)
  NZ_JZOJ01000020.1 (Escherichia coli)
  NZ_JZOJ01000085.1 (Escherichia coli)
  NZ_JZOJ01000086.1 (Escherichia coli)
  NZ_JZOJ01000087.1 (Escherichia coli)
  NZ_JZOJ01000088.1 (Escherichia coli)
  NZ_JZOJ01000021.1 (Escherichia coli)
  NZ_JZOJ01000003.1 (Escherichia coli)
  NZ_JZOJ01000022.1 (Escherichia coli)
  NZ_JZOJ01000089.1 (Escherichia coli)
  NZ_JZOJ01000023.1 (Escherichia coli)
  NZ_JZOJ01000024.1 (Escherichia coli)
  NZ_JZOJ01000025.1 (Escherichia coli)
  NZ_JZOJ01000004.1 (Escherichia coli)
  NZ_JZOJ01000026.1 (Escherichia coli)
  NZ_JZOJ01000027.1 (Escherichia coli)
  NZ_JZOJ01000028.1 (Escherichia coli)
  NZ_JZOJ01000029.1 (Escherichia coli)
  NZ_JZOJ01000030.1 (Escherichia coli)
  NZ_JZOJ01000031.1 (Escherichia coli)
  NZ_JZOJ01000005.1 (Escherichia coli)
  NZ_JZOJ01000032.1 (Escherichia coli)
  NZ_JZOJ01000033.1 (Escherichia coli)
  NZ_JZOJ01000034.1 (Escherichia coli)
  NZ_JZOJ01000035.1 (Escherichia coli)
  NZ_JZOJ01000036.1 (Escherichia coli)
  NZ_JZOJ01000037.1 (Escherichia coli)
  NZ_JZOJ01000038.1 (Escherichia coli)
  NZ_JZOJ01000039.1 (Escherichia coli)
  NZ_JZOJ01000040.1 (Escherichia coli)
  NZ_JZOJ01000041.1 (Escherichia coli)
  NZ_JZOJ01000042.1 (Escherichia coli)
  NZ_JZOJ01000043.1 (Escherichia coli)
  NZ_JZOJ01000044.1 (Escherichia coli)
  NZ_JZOJ01000045.1 (Escherichia coli)
  NZ_JZOJ01000046.1 (Escherichia coli)
  NZ_JZOJ01000047.1 (Escherichia coli)
  NZ_JZOJ01000048.1 (Escherichia coli)
  NZ_JZOJ01000006.1 (Escherichia coli)

Compact view
NZ_JZOJ01000007.1 - Region 1 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,542 - 11,415 nt. (total: 8,874 nt) Show pHMM detection rules used
Region on contig edge.
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

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

No matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.70 out of 32.93
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.97 out of 32.93
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 28.19
Confidence: medium
Additional weak hits (3):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.61 out of 30.22
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.16 out of 27.55
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 25.24 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
LexA variant 3 | Repressor of DNA damage response
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_JZOJ01000072.1 - Region 1 - 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: 103,213 - 129,505 nt. (total: 26,293 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: electron transfer
VE62_RS13560: flavodoxin

smcogs
  SMCOG1134: flavodoxin

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

Reference | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001285.5 |  | 0.34 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0002300.2 |  | 0.30 | NRPS | albomycin delta2, albomycin delta1, albomycin epsilon | Streptomyces sp. ATCC 700974
BGC0001441.5 |  | 0.28 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0002439.3 |  | 0.28 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0000781.3 |  | 0.28 | saccharide | O-antigen | Pseudomonas aeruginosa
BGC0000070.5 |  | 0.27 | PKS | griseofulvin, epidechlorogriseofulvin | Penicillium aethiopicum
BGC0000784.3 |  | 0.27 | saccharide | O-antigen | Pseudomonas aeruginosa
BGC0001302.5 |  | 0.27 | other (other) | lomofungin | Streptomyces lomondensis
BGC0000981.3 |  | 0.26 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E6
BGC0002012.4 |  | 0.25 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001285.5 |  | 0.34 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0002300.2 |  | 0.30 | NRPS | albomycin delta2, albomycin delta1, albomycin epsilon | Streptomyces sp. ATCC 700974
BGC0001441.5 |  | 0.28 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0002439.3 |  | 0.28 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0000781.3 |  | 0.28 | saccharide | O-antigen | Pseudomonas aeruginosa
BGC0000070.5 |  | 0.27 | PKS | griseofulvin, epidechlorogriseofulvin | Penicillium aethiopicum
BGC0000784.3 |  | 0.27 | saccharide | O-antigen | Pseudomonas aeruginosa
BGC0001302.5 |  | 0.27 | other (other) | lomofungin | Streptomyces lomondensis
BGC0000981.3 |  | 0.26 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E6
BGC0002012.4 |  | 0.25 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.32 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.65 out of 28.19
Confidence: medium
Additional weak hits (5):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.73 out of 39.62
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.12 out of 28.14
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.81 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.82 out of 29.38
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.
TFBS Finder
Azole RiPPs
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MexT | Global virulence regulator
ZuR variant 1 | Zinc-responsive repressor

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_JZOJ01000072.1 - Region 2 - 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: 429,040 - 483,994 nt. (total: 54,955 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase reductase
VE62_RS15225: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

VE62_RS15230: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

VE62_RS15260: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

VE62_RS15280: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

VE62_RS15385: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

Transferases: PPTase aminotransferase
VE62_RS15255: aminotransferase

smcogs
  SMCOG1019: aminotransferase

VE62_RS15350: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Hydrolases: esterase hydrolase
VE62_RS15275: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

VE62_RS15285: isochorismatase

smcogs
  SMCOG1027: isochorismatase

VE62_RS15340: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

Isomerases: isomerase
VE62_RS15235: disulfide isomerase/thiol-disulfide oxidase

smcogs
  SMCOG1233: disulfide isomerase/thiol-disulfide oxidase

VE62_RS15295: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
VE62_RS15290: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

VE62_RS15330: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

VE62_RS15370: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

Translocases: permease
VE62_RS15395: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002476.2 |  |  | 1.62 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0002075.3 |  |  | 0.86 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000343.5 |  |  | 0.73 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001833.4 |  |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002413.3 |  |  | 0.67 | NRPS | frederiksenibactin | Yersinia frederiksenii ATCC 33641
BGC0001825.4 |  |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001185.5 |  |  | 0.65 | NRPS | bacillibactin | Bacillus velezensis FZB42

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002476.2 |  | 0.93 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000343.5 |  | 0.69 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002413.3 |  | 0.67 | NRPS | frederiksenibactin | Yersinia frederiksenii ATCC 33641
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001185.5 |  | 0.66 | NRPS | bacillibactin | Bacillus velezensis FZB42

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 26.61 out of 29.38
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
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.84 out of 29.38
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.40 out of 21.55
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 24.40 out of 30.25
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.70 out of 26.85
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.00 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.50 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.06 out of 28.19
Confidence: medium
Additional weak hits (19):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.06 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.18 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.71 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.46 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.06 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.52 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.34 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.09 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.38 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.24 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.02 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.36 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.34 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.08 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.41 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.02 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 22.40
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.06 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 429039 - 483994:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
VE62_RS15290: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (34..437): 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:
    SRSIYAMSSPGGALQVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz AMPAQGVVNK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

VE62_RS15330: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (461..863): 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:
    RWMTFDVSVWEWHFFCSGEHNLYGPTEAAVDVSW
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (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
--- | ---
ArcA | Repressor of carbon oxidation
CRP | Cyclic AMP receptor protein
ColR | Phenol-responsive regulator
FuR variant 1 | Ferric Uptake Regulator
RutR | Regulator of the pyrimidine and purine metabolism
ZuR variant 1 | Zinc-responsive repressor

NZ_JZOJ01000072.1 - Region 3 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 596,430 - 617,329 nt. (total: 20,900 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase synthase
VE62_RS16065: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

VE62_RS16090: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Hydrolases: synthase
VE62_RS16090: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Ligases: synthase synthetase
VE62_RS16055: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

VE62_RS16060: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001361.3 |  | 0.50 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.50 | terpene | sodorifen | Serratia plymuthica
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0001605.3 |  | 0.39 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002219.2 |  | 0.39 | terpene | (-)-(R)-nephthenol | Stereum hirsutum FP-91666 SS1
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0001594.3 |  | 0.38 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000929.3 |  | 0.38 | other (other) | xanthothricin | Burkholderia glumae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001361.3 |  | 0.50 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.50 | terpene | sodorifen | Serratia plymuthica
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0001605.3 |  | 0.39 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002219.2 |  | 0.39 | terpene | (-)-(R)-nephthenol | Stereum hirsutum FP-91666 SS1
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0001594.3 |  | 0.38 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000929.3 |  | 0.38 | other (other) | xanthothricin | Burkholderia glumae

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP

Genes with terpene domains:
VE62_RS16055: PT_FPPS_like
Domain 1 (32 - 299): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  DMAPP, IPP → FPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.79 out of 27.78
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.49 out of 26.85
Confidence: medium
Additional weak hits (5):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.75 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.63 out of 26.06
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.74 out of 29.72
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.94 out of 30.25
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.88 out of 30.98
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
RutR | Regulator of the pyrimidine and purine metabolism

NZ_JZOJ01000078.1 - Region 1 - NRP-metallophore,NRPS,T1PKS,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: 444,371 - 512,382 nt. (total: 68,012 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)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acylase
VE62_RS22165: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase
VE62_RS22175: thioesterase

smcogs
  SMCOG1004: thioesterase

Isomerases: isomerase
VE62_RS22135: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
VE62_RS22160: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

VE62_RS22180: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

VE62_RS22270: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

VE62_RS22290: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | NRP-metallophore | NRPS | T1PKS | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001055.5 |  |  |  |  | 1.76 | NRPS, PKS | yersiniabactin | Escherichia coli
BGC0000467.5 |  |  |  |  | 1.55 | NRPS | yersiniabactin | Yersinia enterocolitica
BGC0001641.4 |  |  |  |  | 0.89 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  | 0.89 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  |  | 0.89 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  |  |  |  | 0.88 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002570.2 |  |  |  |  | 0.64 | NRPS, PKS | yersiniabactin | Pseudomonas syringae pv. tomato str. DC3000
BGC0001843.2 |  |  |  |  | 0.63 | NRPS | tridecaptin M | Paenibacillus sp. M-152
BGC0001363.5 |  |  |  |  | 0.56 | NRPS, PKS | ralsolamycin | Ralstonia solanacearum GMI1000
BGC0002715.2 |  |  |  |  | 0.54 | NRPS, PKS | HTTPCA, prepiscibactin, piscibactin | Photorhabdus laumondii subsp. laumondii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000467.5 |  | 0.79 | NRPS | yersiniabactin | Yersinia enterocolitica
BGC0001055.5 |  | 0.79 | NRPS, PKS | yersiniabactin | Escherichia coli
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002570.2 |  | 0.54 | NRPS, PKS | yersiniabactin | Pseudomonas syringae pv. tomato str. DC3000
BGC0001843.2 |  | 0.54 | NRPS | tridecaptin M | Paenibacillus sp. M-152
BGC0002474.2 |  | 0.52 | NRPS | agrobactin | Agrobacterium tumefaciens

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.22 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.53 out of 26.06
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.91 out of 26.06
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.67 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.09 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.08 out of 26.06
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.29 out of 27.55
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.80 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.86 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.01 out of 26.06
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.34 out of 29.38
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.50 out of 27.78
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.23 out of 29.38
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.51 out of 20.97
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.39 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.64 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.72 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.81 out of 28.19
Confidence: medium
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 27.10 out of 33.14
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.54 out of 27.04
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.11 out of 28.19
Confidence: medium
Additional weak hits (24):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.94 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.12 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.15 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.54 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.36 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.80 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 28.67 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 30.51 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.62 out of 21.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.52 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.15 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.69 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.13 out of 26.06
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.21 out of 32.93
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.41 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.72 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.78 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.71 out of 29.38
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.75 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.57 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.71 out of 30.97
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.88 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.25 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.25 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 444370 - 507570:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 444370 - 497991:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 458078 - 507570:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
VE62_RS22160: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (573..966): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNSMLSGDIAMGGATEASIWSNA
  Nearest Stachelhaus code(s):
    Cys DLYNMSMIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

VE62_RS22165: mal
PKS_AT (552..842): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 62.5%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 132.8
  Methoxymalonyl-CoA: 50.0
  inactive: 45.6
  Methylmalonyl-CoA: 44.0
  Benzoyl-CoA: 42.7
  Propionyl-CoA: 34.5
  Isobutyryl-CoA: 31.1
  fatty_acid: 25.6
  Acetyl-CoA: 25.3
  2-Methylbutyryl-CoA: 24.6
  3-Methylbutyryl-CoA: 19.5
  CHC-CoA: 16.3
  trans-1,2-CPDA: 11.2
  Ethylmalonyl-CoA: 7.1

VE62_RS22180: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (20..422): 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:
    NASLFPLACPGGALQAGGAQQVFGMAEGLLCFTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPAQGVLCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
DasR | N-acetylglucosamine dependent repressor
FuR variant 1 | Ferric Uptake Regulator
GnfM | Regulator of nitrogen-fixation genes
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor
ZuR variant 2 | Zinc-responsive repressor

NZ_JZOJ01000078.1 - Region 2 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 517,864 - 589,026 nt. (total: 71,163 nt) Show pHMM detection rules used
Region on contig edge.
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
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
VE62_RS22470: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

VE62_RS22480: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: PPTase acylase
VE62_RS22465: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

VE62_RS22505: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: amidase esterase hydrolase
VE62_RS22420: thioesterase

smcogs
  SMCOG1004: thioesterase

VE62_RS22425: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

VE62_RS22445: amidase

smcogs
  SMCOG1105: amidase

Ligases: ligase synthase
VE62_RS22430: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

VE62_RS22435: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

VE62_RS22450: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

VE62_RS22455: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

VE62_RS22460: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

VE62_RS22485: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

VE62_RS22490: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000972.5 |  |  | 1.39 | NRPS, PKS | N-myristoyl-D-asparagine, cis-7-tetradecenoyl-D-asparagine, (R)-N1-((S)-5-oxohexan-2-yl)-2-tetradecanamidosuccinamide, colibactin, precolibactin 1489 | Escherichia coli
BGC0002135.2 |  |  | 0.83 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.81 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  |  | 0.77 | NRPS | HC-toxin | Alternaria jesenskae
BGC0002286.3 |  |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  | 0.75 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000972.5 |  | 0.89 | NRPS, PKS | N-myristoyl-D-asparagine, cis-7-tetradecenoyl-D-asparagine, (R)-N1-((S)-5-oxohexan-2-yl)-2-tetradecanamidosuccinamide, colibactin, precolibactin 1489 | Escherichia coli
BGC0002135.2 |  | 0.73 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.71 | NRPS | HC-toxin | Alternaria jesenskae
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.85 out of 25.88
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 28.09 out of 29.38
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 28.57 out of 29.38
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.44 out of 20.97
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.57 out of 25.31
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.52 out of 28.19
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.30 out of 25.31
Confidence: medium
Additional weak hits (9):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.47 out of 26.06
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.11 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.38 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.69 out of 27.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.06 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.50 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.80 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.02 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.32 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 5, location 517863 - 589026:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ala - redmal) + (X) + (mal) + (Gly - Cys) + (Asn)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
VE62_RS22435: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (453..844): Asn
nrpys: Asn

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

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

VE62_RS22450: Gly - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (507..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:
    LDMTFDISFLELQALAGGEWNLYGPTETTIWSLK
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1555..1950): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDANALLSGDISLGGATECAIWSVY
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

VE62_RS22455: mal
PKS_AT (531..813): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 135.2
  inactive: 78.0
  Methoxymalonyl-CoA: 66.0
  Methylmalonyl-CoA: 56.3
  Isobutyryl-CoA: 28.5
  Propionyl-CoA: 26.3
  Ethylmalonyl-CoA: 20.5
  2-Methylbutyryl-CoA: 14.2
  Benzoyl-CoA: 11.6
  trans-1,2-CPDA: 11.4
  CHC-CoA: 9.8
  3-Methylbutyryl-CoA: 6.9
  fatty_acid: 0.0
  Acetyl-CoA: 0.0

VE62_RS22460: Ser - X
Search NORINE for peptide: strict or relaxed
AMP-binding (24..422): 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:
    RWMTFDVSVWEWHFFSSGEINLYGPTEAAIDVSH
  Nearest Stachelhaus code(s):
    Ser DVWHFSLIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (992..1384): X
nrpys: Sam

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:
    LSFTSASFVGEPSTLCGGEVNGYGLTESGICSTY
  Nearest Stachelhaus code(s):
    Sam ASGSLGGICK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

VE62_RS22465: mal
PKS_AT (7..296): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 57.2
  Methoxymalonyl-CoA: 41.1
  Methylmalonyl-CoA: 34.3
  inactive: 30.1
  Ethylmalonyl-CoA: 18.1
  Propionyl-CoA: 16.0
  Acetyl-CoA: 14.6
  Benzoyl-CoA: 12.9
  2-Methylbutyryl-CoA: 12.5
  CHC-CoA: 9.1
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

VE62_RS22490: Ala - mal
Search NORINE for peptide: strict or relaxed
AMP-binding (502..890): Ala
nrpys: Ala

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

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

PKS_AT (1604..1895): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 155.9
  inactive: 95.9
  Methoxymalonyl-CoA: 53.4
  Methylmalonyl-CoA: 38.8
  Propionyl-CoA: 26.7
  Isobutyryl-CoA: 21.1
  fatty_acid: 18.9
  CHC-CoA: 16.9
  2-Methylbutyryl-CoA: 11.0
  Benzoyl-CoA: 10.3
  Ethylmalonyl-CoA: 9.3
  Acetyl-CoA: 8.1
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A
FuR variant 1 | Ferric Uptake Regulator
PsrA | Oleic acid responsive regulator
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_JZOJ01000049.1 - Region 1 - 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: 1 - 6,012 nt. (total: 6,012 nt) Show pHMM detection rules used
Region on contig edge.
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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: Hydrolysis
VE62_RS28925: Hydrolysis

MITE
  MITE0000056Hydrolysis (identity: 97.60%)

VE62_RS28930: Hydrolysis

MITE
  MITE0000056Hydrolysis (identity: 99.00%)

Ligases: Macrolactam formation
VE62_RS06225: Macrolactam formation

MITE
  MITE0000055Macrolactam formation (identity: 99.10%)

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
--- | --- | --- | --- | --- | ---
BGC0000581.6 |  | 0.89 | ribosomal | microcin J25 | Escherichia coli AY25
BGC0002312.2 |  | 0.69 | ribosomal | ubonodin | Burkholderia ubonensis
BGC0002322.3 |  | 0.54 | ribosomal | citrocin | Citrobacter pasteurii
BGC0001639.3 |  | 0.52 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0002747.3 |  | 0.36 | ribosomal | lentinulin A | Lentinula edodes
BGC0000322.3 |  | 0.31 | NRPS | chloroeremomycin | Amycolatopsis orientalis
BGC0001801.5 |  | 0.26 | NRPS | thiazostatin, watasemycin A, watasemycin B, 2-hydroxyphenylthiazoline enantiopyochelin, isopyochelin | Streptomyces venezuelae ATCC 10712
BGC0000347.5 |  | 0.24 | NRPS | equibactin | Streptococcus equi subsp. equi
BGC0000125.5 |  | 0.24 | PKS | pimaricin | Streptomyces natalensis
BGC0001709.5 |  | 0.23 | PKS | nystatin | Streptomyces albulus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000581.6 |  | 0.89 | ribosomal | microcin J25 | Escherichia coli AY25
BGC0002312.2 |  | 0.69 | ribosomal | ubonodin | Burkholderia ubonensis
BGC0002322.3 |  | 0.54 | ribosomal | citrocin | Citrobacter pasteurii
BGC0001639.3 |  | 0.52 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0002747.3 |  | 0.36 | ribosomal | lentinulin A | Lentinula edodes
BGC0000322.3 |  | 0.31 | NRPS | chloroeremomycin | Amycolatopsis orientalis
BGC0001801.5 |  | 0.26 | NRPS | thiazostatin, watasemycin A, watasemycin B, 2-hydroxyphenylthiazoline enantiopyochelin, isopyochelin | Streptomyces venezuelae ATCC 10712
BGC0000347.5 |  | 0.24 | NRPS | equibactin | Streptococcus equi subsp. equi
BGC0000125.5 |  | 0.24 | PKS | pimaricin | Streptomyces natalensis
BGC0001709.5 |  | 0.23 | PKS | nystatin | Streptomyces albulus

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 VE62_RS06215

VE62_RS06215
Leader:
MIKHIHFDKLSSGKKNNVPHPAKGVIQIKKSASQLTK
Full core:
G G A G H V P E Y F V G I G T P I S F Y G
Putative macrolactam:
G G A G H V P E

#### antiSMASH-DB 4.0 matches for VE62_RS06215

100.0%
NZ_AP021947.1 and 16 others:
NZ_CAJGEM010000015.1 Lassopeptides: JMT87_RS21655_lassopeptide NZ_CAJGGU010000008.1 Lassopeptides: JMU20_RS21490_lassopeptide NZ_CP010127.1 Lassopeptides: RG30_RS26380_lassopeptide NZ_CP031107.1 Lassopeptides: DUT84_RS26055_lassopeptide NZ_CP074577.1 Lassopeptides: KHZ70_RS24010_lassopeptide NZ_CP091672.1 Lassopeptides: L6L68_RS00080_lassopeptide NZ_CP097722.1 Lassopeptides: M9O79_RS23190_lassopeptide NZ_CP117571.1 Lassopeptides: PS035_RS23020_lassopeptide NZ_CP117612.1 Lassopeptides: PS038_RS23585_lassopeptide NZ_CP117622.1 Lassopeptides: PS039_RS24320_lassopeptide NZ_FZFT01000070.1 Lassopeptides: CPG75_RS26760_lassopeptide NZ_JABMLY010000084.1 Lassopeptides: HRQ70_RS23615_lassopeptide NZ_JZNY01000005.1 Lassopeptides: VE51_RS00690_lassopeptide NZ_JZOJ01000049.1 Lassopeptides: VE62_RS06215_lassopeptide NZ_MRDN01000066.1 Lassopeptides: BSF34_RS29250_lassopeptide NZ_OW968329.1 Lassopeptides: LQ108_RS23255_lassopeptide
Lassopeptides: H7R07_RS25795_lassopeptide
1
G G A G H V P E Y F V G I G T P I S F Y G
21
G G A G H V P E Y F V G I G T P I S F Y G
1
G G A G H V P E Y F V G I G T P I S F Y G
21
52.4%
NZ_CP016898.1:
Lassopeptides: BEN76_RS17395_lassopeptide
1
G G A G H V P E Y F V G I G T P I S F Y G
21
G G G +P E Y F+ +G +F Y G
1
G G K G P L P E Y F L-M G G G G N F Y G
20
33.3%
NZ_CP077406.1:
Lassopeptides: I6L51_RS27045_lassopeptide
1
G G A G H V P E Y F V G
12
G G G + E Y F+G
1
G G V G K I I E Y F I G
12
with 5 more sequence matches
30.8%
NZ_VYKJ01000032.1:
Lassopeptides: FJU30_RS26370_lassopeptide
1
G G A G H V P E Y F V G I G T P I S
18
G G G +P E Y F P
1
G G D G G I P E Y F E H S N P P T D
18
28.6%
NZ_JADPRT010000002.1:
Lassopeptides: I2501_RS04910_lassopeptide
1
G G A G H V P E Y F V G I G
14
G G G V P++F +
1
G G L G T V P D W F F N M N
14
28.6%
NZ_JAERJD010000009.1:
Lassopeptides: allorf_022741_022872_lassopeptide
1
G G A G H V P E Y F V
11
G G G + E Y F
1
G G G G Q I V E Y F T
11
22.2%
NZ_RBZW01000021.1:
Lassopeptides: D8Y22_RS22300_lassopeptide
6
V P E Y F V G I G T P I S
18
V E +G T P I+
11
V T E A T A A V G T P I T
23
21.9%
NZ_CP031746.1:
Lanthipeptides: allorf_1813979_1814164_lanthipeptide
1
G G A G H V P E Y F V G I G T P I S F
19
G A V P +G G P+++
6
G C A R W V P C S L L G A G C P V T W
24

#### MIBiG 4.0 matches for VE62_RS06215

100.0%
BGC0000581.6 (AAD28494.1):
Lasso peptide: microcin J25
1
G G A G H V P E Y F V G I G T P I S F Y G
21
G G A G H V P E Y F V G I G T P I S F Y G
1
G G A G H V P E Y F V G I G T P I S F Y G
21
33.3%
BGC0002322.3 (CEJ66604.1):
Lasso peptide: citrocin
1
G G A G H V P E Y F V G
12
G G G + E Y F+G
1
G G V G K I I E Y F I G
12

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.44 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.32 out of 29.38
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.

VE62_RS06215 - Class II
  Cleavage pHMM score: 5.40
  RODEO score: 20
  Monoisotopic mass: 2106.0 Da
  Molecular weight: 2107.3 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (0...6012)
VE62_RS28925
  RRE type: Lasso_Fused_RRE
  Location: 3 - 68
  Score: 45.8

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---