Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
2.1
2.2
2.3

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

NZ_CP024199.1 (Thalassospira marina)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | terpene | 490,413 | 511,492 |
Region 1.2 | terpene-precursor | 1,394,822 | 1,415,661 |
Region 1.3 | terpene | 2,014,067 | 2,034,912 |
Region 1.4 | ectoine | 2,096,617 | 2,107,018 | Medium | ectoine | other:other
Region 1.5 | RiPP-like | 2,771,783 | 2,782,730 |
Region 1.6 | arylpolyene | 2,923,800 | 2,967,780 | Low | APE Vf | other:other

NZ_CP024200.1 (Thalassospira marina)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | azole-containing-RiPP,lanthipeptide-class-ii | 456,997 | 486,109 |
Region 2.2 | NRPS | 651,214 | 694,207 |
Region 2.3 | hydrogen-cyanide,NI-siderophore | 796,768 | 846,258 | Low | schizokinen | NRPS:Type IV

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | terpene | 490,413 | 511,492 |
Region 1.2 | terpene-precursor | 1,394,822 | 1,415,661 |
Region 1.3 | terpene | 2,014,067 | 2,034,912 |
Region 1.4 | ectoine | 2,096,617 | 2,107,018 | Medium | ectoine | other:other
Region 1.5 | RiPP-like | 2,771,783 | 2,782,730 |
Region 1.6 | arylpolyene | 2,923,800 | 2,967,780 | Low | APE Vf | other:other
Region 2.1 | azole-containing-RiPP,lanthipeptide-class-ii | 456,997 | 486,109 |
Region 2.2 | NRPS | 651,214 | 694,207 |
Region 2.3 | hydrogen-cyanide,NI-siderophore | 796,768 | 846,258 | Low | schizokinen | NRPS:Type IV

Compact view
NZ_CP024199.1 - 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: 490,413 - 511,492 nt. (total: 21,080 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: dehalogenase
CSC3H3_RS02210: 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0001862.4 |  | 0.40 | ribosomal | pallidocin | Aeribacillus pallidus
BGC0001863.4 |  | 0.38 | ribosomal, terpene | bacillicn CER074 | Bacillus mycoides
BGC0001887.3 |  | 0.38 | ribosomal | huazacin | Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0001210.5 |  | 0.36 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000626.3 |  | 0.36 | ribosomal | thuricin | Bacillus thuringiensis
BGC0000539.5 |  | 0.36 | ribosomal | nukacin ISK-1 | Staphylococcus warneri
BGC0002635.2 |  | 0.35 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000558.5 |  | 0.42 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0001862.4 |  | 0.40 | ribosomal | pallidocin | Aeribacillus pallidus
BGC0001863.4 |  | 0.38 | ribosomal, terpene | bacillicn CER074 | Bacillus mycoides
BGC0001887.3 |  | 0.38 | ribosomal | huazacin | Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0001210.5 |  | 0.36 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000626.3 |  | 0.36 | ribosomal | thuricin | Bacillus thuringiensis
BGC0000539.5 |  | 0.36 | ribosomal | nukacin ISK-1 | Staphylococcus warneri
BGC0002635.2 |  | 0.35 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
CSC3H3_RS02195: PT_phytoene_like
Domain 1 (16 - 316): Prenyltransferase; Phytoene synthase like
Subtype: unknown

Reactions:
  FPP → PSPP
  FPP → diapophytoene
  FPP → squalene
  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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 22.67 out of 26.33
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.87 out of 27.78
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.07 out of 25.31
Confidence: medium
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: 21.87 out of 29.72
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.21 out of 27.78
Confidence: medium
Additional weak hits (7):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.23 out of 23.43
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.78 out of 30.22
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.17 out of 24.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.10 out of 29.25
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.45 out of 20.01
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CatR | H2O2-responsive repressor
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP024199.1 - Region 2 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,394,822 - 1,415,661 nt. (total: 20,840 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CSC3H3_RS06375: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CSC3H3_RS06380: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CSC3H3_RS06385: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Ligases: synthase synthetase
CSC3H3_RS06355: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

CSC3H3_RS06365: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0001605.3 |  | 0.43 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001594.3 |  | 0.41 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0000678.5 |  | 0.41 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000666.5 |  | 0.41 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001184.4 |  | 0.41 | other (other) | bacilysin | Bacillus velezensis FZB42

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0001605.3 |  | 0.43 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001594.3 |  | 0.41 | other (other) | fischerindole L | Fischerella muscicola UTEX 1829
BGC0000678.5 |  | 0.41 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000666.5 |  | 0.41 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001184.4 |  | 0.41 | other (other) | bacilysin | Bacillus velezensis FZB42

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
CSC3H3_RS06355: PT_FPPS_like
Domain 1 (17 - 278): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  DMAPP, IPP → FPP

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.42 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.74 out of 29.38
Confidence: medium
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 28.21 out of 32.74
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.00 out of 28.19
Confidence: medium
Additional weak hits (11):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.08 out of 26.85
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.16 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.95 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.69 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.82 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.78 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.32 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.80 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.72 out of 29.65
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 24.96 out of 30.98
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
FuR variant 1 | Ferric Uptake Regulator
FuR variant 2 | Ferric Uptake Regulator
RpoN | Regulator of nitrogen assimilation and virulence
ZuR variant 1 | Zinc-responsive repressor

NZ_CP024199.1 - Region 3 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,014,067 - 2,034,912 nt. (total: 20,846 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
CSC3H3_RS09275: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001687.3 |  | 0.33 | other (other) | N-tetradecanoyl tyrosine | uncultured bacterium CSL12
BGC0000760.5 |  | 0.29 | saccharide | emulsan | Acinetobacter venetianus RAG-1 = CIP 110063
BGC0000698.5 |  | 0.29 | saccharide | hygromycin A | Streptomyces hygroscopicus
BGC0001637.3 |  | 0.28 | NRPS | kleboxymycin | Klebsiella oxytoca
BGC0000448.5 |  | 0.28 | NRPS | tomaymycin | Streptomyces achromogenes
BGC0001652.5 |  | 0.26 | NRPS | limazepine C, limazepine D, limazepine E, limazepine F, limazepine A | Streptomyces sp. ICBB 8177
BGC0000415.5 |  | 0.26 | NRPS | quinomycin | Streptomyces griseovariabilis subsp. bandungensis
BGC0001228.5 |  | 0.26 | NRPS | retimycin A | Salinispora arenicola CNT005
BGC0002129.4 |  | 0.25 | PKS | metathramycin, premetathramycin | uncultured bacterium
BGC0000339.5 |  | 0.25 | NRPS | echinomycin | Streptomyces lasaliensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001687.3 |  | 0.33 | other (other) | N-tetradecanoyl tyrosine | uncultured bacterium CSL12
BGC0000760.5 |  | 0.29 | saccharide | emulsan | Acinetobacter venetianus RAG-1 = CIP 110063
BGC0000698.5 |  | 0.29 | saccharide | hygromycin A | Streptomyces hygroscopicus
BGC0001637.3 |  | 0.28 | NRPS | kleboxymycin | Klebsiella oxytoca
BGC0000448.5 |  | 0.28 | NRPS | tomaymycin | Streptomyces achromogenes
BGC0001652.5 |  | 0.26 | NRPS | limazepine C, limazepine D, limazepine E, limazepine F, limazepine A | Streptomyces sp. ICBB 8177
BGC0000415.5 |  | 0.26 | NRPS | quinomycin | Streptomyces griseovariabilis subsp. bandungensis
BGC0001228.5 |  | 0.26 | NRPS | retimycin A | Salinispora arenicola CNT005
BGC0002129.4 |  | 0.25 | PKS | metathramycin, premetathramycin | uncultured bacterium
BGC0000339.5 |  | 0.25 | NRPS | echinomycin | Streptomyces lasaliensis

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
CSC3H3_RS09245: PT_phytoene_like
Domain 1 (8 - 276): Prenyltransferase; Phytoene synthase like
Subtype: unknown

Reactions:
  FPP → PSPP
  FPP → diapophytoene
  FPP → squalene
  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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
Additional weak hits (2):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.14 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.44 out of 36.53
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP024199.1 - Region 4 - ectoine
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,096,617 - 2,107,018 nt. (total: 10,402 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
CSC3H3_RS09575: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: phosphatase
CSC3H3_RS09600: 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 | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000856.3 |  | 0.80 | other (other) | ectoine | Methylophaga thalassica
BGC0000859.3 |  | 0.80 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000857.3 |  | 0.80 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.79 | other (other) | ectoine | Methylarcula marina
BGC0000855.3 |  | 0.74 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000852.5 |  | 0.71 | other (other) | ectoine | Sporosarcina pasteurii
BGC0002052.3 |  | 0.68 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.68 | other (other) | ectoine | Streptomyces anulatus
BGC0000854.3 |  | 0.67 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000856.3 |  | 0.80 | other (other) | ectoine | Methylophaga thalassica
BGC0000859.3 |  | 0.80 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000857.3 |  | 0.80 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.79 | other (other) | ectoine | Methylarcula marina
BGC0000855.3 |  | 0.74 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000852.5 |  | 0.71 | other (other) | ectoine | Sporosarcina pasteurii
BGC0002052.3 |  | 0.68 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.68 | other (other) | ectoine | Streptomyces anulatus
BGC0000854.3 |  | 0.67 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus

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:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.64 out of 27.55
Confidence: medium
Additional weak hits (4):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.79 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.94 out of 30.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.86 out of 27.18
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
GnfM | Regulator of nitrogen-fixation genes

NZ_CP024199.1 - Region 5 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,771,783 - 2,782,730 nt. (total: 10,948 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
CSC3H3_RS12665: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000372.5 |  | 0.27 | NRPS | hexadehydroastechrome, terezine-D, astechrome | Aspergillus fumigatus Af293
BGC0000207.5 |  | 0.26 | PKS | chartreusin | Streptomyces chartreusis
BGC0002408.3 |  | 0.25 | NRPS | malleobactin X | Collimonas pratensis
BGC0001285.5 |  | 0.25 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001617.3 |  | 0.25 | terpene | hirsutene | Stereum hirsutum FP-91666 SS1
BGC0000495.5 |  | 0.24 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0001578.3 |  | 0.23 | PKS | duclauxin | Talaromyces stipitatus ATCC 10500
BGC0000935.5 |  | 0.23 | PKS, other (aminocoumarin) | esmeraldin | Streptomyces antibioticus
BGC0002244.3 |  | 0.23 | PKS | 3'-methoxy-1,2-dehydropenicillide, pestalotiollide B, pestalotiollide C, 1,2-dehydropenicillide, 3-methoxy-1,2-dehydropenicillide, 1,2-epoxy-3,4-didehydropenicillide | Neopestalotiopsis clavispora
BGC0000723.5 |  | 0.22 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000372.5 |  | 0.27 | NRPS | hexadehydroastechrome, terezine-D, astechrome | Aspergillus fumigatus Af293
BGC0000207.5 |  | 0.26 | PKS | chartreusin | Streptomyces chartreusis
BGC0002408.3 |  | 0.25 | NRPS | malleobactin X | Collimonas pratensis
BGC0001285.5 |  | 0.25 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001617.3 |  | 0.25 | terpene | hirsutene | Stereum hirsutum FP-91666 SS1
BGC0000495.5 |  | 0.24 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0001578.3 |  | 0.23 | PKS | duclauxin | Talaromyces stipitatus ATCC 10500
BGC0000935.5 |  | 0.23 | PKS, other (aminocoumarin) | esmeraldin | Streptomyces antibioticus
BGC0002244.3 |  | 0.23 | PKS | 3'-methoxy-1,2-dehydropenicillide, pestalotiollide B, pestalotiollide C, 1,2-dehydropenicillide, 3-methoxy-1,2-dehydropenicillide, 1,2-epoxy-3,4-didehydropenicillide | Neopestalotiopsis clavispora
BGC0000723.5 |  | 0.22 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. limoneus

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: 18.25 out of 18.46
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.93 out of 26.33
Confidence: medium
Additional weak hits (4):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.51 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.87 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.81 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.96 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP024199.1 - Region 6 - arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,923,800 - 2,967,780 nt. (total: 43,981 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
CSC3H3_RS13340: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

CSC3H3_RS13435: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase halogenase
CSC3H3_RS13365: acyltransferase

smcogs
  SMCOG1141: acyltransferase

CSC3H3_RS13415: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

Ligases: ligase synthase
CSC3H3_RS13385: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CSC3H3_RS13390: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

CSC3H3_RS13425: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CSC3H3_RS13440: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.74 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002008.3 |  | 0.65 | other (other) | aryl polyenes | Xenorhabdus doucetiae
BGC0000836.5 |  | 0.58 | other (other) | APE Ec | Escherichia coli CFT073
BGC0001160.5 |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001940.3 |  | 0.49 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0000837.4 |  | 0.48 | other (other) | APE Vf | Aliivibrio fischeri ES114
BGC0001987.2 |  | 0.47 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0002711.2 |  | 0.47 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000231.5 |  | 0.47 | PKS | griseusin A, griseusin B | Streptomyces griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.74 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002008.3 |  | 0.65 | other (other) | aryl polyenes | Xenorhabdus doucetiae
BGC0000836.5 |  | 0.58 | other (other) | APE Ec | Escherichia coli CFT073
BGC0001160.5 |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001940.3 |  | 0.49 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0000837.4 |  | 0.48 | other (other) | APE Vf | Aliivibrio fischeri ES114
BGC0001987.2 |  | 0.47 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0002711.2 |  | 0.47 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000231.5 |  | 0.47 | PKS | griseusin A, griseusin B | Streptomyces griseus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.52 out of 27.55
Confidence: medium
Additional weak hits (6):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.60 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.10 out of 39.62
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.28 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.59 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.20 out of 26.12
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.10 out of 27.78
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CSC3H3_RS13385: X
AMP-binding (42..294): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LRVS-----QAWIAFCSGGTEILGSTETGGIAWR
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
GnfM | Regulator of nitrogen-fixation genes

NZ_CP024200.1 - Region 1 - azole-containing-RiPP,lanthipeptide-class-ii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 456,997 - 486,109 nt. (total: 29,113 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase reductase
CSC3H3_RS22295: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CSC3H3_RS22330: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: sulfotransferase
CSC3H3_RS22275: glutathione S-transferase

smcogs
  SMCOG1193: glutathione S-transferase

Hydrolases: hydrolase
CSC3H3_RS22340: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

Lyases: cyclase decarboxylase
CSC3H3_RS22250: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

CSC3H3_RS22310: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | azole-containing-RiPP | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002551.2 |  |  | 0.38 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398
BGC0002485.2 |  |  | 0.38 | other (other), ribosomal | muscoride A, muscoride B | Desmonostoc sp. PCC 7906
BGC0000483.5 |  |  | 0.38 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000565.5 |  |  | 0.37 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000475.5 |  |  | 0.32 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0000480.5 |  |  | 0.32 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0002311.3 |  |  | 0.32 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0000471.4 |  |  | 0.31 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112
BGC0000477.3 |  |  | 0.31 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A
BGC0002584.2 |  |  | 0.31 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002551.2 |  | 0.51 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398
BGC0002485.2 |  | 0.51 | other (other), ribosomal | muscoride A, muscoride B | Desmonostoc sp. PCC 7906
BGC0000483.5 |  | 0.51 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0000565.5 |  | 0.50 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000475.5 |  | 0.47 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0000480.5 |  | 0.47 | ribosomal | tenuecyclamide A, tenuecyclamide C | Nostoc spongiaeforme var. tenue str. Carmeli
BGC0002584.2 |  | 0.46 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0002311.3 |  | 0.46 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0000471.4 |  | 0.46 | ribosomal | viridisamide A | Oscillatoria nigro-viridis PCC 7112
BGC0000477.3 |  | 0.46 | ribosomal | patellin 2, patellin 3 | uncultured Prochloron sp. 06037A

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

No significant matches found.

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

No significant matches found.

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

#### Lanthipeptide(s) for CSC3H3_RS22310

allorf_465136_465309
Leader:
MVAMQRYPSKISNGLGCRNRRPFRPPVPTDQTMPYS
Core:
N T R P A M R W R V F C C G I W R T A C G
Core with dehydrations:
N Dhb R P A M R W R V F Cys Cys G I W R Dhb A Cys G

#### antiSMASH-DB 4.0 matches for allorf_465136_465309

100.0%
NZ_CP024200.1:
Lanthipeptides: allorf_465136_465309_lanthipeptide
1
N T R P A M R W R V F C C G I W R T A C G
21
N T R P A M R W R V F C C G I W R T A C G
1
N T R P A M R W R V F C C G I W R T A C G
21
32.1%
NZ_CP026498.1:
Lanthipeptides: allorf_09403111_09403221_lanthipeptide
2
T R P A M R W R V F C C G I W R T A
19
T R P A+R C C G W +
2
T R P A V R----C C G R W E S G
15
16.7%
NC_002935.2 and 10 others:
NC_016787.1 Lanthipeptides: allorf_0696604_0696828_lanthipeptide NC_016788.1 Lanthipeptides: allorf_0704780_0705004_lanthipeptide NC_016790.1 Lanthipeptides: allorf_0673912_0674136_lanthipeptide NC_016802.1 Lanthipeptides: allorf_0720358_0720582_lanthipeptide NZ_CP038504.1 Lanthipeptides: allorf_0568170_0568394_lanthipeptide NZ_CP040519.1 Lanthipeptides: allorf_0699626_0699850_lanthipeptide NZ_CP040557.1 Lanthipeptides: allorf_0664205_0664429_lanthipeptide NZ_MIOA01000032.1 Lanthipeptides: allorf_03743_03967_lanthipeptide NZ_MIOB01000009.1 Lanthipeptides: allorf_03741_03965_lanthipeptide NZ_MIYS01000053.1 Lanthipeptides: allorf_04053_04277_lanthipeptide
Lanthipeptides: allorf_0736323_0736547_lanthipeptide
8
W R V F C C G I W R T A C G
21
W+ F C +W T A G
25
W Q T F R C C V W I T A P G
38
with 2 more sequence matches
16.1%
NZ_FUXI01000002.1:
Lanthipeptides: B5D30_RS01205_lanthipeptide
13
C G I W R T A C G
21
C ++ T A C G
11
C A V F A T A C G
19
10.2%
NZ_SOCO01000001.1:
Lanthipeptides: allorf_1178421_1178636_lanthipeptide
12
C C G I W R T
18
C C G W R+
28
C C G D W R S
34
allorf_472692_472802
Leader:
MAEFQNACAHTQRVGDALKALPGP
Core:
C V D R E K G N K T L M
Core with dehydrations:
Cys V D R E K G N K Dhb L M

#### antiSMASH-DB 4.0 matches for allorf_472692_472802

100.0%
NZ_CP024200.1:
Lanthipeptides: allorf_472692_472802_lanthipeptide
1
C V D R E K G N K T L M
12
C V D R E K G N K T L M
1
C V D R E K G N K T L M
12
allorf_472810_472938
Leader:
MGSFFPRLGDPFEELPHVLGG
Core:
N M L H F L C S V L R L G D M I L N C S Y
Core with dehydrations:
N M L H F L Cys Dha V L R L G D M I L N Cys Dha Y

#### antiSMASH-DB 4.0 matches for allorf_472810_472938

100.0%
NZ_CP024200.1:
Lanthipeptides: allorf_472810_472938_lanthipeptide
1
N M L H F L C S V L R L G D M I L N C S Y
21
N M L H F L C S V L R L G D M I L N C S Y
1
N M L H F L C S V L R L G D M I L N C S Y
21
12.0%
NZ_CP098485.1:
Lanthipeptides: allorf_6386875_6387051_lanthipeptide
2
M L H F L C S V L R
11
++H F L C+ L R
26
I I H F L C A A L R
35
8.5%
NZ_FOGI01000013.1:
Lanthipeptides: BMY07_RS27410_lanthipeptide
1
N M L H F L C S V L R L G D M I L N C S Y
21
+ H F V ++ C Y
18
R L T H F E A R V R A T A Q T V V K C D Y
38
allorf_478430_478630
Leader:
MDWEMCSVPSERGKAGSVRAGKVSWDVRPNRSGHRCHPCARRFLTAGARAGG
Core:
C H I L I C R L Q S F A S P
Core with dehydrations:
Cys H I L I Cys R L Q Dha F A Dha P

#### antiSMASH-DB 4.0 matches for allorf_478430_478630

100.0%
NZ_CP024200.1:
Lanthipeptides: allorf_478430_478630_lanthipeptide
1
C H I L I C R L Q S F A S P
14
C H I L I C R L Q S F A S P
1
C H I L I C R L Q S F A S P
14
31.8%
NZ_CP106798.1:
Lanthipeptides: allorf_8206062_8206163_lanthipeptide
4
L I C R L Q S F A S P
14
L C R L + A S P
2
L A C R L P A P A S P
12
14.3%
NZ_LISX01000002.1 and 3 others:
NZ_LISX01000002.1 Lanthipeptides: allorf_740969_741205_lanthipeptide NZ_LISX01000002.1 Lanthipeptides: allorf_740969_741205_lanthipeptide NZ_LISX01000002.1 Lanthipeptides: allorf_740969_741205_lanthipeptide
Lanthipeptides: allorf_740969_741205_lanthipeptide
3
I L I C R L Q S F A
12
I+ C R ++F A
8
I I F C R F R T F A
17
allorf_478534_478758
Leader:
MPPLRPAVFNGGGEGRRMPYIDLPIAVICVSLTGG
Core:
H M P C A E Y P G G F A P W C R S D S F K Q A K P W I A Q M N A F G C N L F R
Core with dehydrations:
H M P Cys A E Y P G G F A P W Cys R Dha D Dha F K Q A K P W I A Q M N A F G Cys N L F R

#### antiSMASH-DB 4.0 matches for allorf_478534_478758

100.0%
NZ_CP024200.1:
Lanthipeptides: allorf_478534_478758_lanthipeptide
1
H M P C A E Y P G G F A P W C R S D S F K Q A K P W I A Q M N A F G C N L F R
39
H M P C A E Y P G G F A P W C R S D S F K Q A K P W I A Q M N A F G C N L F R
1
H M P C A E Y P G G F A P W C R S D S F K Q A K P W I A Q M N A F G C N L F R
39
17.9%
NZ_CP071463.1:
Lanthipeptides: allorf_0726528_0726683_lanthipeptide
17
S D S F K Q A K P W I A Q M N A F G C N
36
S D S P W I+ + C+
10
S D S S A S L S P W I S T V G H R R C H
29
16.3%
NZ_FONG01000023.1 and 4 others:
NZ_FONG01000023.1 Lanthipeptides: allorf_100558_100722_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_100558_100722_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_100558_100722_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_100558_100722_lanthipeptide
Lanthipeptides: allorf_100558_100722_lanthipeptide
2
M P C A E Y P G G F A P W C R
16
P C ++P G G P R
28
T P C G Q H P G G C G P H G R
42
with 2 more sequence matches
14.0%
NZ_CP050504.1 and 3 others:
NZ_CP050504.1 Lanthipeptides: HB370_RS40320_lanthipeptide NZ_CP050504.1 Lanthipeptides: HB370_RS40320_lanthipeptide NZ_CP050504.1 Lanthipeptides: HB370_RS40320_lanthipeptide
Lanthipeptides: HB370_RS40320_lanthipeptide
23
A K P W I A Q M N A F G C N L
37
A P W+ F C+L
27
A D P W V T A T T R F A C D L
41
12.8%
NZ_CP010407.1 and 3 others:
NZ_CP010407.1 Lanthipeptides: SVTN_RS37505_lanthipeptide NZ_CP010407.1 Lanthipeptides: SVTN_RS37505_lanthipeptide NZ_CP010407.1 Lanthipeptides: SVTN_RS37505_lanthipeptide
Lanthipeptides: SVTN_RS37505_lanthipeptide
23
A K P W I A Q M N A F G C N L
37
+ P W+ F C+L
16
S D P W V T A T T R F A C D L
30
allorf_485224_485328
Leader:
MADDCNCLPICGYAMIDESSGA
Core:
C A L E K P N R V R E T
Core with dehydrations:
Cys A L E K P N R V R E Dhb

#### antiSMASH-DB 4.0 matches for allorf_485224_485328

100.0%
NZ_CP024200.1:
Lanthipeptides: allorf_485224_485328_lanthipeptide
1
C A L E K P N R V R E T
12
C A L E K P N R V R E T
1
C A L E K P N R V R E T
12
11.8%
NZ_JACHOW010000029.1:
Lanthipeptides: allorf_00086_00274_lanthipeptide
2
A L E K P N R V R E
11
A+E P N R R+
33
A V E A P N R T R Q
42

#### 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: 17.55 out of 18.46
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.43 out of 26.85
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 21.84 out of 21.84
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.04 out of 26.85
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.75 out of 18.57
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.36 out of 20.97
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.58 out of 27.55
Confidence: medium
Additional weak hits (4):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.40 out of 26.12
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.88 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.15 out of 28.19
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
Lanthipeptides
RREFinder
TFBS Finder
Azole RiPPs
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

allorf_465136_465309 - Class II
  Cleavage pHMM score: -4.80
  RODEO score: 0
  Monoisotopic mass: 2463.2 Da
  Molecular weight: 2464.9 Da
  Number of bridges: 2
  Additional modifications: OH
allorf_472692_472802 - Class II
  Cleavage pHMM score: -7.30
  RODEO score: 0
  Monoisotopic mass: 1390.7 Da
  Molecular weight: 1391.6 Da
  Number of bridges: 1
  Additional modifications: OH
allorf_472810_472938 - Class II
  Cleavage pHMM score: -0.50
  RODEO score: 0
  Monoisotopic mass: 2421.2 Da
  Molecular weight: 2422.9 Da
  Number of bridges: 2
  Additional modifications: OH
allorf_478430_478630 - Class II
  Cleavage pHMM score: -6.10
  RODEO score: 0
  Monoisotopic mass: 1566.8 Da
  Molecular weight: 1567.9 Da
  Number of bridges: 2
  Additional modifications: OH
allorf_478534_478758 - Class II
  Cleavage pHMM score: -5.90
  RODEO score: 0
  Monoisotopic mass: 4441.0 Da
  Molecular weight: 4444.1 Da
  Number of bridges: 2
  Additional modifications: OH
allorf_485224_485328 - Class II
  Cleavage pHMM score: -6.00
  RODEO score: 0
  Monoisotopic mass: 1412.7 Da
  Molecular weight: 1413.6 Da
  Number of bridges: 1
  Additional modifications: OH

RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (456996...482043)
CSC3H3_RS22300
  RRE type: Cyanobactin_D_RRE
  Location: 6 - 81
  Score: 64.2
  RRE type: NHLP_CD_RRE
  Location: 5 - 97
  Score: 57.0
  RRE type: Goadsporin_CD_RRE
  Location: 7 - 98
  Score: 40.1
lanthipeptide-class-ii protocluster (462971...486109)
CSC3H3_RS22300
  RRE type: Cyanobactin_D_RRE
  Location: 6 - 81
  Score: 64.2
  RRE type: NHLP_CD_RRE
  Location: 5 - 97
  Score: 57.0
  RRE type: Goadsporin_CD_RRE
  Location: 7 - 98
  Score: 40.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
GnfM | Regulator of nitrogen-fixation genes
MexT | Global virulence regulator
RpoN | Regulator of nitrogen assimilation and virulence
RutR | Regulator of the pyrimidine and purine metabolism
ToxT | Regulator of MSHA biosynthesis

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_CP024200.1 - Region 2 - 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: 651,214 - 694,207 nt. (total: 42,994 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CSC3H3_RS23190: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CSC3H3_RS23210: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

CSC3H3_RS23250: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

CSC3H3_RS23270: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase
CSC3H3_RS23155: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Hydrolases: esterase
CSC3H3_RS23195: thioesterase

smcogs
  SMCOG1004: thioesterase

Isomerases: racemase
CSC3H3_RS23295: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase
CSC3H3_RS23200: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CSC3H3_RS23225: 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
--- | --- | --- | --- | --- | ---
BGC0001166.5 |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002084.4 |  | 0.56 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.56 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0000016.4 |  | 0.54 | other (other) | amphotericin B | Streptomyces nodosus
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002474.2 |  | 0.50 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0000343.5 |  | 0.49 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001475.4 |  | 0.47 | terpene | aspterric acid | Aspergillus terreus NIH2624

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001166.5 |  | 0.65 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002084.4 |  | 0.56 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  | 0.56 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0000016.4 |  | 0.54 | other (other) | amphotericin B | Streptomyces nodosus
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0002474.2 |  | 0.50 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0000343.5 |  | 0.49 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001475.4 |  | 0.47 | terpene | aspterric acid | Aspergillus terreus NIH2624

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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.75 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.16 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.28 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.47 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.23 out of 28.19
Confidence: medium
Additional weak hits (4):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.56 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.78 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.68 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.24 out of 26.06
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 4, location 651213 - 694207:
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).
CSC3H3_RS23200: fatty_acid
CAL_domain (48..492): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 4.1
  AHBA: 3.9
  NH2: 0.2
  shikimic_acid: 0.0
  Acetyl-CoA: -2.9

CSC3H3_RS23225: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (22..385): Asp
nrpys: Asp

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:
    pro (Pro)
  Single AA prediction:
    pro (Pro)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWQTFDVMYRDLHVFFAGEYNLYGPSESTMAKFC
  Nearest Stachelhaus code(s):
    Asp DVRHFALMAK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP024200.1 - Region 3 - NI-siderophore,hydrogen-cyanide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 796,768 - 846,258 nt. (total: 49,491 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase reductase
CSC3H3_RS23795: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CSC3H3_RS23800: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

CSC3H3_RS23810: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CSC3H3_RS23840: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: aminotransferase
CSC3H3_RS25070: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: decarboxylase
CSC3H3_RS25065: 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 | hydrogen-cyanide | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002488.3 |  |  | 0.31 | other (other) | bacillopaline | Paenibacillus mucilaginosus KNP414
BGC0000946.5 |  |  | 0.28 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002487.3 |  |  | 0.27 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0002527.2 |  |  | 0.26 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0002683.2 |  |  | 0.25 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000486.4 |  |  | 0.24 | ribosomal | butyrivibriocin AR10 | Butyrivibrio fibrisolvens
BGC0002698.2 |  |  | 0.24 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0002656.2 |  |  | 0.24 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49
BGC0001289.5 |  |  | 0.24 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000947.5 |  |  | 0.23 | other (other) | vibrioferrin | Vibrio alginolyticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.62 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002527.2 |  | 0.59 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000947.5 |  | 0.57 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000943.5 |  | 0.56 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000939.5 |  | 0.56 | other (other) | aerobactin | Grimontia hollisae
BGC0002471.3 |  | 0.55 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0001870.3 |  | 0.54 | other (other) | putrebactin, avaroferrin | Xenorhabdus budapestensis
BGC0002073.3 |  | 0.54 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0001408.5 |  | 0.54 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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: 19.37 out of 20.47
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.48 out of 18.57
Confidence: strong
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.87 out of 27.55
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.93 out of 26.06
Confidence: medium
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 26.76 out of 32.74
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.36 out of 20.97
Confidence: medium
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 29.03 out of 33.14
Confidence: medium
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 29.03 out of 33.14
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.00 out of 28.19
Confidence: medium
Additional weak hits (16):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.61 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.24 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.22 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.33 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.88 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.67 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.02 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.76 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.87 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.99 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.24 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.21 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.60 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.09 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.55 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.99 out of 20.01
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CcpA | Catabolite control protein A
FuR variant 2 | Ferric Uptake Regulator
GnfM | Regulator of nitrogen-fixation genes
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor
ZuR variant 2 | Zinc-responsive repressor