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
3.1
3.2
4.1
5.1
5.2

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

NZ_CP040272.1 (Nostoc sp. C052)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | mycosporine | 7,790,554 | 6,926 | Low | hexose-palythine-serine/hexose-shinorine | NRPS:Type I
Region 1.2 | lanthipeptide-class-v | 117,984 | 160,413 |
Region 1.3 | NRPS,T1PKS,NRPS-like | 424,485 | 481,501 | Low | heinamide A1/heinamide A2/heinamide A3/heinamide B1/heinamide B2/heinamide B3/heinamide B4/heinamide B5 | NRPS:Type I+PKS
Region 1.4 | T3PKS | 674,221 | 715,531 |
Region 1.5 | NRPS-like,NRPS,microviridin,lanthipeptide-class-v | 1,246,045 | 1,359,377 | High | micropeptin K139 | NRPS:Type I
Region 1.6 | terpene,T1PKS,NRPS | 1,392,271 | 1,537,939 | Medium | nostophycin | NRPS:Type I+PKS
Region 1.7 | proteusin,terpene,lanthipeptide-class-ii | 1,661,947 | 1,691,397 |
Region 1.8 | phosphonate | 1,697,979 | 1,714,414 |
Region 1.9 | NRPS,T1PKS,t3nrps-iterative | 2,107,879 | 2,229,286 | Low | anachelin | NRPS:Type I+PKS
Region 1.10 | terpene-precursor | 2,980,781 | 3,001,713 |  |
Region 1.11 | T1PKS | 3,086,370 | 3,134,817 |
Region 1.12 | terpene | 3,427,539 | 3,448,504 |
Region 1.13 | terpene | 3,548,551 | 3,569,483 |
Region 1.14 | redox-cofactor | 3,922,221 | 3,944,833 |  |
Region 1.15 | NRPS | 4,003,405 | 4,068,783 | High | nostopeptolide A2 | NRPS:Type I+PKS
Region 1.16 | hglE-KS,T1PKS | 4,729,999 | 4,782,307 | High | heterocyst glycolipids | other:other
Region 1.17 | lanthipeptide-class-v,spliceotide,RRE-containing | 4,943,029 | 4,985,369 | Low | PcpA | ribosomal:RiPP
Region 1.18 | terpene | 5,432,852 | 5,454,768 |
Region 1.19 | NRPS | 5,686,058 | 5,731,985 |  |
Region 1.20 | terpene | 6,082,246 | 6,103,076 |
Region 1.21 | lanthipeptide-class-ii | 6,502,743 | 6,526,051 | Low | nostolysamide A/nostolysamide B | ribosomal:RiPP
Region 1.22 | terpene | 6,602,843 | 6,625,200 | High | geosmin | terpene:Sesquiterpene
Region 1.23 | terpene | 7,585,493 | 7,610,055 |
Region 1.24 | NRPS-like | 7,681,020 | 7,724,160 |

NZ_CP040274.1 (Nostoc sp. C052)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | NRPS | 329,734 | 37,934 |  |
Region 3.2 | proteusin | 51,884 | 72,600 |

NZ_CP040275.1 (Nostoc sp. C052)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | T1PKS,NRPS-like,NRPS,terpene | 251,519 | 59,084 | Low | vatiamide A/vatiamide B/vatiamide C/vatiamide D/vatiamide E/vatiamide F | NRPS:Type I+PKS

NZ_CP040276.1 (Nostoc sp. C052)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | terpene | 50,107 | 73,763 | High | 1-heptadecene | PKS:Type I
Region 5.2 | NRPS | 82,054 | 126,889 | High | bovienimide A | NRPS:Type I

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | mycosporine | 7,790,554 | 6,926 | Low | hexose-palythine-serine/hexose-shinorine | NRPS:Type I
Region 1.2 | lanthipeptide-class-v | 117,984 | 160,413 |
Region 1.3 | NRPS,T1PKS,NRPS-like | 424,485 | 481,501 | Low | heinamide A1/heinamide A2/heinamide A3/heinamide B1/heinamide B2/heinamide B3/heinamide B4/heinamide B5 | NRPS:Type I+PKS
Region 1.4 | T3PKS | 674,221 | 715,531 |
Region 1.5 | NRPS-like,NRPS,microviridin,lanthipeptide-class-v | 1,246,045 | 1,359,377 | High | micropeptin K139 | NRPS:Type I
Region 1.6 | terpene,T1PKS,NRPS | 1,392,271 | 1,537,939 | Medium | nostophycin | NRPS:Type I+PKS
Region 1.7 | proteusin,terpene,lanthipeptide-class-ii | 1,661,947 | 1,691,397 |
Region 1.8 | phosphonate | 1,697,979 | 1,714,414 |
Region 1.9 | NRPS,T1PKS,t3nrps-iterative | 2,107,879 | 2,229,286 | Low | anachelin | NRPS:Type I+PKS
Region 1.10 | terpene-precursor | 2,980,781 | 3,001,713 |  |
Region 1.11 | T1PKS | 3,086,370 | 3,134,817 |
Region 1.12 | terpene | 3,427,539 | 3,448,504 |
Region 1.13 | terpene | 3,548,551 | 3,569,483 |
Region 1.14 | redox-cofactor | 3,922,221 | 3,944,833 |  |
Region 1.15 | NRPS | 4,003,405 | 4,068,783 | High | nostopeptolide A2 | NRPS:Type I+PKS
Region 1.16 | hglE-KS,T1PKS | 4,729,999 | 4,782,307 | High | heterocyst glycolipids | other:other
Region 1.17 | lanthipeptide-class-v,spliceotide,RRE-containing | 4,943,029 | 4,985,369 | Low | PcpA | ribosomal:RiPP
Region 1.18 | terpene | 5,432,852 | 5,454,768 |
Region 1.19 | NRPS | 5,686,058 | 5,731,985 |  |
Region 1.20 | terpene | 6,082,246 | 6,103,076 |
Region 1.21 | lanthipeptide-class-ii | 6,502,743 | 6,526,051 | Low | nostolysamide A/nostolysamide B | ribosomal:RiPP
Region 1.22 | terpene | 6,602,843 | 6,625,200 | High | geosmin | terpene:Sesquiterpene
Region 1.23 | terpene | 7,585,493 | 7,610,055 |
Region 1.24 | NRPS-like | 7,681,020 | 7,724,160 |
Region 3.1 | NRPS | 329,734 | 37,934 |  |
Region 3.2 | proteusin | 51,884 | 72,600 |
Region 4.1 | T1PKS,NRPS-like,NRPS,terpene | 251,519 | 59,084 | Low | vatiamide A/vatiamide B/vatiamide C/vatiamide D/vatiamide E/vatiamide F | NRPS:Type I+PKS
Region 5.1 | terpene | 50,107 | 73,763 | High | 1-heptadecene | PKS:Type I
Region 5.2 | NRPS | 82,054 | 126,889 | High | bovienimide A | NRPS:Type I

No secondary metabolite regions were found in these records:
  NZ_CP040273.1 (Nostoc sp. C052)
  NZ_CP040277.1 (Nostoc sp. C052)
  NZ_CP040278.1 (Nostoc sp. C052)
  NZ_CP040279.1 (Nostoc sp. C052)
  NZ_CP040280.1 (Nostoc sp. C052)

Compact view
NZ_CP040272.1 - Region 1 - mycosporine
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: 7,790,554 - 6,926 nt. (total: 44,709 nt) Show pHMM detection rules used
mycosporine: (DHQ_synthase and Methyltransf_3 and ATP-grasp_3)

#### 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
FD723_RS32030: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FD723_RS32050: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: deformylase
FD723_RS32120: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Ligases: synthase
FD723_RS32090: 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 | mycosporine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000427.5 |  | 0.59 | NRPS | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0002276.2 |  | 0.54 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001615.3 |  | 0.50 | NRPS | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0001928.2 |  | 0.50 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000701.5 |  | 0.47 | saccharide | jinggangmycin | Streptomyces hygroscopicus subsp. yingchengensis
BGC0001733.3 |  | 0.44 | ribosomal | PcpA | Pleurocapsa sp. PCC 7327
BGC0000231.5 |  | 0.43 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002218.2 |  | 0.42 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0001197.5 |  | 0.42 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000671.3 |  | 0.41 | terpene | momilactone B | Oryza sativa Japonica Group

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000427.5 |  | 0.59 | NRPS | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0002276.2 |  | 0.54 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001615.3 |  | 0.50 | NRPS | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0001928.2 |  | 0.50 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000701.5 |  | 0.47 | saccharide | jinggangmycin | Streptomyces hygroscopicus subsp. yingchengensis
BGC0001733.3 |  | 0.44 | ribosomal | PcpA | Pleurocapsa sp. PCC 7327
BGC0000231.5 |  | 0.43 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002218.2 |  | 0.42 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0001197.5 |  | 0.42 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000671.3 |  | 0.41 | terpene | momilactone B | Oryza sativa Japonica Group

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.04 out of 26.06
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 22.75 out of 25.31
Confidence: strong
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 24.01 out of 29.25
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.69 out of 27.55
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.67 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.28 out of 27.78
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.57 out of 27.55
Confidence: medium
Additional weak hits (6):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 25.17 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.23 out of 29.38
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.79 out of 32.93
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.85 out of 39.62
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.83 out of 26.12
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
GnfM | Regulator of nitrogen-fixation genes
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
SypG | Regulator of biofilm formation and host colonization
ToxT | Regulator of MSHA biosynthesis

NZ_CP040272.1 - Region 2 - lanthipeptide-class-v
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: 117,984 - 160,413 nt. (total: 42,430 nt) Show pHMM detection rules used
lanthipeptide-class-v: (APH and HopA1)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
FD723_RS00540: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

FD723_RS00615: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: glycosyltransferase
FD723_RS00605: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

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-v | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001633.3 |  | 0.43 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000041.3 |  | 0.41 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001187.4 |  | 0.41 | NRPS, PKS | xenolozoyenone | Glarea lozoyensis
BGC0000194.5 |  | 0.38 | PKS | actinorhodin | Streptomyces coelicolor A3(2)
BGC0001858.2 |  | 0.38 | PKS | alternapyrone B, alternapyrone C, alternapyrone D, alternapyrone E, alternapyrone F | Parastagonospora nodorum SN15
BGC0001521.3 |  | 0.37 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001124.4 |  | 0.37 | PKS | pyranonigrin E | Aspergillus niger ATCC 1015
BGC0000189.4 |  | 0.36 | PKS | 3-(2'-hydroxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-hydroxy-3'-oxo-4'-methylhexyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylhexyl)-indole | Xenorhabdus bovienii SS-2004
BGC0002211.3 |  | 0.36 | PKS | HEx-pks1 polyketide | Paraphaeosphaeria sporulosa
BGC0000045.3 |  | 0.36 | PKS | dehydrocurvularin | Aspergillus terreus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001633.3 |  | 0.43 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000041.3 |  | 0.41 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001187.4 |  | 0.41 | NRPS, PKS | xenolozoyenone | Glarea lozoyensis
BGC0000194.5 |  | 0.38 | PKS | actinorhodin | Streptomyces coelicolor A3(2)
BGC0001858.2 |  | 0.38 | PKS | alternapyrone B, alternapyrone C, alternapyrone D, alternapyrone E, alternapyrone F | Parastagonospora nodorum SN15
BGC0001521.3 |  | 0.37 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001124.4 |  | 0.37 | PKS | pyranonigrin E | Aspergillus niger ATCC 1015
BGC0000189.4 |  | 0.36 | PKS | 3-(2'-hydroxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-hydroxy-3'-oxo-4'-methylhexyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylpentyl)-indole, 3-(2'-acetoxy-3'-oxo-4'-methylhexyl)-indole | Xenorhabdus bovienii SS-2004
BGC0002211.3 |  | 0.36 | PKS | HEx-pks1 polyketide | Paraphaeosphaeria sporulosa
BGC0000045.3 |  | 0.36 | PKS | dehydrocurvularin | Aspergillus terreus

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.
Lanthipeptides - No core peptides 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
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.95 out of 28.19
Confidence: medium
Additional weak hits (3):
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 30.11
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.09 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.57 out of 36.53
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.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP040272.1 - Region 3 - 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: 424,485 - 481,501 nt. (total: 57,017 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
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acylase acyltransferase
FD723_RS01865: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

FD723_RS01875: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: ligase
FD723_RS01855: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS01860: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS01880: 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
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  |  | 1.32 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  |  |  | 1.26 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002286.3 |  |  |  | 1.26 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  |  | 1.24 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5 |  |  |  | 1.23 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001833.4 |  |  |  | 1.18 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  |  | 1.17 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  |  |  | 1.14 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  |  |  | 1.14 | NRPS | AM-toxin | Alternaria alternata
BGC0001758.4 |  |  |  | 1.13 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.71 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.73 out of 18.46
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.61 out of 27.78
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.84 out of 29.38
Confidence: medium
Additional weak hits (13):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.20 out of 30.22
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.55 out of 29.51
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.23 out of 29.38
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.83 out of 26.12
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.00 out of 32.74
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.10 out of 25.88
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.59 out of 30.97
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.03 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.45 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.03 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.78 out of 21.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.08 out of 35.63
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 24.13 out of 32.38
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 3, location 424484 - 481501:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 424484 - 472169:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 434514 - 479470:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 439473 - 481501:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (mal) + (Val) + (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).
FD723_RS01855: X
AMP-binding (548..956): 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:
    HAISCDSFIESPNLMVGGELNAYGSLETTLTATI
  Nearest Stachelhaus code(s):
    Arg DVENVGAITK (62% 8Å match)
    Orn DMENMGAVNK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

FD723_RS01860: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (490..889): 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:
    LDTSFDASTFEGWLLAGGDINGYGPTESTTFTCC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

FD723_RS01875: mal
PKS_AT (538..834): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 164.6
  inactive: 120.1
  Methoxymalonyl-CoA: 80.0
  Methylmalonyl-CoA: 72.9
  Propionyl-CoA: 50.4
  Ethylmalonyl-CoA: 50.1
  Isobutyryl-CoA: 40.1
  2-Methylbutyryl-CoA: 30.5
  CHC-CoA: 25.0
  fatty_acid: 24.9
  Benzoyl-CoA: 24.3
  Acetyl-CoA: 20.6
  3-Methylbutyryl-CoA: 17.9
  trans-1,2-CPDA: 15.0

FD723_RS01880: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (66..465): 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:
    LETAFDASTFEGWLLAGGDINGYGPTENTTFTCC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP040272.1 - Region 4 - 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: 674,221 - 715,531 nt. (total: 41,311 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
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
FD723_RS02780: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

FD723_RS02785: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: methyltransferase
FD723_RS02880: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthase
FD723_RS02820: 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
--- | --- | --- | --- | --- | ---
BGC0002447.3 |  | 0.46 | ribosomal | cerecyclin | Bacillus cereus
BGC0000501.3 |  | 0.45 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0002332.2 |  | 0.44 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0000487.5 |  | 0.44 | ribosomal | carnocyclin | Carnobacterium maltaromaticum
BGC0002442.3 |  | 0.44 | ribosomal | toyoncin | Bacillus toyonensis
BGC0001077.4 |  | 0.44 | 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
BGC0000488.4 |  | 0.42 | ribosomal | circularin A | Clostridium beijerinckii
BGC0002701.2 |  | 0.41 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0001210.5 |  | 0.41 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000497.3 |  | 0.40 | ribosomal | BHT-Aα, BHT-Aβ | Streptococcus ratti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002447.3 |  | 0.46 | ribosomal | cerecyclin | Bacillus cereus
BGC0000501.3 |  | 0.45 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0002332.2 |  | 0.44 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0000487.5 |  | 0.44 | ribosomal | carnocyclin | Carnobacterium maltaromaticum
BGC0002442.3 |  | 0.44 | ribosomal | toyoncin | Bacillus toyonensis
BGC0001077.4 |  | 0.44 | 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
BGC0000488.4 |  | 0.42 | ribosomal | circularin A | Clostridium beijerinckii
BGC0002701.2 |  | 0.41 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0001210.5 |  | 0.41 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000497.3 |  | 0.40 | ribosomal | BHT-Aα, BHT-Aβ | Streptococcus ratti

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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.28 out of 27.78
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.63 out of 27.55
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.75 out of 27.55
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.75 out of 28.19
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.75 out of 23.05
Confidence: medium
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.68 out of 28.14
Confidence: medium
Additional weak hits (6):
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.36 out of 30.11
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.74 out of 26.85
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.05 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.81 out of 30.22
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.31 out of 30.22
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.25 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
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
GnfM | Regulator of nitrogen-fixation genes
PerR | Peroxide regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_CP040272.1 - Region 5 - NRPS,NRPS-like,lanthipeptide-class-v,microviridin
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: 1,246,045 - 1,359,377 nt. (total: 113,333 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
microviridin: (mvd or mvnA)
lanthipeptide-class-v: (APH and HopA1)

#### 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
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
FD723_RS05380: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FD723_RS05400: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: methyltransferase
FD723_RS05365: methyltransferase

smcogs
  SMCOG1089: methyltransferase

FD723_RS05415: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: ligase
FD723_RS05335: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FD723_RS05340: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS05345: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS05350: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS05360: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS-like | NRPS | microviridin | lanthipeptide-class-v | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002049.3 |  |  |  |  | 1.64 | ribosomal | microviridin N9, microviridin N8, microviridin N7, microviridin N6, microviridin N5, microviridin N4, microviridin N3 | Nostoc punctiforme PCC 73102
BGC0000593.4 |  |  |  |  | 1.39 | ribosomal | microviridin J | Microcystis aeruginosa MRC
BGC0000592.5 |  |  |  |  | 0.95 | ribosomal | microviridin B | Microcystis aeruginosa NIES-298
BGC0001641.4 |  |  |  |  | 0.93 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002274.2 |  |  |  |  | 0.82 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0000342.4 |  |  |  |  | 0.81 | NRPS | enniatin | Fusarium equiseti
BGC0001748.4 |  |  |  |  | 0.79 | NRPS, PKS | pseudospumigin A, pseudospumigin B, pseudospumigin C, pseudospumigin D, pseudospumigin E, pseudospumigin F | Nostoc sp. CENA543
BGC0002135.2 |  |  |  |  | 0.78 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  |  |  |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002049.3 |  | 0.79 | ribosomal | microviridin N9, microviridin N8, microviridin N7, microviridin N6, microviridin N5, microviridin N4, microviridin N3 | Nostoc punctiforme PCC 73102
BGC0002135.2 |  | 0.76 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.75 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  | 0.75 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000593.4 |  | 0.73 | ribosomal | microviridin J | Microcystis aeruginosa MRC
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.73 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001132.4 |  | 0.72 | 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.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.31 out of 28.14
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.05 out of 18.16
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.84 out of 29.38
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.53 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.38 out of 28.19
Confidence: medium
Additional weak hits (7):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.68 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.41 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.51 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.72 out of 29.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.02 out of 39.62
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.60 out of 23.43
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
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
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.
No core peptides found.
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 8, location 1246044 - 1359377:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid) + (NMe-Val) + (Thr - Thr - X - X - Phe - NMe-X) + (Ala)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 1246044 - 1290286:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid) + (NMe-Val) + (Thr - Thr - X - X - Phe - NMe-X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 1250287 - 1320961:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid) + (NMe-Val) + (Thr - Thr - X - X - Phe - NMe-X) + (Ala)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
FD723_RS05335: fatty_acid
CAL_domain (353..645): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 23.2
  NH2: 13.6
  Acetyl-CoA: 13.3
  shikimic_acid: 0.0
  AHBA: 0.0

FD723_RS05340: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (536..936): 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:
    LGVAFDASTFEGWLLIGGEVNGYGPTESTTFSCC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

FD723_RS05345: Thr - Thr - X - X - Phe - X
Search NORINE for peptide: strict or relaxed
AMP-binding (541..948): 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:
    LATHFDFSVWEGNQIFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1610..2020): 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:
    LATHFDFSVWEGNQIFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2686..3090): 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:
    LWLSFDLTQKNANCFLGGEVNSYGPTECAVCAAY
  Nearest Stachelhaus code(s):
    Hse DLKNVGSDVK (74% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (3755..4162): X
nrpys: Ahp

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:
    HAIAFDVAAEEPNIAVGGDLNVYGPTEASVTAVV
  Nearest Stachelhaus code(s):
    Ahp DVENAGVVTK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4824..5213): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASIWEMTLIVAGEFNAYGPTETTVCATI
  Nearest Stachelhaus code(s):
    Phe DAWTIAAVCK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5872..6264): X
nrpys: Tyr, Pro

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:
    LAQAFDACISEMTLIVAGEFNAYGPTEASVCATI
  Nearest Stachelhaus code(s):
    Tyr or Pro DASTIAAVCK (97% 8Å match)
    Tyr DASTIAAVCK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

FD723_RS05360: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (259..650): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWATFDLSVFEVNTNLAGEFNLYGPSEDTTYSTF
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (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
--- | ---
ANR | Anaerobic transcriptional regulator
AbrC3 | Antibiotic production activator
FuR variant 1 | Ferric Uptake Regulator
PerR | Peroxide regulator
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP040272.1 - Region 6 - NRPS,T1PKS,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: 1,392,271 - 1,537,939 nt. (total: 145,669 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)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### 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
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
FD723_RS05920: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

FD723_RS06015: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FD723_RS06130: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: halogenase methyltransferase
FD723_RS05925: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

FD723_RS05930: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

FD723_RS06135: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase hydrolase phosphatase
FD723_RS05895: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

smcogs
  SMCOG1283: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

FD723_RS05945: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

FD723_RS06185: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

Ligases: ligase synthase
FD723_RS05935: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

FD723_RS06085: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS06095: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS06100: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS06105: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FD723_RS06140: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS06145: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS06150: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | terpene | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002512.3 |  |  |  | 0.57 | NRPS | anabaenopeptin 788, anabaenopeptin 816, anabaenopeptin 802 | Brasilonema sp. CT11
BGC0001758.4 |  |  |  | 0.47 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  |  | 0.47 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  | 0.47 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  |  |  | 0.46 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  |  |  | 0.46 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001164.3 |  |  |  | 0.46 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002135.2 |  |  |  | 0.46 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  |  | 0.45 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  |  |  | 0.43 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002512.3 |  | 0.82 | NRPS | anabaenopeptin 788, anabaenopeptin 816, anabaenopeptin 802 | Brasilonema sp. CT11
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.77 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.77 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.76 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.74 | NRPS | enniatin | Fusarium equiseti
BGC0000307.4 |  | 0.73 | NRPS | AbT1 | Aureobasidium pullulans

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 |  |  | C15 | C1-C6 | none
diterpene |  |  | C20 | C1-C6 | none
diterpene |  |  | C20 | C1-C7 + C6-C10 | none
sesterterpene |  |  | C25 | C1-C7 + C6-C10 | none

Genes with terpene domains:
FD723_RS05880: TS_UbiA
Domain 1 (62 - 349): UbiA type terpene synthase

Reactions:
  FPP → sesquiterpene_C1-C6
  GGPP → diterpene_C1-C6
  GGPP → diterpene_C1-C7/C6-C10
  GFPP → sesterterpene_C1-C7/C6-C10

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
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: 18.31 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.14 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.03 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.70 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.01 out of 26.06
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.29 out of 27.55
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.53 out of 28.19
Confidence: medium
Additional weak hits (17):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 26.16 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.28 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.51 out of 29.38
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.70 out of 29.51
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.72 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.69 out of 26.06
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.24 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.96 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.22 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.23 out of 33.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.84 out of 21.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.14 out of 32.74
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.37 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.10 out of 35.63
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.53 out of 27.18
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.42 out of 29.72
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.25 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 13, location 1392270 - 1537939:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2) + (X - Thr - Leu - X - NMe-Phe - NMe-X) + (Val) + (Ile - D-Lys) + (Leu) + (X - NMe-Asn) + (Phe)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 16, location 1439924 - 1537939:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2) + (X - Thr - Leu - X - NMe-Phe - NMe-X) + (Val) + (Ile - D-Lys) + (Leu) + (X - NMe-Asn) + (Phe)

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).
FD723_RS05935: mal
PKS_AT (594..889): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 58.3%
  2-Methylbutyryl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 46.0
  Methoxymalonyl-CoA: 35.9
  inactive: 25.8
  Methylmalonyl-CoA: 17.4
  Propionyl-CoA: 15.5
  fatty_acid: 8.9
  trans-1,2-CPDA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

FD723_RS06085: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (541..935): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAISFDASIWETTLVVAGEFNGYGPTESTVCAAI
  Nearest Stachelhaus code(s):
    Phe DAWTIAGVCK (76% 8Å match)
    Tyr DASTVAGVCK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

FD723_RS06095: X - Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (503..897): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LALAFDSSVAEPIVVVGGELNGYGPTESTVGAAI
  Nearest Stachelhaus code(s):
    Ala DMASVGGVFK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1557..1988): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDATITSLKIVLGGEINEYGPTEAVVGCCV
  Nearest Stachelhaus code(s):
    Asn DATKVGEVGK (100% 8Å match)
    OH-Asn or Asn DATKVGEVGK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

FD723_RS06100: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (468..866): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGVSWDGLTLEPFLLFGGEIHAYGPSECTVFTCC
  Nearest Stachelhaus code(s):
    Ile DGFFLGVVFK (59% 8Å match)
  Stachelhaus code match:
    80% (moderate)

FD723_RS06105: Ile - Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (46..485): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNTSFDAATFEGFLLFGGELHVYGPTESTTFACW
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1160..1573): Lys
nrpys: Lys

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:
    FTAAFDASVEEPDLIIGGELNSYGPTEATVITTL
  Nearest Stachelhaus code(s):
    Lys DAEDIGSVIK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

FD723_RS06140: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (541..962): 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:
    LGVAFDASTFEGWLLIGGEINGYGPTEGTTFTCC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

FD723_RS06145: X - Thr - Leu - X - Phe - X
Search NORINE for peptide: strict or relaxed
AMP-binding (549..950): X
nrpys: Val, Glu

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:
    FNYSFDAALMDAHSVLGGEVNGLGPTESTVTLQY
  Nearest Stachelhaus code(s):
    Glu DAMHVGGTAK (74% 8Å match)
    Val DAMFVGGVFK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1610..2048): 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:
    LATHFDFSVWEGNQIFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2711..3122): Leu
nrpys: Leu

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
  Single AA prediction:
    leu (Leu)

Stachelhaus prediction details:
  Stachelhaus sequence:
    NRTSFDPSVFEWVFFCGGEHNLYGPTEAAVDATS
  Nearest Stachelhaus code(s):
    Arg DPWGFGLVDK (82% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (3783..4225): X
nrpys: Ahp

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:
    HAIAFDVAAEEPNIAVGGDLNVYGPTEASVTAIV
  Nearest Stachelhaus code(s):
    Ahp DVENAGVVTK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4893..5321): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASIWELTLIVGGEFNAYGPTEASVCTTI
  Nearest Stachelhaus code(s):
    Leu or Phe DAWTIGGVCK (88% 8Å match)
    Phe DAWTIAAVCK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (6341..6749): X
nrpys: Tyr, Pro

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:
    LAQAFDACISEMTLIVAGEFNAYGPTEASVCATI
  Nearest Stachelhaus code(s):
    Tyr or Pro DASTIAAVCK (97% 8Å match)
    Tyr DASTIAAVCK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

FD723_RS06150: NH2
CAL_domain (351..650): NH2
minowa: NH2

Prediction, score:
  NH2: 14.9
  Acetyl-CoA: 12.0
  fatty_acid: 10.0
  shikimic_acid: 0.0
  AHBA: 0.0

Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP040272.1 - Region 7 - lanthipeptide-class-ii,proteusin,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: 1,661,947 - 1,691,397 nt. (total: 29,451 nt) Show pHMM detection rules used
proteusin: (PoyD or TIGR03793)
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)
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
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase
FD723_RS06755: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: synthase
FD723_RS06765: 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 | proteusin | terpene | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000525.5 |  |  |  | 0.54 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002330.2 |  |  |  | 0.49 | ribosomal | landornamide A | Kamptonema sp. PCC 6506
BGC0002704.2 |  |  |  | 0.48 | ribosomal | archalan β | Halorussus salinus
BGC0000554.4 |  |  |  | 0.43 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000517.4 |  |  |  | 0.40 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0001660.3 |  |  |  | 0.40 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000520.5 |  |  |  | 0.38 | ribosomal | lacticin 3147 A1, lacticin 3147 A2 | Lactococcus lactis
BGC0001210.5 |  |  |  | 0.38 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000598.5 |  |  |  | 0.37 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0002698.2 |  |  |  | 0.37 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002330.2 |  | 0.48 | ribosomal | landornamide A | Kamptonema sp. PCC 6506
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002704.2 |  | 0.47 | ribosomal | archalan β | Halorussus salinus
BGC0001660.3 |  | 0.44 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000517.4 |  | 0.44 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0002698.2 |  | 0.43 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001210.5 |  | 0.43 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000520.5 |  | 0.43 | ribosomal | lacticin 3147 A1, lacticin 3147 A2 | Lactococcus lactis
BGC0000527.5 |  | 0.43 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728

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 FD723_RS06755

allorf_1671706_1671828
Leader:
MRLTSSREGIDSVSNTA
Core:
K A I E D E G V P L N I W G K A P S R C G I L
Core with dehydrations:
K A I E D E G V P L N I W G K A P Dha R Cys G I L

#### antiSMASH-DB 4.0 matches for allorf_1671706_1671828

100.0%
NZ_CP040272.1:
Lanthipeptides: allorf_1671706_1671828_lanthipeptide
1
K A I E D E G V P L N I W G K A P S R C G I L
23
K A I E D E G V P L N I W G K A P S R C G I L
1
K A I E D E G V P L N I W G K A P S R C G I L
23
34.8%
NZ_QLLX01000002.1 and 1 other:
NZ_QLLX01000002.1 Lanthipeptides: allorf_348026_348142_lanthipeptide
Lanthipeptides: allorf_348026_348142_lanthipeptide
7
G V P L N I W G K A P S R C
20
V P G A P S R C
1
A V P R A P N G S A P S R C
14
23.7%
NZ_KQ236748.1:
Lanthipeptides: HMPREF0980_RS19040_lanthipeptide
4
E D E G V P L N I W G K A P S R-C G I L
23
E+ G V P + W A S+ C I+
15
E E V G V P Y S T W T L A C S Q F C T I I
35
with 2 more sequence matches
15.8%
NZ_CP033581.1 and 1 other:
NZ_CP033581.1 Lanthipeptides: allorf_6745013_6745198_lanthipeptide
Lanthipeptides: allorf_6745013_6745198_lanthipeptide
8
V P L N I W G K A P S R C
20
P++ G+A P S C
21
A P V H N R G Q A P S S C
33
10.5%
NZ_AUCI01000015.1 and 1 other:
NZ_AUCI01000015.1 Lanthipeptides: G475_RS0114655_lanthipeptide
Lanthipeptides: G475_RS0114655_lanthipeptide
8
V P L N I W G K A P S R C G
21
+P++ W G ++C
17
I P I S A W G C P T T K C A
30

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
FD723_RS06750: T2TS
Domain 1 (403 - 656): Type 2 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (6):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.26 out of 32.74
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.63 out of 26.12
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.30 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.31 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.31 out of 25.75
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.36 out of 33.14
Confidence: weak
Lanthipeptides
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

allorf_1671706_1671828 - Class II
  Cleavage pHMM score: -6.90
  RODEO score: 0
  Monoisotopic mass: 2447.3 Da
  Molecular weight: 2448.8 Da
  Number of bridges: 1

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

Regulator | Description
--- | ---

NZ_CP040272.1 - Region 8 - phosphonate
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: 1,697,979 - 1,714,414 nt. (total: 16,436 nt) Show pHMM detection rules used
phosphonate: (phosphonates and minimum(1, [2-Hacid_dh_C, Aldedh, Aminotran_1_2, Aminotran_5, AurF, CTP_transf_like, DUF4992, Fe-ADH, HMGL-like, Metallophos_2, NTP_transf_3, NTP_transf_5, PALP, PEP_mutase, TPP_enzyme_C, TPP_enzyme_N, phosphonates]) and not (phosphonatesHydrolase or phosphonatesMeIsocitrateLyase))

#### 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: oxidase
FD723_RS06820: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

Transferases: aminotransferase
FD723_RS06810: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

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

Reference | phosphonate | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000897.5 |  | 0.46 | other (other) | dehydrophos | Streptomyces luridus
BGC0001859.4 |  | 0.45 | other (phosphonate) | fosfomycin | Pseudomonas syringae
BGC0002036.4 |  | 0.44 | other (other) | dehydrofosmidomycin | Streptomyces lavendulae
BGC0000904.5 |  | 0.43 | other (other) | FR-900098 | Streptomyces rubellomurinus
BGC0000926.5 |  | 0.43 | other (other) | rhizocticin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0001739.3 |  | 0.42 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0000937.5 |  | 0.41 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372
BGC0000938.5 |  | 0.40 | other (aminocoumarin) | fosfomycin | Streptomyces fradiae
BGC0002670.2 |  | 0.38 | other (other) | fosfonochlorin | Fusarium oxysporum f. sp. lycopersici 4287
BGC0000807.3 |  | 0.36 | saccharide | phosphonoglycans | Stackebrandtia nassauensis DSM 44728

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000897.5 |  | 0.46 | other (other) | dehydrophos | Streptomyces luridus
BGC0001859.4 |  | 0.45 | other (phosphonate) | fosfomycin | Pseudomonas syringae
BGC0002036.4 |  | 0.44 | other (other) | dehydrofosmidomycin | Streptomyces lavendulae
BGC0000904.5 |  | 0.43 | other (other) | FR-900098 | Streptomyces rubellomurinus
BGC0000926.5 |  | 0.43 | other (other) | rhizocticin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0001739.3 |  | 0.42 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0000937.5 |  | 0.41 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372
BGC0000938.5 |  | 0.40 | other (aminocoumarin) | fosfomycin | Streptomyces fradiae
BGC0002670.2 |  | 0.38 | other (other) | fosfonochlorin | Fusarium oxysporum f. sp. lycopersici 4287
BGC0000807.3 |  | 0.36 | saccharide | phosphonoglycans | Stackebrandtia nassauensis DSM 44728

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:
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.96 out of 30.25
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.76 out of 21.55
Confidence: medium
Additional weak hits (1):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.78 out of 21.55
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
ColR | Phenol-responsive regulator

NZ_CP040272.1 - Region 9 - NRPS,T1PKS,t3nrps-iterative
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,107,879 - 2,229,286 nt. (total: 121,408 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))
t3nrps-iterative: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
FD723_RS08415: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

FD723_RS08485: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

FD723_RS08490: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

FD723_RS08555: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

FD723_RS08570: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

FD723_RS08580: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: aminotransferase glycosyltransferase methyltransferase transferase
FD723_RS08535: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

FD723_RS08635: methyltransferase

smcogs
  SMCOG1089: methyltransferase

FD723_RS08655: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

FD723_RS08700: methyltransferase

smcogs
  SMCOG1248: methyltransferase

FD723_RS08745: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: esterase phosphatase
FD723_RS08565: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

FD723_RS08705: putative esterase

smcogs
  SMCOG1104: putative esterase

Lyases: decarboxylase
FD723_RS08510: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

FD723_RS08650: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
FD723_RS08445: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FD723_RS08495: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS08500: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

FD723_RS08505: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

FD723_RS08515: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS08520: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

FD723_RS08525: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS08530: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS08545: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS08550: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FD723_RS08560: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS08585: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

FD723_RS08590: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | T1PKS | T1PKS | t3nrps-iterative | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  |  | 1.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  |  | 1.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  |  |  | 1.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  |  |  | 1.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  |  | 1.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  |  |  | 1.57 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  |  |  |  | 1.57 | NRPS | enniatin | Fusarium equiseti
BGC0001758.4 |  |  |  |  | 1.57 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  |  |  |  | 1.57 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  |  |  |  | 1.53 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.78 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.78 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.78 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002135.2 |  | 0.78 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.77 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.77 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001249.5 |  | 0.75 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  | 0.75 | NRPS | AM-toxin | Alternaria alternata
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | 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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 18.25 out of 18.46
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.19 out of 26.06
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 21.55
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.51 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.10 out of 26.06
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.88 out of 29.38
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.16 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.53 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.63 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 28.19
Confidence: medium
Additional weak hits (7):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.06 out of 25.88
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.11 out of 26.12
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.60 out of 30.97
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.81 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.71 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.20 out of 30.22
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.85 out of 36.54
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 22, location 2107878 - 2229286:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Ala) + (Me-ohmal) + (Asn - D-Ala) + (X) + (Thr - Ser) + (D-ccmal) + (Ala) + (ohmal) + (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).
FD723_RS08445: X
AMP-binding (96..535): 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:
    YITAWITGSYIGYTGTVGEVDTWWQTETGGIMIT
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

FD723_RS08495: X
AMP-binding (501..903): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    phe (Phe)

Stachelhaus prediction details:
  Stachelhaus sequence:
    GWLTFVDSVWEAVLITSGEINLYGSSEVSANATY
  Nearest Stachelhaus code(s):
    bAla VDWVISLADK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

FD723_RS08500: mal
PKS_AT (535..837): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 165.2
  inactive: 114.7
  Methoxymalonyl-CoA: 58.5
  Methylmalonyl-CoA: 43.1
  Propionyl-CoA: 26.5
  Isobutyryl-CoA: 21.4
  CHC-CoA: 11.9
  2-Methylbutyryl-CoA: 10.4
  Acetyl-CoA: 8.7
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

FD723_RS08505: mal
PKS_AT (538..840): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 91.7%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 172.4
  inactive: 121.3
  Methoxymalonyl-CoA: 70.6
  Methylmalonyl-CoA: 52.5
  Propionyl-CoA: 33.3
  Isobutyryl-CoA: 29.5
  CHC-CoA: 17.7
  2-Methylbutyryl-CoA: 16.9
  Ethylmalonyl-CoA: 15.6
  fatty_acid: 15.2
  trans-1,2-CPDA: 9.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

FD723_RS08515: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (479..880): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MWATFDLSVFEVNTNVAGEFNLYGPSEDTTYSTF
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

FD723_RS08520: mal
PKS_AT (540..865): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 144.0
  inactive: 109.2
  Methoxymalonyl-CoA: 65.5
  Methylmalonyl-CoA: 42.3
  Propionyl-CoA: 25.7
  Acetyl-CoA: 24.9
  Isobutyryl-CoA: 22.1
  Ethylmalonyl-CoA: 18.7
  Benzoyl-CoA: 16.0
  3-Methylbutyryl-CoA: 13.8
  2-Methylbutyryl-CoA: 11.4
  CHC-CoA: 9.6
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0

FD723_RS08525: Thr - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (538..946): 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:
    LATHFDFSVWEGNQIFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1613..2031): 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:
    RWMTFDVSVWEWHFIVSGEHNLYGPTEAAVDVTF
  Nearest Stachelhaus code(s):
    Ser DVWHISLVDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

FD723_RS08530: X
AMP-binding (269..707): 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:
    HAQATDISVWQAELMVVGEVNAYGPTEAADDISQ
  Nearest Stachelhaus code(s):
    Dpr DIWEMTADDK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

FD723_RS08550: Asn - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (463..865): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWCSFDLTITSSKIIIGGEVNEYGPTETVVGCCV
  Nearest Stachelhaus code(s):
    Asn DLTKIGEVGK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1526..1919): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MWATFDLSVFEVNTNVAGEFNLYGPSEDTTYSTF
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

FD723_RS08585: mal
PKS_AT (542..829): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 87.5%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 184.0
  inactive: 123.4
  Methylmalonyl-CoA: 73.2
  Methoxymalonyl-CoA: 72.7
  Benzoyl-CoA: 51.5
  Isobutyryl-CoA: 50.1
  Propionyl-CoA: 45.9
  Ethylmalonyl-CoA: 43.2
  2-Methylbutyryl-CoA: 30.3
  CHC-CoA: 28.7
  Acetyl-CoA: 21.6
  trans-1,2-CPDA: 18.8
  3-Methylbutyryl-CoA: 14.4
  fatty_acid: 13.3

FD723_RS08590: NH2 - Ala
Search NORINE for peptide: strict or relaxed
CAL_domain (157..489): NH2
minowa: NH2

Prediction, score:
  NH2: 135.8
  Acetyl-CoA: 45.1
  AHBA: 22.8
  shikimic_acid: 8.1
  fatty_acid: 5.8

AMP-binding (1166..1561): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWSTFDLSIFEVNTNLAGELNLYGPSEDTTYSTF
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP040272.1 - Region 10 - 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: 2,980,781 - 3,001,713 nt. (total: 20,933 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
Transferases: acyltransferase
FD723_RS11870: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Hydrolases: hydrolase
FD723_RS11940: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: synthetase
FD723_RS11915: 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
--- | --- | --- | --- | --- | ---
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0002397.2 |  | 0.48 | terpene | astallatene | Arabidopsis thaliana
BGC0001526.4 |  | 0.46 | other (other) | bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K | Synechocystis salina LEGE 06099
BGC0001525.3 |  | 0.46 | other (other) | bartoloside B, bartoloside C, bartoloside D | Synechocystis salina LEGE 06155
BGC0002400.2 |  | 0.45 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000589.5 |  | 0.44 | ribosomal | microcin M | Escherichia coli Nissle 1917
BGC0000587.5 |  | 0.44 | ribosomal | microcin H47 | Escherichia coli
BGC0000586.5 |  | 0.42 | ribosomal | microcin E492 | Klebsiella pneumoniae RYC492

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0002397.2 |  | 0.48 | terpene | astallatene | Arabidopsis thaliana
BGC0001526.4 |  | 0.46 | other (other) | bartoloside E, bartoloside F, bartoloside G, bartoloside H, bartoloside I, bartoloside J, bartoloside K | Synechocystis salina LEGE 06099
BGC0001525.3 |  | 0.46 | other (other) | bartoloside B, bartoloside C, bartoloside D | Synechocystis salina LEGE 06155
BGC0002400.2 |  | 0.45 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000589.5 |  | 0.44 | ribosomal | microcin M | Escherichia coli Nissle 1917
BGC0000587.5 |  | 0.44 | ribosomal | microcin H47 | Escherichia coli
BGC0000586.5 |  | 0.42 | ribosomal | microcin E492 | Klebsiella pneumoniae RYC492

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
FD723_RS11915: PT_FPPS_like
Domain 1 (45 - 309): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial or Geranylgeranyl diphosphate synthase or geranylfarnesyl diphosphate synthase, bacterial
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:
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.83 out of 21.55
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.84 out of 20.97
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.38 out of 26.06
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.07 out of 18.46
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.65 out of 28.19
Confidence: medium
Additional weak hits (2):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.08 out of 23.43
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.34 out of 31.73
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
CcpA | Catabolite control protein A
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
ZuR variant 1 | Zinc-responsive repressor

NZ_CP040272.1 - Region 11 - 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: 3,086,370 - 3,134,817 nt. (total: 48,448 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))

#### 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: oxidoreductase oxygenase
FD723_RS12420: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

FD723_RS12425: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

FD723_RS12465: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

FD723_RS12515: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Ligases: synthase
FD723_RS12415: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002191.2 |  | 0.62 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

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

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:
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 22.28 out of 25.88
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.78 out of 20.97
Confidence: medium
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.44 out of 28.14
Confidence: medium
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.44 out of 28.14
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.18 out of 27.78
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 28.19
Confidence: medium
Additional weak hits (2):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.45 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73
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 24, location 3086369 - 3134817:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-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).
FD723_RS12415: pk
PKS_AT (565..863): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  CE-Malonyl-CoA: 62.5%
  Methylmalonyl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 119.9
  Methoxymalonyl-CoA: 103.0
  Malonyl-CoA: 90.5
  Isobutyryl-CoA: 84.2
  Ethylmalonyl-CoA: 84.2
  Benzoyl-CoA: 72.3
  trans-1,2-CPDA: 69.1
  Propionyl-CoA: 68.3
  Acetyl-CoA: 67.8
  2-Methylbutyryl-CoA: 58.7
  3-Methylbutyryl-CoA: 46.9
  fatty_acid: 39.6
  inactive: 31.4
  CHC-CoA: 28.2

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

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
PerR | Peroxide regulator
PsrA | Oleic acid responsive regulator
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_CP040272.1 - Region 12 - 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: 3,427,539 - 3,448,504 nt. (total: 20,966 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: oxygenase
FD723_RS13810: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Lyases: cyclase
FD723_RS13815: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002708.2 |  | 0.75 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0001201.3 |  | 0.56 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002402.2 |  | 0.45 | terpene | Yossoside I, Yossoside II, Yossoside III, Yossoside IV, Yossoside V | Spinacia oleracea
BGC0001969.3 |  | 0.44 | terpene | asperterpenoid A | Talaromyces wortmannii
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001679.3 |  | 0.40 | NRPS | N-Acetyltryptophan | Aspergillus nidulans FGSC A4
BGC0002445.3 |  | 0.37 | terpene | armillyl orsellinate, 8α-hydroxy-6-protoilludene | Armillaria gallica
BGC0001262.3 |  | 0.36 | PKS | AK-toxin I | Alternaria alternata
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000528.5 |  | 0.35 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002708.2 |  | 0.75 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0001201.3 |  | 0.56 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002402.2 |  | 0.45 | terpene | Yossoside I, Yossoside II, Yossoside III, Yossoside IV, Yossoside V | Spinacia oleracea
BGC0001969.3 |  | 0.44 | terpene | asperterpenoid A | Talaromyces wortmannii
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001679.3 |  | 0.40 | NRPS | N-Acetyltryptophan | Aspergillus nidulans FGSC A4
BGC0002445.3 |  | 0.37 | terpene | armillyl orsellinate, 8α-hydroxy-6-protoilludene | Armillaria gallica
BGC0001262.3 |  | 0.36 | PKS | AK-toxin I | Alternaria alternata
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000528.5 |  | 0.35 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

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

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
--- | --- | --- | --- | --- | ---
monoterpene |  |  | C10 | C1-C10 | none
sesquiterpene |  |  | C15 | C1-C10 | none

Genes with terpene domains:
FD723_RS13815: T1TS
Domain 1 (1 - 311): Type 1 terpene synthase
Subtype: Germacrene A synthase type

Reactions:
  GPP → monoterpene_C1-C10
  FPP → sesquiterpene_C1-C10

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.48 out of 20.97
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.38 out of 27.78
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.17 out of 23.79
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.54 out of 21.55
Confidence: medium
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
IolR | Regulator of the inositol catabolism

NZ_CP040272.1 - Region 13 - 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: 3,548,551 - 3,569,483 nt. (total: 20,933 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: dehydrogenase
FD723_RS14465: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: deacetylase
FD723_RS14300: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

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
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.41 | terpene | β-carotein | uncultured bacterium
BGC0000645.3 |  | 0.40 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000664.5 |  | 0.40 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000640.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000641.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000643.3 |  | 0.40 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000642.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000634.3 |  | 0.39 | terpene | carotenoid | Brevundimonas sp. SD212

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.41 | terpene | β-carotein | uncultured bacterium
BGC0000645.3 |  | 0.40 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000664.5 |  | 0.40 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000640.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000641.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000643.3 |  | 0.40 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000642.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000634.3 |  | 0.39 | terpene | carotenoid | Brevundimonas sp. SD212

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:
FD723_RS14470: PT_phytoene_like
Domain 1 (18 - 308): 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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.12 out of 27.78
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 16.78 out of 18.16
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.35 out of 27.78
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.57 out of 27.04
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.10 out of 26.06
Confidence: medium
Additional weak hits (3):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.36 out of 20.01
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.02 out of 32.93
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.05 out of 30.11
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
--- | ---
AbrC3 | Antibiotic production activator
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
DasR | N-acetylglucosamine dependent repressor
MogR | Repressor of flagellar motility genes

NZ_CP040272.1 - Region 14 - redox-cofactor
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: 3,922,221 - 3,944,833 nt. (total: 22,613 nt) Show pHMM detection rules used
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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: kinase
FD723_RS16140: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: phosphatase
FD723_RS16135: 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 | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000878.5 |  | 0.39 | other (other) | puromycin | Streptomyces alboniger
BGC0000916.5 |  | 0.38 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0001521.3 |  | 0.34 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0000017.5 |  | 0.33 | PKS, other (other) | anatoxin-a, homoanatoxin-a | [Oscillatoria] sp. PCC 6506
BGC0001100.5 |  | 0.32 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0000249.5 |  | 0.32 | PKS | nogalamycin | Streptomyces nogalater
BGC0002805.2 |  | 0.32 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0002754.2 |  | 0.32 | NRPS | hectoramide B | Moorena producens JHB
BGC0002294.3 |  | 0.31 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0001076.5 |  | 0.31 | other (nucleoside) | liposidomycin B, liposidomycin A, liposidomycin C, liposidomycin Z, liposidomycin H, liposidomycin G, liposidomycin L, liposidomycin M, liposidomycin K, liposidomycin N | Streptomyces sp. SN-1061M

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000878.5 |  | 0.39 | other (other) | puromycin | Streptomyces alboniger
BGC0000916.5 |  | 0.38 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0001521.3 |  | 0.34 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0000017.5 |  | 0.33 | PKS, other (other) | anatoxin-a, homoanatoxin-a | [Oscillatoria] sp. PCC 6506
BGC0001100.5 |  | 0.32 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0000249.5 |  | 0.32 | PKS | nogalamycin | Streptomyces nogalater
BGC0002805.2 |  | 0.32 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0002754.2 |  | 0.32 | NRPS | hectoramide B | Moorena producens JHB
BGC0002294.3 |  | 0.31 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0001076.5 |  | 0.31 | other (nucleoside) | liposidomycin B, liposidomycin A, liposidomycin C, liposidomycin Z, liposidomycin H, liposidomycin G, liposidomycin L, liposidomycin M, liposidomycin K, liposidomycin N | Streptomyces sp. SN-1061M

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.42 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.30 out of 27.78
Confidence: medium
Additional weak hits (2):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.03 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.81 out of 29.65
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (3922220...3944833)
FD723_RS16170
  RRE type: PqqD_RRE
  Location: 1 - 88
  Score: 78.7
  RRE type: Thurincin_rSAM_RRE
  Location: 32 - 86
  Score: 27.8

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP040272.1 - Region 15 - 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: 4,003,405 - 4,068,783 nt. (total: 65,379 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
FD723_RS16525: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Ligases: ligase
FD723_RS16500: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS16505: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FD723_RS16550: cobaltochelatase subunit CobN

smcogs
  SMCOG1263: cobaltochelatase subunit CobN

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
BGC0000397.5 |  | 0.75 | NRPS | nostocyclopeptide A2 | Nostoc sp. ATCC 53789
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.71 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002071.2 |  | 0.70 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000397.5 |  | 0.75 | NRPS | nostocyclopeptide A2 | Nostoc sp. ATCC 53789
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.71 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002071.2 |  | 0.70 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti

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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.38 out of 26.06
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.00 out of 21.55
Confidence: medium
Additional weak hits (9):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.20 out of 30.22
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.77 out of 32.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.12 out of 26.85
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.15 out of 25.75
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.01 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.48 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.12 out of 27.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.69 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.04 out of 29.38
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 4003404 - 4068783:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Tyr - Gly - D-Gln) + (Ile - Ser - X - Leu)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
FD723_RS16500: Ile - Ser - X - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (476..904): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LETSFDAATFEGFLLFGGELHVYGPTENTTFSSW
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1566..1997): 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:
    RWMTFDVSVWEWHFICSGEHNLYGPTEAAIDVTF
  Nearest Stachelhaus code(s):
    Ser DVWHISLIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2659..3064): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHAFDVSFQETFLITSGEHNHYGPSESHLATSF
  Nearest Stachelhaus code(s):
    4Me-Pro DVQFIAHLAK (97% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3726..4127): Leu
nrpys: Leu

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

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

FD723_RS16505: Tyr - Gly - Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (549..960): 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:
    LAQAFDACISEMTLVVAGEFNAYGPTEASVCATT
  Nearest Stachelhaus code(s):
    Tyr DASTVAAVCK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1622..2023): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAMTFDIAALELQALCGGEWNLYGPTETTIWSSV
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2685..3089): Gln
nrpys: Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWMTFDASVWEAQLFCGGEHNLYGPTEACIDATF
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
MogR | Repressor of flagellar motility genes

NZ_CP040272.1 - Region 16 - T1PKS,hglE-KS
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: 4,729,999 - 4,782,307 nt. (total: 52,309 nt) Show pHMM detection rules used
hglE-KS: (hglE or hglD)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
FD723_RS19580: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acylase glycosyltransferase sulfotransferase
FD723_RS19575: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

FD723_RS19590: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

FD723_RS19640: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

FD723_RS19645: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

Lyases: decarboxylase dehydratase
FD723_RS19550: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

FD723_RS19620: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
FD723_RS19595: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

FD723_RS19605: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: permease
FD723_RS19545: 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 | hglE-KS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000869.5 |  |  | 1.47 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0002276.2 |  |  | 0.59 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001276.3 |  |  | 0.58 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.57 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.57 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  |  | 0.56 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001284.4 |  |  | 0.55 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002648.2 |  |  | 0.54 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  |  | 0.54 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0000863.3 |  |  | 0.54 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000869.5 |  | 0.90 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0002276.2 |  | 0.63 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001276.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.62 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002648.2 |  | 0.61 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  | 0.61 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0000863.3 |  | 0.60 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.68 out of 27.78
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.07 out of 18.46
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 16.33 out of 18.16
Confidence: strong
Additional weak hits (4):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.20 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.69 out of 32.74
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.56 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 29, location 4729998 - 4782307:
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).
FD723_RS19595: mxmal
PKS_AT (1085..1361): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 17.4
  Isobutyryl-CoA: 10.3
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Malonyl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

FD723_RS19605: mal
PKS_AT (629..927): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 86.4
  inactive: 31.4
  Methoxymalonyl-CoA: 30.7
  Methylmalonyl-CoA: 23.6
  Isobutyryl-CoA: 15.1
  CHC-CoA: 14.7
  fatty_acid: 11.3
  Propionyl-CoA: 9.9
  trans-1,2-CPDA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis

NZ_CP040272.1 - Region 17 - RRE-containing,lanthipeptide-class-v,spliceotide
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: 4,943,029 - 4,985,369 nt. (total: 42,341 nt) Show pHMM detection rules used
lanthipeptide-class-v: (APH and HopA1)
spliceotide: (TIGR04103 and TIGR03798)
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase
FD723_RS20480: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Lyases: dehydratase
FD723_RS20325: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

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-v | spliceotide | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001733.3 |  |  |  | 0.88 | ribosomal | PcpA | Pleurocapsa sp. PCC 7327
BGC0001555.4 |  |  |  | 0.59 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  |  |  | 0.57 | ribosomal | microcin N | Escherichia coli
BGC0002005.2 |  |  |  | 0.57 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0002306.2 |  |  |  | 0.55 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000588.5 |  |  |  | 0.53 | ribosomal | microcin L | Escherichia coli
BGC0000558.5 |  |  |  | 0.51 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000617.5 |  |  |  | 0.44 | ribosomal | coagulin | Bacillus coagulans
BGC0000623.3 |  |  |  | 0.43 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0002577.2 |  |  |  | 0.43 | ribosomal | lactococcin G | Lactococcus lactis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001733.3 |  | 0.63 | ribosomal | PcpA | Pleurocapsa sp. PCC 7327
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0002005.2 |  | 0.51 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0002306.2 |  | 0.50 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0000558.5 |  | 0.48 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000623.3 |  | 0.48 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0002674.2 |  | 0.46 | ribosomal | enterocin F4-9 | Enterococcus faecalis
BGC0002699.2 |  | 0.46 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102

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.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 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
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.45 out of 26.33
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.03 out of 30.25
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.23 out of 24.78
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.42 out of 32.93
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.42 out of 26.06
Confidence: medium
Additional weak hits (6):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.13 out of 25.88
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.70 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.28 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 24.07 out of 30.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.96 out of 30.22
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.74 out of 23.43
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.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-v protocluster (4943028...4985369)
FD723_RS20425
  RRE type: PlpY_RRE
  Location: 0 - 66
  Score: 74.6
spliceotide protocluster (4950498...4972663)
FD723_RS20425
  RRE type: PlpY_RRE
  Location: 0 - 66
  Score: 74.6
RRE-containing protocluster (4952689...4972893)
FD723_RS20425
  RRE type: PlpY_RRE
  Location: 0 - 66
  Score: 74.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
ColR | Phenol-responsive regulator
LexA variant 2 | Repressor of DNA damage response
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis

NZ_CP040272.1 - Region 18 - 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: 5,432,852 - 5,454,768 nt. (total: 21,917 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: dehydrogenase oxidoreductase oxygenase
FD723_RS22430: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FD723_RS22440: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

FD723_RS22445: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

FD723_RS22450: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FD723_RS22490: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

Transferases: methyltransferase
FD723_RS22425: methyltransferase

smcogs
  SMCOG1089: methyltransferase

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
--- | --- | --- | --- | --- | ---
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000632.5 |  | 0.41 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001267.3 |  | 0.39 | terpene | elymoclavine, Agroclavine I | Claviceps fusiformis
BGC0002362.3 |  | 0.39 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0002007.2 |  | 0.39 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000811.3 |  | 0.38 | other (other) | fumigaclavine C | Aspergillus fumigatus Af293
BGC0001841.2 |  | 0.37 | NRPS, PKS | detoxin P1, detoxin P2, detoxin P3 | Amycolatopsis jejuensis
BGC0001878.2 |  | 0.36 | NRPS, PKS | detoxin N2, detoxin N3 | Streptomyces sp. NRRL B-1347
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000348.4 |  | 0.36 | NRPS | ergovaline | Epichloe festucae var. lolii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000632.5 |  | 0.41 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001267.3 |  | 0.39 | terpene | elymoclavine, Agroclavine I | Claviceps fusiformis
BGC0002362.3 |  | 0.39 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0002007.2 |  | 0.39 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000811.3 |  | 0.38 | other (other) | fumigaclavine C | Aspergillus fumigatus Af293
BGC0001841.2 |  | 0.37 | NRPS, PKS | detoxin P1, detoxin P2, detoxin P3 | Amycolatopsis jejuensis
BGC0001878.2 |  | 0.36 | NRPS, PKS | detoxin N2, detoxin N3 | Streptomyces sp. NRRL B-1347
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000348.4 |  | 0.36 | NRPS | ergovaline | Epichloe festucae var. lolii

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
FD723_RS22470: T2TS
Domain 1 (4 - 634): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 29.39 out of 32.74
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.34 out of 20.97
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.53 out of 28.19
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.18 out of 32.93
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.47 out of 32.93
Confidence: medium
Additional weak hits (3):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.61 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.77 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.00 out of 31.73
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
FuR variant 2 | Ferric Uptake Regulator
LexA variant 3 | Repressor of DNA damage response
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_CP040272.1 - Region 19 - 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: 5,686,058 - 5,731,985 nt. (total: 45,928 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 oxidoreductase
FD723_RS23570: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

FD723_RS23610: nucleotide sugar dehydrogenase

smcogs
  SMCOG1152: nucleotide sugar dehydrogenase

Transferases: aminotransferase glycosyltransferase
FD723_RS23540: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

FD723_RS23580: sugar transferase

smcogs
  SMCOG1146: sugar transferase

FD723_RS23605: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

FD723_RS23615: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Ligases: ligase
FD723_RS23575: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.67 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  | 0.66 | NRPS | peramine | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.67 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  | 0.66 | NRPS | peramine | 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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.98 out of 27.55
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.44 out of 28.19
Confidence: medium
Additional weak hits (10):
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.01 out of 29.72
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.41 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.88 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.13 out of 29.38
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.65 out of 30.98
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 18.41 out of 30.12
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.21 out of 26.85
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 21.24 out of 30.12
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.88 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.18 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 34, location 5686057 - 5731985:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - 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).
FD723_RS23575: X - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (49..451): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    QWKIFDPSVWQWALVCGGEHNCYGPTEASIDTTF
  Nearest Stachelhaus code(s):
    ohdmTyr DPWGLGLIDK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1108..1505): 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:
    RWMTFDVSVWEWHFFCSGEHNLYGPTEAAIDVTF
  Nearest Stachelhaus code(s):
    Ser DVWHFSLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
GnfM | Regulator of nitrogen-fixation genes
ZuR variant 1 | Zinc-responsive repressor

NZ_CP040272.1 - Region 20 - 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: 6,082,246 - 6,103,076 nt. (total: 20,831 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
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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002700.2 |  | 0.41 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002111.3 |  | 0.39 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0002701.2 |  | 0.32 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0002425.3 |  | 0.28 | ribosomal | stlassin | Streptomyces sp.
BGC0000017.5 |  | 0.25 | PKS, other (other) | anatoxin-a, homoanatoxin-a | [Oscillatoria] sp. PCC 6506
BGC0001060.5 |  | 0.23 | PKS | dynemicin A | Micromonospora chersina
BGC0000023.5 |  | 0.21 | PKS | aurafuron A | Stigmatella aurantiaca DW4/3-1
BGC0000362.5 |  | 0.18 | NRPS | glycopeptidolipid | Mycobacterium avium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002700.2 |  | 0.41 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002111.3 |  | 0.39 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0002701.2 |  | 0.32 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0002425.3 |  | 0.28 | ribosomal | stlassin | Streptomyces sp.
BGC0000017.5 |  | 0.25 | PKS, other (other) | anatoxin-a, homoanatoxin-a | [Oscillatoria] sp. PCC 6506
BGC0001060.5 |  | 0.23 | PKS | dynemicin A | Micromonospora chersina
BGC0000023.5 |  | 0.21 | PKS | aurafuron A | Stigmatella aurantiaca DW4/3-1
BGC0000362.5 |  | 0.18 | NRPS | glycopeptidolipid | Mycobacterium avium

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
FD723_RS25185: PT_phytoene_like
Domain 1 (10 - 206): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.54 out of 18.46
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.38 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.93 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.97 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.08 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.97 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.08 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.97 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.08 out of 26.06
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.32 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.46 out of 27.78
Confidence: medium
Additional weak hits (6):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.89 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.89 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.89 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.50 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.28 out of 31.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.16 out of 33.14
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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP040272.1 - Region 21 - 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: 6,502,743 - 6,526,051 nt. (total: 23,309 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: reductase
FD723_RS26905: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Lyases: cyclase
FD723_RS26890: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002699.2 |  | 0.56 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0002698.2 |  | 0.52 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000554.4 |  | 0.51 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0000527.5 |  | 0.48 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000504.5 |  | 0.48 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001210.5 |  | 0.48 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002699.2 |  | 0.56 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0002698.2 |  | 0.52 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000554.4 |  | 0.51 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0000527.5 |  | 0.48 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000504.5 |  | 0.48 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001210.5 |  | 0.48 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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 FD723_RS26890

allorf_6516183_6516359
Leader:
MEEAIILPLDLTDTLYQRRSSRAA
Core:
I A L N P Q R H Q I V L F R W V S P I S Y K R P S L A G L Y I S R C
Core with dehydrations:
I A L N P Q R H Q I V L F R W V Dha P I Dha Y K R P Dha L A G L Y I Dha R Cys

#### antiSMASH-DB 4.0 matches for allorf_6516183_6516359

100.0%
NZ_CP040272.1:
Lanthipeptides: allorf_6516183_6516359_lanthipeptide
1
I A L N P Q R H Q I V L F R W V S P I S Y K R P S L A G L Y I S R C
34
I A L N P Q R H Q I V L F R W V S P I S Y K R P S L A G L Y I S R C
1
I A L N P Q R H Q I V L F R W V S P I S Y K R P S L A G L Y I S R C
34
17.6%
NZ_BNBJ01000003.1 and 2 others:
NZ_CP079114.1 Lanthipeptides: allorf_4444301_4444447_lanthipeptide NZ_JNZV01000231.1 Lanthipeptides: allorf_40678_40824_lanthipeptide
Lanthipeptides: allorf_001692_001838_lanthipeptide
7
R H Q I V L F R W V S P I S Y K R P S
25
R H+ V W +P + P+
3
R H E C V G A G W T T P A M D R N P T
21
15.6%
NZ_CP010407.1 and 2 others:
NZ_CP010407.1 Lanthipeptides: allorf_8470819_8470980_lanthipeptide NZ_CP010407.1 Lanthipeptides: allorf_8470819_8470980_lanthipeptide
Lanthipeptides: allorf_8470819_8470980_lanthipeptide
15
W V S P I S Y K R P S L A G
28
W S + R P L A G
17
W T S L V D V L R P G L A G
30

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.84 out of 25.88
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.52 out of 26.06
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.90 out of 21.55
Confidence: medium
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 25.60 out of 30.22
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 28.19
Confidence: medium
Additional weak hits (3):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.50 out of 39.62
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.56 out of 27.04
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.76 out of 32.74
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

allorf_6516183_6516359 - Class II
  Cleavage pHMM score: -6.30
  RODEO score: 0
  Monoisotopic mass: 3909.2 Da
  Molecular weight: 3911.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3929.6 Da N = 1
    3947.6 Da N = 2
    3965.7 Da N = 3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
ClgR | Caseinolytic protease gene regulator
MogR | Repressor of flagellar motility genes
PsrA | Oleic acid responsive regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_CP040272.1 - Region 22 - 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: 6,602,843 - 6,625,200 nt. (total: 22,358 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase
FD723_RS27230: 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
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.80 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000657.5 |  | 0.53 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001554.3 |  | 0.39 | other (other) | coenzyme F430 | Methanosarcina barkeri str. Fusaro
BGC0001210.5 |  | 0.32 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000488.4 |  | 0.29 | ribosomal | circularin A | Clostridium beijerinckii
BGC0002425.3 |  | 0.28 | ribosomal | stlassin | Streptomyces sp.
BGC0002747.3 |  | 0.28 | ribosomal | lentinulin A | Lentinula edodes
BGC0000549.3 |  | 0.27 | ribosomal | salivaricin D | Streptococcus salivarius
BGC0002386.2 |  | 0.27 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0002470.2 |  | 0.25 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.80 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000657.5 |  | 0.53 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001554.3 |  | 0.39 | other (other) | coenzyme F430 | Methanosarcina barkeri str. Fusaro
BGC0001210.5 |  | 0.32 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000488.4 |  | 0.29 | ribosomal | circularin A | Clostridium beijerinckii
BGC0002425.3 |  | 0.28 | ribosomal | stlassin | Streptomyces sp.
BGC0002747.3 |  | 0.28 | ribosomal | lentinulin A | Lentinula edodes
BGC0000549.3 |  | 0.27 | ribosomal | salivaricin D | Streptococcus salivarius
BGC0002386.2 |  | 0.27 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0002470.2 |  | 0.25 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002

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

No significant matches found.

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

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

Genes with terpene domains:
FD723_RS27230: T1TS + T1TS
Domain 1 (3 - 335): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (336 - 715): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.56 out of 27.04
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.99 out of 27.55
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.41 out of 25.88
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.14 out of 27.18
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.44 out of 18.16
Confidence: strong
Additional weak hits (2):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.23 out of 33.73
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.24 out of 36.53
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
DasR | N-acetylglucosamine dependent repressor
GnfM | Regulator of nitrogen-fixation genes
NrdR | Represses ribonucleotide reductase encoding genes
PsrA | Oleic acid responsive regulator

NZ_CP040272.1 - Region 23 - 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: 7,585,493 - 7,610,055 nt. (total: 24,563 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: glycosyltransferase sulfotransferase
FD723_RS31295: Sulfotransferase domain

extras
  Sulfotransfer_1: Sulfotransferase domain

FD723_RS31300: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

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
--- | --- | --- | --- | --- | ---
BGC0000734.3 |  | 0.42 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000783.3 |  | 0.40 | saccharide | O-antigen | Xanthomonas oryzae pv. oryzae
BGC0000393.5 |  | 0.39 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0000794.5 |  | 0.39 | saccharide | S-layer glycan | Geobacillus stearothermophilus
BGC0000735.3 |  | 0.37 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000880.4 |  | 0.35 | other (nucleoside) | tunicamycin B1 | Streptomyces chartreusis NRRL 3882
BGC0002302.2 |  | 0.35 | saccharide | glucorhamnan | [Ruminococcus] gnavus ATCC 29149
BGC0000426.5 |  | 0.35 | NRPS | sevadicin | Paenibacillus larvae
BGC0001167.4 |  | 0.32 | ribosomal | piricyclamide 7005E1, piricyclamide 7005E2, piricyclamide 7005E3, piricyclamide 7005E4 | Microcystis aeruginosa PCC 7005
BGC0002641.2 |  | 0.32 | NRPS | bacillothiazol A, bacillothiazol B, bacillothiazol C, bacillothiazol D, bacillothiazol E, bacillothiazol F, bacillothiazol G, bacillothiazol H, bacillothiazol I, bacillothiazol J, bacillothiazol K, bacillothiazol L, bacillothiazol M, bacillothiazol N | Bacillus velezensis FZB42

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000734.3 |  | 0.42 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000783.3 |  | 0.40 | saccharide | O-antigen | Xanthomonas oryzae pv. oryzae
BGC0000393.5 |  | 0.39 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0000794.5 |  | 0.39 | saccharide | S-layer glycan | Geobacillus stearothermophilus
BGC0000735.3 |  | 0.37 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000880.4 |  | 0.35 | other (nucleoside) | tunicamycin B1 | Streptomyces chartreusis NRRL 3882
BGC0002302.2 |  | 0.35 | saccharide | glucorhamnan | [Ruminococcus] gnavus ATCC 29149
BGC0000426.5 |  | 0.35 | NRPS | sevadicin | Paenibacillus larvae
BGC0001167.4 |  | 0.32 | ribosomal | piricyclamide 7005E1, piricyclamide 7005E2, piricyclamide 7005E3, piricyclamide 7005E4 | Microcystis aeruginosa PCC 7005
BGC0002641.2 |  | 0.32 | NRPS | bacillothiazol A, bacillothiazol B, bacillothiazol C, bacillothiazol D, bacillothiazol E, bacillothiazol F, bacillothiazol G, bacillothiazol H, bacillothiazol I, bacillothiazol J, bacillothiazol K, bacillothiazol L, bacillothiazol M, bacillothiazol N | 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:
No product predictions
Genes with terpene domains:
FD723_RS31310: T2TS
Domain 1 (1,057 - 1,287): Type 2 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 15.94 out of 18.46
Confidence: medium
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP040272.1 - Region 24 - 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: 7,681,020 - 7,724,160 nt. (total: 43,141 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
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
FD723_RS31685: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: aminotransferase
FD723_RS31720: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Hydrolases: hydrolase
FD723_RS31680: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: cyclase
FD723_RS31705: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Isomerases: isomerase
FD723_RS31690: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
FD723_RS31695: 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-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.59 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000343.5 |  | 0.46 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0002474.2 |  | 0.44 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0001168.5 |  | 0.44 | NRPS | Livipeptin | Streptomyces lividans 1326
BGC0000922.5 |  | 0.41 | PKS | 2-heptyl-3-hydroxy-4-quinolone, 2,4-Quinolinediol, 2-heptylquinolin-4(1H)-one | Pseudomonas aeruginosa PAO1
BGC0002493.3 |  | 0.41 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0000632.5 |  | 0.40 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001909.3 |  | 0.40 | PKS | strobilurin A | Strobilurus tenacellus
BGC0001850.4 |  | 0.40 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0001868.4 |  | 0.39 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.59 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000343.5 |  | 0.46 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0002474.2 |  | 0.44 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0001168.5 |  | 0.44 | NRPS | Livipeptin | Streptomyces lividans 1326
BGC0000922.5 |  | 0.41 | PKS | 2-heptyl-3-hydroxy-4-quinolone, 2,4-Quinolinediol, 2-heptylquinolin-4(1H)-one | Pseudomonas aeruginosa PAO1
BGC0002493.3 |  | 0.41 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0000632.5 |  | 0.40 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0001909.3 |  | 0.40 | PKS | strobilurin A | Strobilurus tenacellus
BGC0001850.4 |  | 0.40 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0001868.4 |  | 0.39 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338

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: 18.31 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.98 out of 27.78
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.21 out of 24.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.13 out of 26.06
Confidence: medium
Additional weak hits (10):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.81 out of 23.43
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.31 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.20 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.73 out of 30.25
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.01 out of 29.72
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.20 out of 30.22
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.86 out of 20.01
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.99 out of 20.01
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.91 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.46 out of 29.38
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 39, location 7681019 - 7724160:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
FD723_RS31695: X
AMP-binding (25..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:
    NEFLHAYGMLMYHITSSAAKQIYGTTETCVNLHA
  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
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis

NZ_CP040274.1 - Region 1 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 329,734 - 37,934 nt. (total: 44,626 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
FD723_RS34770: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FD723_RS34790: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: ligase
FD723_RS34755: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.65 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.65 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (1):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.30 out of 31.73
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 329733 - 37934:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-Leu)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
FD723_RS34755: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (514..909): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHSFDACGWEPFILTGGDFNNYGPTENTVVTTS
  Nearest Stachelhaus code(s):
    Leu DAWFLGNVVK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---

NZ_CP040274.1 - Region 2 - proteusin
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 51,884 - 72,600 nt. (total: 20,717 nt) Show pHMM detection rules used
proteusin: (PoyD or TIGR03793)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase
FD723_RS34920: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FD723_RS34960: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/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 | proteusin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000888.5 |  | 0.40 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000231.5 |  | 0.38 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.34 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.32 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001768.4 |  | 0.32 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4
BGC0000188.5 |  | 0.31 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0000391.5 |  | 0.31 | NRPS | methylpendolmycin, pendolmycin | Marinactinospora thermotolerans
BGC0001444.5 |  | 0.31 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0002425.3 |  | 0.31 | ribosomal | stlassin | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000888.5 |  | 0.40 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000231.5 |  | 0.38 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.34 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.32 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001768.4 |  | 0.32 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4
BGC0000188.5 |  | 0.31 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0000391.5 |  | 0.31 | NRPS | methylpendolmycin, pendolmycin | Marinactinospora thermotolerans
BGC0001444.5 |  | 0.31 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0002425.3 |  | 0.31 | ribosomal | stlassin | Streptomyces sp.

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

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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.48 out of 26.85
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.16 out of 26.85
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.85 out of 25.88
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.43 out of 26.06
Confidence: medium
Additional weak hits (5):
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.88 out of 30.98
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.86 out of 20.01
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.39 out of 28.14
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.44 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MogR | Repressor of flagellar motility genes
PsrA | Oleic acid responsive regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP040275.1 - Region 1 - NRPS,NRPS-like,T1PKS,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: 251,519 - 59,084 nt. (total: 106,497 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)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase methyltransferase
FD723_RS37395: methyltransferase

smcogs
  SMCOG1089: methyltransferase

FD723_RS37465: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: esterase
FD723_RS37460: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
FD723_RS36370: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

FD723_RS36375: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

FD723_RS36400: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS37375: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS37490: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

FD723_RS37495: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

FD723_RS42275: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

FD723_RS44005: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FD723_RS44290: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | terpene | NRPS-like | T1PKS | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001164.3 |  |  |  |  |  | 1.69 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  |  |  | 1.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001254.3 |  |  |  |  |  | 1.48 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001273.3 |  |  |  |  |  | 1.47 | PKS | asperlactone | Aspergillus ochraceus
BGC0002192.3 |  |  |  |  |  | 1.44 | PKS | FR901512 | fungal sp. No.14919
BGC0001244.3 |  |  |  |  |  | 1.42 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001135.5 |  |  |  |  |  | 1.34 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  |  |  |  | 1.34 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  |  |  |  |  | 1.32 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  |  |  |  | 1.30 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001164.3 |  | 0.76 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.75 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001254.3 |  | 0.75 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  | 0.75 | PKS | FR901512 | fungal sp. No.14919
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001268.4 |  | 0.69 | NRPS, PKS | fusarin C | Fusarium fujikuroi

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
FD723_RS37415: TS_Pyr4
Domain 1 (4 - 196): Pyr4 type terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.64 out of 26.33
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.87 out of 29.72
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.72 out of 29.38
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.15 out of 27.78
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.29 out of 26.85
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.01 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.67 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.64 out of 26.06
Confidence: medium
Additional weak hits (4):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.80 out of 26.12
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.06 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.77 out of 26.06
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.73 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 251518 - 59084:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Me-redmal) + (ccmal) + (ohmal - Me-redmal) + (ccmal) + (Me-ccmal) + (ccmal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 263443 - 50494:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Me-redmal) + (ccmal) + (ohmal - Me-redmal) + (ccmal) + (Me-ccmal) + (ccmal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 10888 - 59084:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ohmal - Me-redmal) + (ccmal) + (Me-ccmal) + (ccmal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 254092 - 295766:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Me-redmal) + (ccmal)
Non-colinear ordering:
  FD723_RS37490 + FD723_RS37495

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).
FD723_RS37490: NH2 - mal
CAL_domain (176..496): NH2
minowa: NH2

Prediction, score:
  NH2: 188.3
  Acetyl-CoA: 36.9
  fatty_acid: 12.8
  shikimic_acid: 0.0
  AHBA: 0.0

PKS_AT (1223..1518): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 201.5
  inactive: 179.2
  Methoxymalonyl-CoA: 64.7
  Methylmalonyl-CoA: 60.0
  Propionyl-CoA: 40.2
  Isobutyryl-CoA: 39.7
  trans-1,2-CPDA: 27.9
  Acetyl-CoA: 23.2
  Benzoyl-CoA: 22.7
  3-Methylbutyryl-CoA: 22.6
  CHC-CoA: 18.9
  2-Methylbutyryl-CoA: 17.1
  Ethylmalonyl-CoA: 11.5
  fatty_acid: 10.4

FD723_RS37495: mal
PKS_AT (568..787): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 54.2%

minowa: inactive

Prediction, score:
  inactive: 68.5
  Malonyl-CoA: 66.9
  Methoxymalonyl-CoA: 17.3
  Propionyl-CoA: 15.5
  Isobutyryl-CoA: 14.9
  Benzoyl-CoA: 13.9
  Methylmalonyl-CoA: 13.6
  trans-1,2-CPDA: 10.8
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

FD723_RS42275: mal - mal
PKS_AT (603..897): mal
ATSignature: Malonyl-CoA, inactive

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 100.0%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.8
  inactive: 169.0
  Methoxymalonyl-CoA: 74.6
  Methylmalonyl-CoA: 60.7
  Isobutyryl-CoA: 37.5
  Propionyl-CoA: 36.6
  Benzoyl-CoA: 31.8
  Ethylmalonyl-CoA: 28.9
  trans-1,2-CPDA: 24.0
  2-Methylbutyryl-CoA: 24.0
  Acetyl-CoA: 19.8
  CHC-CoA: 16.0
  3-Methylbutyryl-CoA: 10.2
  fatty_acid: 9.4

PKS_AT (2155..2447): mal
ATSignature: Malonyl-CoA, inactive

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 100.0%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 195.8
  inactive: 167.6
  Methoxymalonyl-CoA: 68.8
  Methylmalonyl-CoA: 52.8
  Isobutyryl-CoA: 28.2
  Propionyl-CoA: 27.4
  Benzoyl-CoA: 22.9
  Acetyl-CoA: 16.0
  Ethylmalonyl-CoA: 15.5
  2-Methylbutyryl-CoA: 15.4
  trans-1,2-CPDA: 14.5
  CHC-CoA: 12.0
  3-Methylbutyryl-CoA: 6.5
  fatty_acid: 0.0

FD723_RS36370: mal
PKS_AT (574..866): mal
ATSignature: Malonyl-CoA, inactive

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 100.0%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 198.2
  inactive: 165.4
  Methoxymalonyl-CoA: 73.7
  Methylmalonyl-CoA: 59.7
  Isobutyryl-CoA: 37.8
  Propionyl-CoA: 35.6
  Benzoyl-CoA: 30.8
  Acetyl-CoA: 24.8
  2-Methylbutyryl-CoA: 24.2
  trans-1,2-CPDA: 20.5
  CHC-CoA: 15.5
  Ethylmalonyl-CoA: 15.0
  3-Methylbutyryl-CoA: 11.7
  fatty_acid: 9.7

FD723_RS44290: mal
PKS_AT (571..765): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: inactive

Prediction, score:
  inactive: 57.0
  Malonyl-CoA: 40.2
  Benzoyl-CoA: 20.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

FD723_RS36375: mal
PKS_AT (1363..1659): mal
ATSignature: Malonyl-CoA, inactive

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 100.0%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 210.6
  inactive: 184.9
  Methoxymalonyl-CoA: 65.0
  Methylmalonyl-CoA: 62.8
  Isobutyryl-CoA: 43.7
  Propionyl-CoA: 41.2
  Benzoyl-CoA: 30.8
  Ethylmalonyl-CoA: 19.0
  2-Methylbutyryl-CoA: 16.6
  CHC-CoA: 16.0
  Acetyl-CoA: 13.1
  fatty_acid: 9.2
  trans-1,2-CPDA: 8.9
  3-Methylbutyryl-CoA: 8.5

FD723_RS44005: X
A-OX (558..1326): X
No predictions made
FD723_RS36400: X
AMP-binding (537..838): 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:
    HAMAFDISIWQTQILVTGEMNAYGPAECADDVTL
  Nearest Stachelhaus code(s):
    Dpr DIWELTADDK (76% 8Å match)
    Dab DIWELTADDK (74% 8Å match)
    dnmeProp or Dab DIWQSTADDK (62% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
MogR | Repressor of flagellar motility genes
NtrC | Nitrogen regulatory protein C
RutR | Regulator of the pyrimidine and purine metabolism
ToxT | Regulator of MSHA biosynthesis

NZ_CP040276.1 - 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: 50,107 - 73,763 nt. (total: 23,657 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: glycosyltransferase sulfotransferase
FD723_RS37720: Sulfotransferase domain

extras
  Sulfotransfer_1: Sulfotransferase domain

FD723_RS37725: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

FD723_RS37755: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

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
--- | --- | --- | --- | --- | ---
BGC0001164.3 |  | 0.56 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.56 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000734.3 |  | 0.43 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000794.5 |  | 0.43 | saccharide | S-layer glycan | Geobacillus stearothermophilus
BGC0000783.3 |  | 0.42 | saccharide | O-antigen | Xanthomonas oryzae pv. oryzae
BGC0000393.5 |  | 0.41 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0000735.3 |  | 0.40 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000504.5 |  | 0.40 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0002302.2 |  | 0.38 | saccharide | glucorhamnan | [Ruminococcus] gnavus ATCC 29149
BGC0000736.3 |  | 0.38 | saccharide | capsular polysaccharide | Mannheimia haemolytica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001164.3 |  | 0.56 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.56 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000734.3 |  | 0.43 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000794.5 |  | 0.43 | saccharide | S-layer glycan | Geobacillus stearothermophilus
BGC0000783.3 |  | 0.42 | saccharide | O-antigen | Xanthomonas oryzae pv. oryzae
BGC0000393.5 |  | 0.41 | NRPS, PKS | myxoprincomide-c506 | Myxococcus xanthus DK 1622
BGC0000735.3 |  | 0.40 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000504.5 |  | 0.40 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0002302.2 |  | 0.38 | saccharide | glucorhamnan | [Ruminococcus] gnavus ATCC 29149
BGC0000736.3 |  | 0.38 | saccharide | capsular polysaccharide | Mannheimia haemolytica

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
FD723_RS37735: T2TS
Domain 1 (702 - 991): Type 2 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.27 out of 26.06
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.54 out of 26.06
Confidence: medium
Additional weak hits (3):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.27 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.48 out of 31.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.25 out of 30.97
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MogR | Repressor of flagellar motility genes

NZ_CP040276.1 - 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: 82,054 - 126,889 nt. (total: 44,836 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
Lyases: dehydratase
FD723_RS37980: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
FD723_RS37915: 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
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.07 out of 26.06
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.11 out of 23.05
Confidence: medium
Additional weak hits (3):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.69 out of 39.62
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.64 out of 30.97
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 25.19 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 82053 - 126889:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ala)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
FD723_RS37915: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (42..443): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWATFDLSVFEVNTNLAGEFNLYGPTEDTTYSTF
  Nearest Stachelhaus code(s):
    Ala DLFNNALTYK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production
MogR | Repressor of flagellar motility genes