Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
1.11
1.12
1.13
1.14
1.15
1.16
1.17
1.18
1.19
1.20
1.21
1.22
1.23
1.24
1.25
1.26

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

NZ_CP023865.1 (Actinoplanes teichomyceticus ATCC 31121)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | terpene | 156,756 | 178,785 | Low | isorenieratene | terpene
Region 2 | RiPP-like | 335,135 | 345,359 |  |
Region 3 | terpene,indole | 1,701,153 | 1,738,890 | Medium | erdasporine A/erdasporine B/erdasporine C | other:other
Region 4 | terpene | 2,051,276 | 2,072,517 |  |
Region 5 | NRPS-like,betalactone,azole-containing-RiPP | 2,131,950 | 2,198,059 |  |
Region 6 | amglyccycl | 2,419,151 | 2,440,275 |
Region 7 | azoxy-crosslink | 2,815,968 | 2,844,010 |  |
Region 8 | NRPS,T1PKS,NRPS-like | 3,240,989 | 3,290,742 | Medium | coformycin/aristeromycin | other:other
Region 9 | NRPS,T1PKS | 3,360,438 | 3,468,968 | High | antimycin A1B | NRPS:Type I+PKS
Region 10 | NRPS,T3PKS | 3,478,255 | 3,571,815 | High | Teicoplanin A2-1/Teicoplanin A2-2/Teicoplanin A2-3/Teicoplanin A2-4/Teicoplanin A2-5 | NRPS:Type I
Region 11 | NRPS | 3,744,666 | 3,814,862 |  |
Region 12 | NI-siderophore | 4,065,682 | 4,096,626 |
Region 13 | lanthipeptide-class-i | 4,178,711 | 4,203,248 | Low | microbisporicin A2 | ribosomal:RiPP:Lanthipeptide
Region 14 | RiPP-like | 4,296,973 | 4,308,898 |
Region 15 | triceptide | 4,321,755 | 4,343,938 |
Region 16 | NRPS | 4,532,469 | 4,584,549 |  |
Region 17 | melanin | 4,856,206 | 4,868,169 |
Region 18 | lanthipeptide-class-iii | 5,071,704 | 5,094,343 | Medium | catenulipeptin | ribosomal:RiPP:Lanthipeptide
Region 19 | T1PKS,NRPS-like,2dos | 5,609,935 | 5,690,838 | Medium | ansaseomycin A/ansaseomycin B | PKS
Region 20 | NRPS-like | 5,697,072 | 5,740,782 |  |
Region 21 | oligosaccharide,T1PKS | 5,783,792 | 5,851,087 | Low | maduropeptin | PKS:Iterative type I
Region 22 | terpene-precursor,phosphoglycolipid | 6,688,749 | 6,721,072 | High | teichomycin A1 | other:other
Region 23 | terpene-precursor | 6,785,661 | 6,806,206 | Low | fluostatin M/fluostatin N/fluostatin O/fluostatin P/fluostatin Q | PKS:Type II aromatic
Region 24 | NI-siderophore,T1PKS | 6,815,214 | 6,882,336 | Medium | desferrioxamine E | other:other
Region 25 | T3PKS | 7,880,206 | 7,921,264 | Medium | loseolamycin A1/loseolamycin A2 | PKS
Region 26 | deazapurine | 8,104,948 | 8,127,363 | Low | toyocamycin | other:other

NZ_CP023865.1 - 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: 156,756 - 178,785 nt. (total: 22,030 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 oxidoreductase
ACTEI_RS00755: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

ACTEI_RS00775: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Hydrolases: esterase
ACTEI_RS00715: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

Ligases: synthetase
ACTEI_RS00760: 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 |  | 0.55 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.54 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.52 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.52 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000649.3 |  | 0.50 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.49 | terpene | carotenoid | Myxococcus xanthus
BGC0000650.3 |  | 0.48 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002318.2 |  | 0.46 | ribosomal | canucin A, canucin B | Streptomyces canus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.55 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.54 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.52 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.52 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000649.3 |  | 0.50 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.49 | terpene | carotenoid | Myxococcus xanthus
BGC0000650.3 |  | 0.48 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002318.2 |  | 0.46 | ribosomal | canucin A, canucin B | Streptomyces canus

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

No significant matches found.

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

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

Genes with terpene domains:
ACTEI_RS00760: PT_FPPS_like
Domain 1 (44 - 323): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

ACTEI_RS00765: PT_phytoene_like
Domain 1 (5 - 285): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.81 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
Additional weak hits (23):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.38 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.76 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 21.55
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.38 out of 36.53
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.18 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.50 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.99 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.97 out of 31.73
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: 15.65 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.92 out of 26.06
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: 15.10 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.03 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.96 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.47 out of 36.54
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 out of 30.98
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
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
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism

NZ_CP023865.1 - 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: 335,135 - 345,359 nt. (total: 10,225 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
--- | --- | --- | --- | --- | ---
BGC0001948.3 |  | 0.43 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000565.5 |  | 0.38 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002227.3 |  | 0.36 | NRPS | AKML B, AKML D, AKML A, AKML C | Aspergillus luchuensis IFO 4308
BGC0001336.5 |  | 0.33 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000471.4 |  | 0.32 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112
BGC0000477.3 |  | 0.32 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0000480.5 |  | 0.32 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000475.5 |  | 0.32 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0001954.2 |  | 0.32 | NRPS, PKS | wortmanamide A, wortmanamide B | Talaromyces wortmannii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001948.3 |  | 0.43 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000565.5 |  | 0.38 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002227.3 |  | 0.36 | NRPS | AKML B, AKML D, AKML A, AKML C | Aspergillus luchuensis IFO 4308
BGC0001336.5 |  | 0.33 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000471.4 |  | 0.32 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112
BGC0000477.3 |  | 0.32 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0000480.5 |  | 0.32 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0000475.5 |  | 0.32 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0001954.2 |  | 0.32 | NRPS, PKS | wortmanamide A, wortmanamide B | Talaromyces wortmannii

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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (7):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.75 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.42 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.36 out of 29.38
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.61 out of 23.43
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.94 out of 28.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.68 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP023865.1 - Region 3 - indole,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: 1,701,153 - 1,738,890 nt. (total: 37,738 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)
indole: (indsynth or dmat or indole_PTase)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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
ACTEI_RS07910: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

ACTEI_RS07920: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: methyltransferase
ACTEI_RS07915: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

ACTEI_RS07970: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Ligases: synthetase
ACTEI_RS07855: 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 | indole | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001336.5 |  |  | 0.36 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001224.5 |  |  | 0.32 | other (other) | reductasporine | uncultured bacterium
BGC0001948.3 |  |  | 0.31 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000821.5 |  |  | 0.24 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0000688.4 |  |  | 0.24 | terpene | copalyl diphosphate | Diaporthe amygdali
BGC0000678.5 |  |  | 0.22 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000665.5 |  |  | 0.22 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002631.2 |  |  | 0.21 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000817.4 |  |  | 0.21 | other (other) | methylarcyriarubin | uncultured bacterium
BGC0001227.3 |  |  | 0.20 | terpene | isorenieratene | Streptomyces collinus Tu 365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001224.5 |  | 0.66 | other (other) | reductasporine | uncultured bacterium
BGC0001336.5 |  | 0.60 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001223.5 |  | 0.55 | other (other) | hydroxysporine | uncultured bacterium
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000817.4 |  | 0.54 | other (other) | methylarcyriarubin | uncultured bacterium
BGC0001948.3 |  | 0.49 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000677.5 |  | 0.49 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000636.3 |  | 0.49 | terpene | carotenoid | Brevibacterium linens
BGC0000829.5 |  | 0.47 | other (other) | violacein | Chromobacterium violaceum
BGC0000821.5 |  | 0.47 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes

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

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

Genes with terpene domains:
ACTEI_RS07845: Lycopene_cycl
Domain 1 (5 - 93): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

ACTEI_RS07850: Lycopene_cycl
Domain 1 (1 - 91): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

ACTEI_RS07855: PT_FPPS_like
Domain 1 (42 - 354): 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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
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: 19.24 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.11 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.00 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.68 out of 30.12
Confidence: medium
Additional weak hits (8):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.54 out of 20.97
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.62 out of 26.12
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.62 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.64 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.70 out of 35.63
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.32 out of 26.85
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.19 out of 20.01
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP023865.1 - Region 4 - 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: 2,051,276 - 2,072,517 nt. (total: 21,242 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
ACTEI_RS09410: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: aminotransferase methyltransferase
ACTEI_RS09400: methyltransferase

smcogs
  SMCOG1089: methyltransferase

ACTEI_RS09430: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Lyases: cyclase
ACTEI_RS09395: 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
--- | --- | --- | --- | --- | ---
BGC0000657.5 |  | 0.65 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000659.3 |  | 0.62 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000658.3 |  | 0.61 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002128.3 |  | 0.41 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001909.3 |  | 0.40 | PKS | strobilurin A | Strobilurus tenacellus
BGC0002561.3 |  | 0.39 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0000815.4 |  | 0.39 | other (other) | loline, N-acetylnorloline, N-formylloline | Epichloe uncinata
BGC0000843.5 |  | 0.38 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0002007.2 |  | 0.37 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0001285.5 |  | 0.37 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000657.5 |  | 0.65 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000659.3 |  | 0.62 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000658.3 |  | 0.61 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002128.3 |  | 0.41 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001909.3 |  | 0.40 | PKS | strobilurin A | Strobilurus tenacellus
BGC0002561.3 |  | 0.39 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0000815.4 |  | 0.39 | other (other) | loline, N-acetylnorloline, N-formylloline | Epichloe uncinata
BGC0000843.5 |  | 0.38 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0002007.2 |  | 0.37 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0001285.5 |  | 0.37 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida

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 |  | 2-methylisoborneol | C11 | C1-C6 | OH
monoterpene |  | 2-methylenebornane | C11 | C1-C6 | none

Genes with terpene domains:
ACTEI_RS09395: T1TS
Domain 1 (43 - 404): Type 1 terpene synthase
Subtype: 2-Methylisoborneol synthase type

Reactions:
  2-MeGPP → 2-methylisoborneol
  2-MeGPP → 2-methylenebornane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (2):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.83 out of 26.06
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
2-MeGPP | 2-methylgeranyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP023865.1 - Region 5 - NRPS-like,azole-containing-RiPP,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: 2,131,950 - 2,198,059 nt. (total: 66,110 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)
betalactone: (HMGL-like and AMP-binding)
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 electron transfer oxygenase
ACTEI_RS09775: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

ACTEI_RS09800: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

ACTEI_RS09830: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

ACTEI_RS09870: flavodoxin

smcogs
  SMCOG1134: flavodoxin

ACTEI_RS09880: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: acetyltransferase aminotransferase kinase transferase
ACTEI_RS09855: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

ACTEI_RS09890: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

ACTEI_RS09940: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

ACTEI_RS09945: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: esterase hydrolase
ACTEI_RS09760: thioesterase

smcogs
  SMCOG1004: thioesterase

ACTEI_RS09790: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

ACTEI_RS09835: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: cyclase
ACTEI_RS09860: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Isomerases: isomerase
ACTEI_RS09840: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
ACTEI_RS09750: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

ACTEI_RS09785: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

ACTEI_RS09795: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

ACTEI_RS09810: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

Translocases: permease
ACTEI_RS09765: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | NRPS-like | betalactone | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001641.4 |  |  |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  | 0.61 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002277.2 |  |  |  | 0.60 | NRPS | atromentin | Suillus grevillei
BGC0001135.5 |  |  |  | 0.59 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  |  |  | 0.58 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000342.4 |  |  |  | 0.58 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  |  |  | 0.58 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  |  |  | 0.58 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  |  |  | 0.58 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001250.4 |  |  |  | 0.57 | NRPS | epichloenin A | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002277.2 |  | 0.63 | NRPS | atromentin | Suillus grevillei
BGC0001135.5 |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000342.4 |  | 0.63 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0001166.5 |  | 0.62 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001250.4 |  | 0.62 | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 21.15 out of 23.79
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
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: 18.07 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.07 out of 23.79
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.08 out of 26.85
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
Additional weak hits (18):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.88 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.63 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.66 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.48 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.05 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.56 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.39 out of 30.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.04 out of 21.84
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.02 out of 21.55
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.49 out of 19.26
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.79 out of 29.38
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.69 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.83 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.25 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.33 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.61 out of 29.65
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
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 7, location 2131949 - 2198059:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 2131949 - 2173608:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Asp)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
ACTEI_RS09785: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (31..361): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LCRAFDGWWFDRLLFSGGEVNLYGPTEATFATHG
  Nearest Stachelhaus code(s):
    Leu DAFLHGLTAK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

ACTEI_RS09795: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (12..376): Asp
nrpys: Asp

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:
    VDHAFDGCITEWKTINGGGHNAYGLTETTVCNLL
  Nearest Stachelhaus code(s):
    Asp DLTKIGAVNK (47% 8Å match)
    OH-Asp or OMe-Asp DLTKIGAVNK (44% 8Å match)
  Stachelhaus code match:
    80% (moderate)

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (2173603...2198059)
ACTEI_RS09925
  RRE type: Thiopeptide_F_RRE
  Location: 31 - 113
  Score: 34.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism
RutR | Regulator of the pyrimidine and purine metabolism
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_CP023865.1 - Region 6 - amglyccycl
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: 2,419,151 - 2,440,275 nt. (total: 21,125 nt) Show pHMM detection rules used
amglyccycl: (DOIS or ValA or salQ or strH or strK1 or strK2 or NeoL or SpcFG or SpcDK_glyc)

#### 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
ACTEI_RS10895: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

ACTEI_RS10945: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: aminotransferase
ACTEI_RS10955: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: hydrolase
ACTEI_RS10915: HAD-superfamily hydrolase, subfamily IA, variant

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

ACTEI_RS10965: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: synthase
ACTEI_RS10940: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate 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 | amglyccycl | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000701.5 |  | 0.51 | saccharide | jinggangmycin | Streptomyces hygroscopicus subsp. yingchengensis
BGC0001817.5 |  | 0.46 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0000894.4 |  | 0.45 | other (other) | citrinin | Monascus aurantiacus
BGC0000723.5 |  | 0.45 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus
BGC0000867.3 |  | 0.45 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0000719.5 |  | 0.44 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0000720.3 |  | 0.44 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000722.5 |  | 0.44 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. jinggangensis
BGC0000791.3 |  | 0.44 | saccharide | O-antigen | Cronobacter sakazakii
BGC0001928.2 |  | 0.43 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000701.5 |  | 0.51 | saccharide | jinggangmycin | Streptomyces hygroscopicus subsp. yingchengensis
BGC0001817.5 |  | 0.46 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0000894.4 |  | 0.45 | other (other) | citrinin | Monascus aurantiacus
BGC0000723.5 |  | 0.45 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus
BGC0000867.3 |  | 0.45 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0000719.5 |  | 0.44 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0000720.3 |  | 0.44 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000722.5 |  | 0.44 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. jinggangensis
BGC0000791.3 |  | 0.44 | saccharide | O-antigen | Cronobacter sakazakii
BGC0001928.2 |  | 0.43 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.34 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
Additional weak hits (1):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.60 out of 21.55
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism

NZ_CP023865.1 - Region 7 - azoxy-crosslink
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: 2,815,968 - 2,844,010 nt. (total: 28,043 nt) Show pHMM detection rules used
azoxy-crosslink: (azdH and LPG_synthase_C and azdO and vlmB)

#### 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
ACTEI_RS12675: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

ACTEI_RS12680: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

ACTEI_RS12700: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

ACTEI_RS12735: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
ACTEI_RS12685: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Ligases: synthase
ACTEI_RS12635: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

ACTEI_RS12710: 3-oxoacyl-(acyl carrier protein) synthase III

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

ACTEI_RS12720: 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 | azoxy-crosslink | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.56 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002711.2 |  | 0.51 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000852.5 |  | 0.48 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000914.5 |  | 0.48 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000859.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0000858.3 |  | 0.47 | other (other) | ectoine | Methylobacter marinus
BGC0000860.3 |  | 0.47 | other (other) | ectoine | Methylarcula marina
BGC0001987.2 |  | 0.46 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.56 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002711.2 |  | 0.51 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000852.5 |  | 0.48 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000914.5 |  | 0.48 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000859.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0000858.3 |  | 0.47 | other (other) | ectoine | Methylobacter marinus
BGC0000860.3 |  | 0.47 | other (other) | ectoine | Methylarcula marina
BGC0001987.2 |  | 0.46 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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: 17.92 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 23.43
Confidence: medium
Additional weak hits (10):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.29 out of 39.62
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.00 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.17 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.45 out of 31.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.90 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.06 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.35 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.04 out of 23.43
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.15 out of 23.43
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
CatR | H2O2-responsive repressor
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP023865.1 - Region 8 - NRPS,NRPS-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: 3,240,989 - 3,290,742 nt. (total: 49,754 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))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
ACTEI_RS14620: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

ACTEI_RS14720: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

ACTEI_RS14725: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: kinase
ACTEI_RS14565: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: esterase hydrolase
ACTEI_RS14600: hydrolase

smcogs
  SMCOG1179: hydrolase

ACTEI_RS14615: HAD-superfamily hydrolase, subfamily IA, variant

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

ACTEI_RS37770: thioesterase

smcogs
  SMCOG1004: thioesterase

Isomerases: mutase
ACTEI_RS14585: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase synthase
ACTEI_RS14640: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

ACTEI_RS14650: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

ACTEI_RS14655: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

ACTEI_RS14665: 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 | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  |  | 1.26 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001250.4 |  |  |  | 1.06 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  |  | 1.06 | NRPS | epichloenin A | Epichloe festucae
BGC0001132.4 |  |  |  | 1.04 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  | 1.02 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 1.02 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  |  |  | 1.01 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  |  |  | 1.00 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  |  |  | 1.00 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  |  | 0.99 | NRPS | AM-toxin | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001250.4 |  | 0.68 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.68 | NRPS | epichloenin A | Epichloe festucae
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  | 0.67 | NRPS | peramine | Epichloe festucae
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.66 | 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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (11):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.07 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.73 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.19 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.66 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.52 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.20 out of 21.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.39 out of 26.85
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.30 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 12, location 3240988 - 3290742:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (mal) + (Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 3240988 - 3284477:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (mal) + (Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 14, location 3244480 - 3287468:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (mal) + (Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 15, location 3248924 - 3290742:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (mal) + (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).
ACTEI_RS14650: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (540..931): 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:
    LRAAFDASTLEAWLLTGGDSNGYGPTENTTFTTV
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (85% 8Å match)
    bOH-Val DALWLGGTFK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

ACTEI_RS14655: mal
PKS_AT (522..805): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 159.2
  inactive: 92.5
  Methoxymalonyl-CoA: 60.3
  Methylmalonyl-CoA: 42.7
  Propionyl-CoA: 25.5
  trans-1,2-CPDA: 18.4
  2-Methylbutyryl-CoA: 15.6
  fatty_acid: 13.4
  CHC-CoA: 12.5
  Acetyl-CoA: 11.5
  Ethylmalonyl-CoA: 10.4
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  Isobutyryl-CoA: -0.3

ACTEI_RS14665: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (37..433): 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:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LATHFDVSVYEGSQLFAGELNLYGITETTVHTTL
  Nearest Stachelhaus code(s):
    Ser DVYSLALVHK (82% 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
OsdR | Development and stress management regulator

NZ_CP023865.1 - Region 9 - 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: 3,360,438 - 3,468,968 nt. (total: 108,531 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))

#### 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
ACTEI_RS15115: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

ACTEI_RS15320: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

ACTEI_RS15365: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase formyltransferase
ACTEI_RS15095: aminotransferase

smcogs
  SMCOG1019: aminotransferase

ACTEI_RS15130: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: esterase hydrolase
ACTEI_RS15080: putative esterase

smcogs
  SMCOG1104: putative esterase

ACTEI_RS15125: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: ligase synthase
ACTEI_RS15105: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

ACTEI_RS15135: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

ACTEI_RS15305: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

ACTEI_RS15315: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

ACTEI_RS15330: 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 | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000958.5 |  |  |  | 1.22 | NRPS, PKS | antimycin | Streptomyces sp. S4
BGC0001216.5 |  |  |  | 1.13 | NRPS, PKS | splenocin C | Streptomyces sp. CNQ431
BGC0001833.4 |  |  |  | 1.13 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  |  |  | 1.13 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  |  | 1.12 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  | 1.11 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001455.6 |  |  |  | 1.10 | NRPS, PKS | antimycin A1B | Streptomyces argillaceus
BGC0001825.4 |  |  |  | 1.10 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  |  |  | 1.10 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  | 1.06 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000958.5 |  | 0.81 | NRPS, PKS | antimycin | Streptomyces sp. S4
BGC0001455.6 |  | 0.80 | NRPS, PKS | antimycin A1B | Streptomyces argillaceus
BGC0001216.5 |  | 0.78 | NRPS, PKS | splenocin C | Streptomyces sp. CNQ431
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
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
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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: 17.92 out of 20.47
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.74 out of 29.72
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.20 out of 29.51
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.36 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.90 out of 30.12
Confidence: medium
Additional weak hits (39):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.09 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.92 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.03 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.79 out of 36.54
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.01 out of 20.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.96 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.14 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.23 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.60 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.15 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.88 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.85 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.26 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.25 out of 31.73
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.55 out of 25.88
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.32 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.03 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.71 out of 27.78
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: 16.23 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.98 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 12.81 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.22 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.76 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.61 out of 26.06
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.44 out of 30.22
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.35 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.54 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.85 out of 27.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.54 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.95 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 32.93
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.08 out of 32.38
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 20.77 out of 32.93
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 27.04
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.77 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.03 out of 23.43
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.69 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.68 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 16, location 3360437 - 3468968:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X - D-Hpg - Ser) + (Hpg) + (Thr - shikimic_acid) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 17, location 3360437 - 3418673:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X - D-Hpg - Ser) + (Hpg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 18, location 3416445 - 3465121:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - shikimic_acid) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 19, location 3425125 - 3468968:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - shikimic_acid) + (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).
ACTEI_RS15105: X
AMP-binding (17..423): 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:
    LFWMW-LSGPTPTMVYHSSLQSYGQTETKMISAL
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

ACTEI_RS15130: X - X - Hpg
Search NORINE for peptide: strict or relaxed
AMP-binding (574..967): X
nrpys: (unknown)

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:
    RWWAFDISVWEAHLVTGGEVQAYGPTEASISVLH
  Nearest Stachelhaus code(s):
    Hpg DIWHVGAITK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1622..2020): 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:
    HWACFDVMVEEPNLVIGGELNAYGPTETTVGATV
  Nearest Stachelhaus code(s):
    Arg DVENVGAIGK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2666..3050): Hpg
nrpys: Hpg

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:
    QWSAFDISLWEHHLVCGGEHHTYGPTEASIIVTH
  Nearest Stachelhaus code(s):
    Hpg DIWHVGTIIK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

ACTEI_RS15135: Ser - Hpg
Search NORINE for peptide: strict or relaxed
AMP-binding (44..441): 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:
    RWMTFDVSVWELHFVCSGEHNLYGPTEATIDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHVSLIDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1112..1507): Hpg
nrpys: Hpg

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:
    RWSAFDIALWEFHLLSGGEHQAYGPTEASISVTH
  Nearest Stachelhaus code(s):
    Hpg DIWHLGAISK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

ACTEI_RS15310: Thr - shikimic_acid
Search NORINE for peptide: strict or relaxed
AMP-binding (461..876): 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:
    LAAHFDFSVWEGNQVFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

CAL_domain (1813..2119): shikimic_acid
minowa: shikimic_acid

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

ACTEI_RS15315: mal
PKS_AT (540..822): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 66.7%
  inactive: 62.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 106.2
  inactive: 70.3
  Methoxymalonyl-CoA: 63.5
  Methylmalonyl-CoA: 45.3
  Ethylmalonyl-CoA: 20.1
  Propionyl-CoA: 17.3
  Isobutyryl-CoA: 17.0
  Benzoyl-CoA: 11.0
  Acetyl-CoA: 10.8
  2-Methylbutyryl-CoA: 9.3
  fatty_acid: 9.2
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

ACTEI_RS15330: X
AMP-binding (7..400): X
nrpys: Pyv, Ant

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:
    IGWCHGSMVVSTWMLYGAARQVYGMTEVGGFVTL
  Nearest Stachelhaus code(s):
    Pyv or Ant GSVWLGVGFK (100% 8Å match)
    Ant GSVWLGVGFK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP023865.1 - Region 10 - 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: 3,478,255 - 3,571,815 nt. (total: 93,561 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: dehydrogenase oxygenase
ACTEI_RS15510: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

ACTEI_RS15520: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

ACTEI_RS15610: Cyclization

MITE
  MITE0000038Cyclization (identity: 74.90%)
smcogs
  SMCOG1007: cytochrome P450

ACTEI_RS15615: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

ACTEI_RS15620: Cyclization

MITE
  MITE0000041Cyclization (identity: 73.10%)
smcogs
  SMCOG1007: cytochrome P450

ACTEI_RS15630: Cyclization

MITE
  MITE0000027Cyclization (identity: 69.50%)
smcogs
  SMCOG1007: cytochrome P450

Transferases: acyltransferase aminotransferase glycosyltransferase halogenase
ACTEI_RS15555: Glycosylation

MITE
  MITE0000034Glycosylation (identity: 100.00%)
smcogs
  SMCOG1102: glycosyltransferase

ACTEI_RS15570: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

ACTEI_RS15625: flavin-dependent tyrosine-like hpg halogenase

halogenases
  flavin-dependent tyrosine-like hpg halogenase
MITE
  MITE0000028Halogenation (identity: 84.50%)
smcogs
  SMCOG1119: halogenase

ACTEI_RS15635: Glycosylation

MITE
  MITE0000033Glycosylation (identity: 100.00%)
smcogs
  SMCOG1102: glycosyltransferase

ACTEI_RS15700: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: Acylation esterase
ACTEI_RS15640: Acylation, Hydrolysis

MITE
  MITE0000035Acylation, Hydrolysis (identity: 100.00%)

ACTEI_RS15735: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: hydratase
ACTEI_RS15680: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

ACTEI_RS15685: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: Acylation ligase synthase
ACTEI_RS15560: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

ACTEI_RS15565: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

ACTEI_RS15575: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

ACTEI_RS15640: Acylation, Hydrolysis

MITE
  MITE0000035Acylation, Hydrolysis (identity: 100.00%)

ACTEI_RS15650: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

ACTEI_RS15670: 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
--- | --- | --- | --- | --- | --- | ---
BGC0000440.5 |  |  | 1.06 | NRPS | Teicoplanin A2-1, Teicoplanin A2-2, Teicoplanin A2-3, Teicoplanin A2-4, Teicoplanin A2-5 | Actinoplanes teichomyceticus
BGC0002341.2 |  |  | 0.94 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0000441.4 |  |  | 0.94 | NRPS | teicoplanin | Actinoplanes teichomyceticus
BGC0002608.2 |  |  | 0.91 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0001164.3 |  |  | 0.51 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.51 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002347.3 |  |  | 0.47 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6
BGC0002084.4 |  |  | 0.46 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  |  | 0.46 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0001261.3 |  |  | 0.45 | NRPS | AM-toxin | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000441.4 |  | 0.95 | NRPS | teicoplanin | Actinoplanes teichomyceticus
BGC0000440.5 |  | 0.95 | NRPS | Teicoplanin A2-1, Teicoplanin A2-2, Teicoplanin A2-3, Teicoplanin A2-4, Teicoplanin A2-5 | Actinoplanes teichomyceticus
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002608.2 |  | 0.76 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0001261.3 |  | 0.75 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  | 0.75 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002135.2 |  | 0.73 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 26.06 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 26.66 out of 30.11
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.68 out of 30.12
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (23):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.21 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.81 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.76 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.56 out of 21.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.75 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.46 out of 27.78
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: 15.39 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.57 out of 26.06
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.67 out of 29.51
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.61 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.58 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.82 out of 21.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.33 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.82 out of 30.98
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 23.43
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.62 out of 36.54
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.96 out of 29.65
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.07 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 20, location 3478254 - 3571815:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpg - D-Tyr) + (Dhpg) + (D-Hpg - D-Hpg - Tyr) + (Dhpg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 21, location 3478254 - 3545531:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpg - D-Tyr) + (Dhpg) + (D-Hpg - D-Hpg - Tyr) + (Dhpg)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
ACTEI_RS15560: Hpg - Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (15..402): Hpg
nrpys: Hpg

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:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNPAFDASLFEVHLLTGGDRHLYGPTETTLCATW
  Nearest Stachelhaus code(s):
    Hpg DAFHLGLLCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1037..1423): Tyr
nrpys: Tyr

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

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

ACTEI_RS15565: Dhpg
Search NORINE for peptide: strict or relaxed
AMP-binding (442..830): Dhpg
nrpys: Dhpg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPAFDASLYDVNFLAGGDWHTYGPTETTLCATW
  Nearest Stachelhaus code(s):
    Dhpg DAYNLGTLCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

ACTEI_RS15570: Hpg - Hpg - Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (459..852): Hpg
nrpys: Hpg

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:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPAFDISLFEVHLLTGGDRHLYGPTETTLCATW
  Nearest Stachelhaus code(s):
    Hpg DIFHLGLLCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1956..2348): Hpg
nrpys: Hpg

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:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPAFDASLLEVHLLTGGDRHLYGPTETTLCATW
  Nearest Stachelhaus code(s):
    Hpg DALHLGLLCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3467..3853): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDAAISEMTVIVAGEINGYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Tyr DASTIAGVCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

ACTEI_RS15575: Dhpg
Search NORINE for peptide: strict or relaxed
AMP-binding (470..870): Dhpg
nrpys: Dhpg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDAAFDPSLYEVHLGTGGDRNTYGPTETTLCATW
  Nearest Stachelhaus code(s):
    Dhpg DPYHGGTLCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

ACTEI_RS15650: NH2
CAL_domain (44..471): NH2
minowa: NH2

Prediction, score:
  NH2: 94.7
  fatty_acid: 48.3
  AHBA: 3.8
  Acetyl-CoA: 3.4
  shikimic_acid: 0.0

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

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP023865.1 - Region 11 - 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: 3,744,666 - 3,814,862 nt. (total: 70,197 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 oxygenase
ACTEI_RS16575: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

ACTEI_RS16640: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

ACTEI_RS16700: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: acyltransferase
ACTEI_RS16615: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: dehalogenase hydrolase
ACTEI_RS16580: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

ACTEI_RS16610: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase
ACTEI_RS16620: 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
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001133.4 |  | 0.69 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001240.4 |  | 0.68 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001133.4 |  | 0.69 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001240.4 |  | 0.68 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

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

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: 17.23 out of 19.52
Confidence: medium
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: 18.92 out of 23.79
Confidence: medium
Additional weak hits (19):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.04 out of 21.55
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.58 out of 27.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.25 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.86 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 15.87 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.86 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.35 out of 18.57
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.36 out of 21.84
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.08 out of 19.26
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.21 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.70 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.39 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.75 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.78 out of 29.65
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.43 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.68 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.30 out of 20.01
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 23, location 3744665 - 3814862:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - D-Leu - Ser) + (D-Orn - Lys - D-X - Ser - D-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).
ACTEI_RS16615: Leu - Leu - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (269..664): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAEAFDASVLELLILVGGEINAYGPTETTVVATW
  Nearest Stachelhaus code(s):
    Leu DALLLGAVVK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1319..1717): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAEAFDASVLEMLVVVGGDINAYGPTECTVVSTW
  Nearest Stachelhaus code(s):
    Leu DALLVGAVVK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2820..3205): 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:
    RWMTFDVSVWEWHFICSGEHNLYGPTEAAVDVTH
  Nearest Stachelhaus code(s):
    Ser DVWHISLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

ACTEI_RS16620: Orn - Lys - X - Ser - X
Search NORINE for peptide: strict or relaxed
AMP-binding (505..906): Orn
nrpys: 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:
    LQHAFDTSWEGLDVMLGGEYNFYGPTECTVDAVS
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2012..2416): Lys
nrpys: Lys

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:
    LDHAFDTSWEGFDLMLGGEYNYYGPTECAVDAVW
  Nearest Stachelhaus code(s):
    Lys DTEDMGYVDK (88% 8Å match)
    Orn DTEDMGYVDK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3070..3471): 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:
    LHLAFDSSWEELDVLVGGEYNMYGPTECAVDAVA
  Nearest Stachelhaus code(s):
    Orn DSEDLGFVDK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4590..4973): 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:
    RWMTFDVSVWEWHFLCSGEHNLYGPTEASVDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5630..6027): X
nrpys: Leu, 3OH-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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAEAFDASVLEMLIIAGGDINAYGPTEATVVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (79% 8Å match)
    Leu DALLIGAVVK (65% 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
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP023865.1 - Region 12 - 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: 4,065,682 - 4,096,626 nt. (total: 30,945 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: acetyltransferase
ACTEI_RS18065: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: hydrolase
ACTEI_RS17935: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: decarboxylase dehydratase
ACTEI_RS18000: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

ACTEI_RS18020: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.52 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0001408.5 |  | 0.50 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002527.2 |  | 0.50 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000947.5 |  | 0.44 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000866.5 |  | 0.43 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000943.5 |  | 0.42 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000923.3 |  | 0.41 | other (other) | paerucumarin | Pseudomonas aeruginosa PAO1
BGC0000867.3 |  | 0.41 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001592.5 |  | 0.38 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0002284.3 |  | 0.38 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.52 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0001408.5 |  | 0.50 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002527.2 |  | 0.50 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000947.5 |  | 0.44 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000866.5 |  | 0.43 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000943.5 |  | 0.42 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000923.3 |  | 0.41 | other (other) | paerucumarin | Pseudomonas aeruginosa PAO1
BGC0000867.3 |  | 0.41 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0001592.5 |  | 0.38 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0002284.3 |  | 0.38 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 18.15 out of 18.46
Confidence: strong
Additional weak hits (4):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.23 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.97 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.62 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP023865.1 - Region 13 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,178,711 - 4,203,248 nt. (total: 24,538 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
ACTEI_RS18470: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

ACTEI_RS18475: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002635.2 |  | 0.74 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000544.4 |  | 0.55 | ribosomal | planosporicin | Planomonospora alba
BGC0001289.5 |  | 0.55 | ribosomal | penisin | Paenibacillus ehimensis
BGC0001579.4 |  | 0.53 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000542.3 |  | 0.53 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.53 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0001660.3 |  | 0.51 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000529.5 |  | 0.51 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000563.4 |  | 0.49 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002635.2 |  | 0.74 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000544.4 |  | 0.55 | ribosomal | planosporicin | Planomonospora alba
BGC0001289.5 |  | 0.55 | ribosomal | penisin | Paenibacillus ehimensis
BGC0001579.4 |  | 0.53 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000542.3 |  | 0.53 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.53 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0001660.3 |  | 0.51 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000529.5 |  | 0.51 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000563.4 |  | 0.49 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712

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 ACTEI_RS18475

ACTEI_RS18480
Leader:
MPIDLFTQLPPADETIDDVFDLDVEVTVETTTSAI
Core:
Y H S G L I C T P T C I S P N G G S F C S F C C
Core with dehydrations:
Y H Dha G L I Cys Dhb P Dhb Cys I Dha P N G G Dha F Cys Dha F Cys Cys

#### antiSMASH-DB 4.0 matches for ACTEI_RS18480

100.0%
NZ_CP023865.1:
Lanthipeptides: ACTEI_RS18480_lanthipeptide
1
Y H S G L I C T P T C I S P N G G S F C S F C C
24
Y H S G L I C T P T C I S P N G G S F C S F C C
1
Y H S G L I C T P T C I S P N G G S F C S F C C
24
60.0%
NZ_CP059572.1:
Lanthipeptides: AGRA3207_RS17530_lanthipeptide
3
S G L I C T P T C I S P N G G S F C S F C C
24
S +C T P C S P G G S F C S+C C
3
S H A V C T P G C T S P G G G S F C S W C C
24
58.3%
NZ_FMZZ01000002.1 and 1 other:
NZ_KI866523.1 Lanthipeptides: MPTA5024_RS39835_lanthipeptide
Lanthipeptides: BLS56_RS30480_lanthipeptide
6
I C T P T C I S P N G G S F C S F C C
24
+C T P C S P G G S C S F C C
6
L C T P G C T S P G G G S N C S F C C
24
with 30 more sequence matches
Only the first 10 are displayed here.
57.7%
NZ_CP071248.1:
Lanthipeptides: BLI009_RS04985_lanthipeptide
6
I C T P T C I S P N G G S F C S F C C
24
+C T P C S P N G G S C S F C C
8
L C T P G C T S P N G G S G C S F C C
26
54.2%
NZ_AP023356.1:
Lanthipeptides: Aiant_RS23765_lanthipeptide
6
I C T P T C I S P N G G S F C S F C C
24
+C T P C S G G S C S F C C
6
L C T P G C T S A G G G S Q C S F C C
24
54.2%
NZ_AXWW01000016.1 and 1 other:
NZ_JAMTCO010000009.1 Lanthipeptides: LV75_RS20160_lanthipeptide
Lanthipeptides: H504_RS39505_lanthipeptide
6
I C T P T C I S P N G G S F C S F C C
24
+C T P C S G G S C S F C C
6
L C T P G C T S A G G G S N C S F C C
24
50.0%
NC_006582.1 and 6 others:
NZ_BOQQ01000001.1 Lanthipeptides: KI354_RS00530_lanthipeptide NZ_BOQS01000001.1 Lanthipeptides: KI364_RS00675_lanthipeptide NZ_CP019985.1 Lanthipeptides: BC8716_RS09795_lanthipeptide NZ_CP104963.1 Lanthipeptides: N7M99_RS07725_lanthipeptide NZ_FRBS01000002.1 Lanthipeptides: BUC05_RS08990_lanthipeptide NZ_JAODPB010000001.1 Lanthipeptides: N6H06_RS03040_lanthipeptide
Lanthipeptides: ABC_RS22115_lanthipeptide
1
Y H S G L I C T P T C I S P N G G S F C S F C C
24
+ S C T P C G S F S F C C
1
F T S V S F C T P G C--G E T G S F N S F C C
22
50.0%
NC_022873.1 and 93 others:
NC_022873.1 Lanthipeptides: YBT1518_RS19670_lanthipeptide NZ_CM000742.1 Lanthipeptides: BMYCO0001_RS26515_lanthipeptide NZ_CP011151.1 Lanthipeptides: WR47_RS18180_lanthipeptide NZ_CP011151.1 Lanthipeptides: WR47_RS18175_lanthipeptide NZ_CP011151.1 Lanthipeptides: WR47_RS18170_lanthipeptide NZ_CP011151.1 Lanthipeptides: WR47_RS18165_lanthipeptide NZ_CP015350.1 Lanthipeptides: BT246_RS19775_lanthipeptide NZ_CP015350.1 Lanthipeptides: BT246_RS19770_lanthipeptide NZ_CP015350.1 Lanthipeptides: BT246_RS19765_lanthipeptide NZ_CP017060.1 Lanthipeptides: FORC47_RS18710_lanthipeptide NZ_CP017060.1 Lanthipeptides: FORC47_RS18705_lanthipeptide NZ_CP017060.1 Lanthipeptides: FORC47_RS18700_lanthipeptide NZ_CP026678.1 Lanthipeptides: C2I25_RS21370_lanthipeptide NZ_CP026678.1 Lanthipeptides: C2I25_RS21365_lanthipeptide NZ_CP026678.1 Lanthipeptides: C2I25_RS21360_lanthipeptide NZ_CP035965.1 Lanthipeptides: EXW35_RS16385_lanthipeptide NZ_CP035965.1 Lanthipeptides: EXW35_RS16380_lanthipeptide NZ_CP035994.1 Lanthipeptides: EXW32_RS16155_lanthipeptide NZ_CP035994.1 Lanthipeptides: EXW32_RS16150_lanthipeptide NZ_CP035994.1 Lanthipeptides: EXW32_RS16145_lanthipeptide NZ_CP035994.1 Lanthipeptides: EXW32_RS16140_lanthipeptide NZ_CP035999.1 Lanthipeptides: EXW27_RS26195_lanthipeptide NZ_CP035999.1 Lanthipeptides: EXW27_RS26190_lanthipeptide NZ_CP035999.1 Lanthipeptides: EXW27_RS26185_lanthipeptide NZ_CP035999.1 Lanthipeptides: EXW27_RS26180_lanthipeptide NZ_CP036099.1 Lanthipeptides: EXW47_RS16265_lanthipeptide NZ_CP036099.1 Lanthipeptides: EXW47_RS16260_lanthipeptide NZ_CP036099.1 Lanthipeptides: EXW47_RS16255_lanthipeptide NZ_CP036099.1 Lanthipeptides: EXW47_RS16250_lanthipeptide NZ_CP036117.1 Lanthipeptides: EXW43_RS16620_lanthipeptide NZ_CP036117.1 Lanthipeptides: EXW43_RS16615_lanthipeptide NZ_CP036117.1 Lanthipeptides: EXW43_RS16610_lanthipeptide NZ_CP036117.1 Lanthipeptides: EXW43_RS16605_lanthipeptide NZ_CP036145.1 Lanthipeptides: EXW57_RS16110_lanthipeptide NZ_CP036145.1 Lanthipeptides: EXW57_RS16105_lanthipeptide NZ_CP036145.1 Lanthipeptides: EXW57_RS16100_lanthipeptide NZ_CP036145.1 Lanthipeptides: EXW57_RS16095_lanthipeptide NZ_CP040334.1 Lanthipeptides: EUC39_RS14125_lanthipeptide NZ_CP040334.1 Lanthipeptides: EUC39_RS14120_lanthipeptide NZ_CP040334.1 Lanthipeptides: EUC39_RS14115_lanthipeptide NZ_CP045606.2 Lanthipeptides: GE376_RS18355_lanthipeptide NZ_CP045606.2 Lanthipeptides: GE376_RS18350_lanthipeptide NZ_CP045606.2 Lanthipeptides: GE376_RS18345_lanthipeptide NZ_CP047366.1 Lanthipeptides: GSN03_RS15835_lanthipeptide NZ_CP047366.1 Lanthipeptides: GSN03_RS15830_lanthipeptide NZ_CP071811.1 Lanthipeptides: EXW36_RS16415_lanthipeptide NZ_CP071811.1 Lanthipeptides: EXW36_RS16410_lanthipeptide NZ_CP071811.1 Lanthipeptides: EXW36_RS16405_lanthipeptide NZ_CP072061.1 Lanthipeptides: J5V93_RS15130_lanthipeptide NZ_CP072061.1 Lanthipeptides: J5V93_RS15125_lanthipeptide NZ_CP072061.1 Lanthipeptides: J5V93_RS15120_lanthipeptide NZ_CP084035.1 Lanthipeptides: LCF45_RS15990_lanthipeptide NZ_CP084035.1 Lanthipeptides: LCF45_RS15985_lanthipeptide NZ_CP084035.1 Lanthipeptides: LCF45_RS15980_lanthipeptide NZ_CP084035.1 Lanthipeptides: LCF45_RS15975_lanthipeptide NZ_CP093291.1 Lanthipeptides: MN093_RS25975_lanthipeptide NZ_CP093291.1 Lanthipeptides: MN093_RS25970_lanthipeptide NZ_CP093291.1 Lanthipeptides: MN093_RS25965_lanthipeptide NZ_CP093291.1 Lanthipeptides: MN093_RS25960_lanthipeptide NZ_CP093835.1 Lanthipeptides: MN034_RS15810_lanthipeptide NZ_CP093835.1 Lanthipeptides: MN034_RS15805_lanthipeptide NZ_CP093835.1 Lanthipeptides: MN034_RS15800_lanthipeptide NZ_CP093835.1 Lanthipeptides: MN034_RS15795_lanthipeptide NZ_JAIPUK010000008.1 Lanthipeptides: K9P71_RS24265_lanthipeptide NZ_JAIPUK010000008.1 Lanthipeptides: K9P71_RS24260_lanthipeptide NZ_JANCTB010000001.1 Lanthipeptides: NMG90_RS06155_lanthipeptide NZ_JANCTB010000001.1 Lanthipeptides: NMG90_RS06150_lanthipeptide NZ_JANCTB010000001.1 Lanthipeptides: NMG90_RS06145_lanthipeptide NZ_JANCTB010000001.1 Lanthipeptides: NMG90_RS06140_lanthipeptide NZ_JH792114.1 Lanthipeptides: II3_RS21535_lanthipeptide NZ_JH792114.1 Lanthipeptides: II3_RS21530_lanthipeptide NZ_JH792114.1 Lanthipeptides: II3_RS21525_lanthipeptide NZ_JH792251.1 Lanthipeptides: III_RS11095_lanthipeptide NZ_JH792251.1 Lanthipeptides: III_RS11090_lanthipeptide NZ_JH792251.1 Lanthipeptides: III_RS11085_lanthipeptide NZ_JH792251.1 Lanthipeptides: III_RS11080_lanthipeptide NZ_JH792251.1 Lanthipeptides: III_RS11075_lanthipeptide NZ_LDGT01000041.1 Lanthipeptides: ABE17_RS18900_lanthipeptide NZ_LDGT01000041.1 Lanthipeptides: ABE17_RS18895_lanthipeptide NZ_LDGT01000041.1 Lanthipeptides: ABE17_RS18890_lanthipeptide NZ_LDGT01000041.1 Lanthipeptides: ABE17_RS18885_lanthipeptide NZ_LDHL01000037.1 Lanthipeptides: ABD98_RS26430_lanthipeptide NZ_LDHL01000037.1 Lanthipeptides: ABD98_RS26425_lanthipeptide NZ_MOOL01000076.1 Lanthipeptides: BK733_RS27280_lanthipeptide NZ_MOOL01000076.1 Lanthipeptides: BK733_RS27275_lanthipeptide NZ_MOOL01000076.1 Lanthipeptides: BK733_RS27270_lanthipeptide NZ_MSTN01000016.1 Lanthipeptides: BVF97_RS28620_lanthipeptide NZ_NIUP01000011.1 Lanthipeptides: CEU84_RS08145_lanthipeptide NZ_NIUP01000011.1 Lanthipeptides: CEU84_RS08140_lanthipeptide NZ_NKAX01000026.1 Lanthipeptides: CE086_RS26165_lanthipeptide NZ_NKAX01000026.1 Lanthipeptides: CE086_RS26160_lanthipeptide NZ_NVGU01000011.1 Lanthipeptides: COL71_RS14760_lanthipeptide NZ_NVGU01000011.1 Lanthipeptides: COL71_RS14755_lanthipeptide
Lanthipeptides: YBT1518_RS19675_lanthipeptide
7
C T P T C I S P N G G S F C S F C C
24
C T P C N G S F S F C C
7
C T P G C--G N T G S F N S F C C
22
50.0%
NZ_CP007699.2 and 2 others:
NZ_JACHEM010000003.1 Lanthipeptides: HNQ79_RS07795_lanthipeptide NZ_LIVZ01000011.1 Lanthipeptides: AMK31_RS29125_lanthipeptide
Lanthipeptides: T261_RS08380_lanthipeptide
7
C T P T C I S P N G G S F C S F C C
24
C T P C S G G S C S C C
7
C T P G C T S D G G G S G C S H C C
24
50.0%
NZ_CP047792.1 and 1 other:
NZ_JAGSAY010000004.1 Lanthipeptides: KC186_RS06745_lanthipeptide
Lanthipeptides: E3S88_RS07345_lanthipeptide
6
I C T P T C I S P N G G S F C S F C C
24
+C T P C N G S F S F C C
7
L C T P G C--A N T G S F N S F C C
23
50.0%
NZ_CP048882.1 and 8 others:
NZ_CP048882.1 Lanthipeptides: G4Z16_RS06545_lanthipeptide NZ_FMHI01000015.1 Lanthipeptides: H180DRAFT_RS21560_lanthipeptide NZ_JAMHJQ010000009.1 Lanthipeptides: M1203_RS22635_lanthipeptide NZ_JAMTCQ010000009.1 Lanthipeptides: LY41_RS11610_lanthipeptide NZ_KB905819.1 Lanthipeptides: F603_RS34750_lanthipeptide NZ_KN039946.1 Lanthipeptides: FM21_RS35825_lanthipeptide NZ_LIPF01000002.1 Lanthipeptides: AMK11_RS10850_lanthipeptide NZ_LIXJ01000007.1 Lanthipeptides: AMK22_RS13160_lanthipeptide
Lanthipeptides: G4Z16_RS06545_lanthipeptide
7
C T P T C I S P N G G S F C S F C C
24
C T P C S G G S C S C C
7
C T P G C T S E G G G S G C S H C C
24
50.0%
NZ_CP090942.1:
Lanthipeptides: LZT96_RS12010_lanthipeptide
3
S G L I C T P T C I S P N G G S F C S F C C
24
S I C T P C G S F S+C C
3
S K F I C T P G C--A K T G S F N S Y C C
22
50.0%
NZ_JADDUE010000020.1:
Lanthipeptides: INP57_RS28495_lanthipeptide
7
C T P T C I S P N G G S F C S F C C
24
C T P C S G G S C S C C
7
C T P G C T S E G G G S N C S H C C
24

#### MIBiG 4.0 matches for ACTEI_RS18480

11.8%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
6
I C T P T C
11
+C T P C
6
L C T P G C
11
10.0%
BGC0002110.3 (QKV49893.1):
Lanthipeptide: birimositide
15
N G G S F C S F
22
N G +C+
14
N N G G W C T L
21

#### 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:
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.34 out of 20.01
Confidence: medium
Additional weak hits (6):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.01 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.95 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.85 out of 30.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.77 out of 33.73
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.31 out of 35.63
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

ACTEI_RS18480 - Class I
  Cleavage pHMM score: 1.80
  RODEO score: 23
  Monoisotopic mass: 2342.0 Da
  Molecular weight: 2343.7 Da
  Number of bridges: 4
  Additional modifications: AviCys
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2361.8 Da N = 1

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (4178710...4203248)
ACTEI_RS18475
  RRE type: Lanthipeptide_LanB_RRE
  Location: 163 - 251
  Score: 49.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes

NZ_CP023865.1 - Region 14 - 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: 4,296,973 - 4,308,898 nt. (total: 11,926 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
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.38 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000470.6 |  | 0.36 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.35 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.35 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.34 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000598.5 |  | 0.31 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0001484.3 |  | 0.31 | other (other) | 2'-chloropentostatin, 2'-amino-2'-deoxyadenosine | Actinomadura sp. ATCC 39365
BGC0001753.3 |  | 0.30 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus
BGC0001561.4 |  | 0.28 | NRPS | curacomycin | Streptomyces curacoi
BGC0001605.3 |  | 0.28 | terpene | gibberellin | Sinorhizobium fredii NGR234

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.38 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000470.6 |  | 0.36 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.35 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.35 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.34 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000598.5 |  | 0.31 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0001484.3 |  | 0.31 | other (other) | 2'-chloropentostatin, 2'-amino-2'-deoxyadenosine | Actinomadura sp. ATCC 39365
BGC0001753.3 |  | 0.30 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus
BGC0001561.4 |  | 0.28 | NRPS | curacomycin | Streptomyces curacoi
BGC0001605.3 |  | 0.28 | terpene | gibberellin | Sinorhizobium fredii NGR234

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84
Confidence: medium
Additional weak hits (2):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.83 out of 27.04
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP023865.1 - Region 15 - triceptide
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: 4,321,755 - 4,343,938 nt. (total: 22,184 nt) Show pHMM detection rules used
triceptide: ((cds(PF04055 and (TIGR04085 or SPASM)) and triceptide_precursor) or triceptide_rSAM)

#### 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
ACTEI_RS19140: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Hydrolases: dehalogenase
ACTEI_RS19180: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

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

Reference | triceptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000874.5 |  | 0.36 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0001636.4 |  | 0.34 | NRPS | KK-1 | Curvularia clavata
BGC0002673.2 |  | 0.28 | PKS, other (other) | iminimycin A, iminimycin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002282.2 |  | 0.28 | other (other) | formycin A | Streptomyces kaniharaensis
BGC0002040.3 |  | 0.27 | other (other) | coformycin, formycin A | Streptomyces kaniharaensis
BGC0002039.3 |  | 0.26 | other (other) | coformycin, formycin A | Nocardia interforma ATCC 21072
BGC0001370.4 |  | 0.25 | NRPS | lipopeptide 8D1-1, lipopeptide 8D1-2 | Streptomyces rochei
BGC0001016.5 |  | 0.24 | NRPS, PKS | microcystin | Anabaena sp. 90
BGC0000290.5 |  | 0.23 | NRPS | A-47934 | Streptomyces toyocaensis
BGC0001955.4 |  | 0.23 | NRPS, saccharide | keratinimicin A, keratinimicin B, keratinimicin C, keratinimicin D | Amycolatopsis keratiniphila NRRL B24117

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000874.5 |  | 0.36 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0001636.4 |  | 0.34 | NRPS | KK-1 | Curvularia clavata
BGC0002673.2 |  | 0.28 | PKS, other (other) | iminimycin A, iminimycin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002282.2 |  | 0.28 | other (other) | formycin A | Streptomyces kaniharaensis
BGC0002040.3 |  | 0.27 | other (other) | coformycin, formycin A | Streptomyces kaniharaensis
BGC0002039.3 |  | 0.26 | other (other) | coformycin, formycin A | Nocardia interforma ATCC 21072
BGC0001370.4 |  | 0.25 | NRPS | lipopeptide 8D1-1, lipopeptide 8D1-2 | Streptomyces rochei
BGC0001016.5 |  | 0.24 | NRPS, PKS | microcystin | Anabaena sp. 90
BGC0000290.5 |  | 0.23 | NRPS | A-47934 | Streptomyces toyocaensis
BGC0001955.4 |  | 0.23 | NRPS, saccharide | keratinimicin A, keratinimicin B, keratinimicin C, keratinimicin D | Amycolatopsis keratiniphila NRRL B24117

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 25.31
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.76 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.67 out of 30.11
Confidence: medium
Additional weak hits (17):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.06 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.61 out of 30.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.70 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.75 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.05 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.83 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.88 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.45 out of 20.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.03 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.10 out of 20.97
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.76 out of 26.85
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.12 out of 36.53
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.00 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CatR | H2O2-responsive repressor
CelR | Cellobiose uptake repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP023865.1 - Region 16 - 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: 4,532,469 - 4,584,549 nt. (total: 52,081 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
ACTEI_RS20135: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

ACTEI_RS20175: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

ACTEI_RS20215: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: cyclase
ACTEI_RS20080: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

ACTEI_RS20190: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: synthase
ACTEI_RS20160: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

ACTEI_RS20245: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001160.5 |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000894.4 |  | 0.50 | other (other) | citrinin | Monascus aurantiacus
BGC0001844.4 |  | 0.48 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0002158.2 |  | 0.45 | NRPS, PKS | tenuazonic acid | Pyricularia oryzae 70-15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001160.5 |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000894.4 |  | 0.50 | other (other) | citrinin | Monascus aurantiacus
BGC0001844.4 |  | 0.48 | NRPS | holrhizin A, holrhizin B, holrhizin C, holrhizin D | Paraburkholderia rhizoxinica HKI 454
BGC0002158.2 |  | 0.45 | NRPS, PKS | tenuazonic acid | Pyricularia oryzae 70-15

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.00 out of 20.47
Confidence: strong
Additional weak hits (12):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 15.84 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.75 out of 29.38
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.05 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.06 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.19 out of 35.63
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.60 out of 29.25
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
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.01 out of 39.62
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.61 out of 25.31
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.12 out of 28.14
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 28, location 4532468 - 4584549:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - 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).
ACTEI_RS20160: fatty_acid - X
CAL_domain (129..460): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 48.3
  NH2: 37.7
  shikimic_acid: 0.0
  Acetyl-CoA: 0.0
  AHBA: 0.0

AMP-binding (2653..3041): 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:
    YWAAFDASVRQASSHVGGEANLYGPTETTINATF
  Nearest Stachelhaus code(s):
    Gln DACSTGVINK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

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_CP023865.1 - Region 17 - melanin
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: 4,856,206 - 4,868,169 nt. (total: 11,964 nt) Show pHMM detection rules used
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
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 phosphatase
ACTEI_RS21450: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

ACTEI_RS21485: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

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

Reference | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000911.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.59 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001164.3 |  | 0.56 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000909.3 |  | 0.53 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.48 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.39 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000662.5 |  | 0.39 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000043.5 |  | 0.39 | PKS | curacin A | Moorea producens 19L
BGC0000889.5 |  | 0.38 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000911.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.59 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001164.3 |  | 0.56 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000909.3 |  | 0.53 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.48 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.39 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000662.5 |  | 0.39 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000043.5 |  | 0.39 | PKS | curacin A | Moorea producens 19L
BGC0000889.5 |  | 0.38 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 25.31
Confidence: medium
Additional weak hits (17):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.27 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.61 out of 21.55
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: 18.86 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.74 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.35 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.33 out of 30.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.97 out of 28.14
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
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.26 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.22 out of 30.22
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.66 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
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.80 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor

NZ_CP023865.1 - Region 18 - 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: 5,071,704 - 5,094,343 nt. (total: 22,640 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
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 | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000496.5 |  | 0.63 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000501.3 |  | 0.62 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.61 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000553.3 |  | 0.52 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000518.3 |  | 0.52 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002698.2 |  | 0.51 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000546.3 |  | 0.49 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0002005.2 |  | 0.41 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000496.5 |  | 0.63 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000501.3 |  | 0.62 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.61 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000553.3 |  | 0.52 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000518.3 |  | 0.52 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002698.2 |  | 0.51 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000546.3 |  | 0.49 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0002005.2 |  | 0.41 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae

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 ACTEI_RS22425

ACTEI_RS22430
Leader:
MALLDLQGLEMSGLETGGGSS
Core:
S S T G C G V E S T A S L V V C A A S S L S L V T C H
Core with dehydrations:
Dha Dha Dhb G Cys G V E Dha Dhb A Dha L V V Cys A A Dha Dha L Dha L V Dhb Cys H

#### antiSMASH-DB 4.0 matches for ACTEI_RS22430

100.0%
NZ_CP023865.1:
Lanthipeptides: ACTEI_RS22430_lanthipeptide
1
S S T G C G V E S T A S L V V C A A S S L S L V T C H
27
S S T G C G V E S T A S L V V C A A S S L S L V T C H
1
S S T G C G V E S T A S L V V C A A S S L S L V T C H
27
96.3%
NZ_JAGFNS010000004.1:
Lanthipeptides: J5X75_RS08295_lanthipeptide
1
S S T G C G V E S T A S L V V C A A S S L S L V T C H
27
S S G C G V E S T A S L V V C A A S S L S L V T C H
1
S S A G C G V E S T A S L V V C A A S S L S L V T C H
27
51.9%
NZ_CP102509.1:
Lanthipeptides: JIW86_RS37035_lanthipeptide
6
G V E S T A S L V V C A A S S L S L V T C H
27
G S A S L++C S S L S L T C H
2
G G G S R A S L L L C G D S S L S L T T C H
23
with 88 more sequence matches
Only the first 10 are displayed here.
51.9%
NZ_JACHJG010000001.1:
Lanthipeptides: FHS38_RS02665_lanthipeptide
4
G C G V E S T A S L V V C A A S S L S L V T C H
27
G G S A S L++C S S L S+V T C+
1
G G G G G S R A S L L L C G D S S L S V V T C N
24
48.3%
NZ_CP080519.1:
Lanthipeptides: K1T34_RS20225_lanthipeptide
4
G C G V E S T A S L V V-C A A S S L S L V T C H
27
G G S S L+ C A S+L S L+T C H
5
G H G A P S N L S L L A S C A H S T L S L L T C H
29
48.1%
NZ_BMVE01000003.1 and 13 others:
NZ_BMVL01000005.1 Lanthipeptides: IE257_RS16230_lanthipeptide NZ_CP011664.1 Lanthipeptides: M444_RS30240_lanthipeptide NZ_CP020039.1 Lanthipeptides: B4U39_RS34445_lanthipeptide NZ_CP020555.1 Lanthipeptides: B6R96_RS03515_lanthipeptide NZ_CP029189.1 Lanthipeptides: DEJ51_RS31910_lanthipeptide NZ_CP033581.1 Lanthipeptides: EES41_RS31595_lanthipeptide NZ_CP034350.1 Lanthipeptides: D1J60_RS32970_lanthipeptide NZ_CP115936.1 Lanthipeptides: PET44_RS28650_lanthipeptide NZ_JAFLQY010000003.1 Lanthipeptides: J0X20_RS29030_lanthipeptide NZ_LIVP01000027.1 Lanthipeptides: AMK15_RS28680_lanthipeptide NZ_LWLD01000038.1 Lanthipeptides: A6A28_RS28600_lanthipeptide NZ_ML123038.1 Lanthipeptides: EES37_RS30340_lanthipeptide NZ_NNBM01000002.1 Lanthipeptides: CG724_RS07855_lanthipeptide
Lanthipeptides: IE248_RS10435_lanthipeptide
4
G C G V E S T A S L V V C A A S S L S L V T C H
27
G G S A S L++C S S L S+ T C+
1
G G G G G S R A S L L L C G D S S L S I T T C N
24
48.1%
NZ_FOEF01000044.1:
Lanthipeptides: BMY97_RS44620_lanthipeptide
4
G C G V E S T A S L V V-C A A S S L S L V T C H
27
G G S S L+ C S+L S L+T C H
2
G G G A P S N L S L L A S C T N S T L S L L T C H
26
48.1%
NZ_FOWW01000003.1:
Lanthipeptides: BM051_RS10305_lanthipeptide
6
G V E S T A S L V V-C A A S S L S L V T C H
27
G S S L V C A S++S L+T C H
1
G G G S N L S L V A S C A N S T V S L L T C H
23
44.4%
NZ_BIFH01000016.1:
Lanthipeptides: EMA17_RS12985_lanthipeptide
6
G V E S T A S L V V C A A S S L S L V T C H
27
G S S L++C S S L S L+ C H
1
G G G S N V S L L L C G N S S L S L L Q C H
22
44.4%
NZ_BMVC01000011.1:
Lanthipeptides: IE282_RS26650_lanthipeptide
9
S T A S L V V C A A S S L S L V T C H
27
S A S L++C S S L S+ T C H
8
S R A S L L L C G D S S L S V T T C H
26
44.4%
NZ_BMXJ01000002.1 and 3 others:
NZ_CP099837.1 Lanthipeptides: NE857_RS18075_lanthipeptide NZ_KI911536.1 Lanthipeptides: B042_RS0117070_lanthipeptide NZ_VWVU01000023.1 Lanthipeptides: FYX01_RS21045_lanthipeptide
Lanthipeptides: IE195_RS04480_lanthipeptide
9
S T A S L V V C A A S S L S L V T C
26
S T A S L++C S S L S+ T C
2
S T A S L L L C G D S S L S V T T C
19
44.4%
NZ_CP020042.1 and 9 others:
NZ_CP023202.1 Lanthipeptides: SXIN_RS23100_lanthipeptide NZ_CP023692.1 Lanthipeptides: CP980_RS04735_lanthipeptide NZ_CP028158.1 Lanthipeptides: C6361_RS04660_lanthipeptide NZ_CP028159.1 Lanthipeptides: C6W10_RS01185_lanthipeptide NZ_FNHI01000003.1 Lanthipeptides: BLT82_RS06465_lanthipeptide NZ_JAGPXX010000007.1 Lanthipeptides: KBZ10_RS10785_lanthipeptide NZ_JAPNLM010000003.1 Lanthipeptides: OTB16_RS07305_lanthipeptide NZ_LIVQ01000005.1 Lanthipeptides: AMK16_RS35205_lanthipeptide NZ_LIVQ01000005.1 Lanthipeptides: AMK16_RS35205_lanthipeptide
Lanthipeptides: B4U46_RS32710_lanthipeptide
6
G V E S T A S L V V C A A S S L S L V T C H
27
G S A S L++C S S L S+ T C+
6
G G G S R A S L L L C G D S S L S V T T C N
27
44.4%
NZ_CP023701.1 and 2 others:
NZ_CP043638.1 Lanthipeptides: F1D59_RS34930_lanthipeptide NZ_CP116355.1 Lanthipeptides: KPP03845_RS32700_lanthipeptide
Lanthipeptides: CP968_RS29065_lanthipeptide
6
G V E S T A S L V V C A A S S L S L V T C H
27
G S A S L++C S S L S+ T C+
6
G G G S R A S L L L C G D S S L S I T T C N
27

#### MIBiG 4.0 matches for ACTEI_RS22430

40.7%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
9
S T A S L V V C A A S S L S L V T C
26
S S L+V C S S L S+V C
3
S Q V S L L V C E Y S S L S V V L C
20

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 18.15 out of 18.46
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.17 out of 23.79
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (17):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.70 out of 26.33
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
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.91 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.07 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.08 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.50 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.51 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.53 out of 36.54
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.32 out of 26.12
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.64 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.83 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.46 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.74 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.61 out of 25.31
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.

ACTEI_RS22430 - Class III
  Cleavage pHMM score: 2.30
  RODEO score: 0
  Monoisotopic mass: 2388.2 Da
  Molecular weight: 2389.7 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2407.7 Da N = 1
    2425.7 Da N = 2
    2443.7 Da N = 3
    2461.8 Da N = 4
    2479.8 Da N = 5
    2497.8 Da N = 6
    2515.8 Da N = 7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP023865.1 - Region 19 - 2dos,NRPS-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: 5,609,935 - 5,690,838 nt. (total: 80,904 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
2dos: ((DOIS or DHQ_synthase or ValA or salQ) and DegT_DnrJ_EryC1 and (LipV or ADSI-DH or cds(ADH_N and ADH_zinc_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: dehydrogenase oxidase oxidoreductase oxygenase
ACTEI_RS24775: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

ACTEI_RS24785: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

ACTEI_RS24810: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

ACTEI_RS24820: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

ACTEI_RS24845: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

ACTEI_RS24870: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

ACTEI_RS24885: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: PPTase acylase aminotransferase methyltransferase
ACTEI_RS24765: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

ACTEI_RS24780: methyltransferase

smcogs
  SMCOG1089: methyltransferase

ACTEI_RS24830: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

ACTEI_RS24875: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: esterase hydrolase
ACTEI_RS24805: thioesterase

smcogs
  SMCOG1004: thioesterase

ACTEI_RS24865: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: synthase
ACTEI_RS24815: 3-oxoacyl-(acyl carrier protein) synthase III

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

ACTEI_RS24835: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

ACTEI_RS24840: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

ACTEI_RS24855: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

ACTEI_RS24860: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

ACTEI_RS37645: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | NRPS-like | 2dos | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  |  | 1.32 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  | 1.30 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  |  | 1.29 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  |  |  | 1.20 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001164.3 |  |  |  | 1.05 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001276.3 |  |  |  | 1.05 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  |  |  | 1.04 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000067.5 |  |  |  | 0.90 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0002191.2 |  |  |  | 0.89 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  |  |  | 0.86 | PKS | alternariol | Parastagonospora nodorum SN15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.72 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001164.3 |  | 0.68 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.68 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000018.5 |  | 0.67 | PKS | angolamycin | Streptomyces eurythermus
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 25.39 out of 29.51
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
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.45 out of 28.19
Confidence: medium
Additional weak hits (29):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.18 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.49 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 12.81 out of 18.57
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.96 out of 30.22
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.36 out of 30.22
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
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.73 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.30 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.04 out of 21.84
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.24 out of 20.97
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.04 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.72 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.39 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.97 out of 30.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.27 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.65 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.46 out of 29.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 14.81 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.16 out of 22.40
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.46 out of 29.65
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.24 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.05 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 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 31, location 5609934 - 5690838:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - ccmal - mal - ohmal) + (redmal) + (Me-redmal) + (emal) + (ccmal) + (Me-ccmal)
Non-colinear ordering:
  ACTEI_RS24855 + ACTEI_RS37645 + ACTEI_RS24845 + ACTEI_RS24840 + ACTEI_RS24835 + ACTEI_RS24830

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).
ACTEI_RS24830: mmal
PKS_AT (569..861): 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: 197.1
  Ethylmalonyl-CoA: 185.7
  Methoxymalonyl-CoA: 165.2
  2-Methylbutyryl-CoA: 139.0
  trans-1,2-CPDA: 115.8
  Propionyl-CoA: 94.7
  Malonyl-CoA: 94.3
  CHC-CoA: 85.5
  Isobutyryl-CoA: 84.8
  Benzoyl-CoA: 59.2
  Acetyl-CoA: 52.4
  inactive: 41.5
  fatty_acid: 32.1
  3-Methylbutyryl-CoA: 31.4

ACTEI_RS24835: mal
PKS_AT (557..844): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 184.6
  inactive: 82.2
  Methoxymalonyl-CoA: 62.7
  Methylmalonyl-CoA: 46.1
  Propionyl-CoA: 36.8
  Acetyl-CoA: 22.9
  Ethylmalonyl-CoA: 20.5
  Isobutyryl-CoA: 20.0
  2-Methylbutyryl-CoA: 16.6
  Benzoyl-CoA: 11.7
  trans-1,2-CPDA: 10.1
  CHC-CoA: 0.8
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

ACTEI_RS24840: emal
PKS_AT (561..861): emal
ATSignature: Ethylmalonyl-CoA, Methylmalonyl-CoA, Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 183.9
  Methylmalonyl-CoA: 183.4
  Methoxymalonyl-CoA: 159.5
  trans-1,2-CPDA: 119.3
  2-Methylbutyryl-CoA: 111.0
  CHC-CoA: 96.8
  Isobutyryl-CoA: 92.6
  Malonyl-CoA: 89.4
  Propionyl-CoA: 87.6
  Benzoyl-CoA: 65.8
  Acetyl-CoA: 48.0
  fatty_acid: 45.0
  3-Methylbutyryl-CoA: 37.2
  inactive: 21.7

ACTEI_RS24845: mmal
PKS_AT (562..858): 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: 209.1
  Ethylmalonyl-CoA: 198.1
  Methoxymalonyl-CoA: 174.7
  2-Methylbutyryl-CoA: 148.6
  trans-1,2-CPDA: 132.5
  Propionyl-CoA: 122.0
  CHC-CoA: 98.8
  Malonyl-CoA: 87.5
  Isobutyryl-CoA: 75.3
  Benzoyl-CoA: 59.5
  Acetyl-CoA: 54.5
  fatty_acid: 46.8
  3-Methylbutyryl-CoA: 38.1
  inactive: 20.1

ACTEI_RS37645: mal
PKS_AT (558..822): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 193.1
  inactive: 109.5
  Methoxymalonyl-CoA: 67.8
  Methylmalonyl-CoA: 59.0
  Propionyl-CoA: 34.7
  Isobutyryl-CoA: 34.3
  Acetyl-CoA: 23.3
  Ethylmalonyl-CoA: 21.0
  2-Methylbutyryl-CoA: 17.4
  CHC-CoA: 16.7
  Benzoyl-CoA: 15.0
  trans-1,2-CPDA: 14.7
  fatty_acid: 9.7
  3-Methylbutyryl-CoA: 0.0

ACTEI_RS24855: AHBA - mal - mal - mal
CAL_domain (35..439): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 386.4
  shikimic_acid: 231.1
  fatty_acid: 0.0
  NH2: 0.0
  Acetyl-CoA: 0.0

PKS_AT (1411..1675): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 193.1
  inactive: 109.5
  Methoxymalonyl-CoA: 67.8
  Methylmalonyl-CoA: 59.0
  Propionyl-CoA: 34.7
  Isobutyryl-CoA: 34.3
  Acetyl-CoA: 23.3
  Ethylmalonyl-CoA: 21.0
  2-Methylbutyryl-CoA: 17.4
  CHC-CoA: 16.7
  Benzoyl-CoA: 15.0
  trans-1,2-CPDA: 14.7
  fatty_acid: 9.7
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2991..3266): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 206.1
  inactive: 96.5
  Methoxymalonyl-CoA: 63.0
  Methylmalonyl-CoA: 46.9
  Ethylmalonyl-CoA: 25.2
  Propionyl-CoA: 25.0
  Acetyl-CoA: 23.1
  Benzoyl-CoA: 17.8
  Isobutyryl-CoA: 12.6
  trans-1,2-CPDA: 10.2
  CHC-CoA: 10.0
  fatty_acid: 8.7
  2-Methylbutyryl-CoA: 8.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3977..4241): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 193.1
  inactive: 109.5
  Methoxymalonyl-CoA: 67.8
  Methylmalonyl-CoA: 59.0
  Propionyl-CoA: 34.7
  Isobutyryl-CoA: 34.3
  Acetyl-CoA: 23.3
  Ethylmalonyl-CoA: 21.0
  2-Methylbutyryl-CoA: 17.4
  CHC-CoA: 16.7
  Benzoyl-CoA: 15.0
  trans-1,2-CPDA: 14.7
  fatty_acid: 9.7
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
DosR | Hypoxia stress response regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_CP023865.1 - Region 20 - 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: 5,697,072 - 5,740,782 nt. (total: 43,711 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
Transferases: sulfotransferase
ACTEI_RS25065: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

Hydrolases: back translocase dehalogenase
ACTEI_RS25050: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

ACTEI_RS25080: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Lyases: lyase
ACTEI_RS25125: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
ACTEI_RS25040: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

ACTEI_RS25055: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

ACTEI_RS25115: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

Translocases: transporter
ACTEI_RS25020: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.71 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  | 0.65 | NRPS | peramine | Epichloe festucae
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.71 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  | 0.65 | NRPS | peramine | Epichloe festucae
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.83 out of 20.47
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.41 out of 27.78
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 23.52 out of 26.33
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 25.13 out of 28.19
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.89 out of 30.11
Confidence: medium
Additional weak hits (24):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.83 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.59 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.50 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.21 out of 20.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.23 out of 20.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.23 out of 20.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.71 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.22 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.23 out of 20.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.90 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.51 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.85 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.12 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.40 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.55 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.42 out of 20.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.42 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.00 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.56 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.52 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.44 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.69 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 32, location 5697071 - 5740782:
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).
ACTEI_RS25045: Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (11..406): Gln
nrpys: Gln

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:
    QWLTFDAAQWEAQCFTGGEVNLYGPTECTINTSA
  Nearest Stachelhaus code(s):
    Gln DAWQFGLINK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

ACTEI_RS25055: X
AMP-binding (69..458): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    GPRFHSSGYSYMTGISTADLDGLGASEMGMALFL
  Nearest Stachelhaus code(s):
    bTyr or Tyr DGSTITAVAK (24% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CelR | Cellobiose uptake repressor
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_CP023865.1 - Region 21 - T1PKS,oligosaccharide
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: 5,783,792 - 5,851,087 nt. (total: 67,296 nt) Show pHMM detection rules used
oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))
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 oxygenase reductase
ACTEI_RS25340: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

ACTEI_RS25370: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

ACTEI_RS25385: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

ACTEI_RS25415: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

ACTEI_RS25420: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

ACTEI_RS25465: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

ACTEI_RS25475: alkyl hydroperoxide reductase/ Thiol specific

smcogs
  SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

ACTEI_RS25485: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

ACTEI_RS25580: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: acyltransferase glycosyltransferase transferase
ACTEI_RS25360: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

ACTEI_RS25380: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

ACTEI_RS25395: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

ACTEI_RS25400: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

ACTEI_RS25470: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Hydrolases: hydrolase
ACTEI_RS25355: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

ACTEI_RS25390: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

ACTEI_RS25570: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: dehydratase
ACTEI_RS25525: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
ACTEI_RS25430: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

ACTEI_RS25510: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

ACTEI_RS25515: 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 | oligosaccharide | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001276.3 |  |  | 0.48 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002043.3 |  |  | 0.43 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0000277.5 |  |  | 0.42 | PKS | urdamycin | Streptomyces fradiae
BGC0001201.3 |  |  | 0.40 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0000660.5 |  |  | 0.40 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0002347.3 |  |  | 0.39 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6
BGC0001310.5 |  |  | 0.38 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001948.3 |  |  | 0.35 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0001275.3 |  |  | 0.34 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  |  | 0.34 | PKS | asperlactone | Aspergillus ochraceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.77 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.67 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001268.4 |  | 0.63 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (8):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.06 out of 31.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.16 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.93 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.22 out of 30.98
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.48 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.97 out of 23.43
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
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 33, location 5783791 - 5851087:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 35, location 5784247 - 5851087:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
ACTEI_RS25430: mal
PKS_AT (616..843): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 77.1
  Methoxymalonyl-CoA: 42.2
  inactive: 40.3
  Methylmalonyl-CoA: 39.2
  Propionyl-CoA: 31.2
  Isobutyryl-CoA: 28.9
  Benzoyl-CoA: 16.9
  fatty_acid: 11.0
  trans-1,2-CPDA: 6.8
  Ethylmalonyl-CoA: 6.7
  2-Methylbutyryl-CoA: 6.4
  Acetyl-CoA: 6.3
  3-Methylbutyryl-CoA: 0.0
  CHC-CoA: -1.4

ACTEI_RS25510: pk
PKS_AT (539..832): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 70.8%
  Methylmalonyl-CoA: 66.7%
  Ethylmalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 107.4
  Methoxymalonyl-CoA: 93.2
  Malonyl-CoA: 77.1
  Ethylmalonyl-CoA: 70.1
  2-Methylbutyryl-CoA: 62.7
  Propionyl-CoA: 54.0
  trans-1,2-CPDA: 44.3
  Isobutyryl-CoA: 43.7
  CHC-CoA: 43.5
  3-Methylbutyryl-CoA: 38.9
  inactive: 32.9
  Benzoyl-CoA: 31.8
  Acetyl-CoA: 31.0
  fatty_acid: 20.5

ACTEI_RS25515: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (39..450): 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:
    MTALYPMAGPGGSLQVAGSQQVYGMAEGLLCMTR
  Nearest Stachelhaus code(s):
    Hpa TWPSQGVLCK (59% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

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

NZ_CP023865.1 - Region 22 - phosphoglycolipid,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: 6,688,749 - 6,721,072 nt. (total: 32,324 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)
phosphoglycolipid: (MoeO5 or moeGT)

#### 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
ACTEI_RS29310: nucleotide sugar dehydrogenase

smcogs
  SMCOG1152: nucleotide sugar dehydrogenase

Transferases: methyltransferase
ACTEI_RS29330: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
ACTEI_RS29365: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

ACTEI_RS29410: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: dehydratase
ACTEI_RS29305: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

ACTEI_RS29415: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase synthetase
ACTEI_RS29320: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

ACTEI_RS29350: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

ACTEI_RS29355: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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

Reference | terpene-precursor | phosphoglycolipid | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001395.5 |  |  | 1.32 | other (other) | teichomycin A1 | Actinoplanes teichomyceticus
BGC0000820.5 |  |  | 0.36 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0002309.2 |  |  | 0.33 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000677.5 |  |  | 0.31 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001880.3 |  |  | 0.29 | ribosomal | scytodecamide | Scytonema sp. UIC 10036
BGC0001911.3 |  |  | 0.28 | terpene | raimonol | Streptomyces anulatus
BGC0000885.3 |  |  | 0.28 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0001910.4 |  |  | 0.28 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000664.5 |  |  | 0.28 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  |  | 0.28 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001395.5 |  | 1.00 | other (other) | teichomycin A1 | Actinoplanes teichomyceticus
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001758.4 |  | 0.59 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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

No significant matches found.

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:
ACTEI_RS29350: PT_FPPS_like
Domain 1 (58 - 360): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.32 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.61 out of 26.06
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.72 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP023865.1 - Region 23 - 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: 6,785,661 - 6,806,206 nt. (total: 20,546 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
ACTEI_RS29805: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Ligases: synthetase
ACTEI_RS29765: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.39 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3 |  | 0.35 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.34 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000664.5 |  | 0.33 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001227.3 |  | 0.32 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000648.3 |  | 0.31 | terpene | carotenoid | Myxococcus xanthus
BGC0000633.3 |  | 0.31 | terpene | carotenoid | Streptomyces avermitilis
BGC0000644.3 |  | 0.31 | terpene | carotenoid | Dietzia sp. CQ4
BGC0001456.3 |  | 0.31 | terpene | isorenieratene | Streptomyces argillaceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.39 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3 |  | 0.35 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.34 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000664.5 |  | 0.33 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001227.3 |  | 0.32 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000648.3 |  | 0.31 | terpene | carotenoid | Myxococcus xanthus
BGC0000633.3 |  | 0.31 | terpene | carotenoid | Streptomyces avermitilis
BGC0000644.3 |  | 0.31 | terpene | carotenoid | Dietzia sp. CQ4
BGC0001456.3 |  | 0.31 | terpene | isorenieratene | Streptomyces argillaceus

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:
ACTEI_RS29765: PT_FPPS_like
Domain 1 (20 - 164): 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: 29.02 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
Additional weak hits (4):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.64 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.44 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.06 out of 36.54
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.68 out of 39.62
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

NZ_CP023865.1 - Region 24 - NI-siderophore,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: 6,815,214 - 6,882,336 nt. (total: 67,123 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC
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 oxygenase
ACTEI_RS29930: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

ACTEI_RS29975: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

ACTEI_RS30055: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: cyclase decarboxylase dehydratase
ACTEI_RS29935: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

ACTEI_RS29980: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

ACTEI_RS30065: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

ACTEI_RS30070: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: ligase synthase
ACTEI_RS30020: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

ACTEI_RS30035: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

ACTEI_RS30090: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

Translocases: transport transporter
ACTEI_RS29960: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

ACTEI_RS30025: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | NI-siderophore | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001572.3 |  |  | 0.41 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0001478.5 |  |  | 0.33 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0001244.3 |  |  | 0.32 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  |  | 0.32 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.32 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  |  | 0.32 | PKS | asperlactone | Aspergillus ochraceus
BGC0000941.3 |  |  | 0.31 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  |  | 0.29 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002192.3 |  |  | 0.27 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  |  | 0.27 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001572.3 |  | 0.72 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0001478.5 |  | 0.67 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0000941.3 |  | 0.64 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.63 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.92 out of 20.97
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.57 out of 36.53
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 22.28 out of 23.43
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
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: 18.37 out of 20.47
Confidence: medium
Additional weak hits (21):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.34 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.09 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.61 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.53 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.70 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.14 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.76 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.86 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
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.52 out of 26.12
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.76 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.47 out of 30.98
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.29 out of 23.43
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.66 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.04 out of 29.65
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.22 out of 30.98
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.67 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 40, location 6815213 - 6882336:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 42, location 6837761 - 6882336:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).
ACTEI_RS30020: mal
PKS_AT (550..839): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 67.5
  Methylmalonyl-CoA: 39.4
  Methoxymalonyl-CoA: 36.0
  Propionyl-CoA: 29.6
  inactive: 23.9
  fatty_acid: 22.1
  Ethylmalonyl-CoA: 21.0
  Isobutyryl-CoA: 14.7
  2-Methylbutyryl-CoA: 13.6
  trans-1,2-CPDA: 9.3
  Benzoyl-CoA: 2.8
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

ACTEI_RS30035: X
AMP-binding (48..446): 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:
    GSTSWAKHAWSACAVGAGERDGFGQTETSVQIAN
  Nearest Stachelhaus code(s):
    Phe or Tyr DAACVAGVAK (35% 8Å match)
  Stachelhaus code match:
    60% (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
AfsR | Pleiotropic regulatory for antibiotic production
BldD | Development and antibiotic global regulator
CcpA | Catabolite control protein A
CelR | Cellobiose uptake repressor
DmdR1 | Iron(II)-dependent repressor
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP023865.1 - Region 25 - 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: 7,880,206 - 7,921,264 nt. (total: 41,059 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
Transferases: Prenylation aminotransferase methyltransferase
ACTEI_RS34785: aminotransferase

smcogs
  SMCOG1019: aminotransferase

ACTEI_RS34845: Methylation

MITE
  MITE0000082Methylation (identity: 71.20%)
smcogs
  SMCOG1089: methyltransferase

ACTEI_RS34850: Prenylation

MITE
  MITE0000083Prenylation (identity: 74.30%)

Hydrolases: deformylase
ACTEI_RS34880: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Lyases: lyase
ACTEI_RS34750: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: synthase
ACTEI_RS34840: 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
--- | --- | --- | --- | --- | ---
BGC0001077.4 |  | 0.68 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431
BGC0002362.3 |  | 0.67 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001896.4 |  | 0.43 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0001206.5 |  | 0.43 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0000918.3 |  | 0.42 | other (other) | ochronotic pigment | Streptomyces avermitilis
BGC0002554.2 |  | 0.42 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
BGC0001903.3 |  | 0.41 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0002584.2 |  | 0.41 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002007.2 |  | 0.41 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001077.4 |  | 0.68 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431
BGC0002362.3 |  | 0.67 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0001485.4 |  | 0.43 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001896.4 |  | 0.43 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0001206.5 |  | 0.43 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0000918.3 |  | 0.42 | other (other) | ochronotic pigment | Streptomyces avermitilis
BGC0002554.2 |  | 0.42 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
BGC0001903.3 |  | 0.41 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0002584.2 |  | 0.41 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002007.2 |  | 0.41 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina

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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.90 out of 26.85
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
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.64 out of 26.33
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.59 out of 24.78
Confidence: medium
Additional weak hits (11):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.57 out of 20.97
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.33 out of 27.18
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.83 out of 24.78
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.46 out of 23.43
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.14 out of 31.73
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.00 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.14 out of 21.84
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.63 out of 27.18
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CRP | Cyclic AMP receptor protein
LexA variant 2 | Repressor of DNA damage response
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP023865.1 - Region 26 - deazapurine
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: 8,104,948 - 8,127,363 nt. (total: 22,416 nt) Show pHMM detection rules used
deazapurine: (GTP_cyclohydroI and PTPS and QueE and QueC and not (dpdA1 or bTGT))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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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
Lyases: lyase
ACTEI_RS35785: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

ACTEI_RS35825: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

ACTEI_RS35830: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

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 | deazapurine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002354.4 |  | 0.64 | other (other) | huimycin | Kutzneria albida DSM 43870
BGC0000881.3 |  | 0.62 | other (other) | toyocamycin | Streptomyces ahygroscopicus subsp. wuzhouensis
BGC0001808.5 |  | 0.62 | other (other) | toyocamycin | Streptomyces diastatochromogenes
BGC0000802.5 |  | 0.60 | saccharide | succinoglycan | Sinorhizobium meliloti
BGC0001937.4 |  | 0.57 | other (other) | tubercidin | Streptomyces tubercidicus
BGC0001994.4 |  | 0.53 | other (other) | β-ethynylserine | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000387.5 |  | 0.49 | NRPS | mangotoxin | Pseudomonas syringae pv. syringae
BGC0002313.3 |  | 0.48 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000879.5 |  | 0.45 | other (other) | toyocamycin, sangivamycin | Streptomyces rimosus
BGC0000876.5 |  | 0.45 | other (other) | neopolyoxin C | Streptomyces tendae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002354.4 |  | 0.64 | other (other) | huimycin | Kutzneria albida DSM 43870
BGC0000881.3 |  | 0.62 | other (other) | toyocamycin | Streptomyces ahygroscopicus subsp. wuzhouensis
BGC0001808.5 |  | 0.62 | other (other) | toyocamycin | Streptomyces diastatochromogenes
BGC0000802.5 |  | 0.60 | saccharide | succinoglycan | Sinorhizobium meliloti
BGC0001937.4 |  | 0.57 | other (other) | tubercidin | Streptomyces tubercidicus
BGC0001994.4 |  | 0.53 | other (other) | β-ethynylserine | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000387.5 |  | 0.49 | NRPS | mangotoxin | Pseudomonas syringae pv. syringae
BGC0002313.3 |  | 0.48 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000879.5 |  | 0.45 | other (other) | toyocamycin, sangivamycin | Streptomyces rimosus
BGC0000876.5 |  | 0.45 | other (other) | neopolyoxin C | Streptomyces tendae

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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
Additional weak hits (3):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.47 out of 30.97
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.04 out of 30.11
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.43 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator