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
2.1
3.1
4.1
6.1

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

NC_010628.1 (Nostoc punctiforme PCC 73102 (Nostoc punctiforme ATCC 29133))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | hglE-KS,T1PKS | 41,892 | 94,238 | High | heterocyst glycolipids | other:other
Region 1.2 | T1PKS,hglE-KS | 1,540,661 | 1,591,247 | Medium | heterocyst glycolipids | other:other
Region 1.3 | T1PKS,NRPS-like | 2,503,324 | 2,568,631 | High | nostoclide N1/nostoclide N2 | other:other
Region 1.4 | T1PKS,NRPS,microviridin | 2,633,241 | 2,723,454 | High | nostopeptolide A2 | NRPS:Type I+PKS
Region 1.5 | NRPS,betalactone | 3,035,744 | 3,097,661 | High | anabaenopeptin | NRPS:Type I
Region 1.6 | lanthipeptide-class-v | 3,337,159 | 3,379,575 |
Region 1.7 | terpene | 3,407,916 | 3,446,813 | High | geosmin | terpene:Sesquiterpene
Region 1.8 | lanthipeptide-class-v | 3,490,154 | 3,532,515 | Low | anacyclamide A10 | ribosomal:RiPP:Cyanobactin
Region 1.9 | terpene | 3,596,279 | 3,617,109 |
Region 1.10 | NRPS,T1PKS | 3,702,118 | 3,800,010 | Low | nostophycin | NRPS:Type I+PKS
Region 1.11 | T1PKS,NRPS | 3,881,285 | 3,975,345 | Low | stigmatellin | NRPS:Type I+PKS:Type I
Region 1.12 | lanthipeptide-class-ii,proteusin,NAPAA | 3,979,164 | 4,032,282 | Low | landornamide A | ribosomal:RiPP
Region 1.13 | lanthipeptide-class-ii | 4,108,476 | 4,131,793 |
Region 1.14 | T1PKS,transAT-PKS-like,lanthipeptide-class-v,RRE-containing,spliceotide,NRP-metallophore,NRPS | 4,166,429 | 4,350,413 | Low | nostophycin | NRPS:Type I+PKS
Region 1.15 | terpene-precursor | 4,744,556 | 4,765,488 |
Region 1.16 | terpene | 4,829,312 | 4,850,283 |
Region 1.17 | lanthipeptide-class-ii | 6,241,419 | 6,264,724 | Low | nostolysamide A/nostolysamide B | ribosomal:RiPP
Region 1.18 | NRPS-like | 6,769,638 | 6,812,394 | Low | aeruginoside 126B/aeruginoside 126A | NRPS:Type I+PKS+saccharide:hybrid/tailoring
Region 1.19 | mycosporine | 6,889,563 | 6,934,355 | Low | hexose-palythine-serine/hexose-shinorine | NRPS:Type I
Region 1.20 | terpene | 7,714,881 | 7,736,797 | Low | hexose-palythine-serine/hexose-shinorine | NRPS:Type I
Region 1.21 | NRPS-like | 7,804,661 | 7,847,765 |
Region 1.22 | NRPS,T1PKS,NRPS-like | 8,130,738 | 8,187,006 | Low | nostopeptolide A2 | NRPS:Type I+PKS

NC_010631.1 (Nostoc punctiforme PCC 73102 (Nostoc punctiforme ATCC 29133))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | lanthipeptide-class-ii | 84,655 | 108,005 | High | nostolysamide A/nostolysamide B | ribosomal:RiPP

NC_010632.1 (Nostoc punctiforme PCC 73102 (Nostoc punctiforme ATCC 29133))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | terpene | 113,694 | 134,341 |

NC_010630.1 (Nostoc punctiforme PCC 73102 (Nostoc punctiforme ATCC 29133))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | NRPS,T1PKS | 62,034 | 3,789 | Low | cyanochelin A | NRPS:Type I+PKS

NC_010629.1 (Nostoc punctiforme PCC 73102 (Nostoc punctiforme ATCC 29133))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 6.1 | RiPP-like | 18,867 | 2,675 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | hglE-KS,T1PKS | 41,892 | 94,238 | High | heterocyst glycolipids | other:other
Region 1.2 | T1PKS,hglE-KS | 1,540,661 | 1,591,247 | Medium | heterocyst glycolipids | other:other
Region 1.3 | T1PKS,NRPS-like | 2,503,324 | 2,568,631 | High | nostoclide N1/nostoclide N2 | other:other
Region 1.4 | T1PKS,NRPS,microviridin | 2,633,241 | 2,723,454 | High | nostopeptolide A2 | NRPS:Type I+PKS
Region 1.5 | NRPS,betalactone | 3,035,744 | 3,097,661 | High | anabaenopeptin | NRPS:Type I
Region 1.6 | lanthipeptide-class-v | 3,337,159 | 3,379,575 |
Region 1.7 | terpene | 3,407,916 | 3,446,813 | High | geosmin | terpene:Sesquiterpene
Region 1.8 | lanthipeptide-class-v | 3,490,154 | 3,532,515 | Low | anacyclamide A10 | ribosomal:RiPP:Cyanobactin
Region 1.9 | terpene | 3,596,279 | 3,617,109 |
Region 1.10 | NRPS,T1PKS | 3,702,118 | 3,800,010 | Low | nostophycin | NRPS:Type I+PKS
Region 1.11 | T1PKS,NRPS | 3,881,285 | 3,975,345 | Low | stigmatellin | NRPS:Type I+PKS:Type I
Region 1.12 | lanthipeptide-class-ii,proteusin,NAPAA | 3,979,164 | 4,032,282 | Low | landornamide A | ribosomal:RiPP
Region 1.13 | lanthipeptide-class-ii | 4,108,476 | 4,131,793 |
Region 1.14 | T1PKS,transAT-PKS-like,lanthipeptide-class-v,RRE-containing,spliceotide,NRP-metallophore,NRPS | 4,166,429 | 4,350,413 | Low | nostophycin | NRPS:Type I+PKS
Region 1.15 | terpene-precursor | 4,744,556 | 4,765,488 |
Region 1.16 | terpene | 4,829,312 | 4,850,283 |
Region 1.17 | lanthipeptide-class-ii | 6,241,419 | 6,264,724 | Low | nostolysamide A/nostolysamide B | ribosomal:RiPP
Region 1.18 | NRPS-like | 6,769,638 | 6,812,394 | Low | aeruginoside 126B/aeruginoside 126A | NRPS:Type I+PKS+saccharide:hybrid/tailoring
Region 1.19 | mycosporine | 6,889,563 | 6,934,355 | Low | hexose-palythine-serine/hexose-shinorine | NRPS:Type I
Region 1.20 | terpene | 7,714,881 | 7,736,797 | Low | hexose-palythine-serine/hexose-shinorine | NRPS:Type I
Region 1.21 | NRPS-like | 7,804,661 | 7,847,765 |
Region 1.22 | NRPS,T1PKS,NRPS-like | 8,130,738 | 8,187,006 | Low | nostopeptolide A2 | NRPS:Type I+PKS
Region 2.1 | lanthipeptide-class-ii | 84,655 | 108,005 | High | nostolysamide A/nostolysamide B | ribosomal:RiPP
Region 3.1 | terpene | 113,694 | 134,341 |
Region 4.1 | NRPS,T1PKS | 62,034 | 3,789 | Low | cyanochelin A | NRPS:Type I+PKS
Region 6.1 | RiPP-like | 18,867 | 2,675 |

No secondary metabolite regions were found in these records:
  NC_010633.1 (Nostoc punctiforme PCC 73102 (Nostoc punctiforme ATCC 29133))

Compact view
NC_010628.1 - Region 1 - 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: 41,892 - 94,238 nt. (total: 52,347 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
NPUN_RS00205: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acylase glycosyltransferase
NPUN_RS00200: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

NPUN_RS00215: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

NPUN_RS00265: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Lyases: dehydratase
NPUN_RS00245: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
NPUN_RS00145: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

NPUN_RS00220: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

NPUN_RS00230: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | hglE-KS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000869.5 |  |  | 1.42 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001276.3 |  |  | 0.58 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.57 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001284.4 |  |  | 0.55 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002276.2 |  |  | 0.54 | NRPS | choline | Aspergillus nidulans FGSC A4
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
BGC0001257.3 |  |  | 0.52 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  |  | 0.51 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000869.5 |  | 0.89 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002276.2 |  | 0.61 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002648.2 |  | 0.60 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  | 0.60 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0000863.3 |  | 0.60 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0001257.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.59 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
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: 22.40 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.03 out of 26.06
Confidence: medium
Additional weak hits (3):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.61 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.96 out of 31.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.70 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 41891 - 94238:
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).
NPUN_RS00220: mxmal
PKS_AT (1085..1361): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 17.4
  Isobutyryl-CoA: 8.2
  Malonyl-CoA: 8.1
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-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

NPUN_RS00230: mal
PKS_AT (637..935): 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: 86.2
  inactive: 31.6
  Methoxymalonyl-CoA: 30.7
  Methylmalonyl-CoA: 23.5
  Isobutyryl-CoA: 15.1
  CHC-CoA: 14.5
  Propionyl-CoA: 11.8
  fatty_acid: 11.2
  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
--- | ---
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis

NC_010628.1 - Region 2 - 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: 1,540,661 - 1,591,247 nt. (total: 50,587 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))
hglE-KS: (hglE or hglD)

#### 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
NPUN_RS06660: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase glycosyltransferase
NPUN_RS06555: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

NPUN_RS06590: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: amidase hydrolase
NPUN_RS06645: HAD-superfamily hydrolase, subfamily IA, variant

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

NPUN_RS06670: amidase

smcogs
  SMCOG1105: amidase

Ligases: synthase
NPUN_RS06595: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS06600: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000869.5 |  |  | 0.57 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001284.4 |  |  | 0.55 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001244.3 |  |  | 0.55 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  |  | 0.55 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.55 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  |  | 0.54 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002648.2 |  |  | 0.52 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  |  | 0.52 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0001257.3 |  |  | 0.52 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  |  | 0.52 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001244.3 |  | 0.63 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000869.5 |  | 0.62 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002648.2 |  | 0.60 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  | 0.60 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0001257.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.59 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.94 out of 21.55
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 25.31
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 20.10 out of 21.84
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.76 out of 30.25
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.70 out of 32.93
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.70 out of 25.88
Confidence: medium
Additional weak hits (15):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.16 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.89 out of 30.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.29 out of 25.88
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.44 out of 30.22
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.44 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.18 out of 31.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.38 out of 29.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.70 out of 27.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.83 out of 39.62
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 24.68 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.40 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.88 out of 30.98
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.14 out of 22.40
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 24.28 out of 30.98
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 20.83 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 2, location 1540660 - 1591247:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 1540660 - 1583966:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 1544128 - 1591247:
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).
NPUN_RS06595: mxmal
PKS_AT (551..871): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 19.2
  Isobutyryl-CoA: 10.6
  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

NPUN_RS06600: mal
PKS_AT (631..929): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 110.9
  inactive: 46.0
  Methoxymalonyl-CoA: 36.9
  Methylmalonyl-CoA: 28.9
  CHC-CoA: 21.0
  fatty_acid: 10.7
  Isobutyryl-CoA: 10.0
  trans-1,2-CPDA: 0.0
  Propionyl-CoA: 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
--- | ---
ArcA | Repressor of carbon oxidation
CatR | H2O2-responsive repressor
ColR | Phenol-responsive regulator
LexA variant 3 | Repressor of DNA damage response
MexT | Global virulence regulator
PsrA | Oleic acid responsive regulator

NC_010628.1 - Region 3 - 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: 2,503,324 - 2,568,631 nt. (total: 65,308 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)

#### 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 oxidase oxygenase
NPUN_RS10395: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

NPUN_RS10490: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

NPUN_RS10540: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

NPUN_RS10555: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase
NPUN_RS10515: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase phosphatase
NPUN_RS10450: thioesterase

smcogs
  SMCOG1004: thioesterase

NPUN_RS10505: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Ligases: ligase synthase
NPUN_RS10390: 3-oxoacyl-(acyl carrier protein) synthase III

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

NPUN_RS10400: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

NPUN_RS10410: 3-oxoacyl-(acyl carrier protein) synthase III

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

NPUN_RS10415: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS10460: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS10465: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

NPUN_RS10470: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

NPUN_RS10475: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

NPUN_RS10485: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

NPUN_RS10510: 3-oxoacyl-(acyl carrier protein) synthase III

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

NPUN_RS10545: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002677.2 |  |  | 1.36 | other (other) | nostoclide N1, nostoclide N2 | Nostoc punctiforme PCC 73102
BGC0002711.2 |  |  | 1.28 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0001273.3 |  |  | 0.86 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.85 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  |  | 0.85 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001244.3 |  |  | 0.84 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  |  | 0.83 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001163.3 |  |  | 0.64 | PKS | 1-heptadecene | Moorea producens 3L
BGC0001254.3 |  |  | 0.60 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002191.2 |  |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002711.2 |  | 1.00 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0002677.2 |  | 0.95 | other (other) | nostoclide N1, nostoclide N2 | Nostoc punctiforme PCC 73102
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  | 0.74 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.73 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001163.3 |  | 0.65 | PKS | 1-heptadecene | Moorea producens 3L
BGC0002193.2 |  | 0.65 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001254.3 |  | 0.64 | PKS | ACT-Toxin II | Alternaria alternata

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

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: 21.64 out of 27.78
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.77 out of 20.97
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.26 out of 27.78
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.98 out of 25.88
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.70 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.17 out of 27.78
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.09 out of 26.85
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.74 out of 26.85
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.98 out of 26.85
Confidence: medium
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 22.86 out of 26.12
Confidence: medium
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 23.04 out of 29.25
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.35 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 28.19
Confidence: medium
Additional weak hits (13):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.85 out of 30.22
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.49 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.53 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.52 out of 26.06
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.72 out of 32.93
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.59 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.86 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.81 out of 26.06
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.71 out of 26.85
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.72 out of 32.93
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.12 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.79 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.88 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 5, location 2503323 - 2568631:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (NH2) + (ccmal) + (Me-ohmal) + (ccmal) + (pk)
Non-colinear ordering:
  NPUN_RS10485 + NPUN_RS10475 + NPUN_RS10470 + NPUN_RS10465 + NPUN_RS10460

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 2503323 - 2564381:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (NH2) + (ccmal) + (Me-ohmal) + (ccmal) + (pk)
Non-colinear ordering:
  NPUN_RS10485 + NPUN_RS10475 + NPUN_RS10470 + NPUN_RS10465 + NPUN_RS10460

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 2524776 - 2568631:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (NH2) + (ccmal) + (Me-ohmal) + (ccmal) + (pk)
Non-colinear ordering:
  NPUN_RS10485 + NPUN_RS10475 + NPUN_RS10470 + NPUN_RS10465 + NPUN_RS10460

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).
NPUN_RS10400: X
AMP-binding (13..405): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    NCALHCFGQNANFGFSAAAHEGYGLTETSPFAAY
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

NPUN_RS10460: pk
PKS_AT (579..846): pk
ATSignature: (unknown)
No matches above 50%
minowa: inactive

Prediction, score:
  inactive: 58.7
  Malonyl-CoA: 50.8
  Propionyl-CoA: 13.7
  Methoxymalonyl-CoA: 13.3
  Methylmalonyl-CoA: 12.9
  Isobutyryl-CoA: 10.4
  Acetyl-CoA: 10.2
  Benzoyl-CoA: 9.7
  2-Methylbutyryl-CoA: 9.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

NPUN_RS10465: mal
PKS_AT (592..884): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 192.8
  inactive: 130.3
  Methoxymalonyl-CoA: 51.2
  Methylmalonyl-CoA: 50.1
  Propionyl-CoA: 24.4
  Ethylmalonyl-CoA: 23.2
  Benzoyl-CoA: 22.9
  Isobutyryl-CoA: 20.9
  2-Methylbutyryl-CoA: 19.5
  fatty_acid: 16.1
  Acetyl-CoA: 13.9
  CHC-CoA: 9.9
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

NPUN_RS10470: mal
PKS_AT (566..859): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 197.3
  inactive: 126.0
  Methylmalonyl-CoA: 52.8
  Methoxymalonyl-CoA: 44.9
  Propionyl-CoA: 28.5
  2-Methylbutyryl-CoA: 19.2
  Isobutyryl-CoA: 17.5
  Benzoyl-CoA: 17.0
  Ethylmalonyl-CoA: 16.2
  Acetyl-CoA: 14.2
  CHC-CoA: 13.7
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

NPUN_RS10475: mal
PKS_AT (571..863): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 187.1
  inactive: 140.8
  Methylmalonyl-CoA: 50.7
  Methoxymalonyl-CoA: 50.7
  Propionyl-CoA: 28.6
  Acetyl-CoA: 22.2
  Isobutyryl-CoA: 22.0
  Benzoyl-CoA: 21.7
  2-Methylbutyryl-CoA: 19.2
  Ethylmalonyl-CoA: 16.2
  fatty_acid: 12.7
  CHC-CoA: 11.7
  trans-1,2-CPDA: 11.4
  3-Methylbutyryl-CoA: 0.0

NPUN_RS10485: NH2
CAL_domain (172..493): NH2
minowa: NH2

Prediction, score:
  NH2: 155.0
  Acetyl-CoA: 51.1
  AHBA: 12.2
  shikimic_acid: 10.1
  fatty_acid: -1.1

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
LuxO | Repressor of luminescence
MogR | Repressor of flagellar motility genes
PsrA | Oleic acid responsive regulator
RpoN | Regulator of nitrogen assimilation and virulence
RutR | Regulator of the pyrimidine and purine metabolism
SypG | Regulator of biofilm formation and host colonization
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NC_010628.1 - Region 4 - NRPS,T1PKS,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: 2,633,241 - 2,723,454 nt. (total: 90,214 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: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
microviridin: (mvd or mvnA)

#### 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
NPUN_RS10935: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

NPUN_RS10995: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

NPUN_RS11035: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: PPTase acylase
NPUN_RS10940: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

NPUN_RS10945: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: ligase synthase
NPUN_RS10970: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS10975: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

NPUN_RS40615: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS40620: 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 | T1PKS | NRPS | T1PKS | microviridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002049.3 |  |  |  |  | 2.00 | ribosomal | microviridin N9, microviridin N8, microviridin N7, microviridin N6, microviridin N5, microviridin N4, microviridin N3 | Nostoc punctiforme PCC 73102
BGC0001028.5 |  |  |  |  | 1.12 | NRPS, PKS | nostopeptolide A2 | Nostoc sp. GSV224
BGC0001758.4 |  |  |  |  | 0.93 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  |  |  |  | 0.89 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  |  | 0.89 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  |  | 0.85 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  |  |  |  | 0.85 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001135.5 |  |  |  |  | 0.84 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  |  |  | 0.84 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000593.4 |  |  |  |  | 0.84 | ribosomal | microviridin J | Microcystis aeruginosa MRC

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002049.3 |  | 1.00 | ribosomal | microviridin N9, microviridin N8, microviridin N7, microviridin N6, microviridin N5, microviridin N4, microviridin N3 | Nostoc punctiforme PCC 73102
BGC0001028.5 |  | 0.86 | NRPS, PKS | nostopeptolide A2 | Nostoc sp. GSV224
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000593.4 |  | 0.73 | ribosomal | microviridin J | Microcystis aeruginosa MRC

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: 22.87 out of 26.06
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.59 out of 25.88
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.01 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
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.15 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 25.86 out of 28.19
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.24 out of 27.04
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.21 out of 28.19
Confidence: medium
Additional weak hits (11):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.03 out of 32.74
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.07 out of 31.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.02 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.82 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.96 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.91 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.29 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.10 out of 31.73
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.87 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.10 out of 29.65
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.61 out of 28.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 8, location 2633240 - 2723454:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 2633240 - 2679933:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ile - Ser - X - Leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 2647204 - 2723454:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

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).
NPUN_RS10945: mal
PKS_AT (210..502): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 40.7
  Methoxymalonyl-CoA: 24.8
  Methylmalonyl-CoA: 19.4
  inactive: 9.3
  Benzoyl-CoA: 8.8
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-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

NPUN_RS10970: Ile - Ser - X - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (483..880): 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:
    LNTAFDAATFEGFLLFGGELHVYGPTENTTFSSW
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1574..1971): 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:
    RWMTFDVSVWEWHFICSGEHNLYGPTEAAIDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHISLIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2649..3075): X
nrpys: 4Me-Pro

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:
    LWHAFDVSFQETFLITAGEHNHYGPSESHLATSF
  Nearest Stachelhaus code(s):
    4Me-Pro DVQFIAHLAK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3757..4153): 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:
    LWHAFDAAVWEPFLLTGGDVNNYGPTENTVVTTS
  Nearest Stachelhaus code(s):
    Leu DAWFLGNVVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

NPUN_RS10975: mal
PKS_AT (557..853): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 87.5%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 178.0
  inactive: 122.0
  Methoxymalonyl-CoA: 74.3
  Methylmalonyl-CoA: 66.1
  Propionyl-CoA: 51.0
  Isobutyryl-CoA: 37.0
  Ethylmalonyl-CoA: 34.1
  2-Methylbutyryl-CoA: 32.1
  Benzoyl-CoA: 29.4
  CHC-CoA: 26.2
  Acetyl-CoA: 20.5
  trans-1,2-CPDA: 15.8
  fatty_acid: 12.8
  3-Methylbutyryl-CoA: 7.6

NPUN_RS40615: Leu - Gly - Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (537..957): 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:
    LWHAFDAAVWEPFLVTGGDVNNYGPTENTVVTTS
  Nearest Stachelhaus code(s):
    Leu DAWFVGNVVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1705..2121): 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:
    FSMTFDIAALELQALCGGEWNLYGPTETTIWSSI
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3256..3673): 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)

NPUN_RS40620: X - Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (469..889): 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:
    LAQAFDASISEMTLIVAGEFNAYGPTEASVCATI
  Nearest Stachelhaus code(s):
    Tyr or Pro DASTIAAVCK (100% 8Å match)
    Tyr DASTIAAVCK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1623..2038): Tyr
nrpys: Tyr

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:
    LWQAFDVSFQESFVITAGEHNHYGPSESHVIITF
  Nearest Stachelhaus code(s):
    Tyr DVQFIAHVIK (100% 8Å match)
    Pro DVQFIAHVIK (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
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
DasR | N-acetylglucosamine dependent repressor
MogR | Repressor of flagellar motility genes
PsrA | Oleic acid responsive regulator
RpoN | Regulator of nitrogen assimilation and virulence
ZuR variant 1 | Zinc-responsive repressor

NC_010628.1 - Region 5 - NRPS,betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,035,744 - 3,097,661 nt. (total: 61,918 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
betalactone: (HMGL-like and AMP-binding)

#### 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: aminotransferase glycosyltransferase
NPUN_RS12285: sugar transferase

smcogs
  SMCOG1146: sugar transferase

NPUN_RS12310: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: hydrolase
NPUN_RS12395: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: ligase synthase
NPUN_RS12350: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

NPUN_RS12355: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS12360: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS12365: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS12370: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

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

Reference | NRPS | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000301.5 |  |  | 0.94 | NRPS | anabaenopeptin 908, anabaenopeptin 915 | Planktothrix agardhii NIVA-CYA 126/8
BGC0001132.4 |  |  | 0.93 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  |  | 0.87 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000342.4 |  |  | 0.87 | NRPS | enniatin | Fusarium equiseti
BGC0001128.4 |  |  | 0.87 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.84 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.84 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  | 0.83 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  |  | 0.83 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  |  | 0.82 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000301.5 |  | 0.77 | NRPS | anabaenopeptin 908, anabaenopeptin 915 | Planktothrix agardhii NIVA-CYA 126/8
BGC0001132.4 |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000342.4 |  | 0.74 | NRPS | enniatin | Fusarium equiseti
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.73 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
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: 22.45 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.75 out of 28.19
Confidence: medium
Additional weak hits (5):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.78 out of 21.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.14 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.99 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.76 out of 28.14
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.45 out of 30.97
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 12, location 3035743 - 3097661:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe - D-Lys) + (Ile) + (X - NMe-Gly) + (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).
NPUN_RS12350: Phe - Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (46..436): 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:
    LAQAFDASVWEMTLIVAGEFNAYGPTESTICATV
  Nearest Stachelhaus code(s):
    Phe DAWTIAAICK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1111..1513): 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:
    FTAAFDASVEEPDLIIGGELNSYGPTEATVIATL
  Nearest Stachelhaus code(s):
    Lys DAEDIGSVIK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

NPUN_RS12355: Ile
Search NORINE for peptide: strict or relaxed
AMP-binding (469..867): 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:
    leu (Leu)

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

NPUN_RS12360: X - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (511..903): X
nrpys: Hph, Hty

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:
    LAWGFDLSIGETTLIVGGEFNCYGPTESTVIASI
  Nearest Stachelhaus code(s):
    Hph or Hty DLGTIGCVIK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1563..1969): 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:
    FSMTFDIAALELQALCGGEWNVYGPTETTIWSDI
  Nearest Stachelhaus code(s):
    Gly DILQLGVIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

NPUN_RS12365: X
AMP-binding (540..942): X
nrpys: Hph, Hty

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:
    LAWGFDLSIGETFLTVGGEFNCYGPTESTVNAAL
  Nearest Stachelhaus code(s):
    Hph or Hty DLGFTGCVNK (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
--- | ---
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NC_010628.1 - Region 6 - 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: 3,337,159 - 3,379,575 nt. (total: 42,417 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 oxidoreductase
NPUN_RS13675: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

NPUN_RS13705: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: glycosyltransferase
NPUN_RS13670: 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
--- | --- | --- | --- | --- | ---
BGC0000189.4 |  | 0.37 | 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
BGC0001304.3 |  | 0.37 | PKS | aflavarin | Aspergillus flavus NRRL3357
BGC0000709.5 |  | 0.34 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000430.5 |  | 0.34 | NRPS, PKS | spumigin E, Spumigin E | Nodularia spumigena CCY9414
BGC0001483.4 |  | 0.32 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001575.4 |  | 0.31 | NRPS | PZN5, PZN6, PZN7, PZN9, PZN10, PZN11 | Ruminococcus sp. 5_1_39BFAA
BGC0000689.3 |  | 0.30 | saccharide | 2-deoxystreptamine | Micromonospora echinospora
BGC0002713.2 |  | 0.30 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0001179.5 |  | 0.29 | PKS | rishirilide B, rishirilide A | Streptomyces bottropensis
BGC0002093.2 |  | 0.29 | NRPS, PKS | ilicicolin H | Talaromyces variabilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000189.4 |  | 0.37 | 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
BGC0001304.3 |  | 0.37 | PKS | aflavarin | Aspergillus flavus NRRL3357
BGC0000709.5 |  | 0.34 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000430.5 |  | 0.34 | NRPS, PKS | spumigin E, Spumigin E | Nodularia spumigena CCY9414
BGC0001483.4 |  | 0.32 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001575.4 |  | 0.31 | NRPS | PZN5, PZN6, PZN7, PZN9, PZN10, PZN11 | Ruminococcus sp. 5_1_39BFAA
BGC0000689.3 |  | 0.30 | saccharide | 2-deoxystreptamine | Micromonospora echinospora
BGC0002713.2 |  | 0.30 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0001179.5 |  | 0.29 | PKS | rishirilide B, rishirilide A | Streptomyces bottropensis
BGC0002093.2 |  | 0.29 | NRPS, PKS | ilicicolin H | Talaromyces variabilis

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:
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: 22.18 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.98 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.13 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.42 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.41 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.20 out of 27.78
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.13 out of 24.78
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.68 out of 27.04
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.88 out of 26.06
Confidence: medium
Additional weak hits (5):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.98 out of 26.12
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.37 out of 32.38
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.14 out of 25.88
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.51 out of 30.98
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
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
DasR | N-acetylglucosamine dependent repressor
LexA variant 2 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis

NC_010628.1 - Region 7 - 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: 3,407,916 - 3,446,813 nt. (total: 38,898 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
NPUN_RS13950: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

NPUN_RS14005: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: deacetylase
NPUN_RS14120: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

Lyases: cyclase
NPUN_RS13920: 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 |  | 0.58 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.44 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.43 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000664.5 |  | 0.42 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000641.3 |  | 0.42 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000642.3 |  | 0.42 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0001456.3 |  | 0.42 | terpene | isorenieratene | Streptomyces argillaceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.80 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000657.5 |  | 0.58 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.44 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.43 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000664.5 |  | 0.42 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000641.3 |  | 0.42 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000642.3 |  | 0.42 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0001456.3 |  | 0.42 | terpene | isorenieratene | Streptomyces argillaceus

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

No significant matches found.

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

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

Genes with terpene domains:
NPUN_RS13920: T1TS + T1TS
Domain 1 (1 - 331): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (332 - 711): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

NPUN_RS14000: PT_phytoene_like
Domain 1 (18 - 308): Prenyltransferase; Phytoene synthase like
Subtype: unknown

Reactions:
  FPP → diapophytoene
  FPP → squalene
  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:
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.60 out of 30.25
Confidence: medium
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: 23.99 out of 27.78
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.22 out of 23.43
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.55 out of 19.26
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.85 out of 20.97
Confidence: medium
Additional weak hits (7):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.20 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.48 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.84 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
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.92 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.04 out of 30.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.63 out of 26.12
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ColR | Phenol-responsive regulator
RpoN | Regulator of nitrogen assimilation and virulence

NC_010628.1 - Region 8 - 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: 3,490,154 - 3,532,515 nt. (total: 42,362 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
Transferases: glycosyltransferase
NPUN_RS14375: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

NPUN_RS14385: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: hydrolase peptidase
NPUN_RS14395: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

NPUN_RS14515: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

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
--- | --- | --- | --- | --- | ---
BGC0002701.2 |  | 0.46 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0002303.3 |  | 0.44 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000571.3 |  | 0.42 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0000517.4 |  | 0.41 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0000504.5 |  | 0.40 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0002284.3 |  | 0.40 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000711.5 |  | 0.39 | saccharide | neomycin | Streptomyces fradiae
BGC0001407.5 |  | 0.39 | ribosomal | bicereucin | Bacillus cereus SJ1
BGC0002130.3 |  | 0.38 | ribosomal | cacaoidin | Streptomyces cacaoi CA-170360

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002701.2 |  | 0.46 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0002303.3 |  | 0.44 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000571.3 |  | 0.42 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0000517.4 |  | 0.41 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0000504.5 |  | 0.40 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0002284.3 |  | 0.40 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000711.5 |  | 0.39 | saccharide | neomycin | Streptomyces fradiae
BGC0001407.5 |  | 0.39 | ribosomal | bicereucin | Bacillus cereus SJ1
BGC0002130.3 |  | 0.38 | ribosomal | cacaoidin | Streptomyces cacaoi CA-170360

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
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.64 out of 26.06
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 16.31 out of 18.16
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.90 out of 27.78
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.79 out of 21.84
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.06 out of 26.85
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.35 out of 29.72
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.36 out of 26.85
Confidence: medium
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
Additional weak hits (5):
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.57 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.61 out of 30.11
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 22.66 out of 26.12
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.50 out of 23.43
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
--- | ---
AbrC3 | Antibiotic production activator
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MexT | Global virulence 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

NC_010628.1 - Region 9 - 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: 3,596,279 - 3,617,109 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
--- | --- | --- | --- | --- | ---
BGC0001879.4 |  | 0.38 | other (other) | type R and F tailocins | Pseudomonas fluorescens
BGC0000017.5 |  | 0.23 | PKS, other (other) | anatoxin-a, homoanatoxin-a | [Oscillatoria] sp. PCC 6506

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001879.4 |  | 0.38 | other (other) | type R and F tailocins | Pseudomonas fluorescens
BGC0000017.5 |  | 0.23 | PKS, other (other) | anatoxin-a, homoanatoxin-a | [Oscillatoria] sp. PCC 6506

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:
NPUN_RS14870: PT_phytoene_like
Domain 1 (10 - 207): 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:
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 29.39 out of 32.74
Confidence: medium
Additional weak hits (9):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.32 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.78 out of 35.63
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.70 out of 28.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.40 out of 36.53
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.58 out of 31.73
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.21 out of 27.55
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 24.68 out of 30.98
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.46 out of 36.53
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
FuR variant 2 | Ferric Uptake Regulator

NC_010628.1 - Region 10 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,702,118 - 3,800,010 nt. (total: 97,893 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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: acyltransferase
NPUN_RS15375: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Ligases: ligase synthase
NPUN_RS15370: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS15380: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

NPUN_RS43285: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  | 1.31 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  | 1.27 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 1.23 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  | 1.23 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  |  | 1.22 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  |  | 1.20 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  |  | 1.20 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  |  | 1.19 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  |  |  | 1.14 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000342.4 |  |  |  | 1.13 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.78 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  | 0.73 | NRPS | HC-toxin | Alternaria jesenskae

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: 22.42 out of 26.06
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.52 out of 27.55
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 25.28 out of 27.78
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.22 out of 27.78
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.18 out of 21.55
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.34 out of 32.93
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.67 out of 26.06
Confidence: medium
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.02 out of 29.38
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.07 out of 39.62
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.87 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.84 out of 23.43
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.86 out of 27.18
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.99 out of 36.53
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 16.71 out of 20.47
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 17, location 3702117 - 3800010:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - mal - Orn - D-Phe) + (D-Thr - D-Leu - D-Ala) + (Thr - Phe - Ile) + (ohmal) + (D-X - D-Thr - Orn)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
NPUN_RS43285: X - Thr - Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (507..909): 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:
    FAAAFDVAAEEPDLIIGGEINAYGPTETTVEATV
  Nearest Stachelhaus code(s):
    Lys or Arg DVEDIGSVAK (82% 8Å match)
    Arg DVGDIGAVTK (76% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2047..2455): 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 (3581..3988): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAWAFDVFSGDREFIVGSDINSYGVTEATIDSSY
  Nearest Stachelhaus code(s):
    Orn DVGEIGSIDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

NPUN_RS15370: mal
PKS_AT (537..833): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 159.4
  inactive: 104.2
  Methoxymalonyl-CoA: 68.4
  Methylmalonyl-CoA: 56.6
  Propionyl-CoA: 39.7
  Ethylmalonyl-CoA: 33.4
  Benzoyl-CoA: 30.0
  Isobutyryl-CoA: 27.2
  CHC-CoA: 23.1
  2-Methylbutyryl-CoA: 22.9
  Acetyl-CoA: 20.2
  fatty_acid: 18.6
  trans-1,2-CPDA: 14.3
  3-Methylbutyryl-CoA: 0.0

NPUN_RS15375: Thr - Phe - Ile
Search NORINE for peptide: strict or relaxed
AMP-binding (476..884): 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 (1561..1959): 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:
    LAQAFDASIWEMTLIVAGEFNAYGPTETTVCATV
  Nearest Stachelhaus code(s):
    Phe DAWTIAAVCK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2621..3018): 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:
    LNTAFDAATFEGFLLFGGELHVYGPTESTTFSSW
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

NPUN_RS15380: Thr - Leu - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (484..892): 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 (2015..2422): 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:
    LWHAFDASVWEPFVLTGGDVNNYGPTENTVVTTS
  Nearest Stachelhaus code(s):
    Leu DAWFLGNVVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3555..3959): 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)

NPUN_RS42520: NH2 - mal - Orn - Phe
Search NORINE for peptide: strict or relaxed
CAL_domain (39..482): NH2
minowa: NH2

Prediction, score:
  NH2: 174.8
  AHBA: 22.3
  fatty_acid: 9.5
  shikimic_acid: 0.0
  Acetyl-CoA: -0.5

PKS_AT (1647..1952): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 203.6
  inactive: 165.3
  Methylmalonyl-CoA: 62.9
  Methoxymalonyl-CoA: 61.2
  Propionyl-CoA: 36.4
  Isobutyryl-CoA: 35.1
  2-Methylbutyryl-CoA: 24.3
  Ethylmalonyl-CoA: 19.8
  Acetyl-CoA: 17.9
  Benzoyl-CoA: 17.0
  trans-1,2-CPDA: 14.6
  3-Methylbutyryl-CoA: 13.4
  fatty_acid: 0.0
  CHC-CoA: 0.0

AMP-binding (3219..3626): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AGWAFDVFTGDREFAVGSDINSYGVSEATIDSCY
  Nearest Stachelhaus code(s):
    Orn DVGEVGSIDK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4289..4693): 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:
    LAQAFDASIWEMTLIVAGEFNAYGPTETTVCATV
  Nearest Stachelhaus code(s):
    Phe DAWTIAAVCK (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
--- | ---
ArcA | Repressor of carbon oxidation
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
GnfM | Regulator of nitrogen-fixation genes
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes

NC_010628.1 - Region 11 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,881,285 - 3,975,345 nt. (total: 94,061 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: 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
NPUN_RS16010: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: esterase
NPUN_RS15985: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: hydratase
NPUN_RS16020: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

NPUN_RS16025: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
NPUN_RS15975: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

NPUN_RS16000: 1-deoxy-D-xylulose-5-phosphate synthase

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

NPUN_RS16005: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS16015: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

NPUN_RS16045: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS16050: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS16055: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

NPUN_RS16060: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

NPUN_RS37685: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.87 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  | 0.85 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  | 0.84 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  |  | 0.72 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0001758.4 |  |  | 0.62 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  |  | 0.61 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.61 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002192.3 |  | 0.64 | PKS | FR901512 | fungal sp. No.14919
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.99 out of 27.55
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.99 out of 27.78
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: 23.58 out of 27.78
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 25.31
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.10 out of 29.38
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.61 out of 28.19
Confidence: medium
Additional weak hits (4):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.65 out of 21.55
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.97 out of 25.88
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.03 out of 26.12
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 18, location 3881284 - 3975345:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-ohmal) + (ccmal) + (ohmal) + (mal - ccmal) + (ohmal) + (ccmal) + (pk) + (Cys)

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).
NPUN_RS15975: mmal
PKS_AT (595..892): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Malonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 176.4
  Ethylmalonyl-CoA: 152.1
  Methoxymalonyl-CoA: 133.4
  Malonyl-CoA: 112.5
  Benzoyl-CoA: 111.3
  Isobutyryl-CoA: 109.3
  2-Methylbutyryl-CoA: 104.2
  trans-1,2-CPDA: 91.4
  Propionyl-CoA: 87.0
  CHC-CoA: 82.0
  Acetyl-CoA: 62.7
  3-Methylbutyryl-CoA: 45.0
  inactive: 40.0
  fatty_acid: 35.8

NPUN_RS16005: mal
PKS_AT (576..875): 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: 194.6
  inactive: 162.8
  Methoxymalonyl-CoA: 72.4
  Methylmalonyl-CoA: 67.5
  Ethylmalonyl-CoA: 36.7
  Benzoyl-CoA: 31.8
  Isobutyryl-CoA: 30.6
  Propionyl-CoA: 27.2
  CHC-CoA: 21.1
  2-Methylbutyryl-CoA: 18.1
  fatty_acid: 17.9
  trans-1,2-CPDA: 17.2
  Acetyl-CoA: 14.4
  3-Methylbutyryl-CoA: 12.8

NPUN_RS16010: mal - pk
PKS_AT (571..878): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  Methylmalonyl-CoA: 70.8%
  Ethylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 129.4
  Methylmalonyl-CoA: 120.3
  Isobutyryl-CoA: 107.8
  Methoxymalonyl-CoA: 104.8
  Benzoyl-CoA: 82.9
  Ethylmalonyl-CoA: 73.9
  2-Methylbutyryl-CoA: 73.0
  Acetyl-CoA: 68.9
  Propionyl-CoA: 68.4
  CHC-CoA: 49.4
  inactive: 46.2
  trans-1,2-CPDA: 42.6
  fatty_acid: 26.9
  3-Methylbutyryl-CoA: 26.2

PKS_AT (2048..2242): pk
ATSignature: (unknown)
No matches above 50%
minowa: inactive

Prediction, score:
  inactive: 39.3
  Malonyl-CoA: 28.3
  Isobutyryl-CoA: 10.9
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-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

NPUN_RS37685: mal - mal
PKS_AT (550..842): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 70.8%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 139.5
  inactive: 119.0
  Methoxymalonyl-CoA: 60.8
  Methylmalonyl-CoA: 60.4
  Isobutyryl-CoA: 41.1
  Propionyl-CoA: 34.0
  Ethylmalonyl-CoA: 28.9
  2-Methylbutyryl-CoA: 28.3
  Acetyl-CoA: 22.9
  Benzoyl-CoA: 22.5
  CHC-CoA: 15.9
  3-Methylbutyryl-CoA: 13.8
  trans-1,2-CPDA: 10.5
  fatty_acid: 0.0

PKS_AT (1565..1864): 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: 187.1
  inactive: 163.0
  Methoxymalonyl-CoA: 65.2
  Methylmalonyl-CoA: 62.9
  Isobutyryl-CoA: 37.9
  Propionyl-CoA: 31.5
  Benzoyl-CoA: 31.0
  Ethylmalonyl-CoA: 27.2
  trans-1,2-CPDA: 20.1
  fatty_acid: 18.6
  Acetyl-CoA: 17.6
  2-Methylbutyryl-CoA: 16.0
  CHC-CoA: 14.3
  3-Methylbutyryl-CoA: 11.5

NPUN_RS16045: mal
PKS_AT (575..874): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 184.3
  inactive: 141.1
  Methoxymalonyl-CoA: 70.4
  Methylmalonyl-CoA: 65.7
  Isobutyryl-CoA: 36.2
  Ethylmalonyl-CoA: 29.0
  Benzoyl-CoA: 27.7
  Propionyl-CoA: 27.5
  Acetyl-CoA: 19.4
  trans-1,2-CPDA: 18.8
  CHC-CoA: 16.9
  2-Methylbutyryl-CoA: 15.1
  fatty_acid: 14.7
  3-Methylbutyryl-CoA: 12.8

NPUN_RS16050: mal
PKS_AT (583..882): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 184.3
  inactive: 141.1
  Methoxymalonyl-CoA: 70.4
  Methylmalonyl-CoA: 65.7
  Isobutyryl-CoA: 36.2
  Ethylmalonyl-CoA: 29.0
  Benzoyl-CoA: 27.7
  Propionyl-CoA: 27.5
  Acetyl-CoA: 19.4
  trans-1,2-CPDA: 18.8
  CHC-CoA: 16.9
  2-Methylbutyryl-CoA: 15.1
  fatty_acid: 14.7
  3-Methylbutyryl-CoA: 12.8

NPUN_RS16055: pk
PKS_AT (562..857): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  Methylmalonyl-CoA: 70.8%
  Propionyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 134.5
  Malonyl-CoA: 129.5
  Methoxymalonyl-CoA: 118.2
  Isobutyryl-CoA: 104.6
  Ethylmalonyl-CoA: 94.5
  2-Methylbutyryl-CoA: 80.8
  Propionyl-CoA: 77.1
  Benzoyl-CoA: 73.6
  CHC-CoA: 66.9
  trans-1,2-CPDA: 46.8
  Acetyl-CoA: 45.2
  inactive: 41.2
  fatty_acid: 40.2
  3-Methylbutyryl-CoA: 38.7

NPUN_RS16060: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (546..947): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNSMMSGDISLGGATEASIWSIF
  Nearest Stachelhaus code(s):
    Cys DLYNMSLIWK (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
--- | ---
ANR | Anaerobic transcriptional regulator
CatR | H2O2-responsive repressor
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
GnfM | Regulator of nitrogen-fixation genes
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NC_010628.1 - Region 12 - NAPAA,lanthipeptide-class-ii,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: 3,979,164 - 4,032,282 nt. (total: 53,119 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)
proteusin: (PoyD or TIGR03793)
NAPAA: (AMP-binding and TIGR02353)

#### 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
NPUN_RS16225: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: cyclase
NPUN_RS16220: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: ligase
NPUN_RS16330: 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 | lanthipeptide-class-ii | proteusin | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002699.2 |  |  |  | 0.56 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0002330.2 |  |  |  | 0.43 | ribosomal | landornamide A | Kamptonema sp. PCC 6506
BGC0002174.2 |  |  |  | 0.42 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0000554.4 |  |  |  | 0.41 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001229.4 |  |  |  | 0.41 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0001210.5 |  |  |  | 0.38 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000525.5 |  |  |  | 0.36 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000527.5 |  |  |  | 0.34 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0002663.2 |  |  |  | 0.32 | ribosomal | amyloliquecidin GF610 | Bacillus amyloliquefaciens UMAF6639
BGC0000502.5 |  |  |  | 0.32 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.73 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0002699.2 |  | 0.63 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.60 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.60 | 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.

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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.83 out of 26.33
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.04 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.93 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.10 out of 26.06
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 16.78 out of 18.16
Confidence: strong
Additional weak hits (3):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 25.11 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
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 19, location 3979163 - 4032282:
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

For candidate cluster 22, location 3998271 - 4032282:
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).
NPUN_RS16330: X
AMP-binding (40..431): 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:
    FICIFDFSFEEPYCIVGGELNTYGPTETTITALW
  Nearest Stachelhaus code(s):
    Lys DIESIGTVTK (62% 8Å match)
    Arg DAEDIGAITK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

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
MogR | Repressor of flagellar motility genes

NC_010628.1 - Region 13 - 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: 4,108,476 - 4,131,793 nt. (total: 23,318 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
Lyases: cyclase
NPUN_RS16790: 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
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002704.2 |  | 0.46 | ribosomal | archalan β | Halorussus salinus
BGC0000528.5 |  | 0.45 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002703.2 |  | 0.45 | ribosomal | archalan α | Halorussus salinus
BGC0002699.2 |  | 0.44 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0000554.4 |  | 0.43 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002698.2 |  | 0.39 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000527.5 |  | 0.39 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000517.4 |  | 0.38 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002704.2 |  | 0.46 | ribosomal | archalan β | Halorussus salinus
BGC0000528.5 |  | 0.45 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002703.2 |  | 0.45 | ribosomal | archalan α | Halorussus salinus
BGC0002699.2 |  | 0.44 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0000554.4 |  | 0.43 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002698.2 |  | 0.39 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000527.5 |  | 0.39 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000517.4 |  | 0.38 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125

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

No significant matches found.

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

No significant matches found.

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

#### Lanthipeptide(s) for NPUN_RS16790

allorf_4110968_4111171
Leader:
MGYITRRLGNIISGLHQLIAM
Core:
V S K F V V R T L V L T T N L K T S G S K V L G N H G W L F P S C Q F A D L G D L L D N S D
Core with dehydrations:
V Dha K F V V R Dhb L V L Dhb Dhb N L K Dhb Dha G Dha K V L G N H G W L F P Dha Cys Q F A D L G D L L D N Dha D

#### antiSMASH-DB 4.0 matches for allorf_4110968_4111171

100.0%
NC_010628.1:
Lanthipeptides: allorf_4110968_4111171_lanthipeptide
1
V S K F V V R T L V L T T N L K T S G S K V L G N H G W L F P S C Q F A D L G D L L D N S D
46
V S K F V V R T L V L T T N L K T S G S K V L G N H G W L F P S C Q F A D L G D L L D N S D
1
V S K F V V R T L V L T T N L K T S G S K V L G N H G W L F P S C Q F A D L G D L L D N S D
46
28.3%
NZ_CP009280.1 and 1 other:
NZ_CP009280.1 Lanthipeptides: P40081_RS01820_lanthipeptide
Lanthipeptides: P40081_RS01820_lanthipeptide
8
T L V L T T N L K T S G S K V L G N H G W L-------F P S C Q
34
T L T T+ S+ L G N G W+ P S C
3
T N T L T T S T S I F I S R G L G N D G W V C T W S K E C M P S C N
36
26.1%
NZ_CP009288.1 and 3 others:
NZ_CP009288.1 Lanthipeptides: PDUR_RS25150_lanthipeptide NZ_CP076607.1 Lanthipeptides: KP014_RS01580_lanthipeptide NZ_CP076607.1 Lanthipeptides: KP014_RS01580_lanthipeptide
Lanthipeptides: PDUR_RS25150_lanthipeptide
10
V L T T N L K T S G S K V L G N H G W L-------F P S C Q
34
L T T+ S L G N+G W+ P S C
5
T L T T S T S I L I S M T L G N N G W V C T A T K E C M P S C N
36
with 3 more sequence matches
23.9%
NZ_NTWJ01000043.1 and 5 others:
NZ_NTWJ01000043.1 Lanthipeptides: CN427_RS29365_lanthipeptide NZ_NTWJ01000043.1 Lanthipeptides: CN427_RS29360_lanthipeptide NZ_NTWJ01000043.1 Lanthipeptides: CN427_RS29370_lanthipeptide NZ_NTWJ01000043.1 Lanthipeptides: CN427_RS29365_lanthipeptide NZ_NTWJ01000043.1 Lanthipeptides: CN427_RS29360_lanthipeptide
Lanthipeptides: CN427_RS29370_lanthipeptide
10
V L T T N L K T S G S K V L G N H G
27
V L T T L G S L G N G
9
V L T T L L C F V G S Y T L G N D G
26
21.7%
NC_006322.1 and 7 others:
NC_006322.1 Lanthipeptides: BLI_RS20295_lanthipeptide NZ_CP033218.1 Lanthipeptides: D9Y32_RS07805_lanthipeptide NZ_CP033218.1 Lanthipeptides: D9Y32_RS07805_lanthipeptide NZ_LQYL01000021.1 Lanthipeptides: B4090_RS08835_lanthipeptide NZ_LQYL01000021.1 Lanthipeptides: B4090_RS08835_lanthipeptide NZ_NIMP01000036.1 Lanthipeptides: CHCC14566_RS11865_lanthipeptide NZ_NIMP01000036.1 Lanthipeptides: CHCC14566_RS11865_lanthipeptide
Lanthipeptides: BLI_RS20295_lanthipeptide
20
S K V L G N H G W L-------F P S C Q
34
S K L G N+G+L P S C
11
S K P L G N N G Y L C T V T K E C M P S C N
32
17.4%
NC_018089.1 and 13 others:
NC_018089.1 Lanthipeptides: SMUGS5_RS08725_lanthipeptide NZ_CP043405.1 Lanthipeptides: FY406_RS04355_lanthipeptide NZ_CP043405.1 Lanthipeptides: FY406_RS04355_lanthipeptide NZ_CP044493.1 Lanthipeptides: FSA40_RS09065_lanthipeptide NZ_CP044493.1 Lanthipeptides: FSA40_RS09065_lanthipeptide NZ_CP050270.1 Lanthipeptides: HB753_RS00325_lanthipeptide NZ_CP050270.1 Lanthipeptides: HB753_RS00325_lanthipeptide NZ_JADPAN010000004.1 Lanthipeptides: I4U28_RS03985_lanthipeptide NZ_JADPAN010000004.1 Lanthipeptides: I4U28_RS03985_lanthipeptide NZ_JALDUN010000005.1 Lanthipeptides: M1F82_RS08120_lanthipeptide NZ_JALDUN010000005.1 Lanthipeptides: M1F82_RS08120_lanthipeptide NZ_JAQCYD010000003.1 Lanthipeptides: PGX70_RS05515_lanthipeptide NZ_JAQCYD010000003.1 Lanthipeptides: PGX70_RS05515_lanthipeptide
Lanthipeptides: SMUGS5_RS08725_lanthipeptide
12
T T N L K T S G S K V L G N H G W L
29
T T + ++ S V L G N G++
3
T T V V N S T F S I V L G N K G Y I
20

#### MIBiG 4.0 matches for allorf_4110968_4111171

19.6%
BGC0002110.3 (QKV49893.1):
Lanthipeptide: birimositide
11
L T T N L K T S G S K V L G N H G W--L F P S C Q
34
T T N + + + N G W L C Q
1
C T T N T F S L S N A L G N N G G W C T L T K E C Q
26
allorf_4111164_4111226
Leader:
MIKEASACCGS
Core:
R S C L A G S G S
Core with dehydrations:
R Dha Cys L A G Dha G Dha

#### antiSMASH-DB 4.0 matches for allorf_4111164_4111226

100.0%
NC_010628.1:
Lanthipeptides: allorf_4111164_4111226_lanthipeptide
1
R S C L A G S G S
9
R S C L A G S G S
1
R S C L A G S G S
9
10.0%
NZ_JACHGN010000015.1:
Lanthipeptides: allorf_120347_120571_lanthipeptide
1
R S C L A G S G S
9
R+C A G+G S
36
R A C T A G A G S
44
allorf_4116120_4116236
Leader:
MDHLISGNSLTSSVKKIYLDFLFIQASELGT
Core:
S S F L L E C
Core with dehydrations:
Dha Dha F L L E Cys

#### antiSMASH-DB 4.0 matches for allorf_4116120_4116236

100.0%
NC_010628.1:
Lanthipeptides: allorf_4116120_4116236_lanthipeptide
1
S S F L L E C
7
S S F L L E C
1
S S F L L E C
7

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.89 out of 23.79
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.22 out of 23.43
Confidence: medium
Additional weak hits (4):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.93 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.55 out of 29.38
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.97 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.56 out of 33.14
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_4110968_4111171 - Class II
  Cleavage pHMM score: -2.30
  RODEO score: 0
  Monoisotopic mass: 4829.6 Da
  Molecular weight: 4832.5 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4850.5 Da N = 1
    4868.5 Da N = 2
    4886.5 Da N = 3
    4904.5 Da N = 4
    4922.6 Da N = 5
    4940.6 Da N = 6
    4958.6 Da N = 7
    4976.6 Da N = 8
allorf_4111164_4111226 - Class II
  Cleavage pHMM score: -4.80
  RODEO score: 0
  Monoisotopic mass: 782.4 Da
  Molecular weight: 782.9 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    800.9 Da N = 1
    818.9 Da N = 2
allorf_4116120_4116236 - Class II
  Cleavage pHMM score: -6.40
  RODEO score: 0
  Monoisotopic mass: 761.4 Da
  Molecular weight: 761.9 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    779.9 Da N = 1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
IolR | Regulator of the inositol catabolism

NC_010628.1 - Region 14 - NRP-metallophore,NRPS,RRE-containing,T1PKS,lanthipeptide-class-v,spliceotide,transAT-PKS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,166,429 - 4,350,413 nt. (total: 183,985 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))
transAT-PKS-like: cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS) and not PKS_AT)
lanthipeptide-class-v: (APH and HopA1)
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])
spliceotide: (TIGR04103 and TIGR03798)
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
binding site
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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 oxidase oxidoreductase oxygenase
NPUN_RS17040: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

NPUN_RS17045: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

NPUN_RS17050: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

NPUN_RS17305: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

NPUN_RS17315: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

NPUN_RS17335: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

NPUN_RS17380: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

NPUN_RS17395: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

NPUN_RS17405: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

NPUN_RS17435: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

NPUN_RS17450: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Transferases: acylase aminotransferase glycosyltransferase methyltransferase
NPUN_RS17020: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

NPUN_RS17065: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

NPUN_RS17310: methyltransferase

smcogs
  SMCOG1248: methyltransferase

NPUN_RS17350: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

NPUN_RS17365: methyltransferase

smcogs
  SMCOG1248: methyltransferase

NPUN_RS17425: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

NPUN_RS17430: methyltransferase

smcogs
  SMCOG1248: methyltransferase

NPUN_RS17440: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

NPUN_RS17485: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

NPUN_RS37760: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase phosphatase
NPUN_RS17000: thioesterase

smcogs
  SMCOG1004: thioesterase

NPUN_RS17290: thioesterase

smcogs
  SMCOG1004: thioesterase

NPUN_RS17390: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

NPUN_RS44140: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

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

Lyases: dehydratase
NPUN_RS17055: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
NPUN_RS17005: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

NPUN_RS17025: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

NPUN_RS17030: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS17320: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS17330: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS17340: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS17345: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS17355: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS17360: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS17370: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS17375: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

NPUN_RS17385: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS17420: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

NPUN_RS17445: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS17455: 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 | T1PKS | transAT-PKS-like | lanthipeptide-class-v | RRE-containing | spliceotide | T1PKS | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001164.3 |  |  |  |  |  |  |  |  | 1.81 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  |  |  |  |  |  | 1.80 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001254.3 |  |  |  |  |  |  |  |  | 1.54 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001276.3 |  |  |  |  |  |  |  |  | 1.52 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  |  |  |  |  |  |  | 1.52 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002191.2 |  |  |  |  |  |  |  |  | 1.51 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001244.3 |  |  |  |  |  |  |  |  | 1.51 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001273.3 |  |  |  |  |  |  |  |  | 1.50 | PKS | asperlactone | Aspergillus ochraceus
BGC0000107.3 |  |  |  |  |  |  |  |  | 1.50 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001257.3 |  |  |  |  |  |  |  |  | 1.50 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.72 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001164.3 |  | 0.70 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001160.5 |  | 0.70 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001825.4 |  | 0.70 | 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.

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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.13 out of 27.78
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.81 out of 32.93
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 16.69 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
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
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.69 out of 26.06
Confidence: medium
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 25.79 out of 29.25
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.33 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.43 out of 29.38
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.76 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.93 out of 26.06
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.08 out of 29.38
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
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.73 out of 28.19
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.58 out of 24.78
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 16.33 out of 18.16
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 16.60 out of 18.16
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.10 out of 26.06
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.11 out of 28.19
Confidence: medium
Additional weak hits (21):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.49 out of 30.22
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.22 out of 25.88
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.10 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.07 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.59 out of 30.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.62 out of 21.55
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.50 out of 23.43
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 26.77 out of 31.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.62 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.83 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.32 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.93 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.93 out of 30.25
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.15 out of 30.98
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.98 out of 29.25
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.99 out of 20.01
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.06 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.54 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
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.
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 4166428 - 4220200:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ohmal) + (redmal) + (mal)
Non-colinear ordering:
  NPUN_RS17020 + NPUN_RS17025 + NPUN_RS17030

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 25, location 4166428 - 4217833:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ohmal) + (redmal) + (mal)
Non-colinear ordering:
  NPUN_RS17020 + NPUN_RS17025 + NPUN_RS17030

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 26, location 4177878 - 4220200:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ohmal) + (redmal) + (mal)
Non-colinear ordering:
  NPUN_RS17020 + NPUN_RS17025 + NPUN_RS17030

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 27, location 4214161 - 4350413:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid) + (Asn) + (mal) + (D-Asn) + (Asp) + (mal) + (Thr) + (Me-ohmal) + (His) + (mal) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 31, location 4243099 - 4350413:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid) + (Asn) + (mal) + (D-Asn) + (Asp) + (mal) + (Thr) + (Me-ohmal) + (His) + (mal) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 32, location 4253514 - 4350413:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid) + (Asn) + (mal) + (D-Asn) + (Asp) + (mal) + (Thr) + (Me-ohmal) + (His) + (mal) + (ohmal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
NPUN_RS17005: NH2
CAL_domain (46..491): NH2
minowa: NH2

Prediction, score:
  NH2: 185.9
  fatty_acid: 34.0
  AHBA: 20.3
  Acetyl-CoA: 2.5
  shikimic_acid: -0.1

NPUN_RS17020: mal
PKS_AT (536..831): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 95.8%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 209.8
  inactive: 184.7
  Methoxymalonyl-CoA: 69.0
  Methylmalonyl-CoA: 57.2
  Isobutyryl-CoA: 39.7
  Propionyl-CoA: 32.6
  Benzoyl-CoA: 31.2
  Acetyl-CoA: 22.0
  Ethylmalonyl-CoA: 20.3
  3-Methylbutyryl-CoA: 17.7
  2-Methylbutyryl-CoA: 17.1
  CHC-CoA: 9.6
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0

NPUN_RS17025: mal
PKS_AT (578..872): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 95.8%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 204.0
  inactive: 174.7
  Methoxymalonyl-CoA: 67.0
  Methylmalonyl-CoA: 54.5
  Isobutyryl-CoA: 32.5
  Propionyl-CoA: 26.6
  Benzoyl-CoA: 24.8
  Acetyl-CoA: 20.8
  Ethylmalonyl-CoA: 20.5
  3-Methylbutyryl-CoA: 17.5
  2-Methylbutyryl-CoA: 15.6
  CHC-CoA: 9.5
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0

NPUN_RS17320: mal
PKS_AT (539..825): 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: 164.7
  inactive: 115.3
  Methoxymalonyl-CoA: 79.9
  Methylmalonyl-CoA: 65.3
  Propionyl-CoA: 44.4
  Ethylmalonyl-CoA: 40.6
  2-Methylbutyryl-CoA: 31.5
  Benzoyl-CoA: 28.2
  Isobutyryl-CoA: 24.5
  Acetyl-CoA: 21.9
  CHC-CoA: 21.5
  trans-1,2-CPDA: 11.6
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

NPUN_RS37760: mal
PKS_AT (538..831): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 177.7
  inactive: 102.0
  Methoxymalonyl-CoA: 74.8
  Methylmalonyl-CoA: 65.9
  Propionyl-CoA: 53.1
  Ethylmalonyl-CoA: 40.3
  Isobutyryl-CoA: 35.2
  2-Methylbutyryl-CoA: 29.6
  Benzoyl-CoA: 24.8
  trans-1,2-CPDA: 23.7
  CHC-CoA: 20.4
  Acetyl-CoA: 9.8
  fatty_acid: 8.3
  3-Methylbutyryl-CoA: 7.6

NPUN_RS17330: His
Search NORINE for peptide: strict or relaxed
AMP-binding (466..866): His
nrpys: His

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    SARSFDSSVAGWLSIVAGEFNEYGPTEGTVWSSV
  Nearest Stachelhaus code(s):
    His DSALIAEVWK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

NPUN_RS17345: mal
PKS_AT (542..828): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 83.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 175.6
  inactive: 127.8
  Methoxymalonyl-CoA: 68.8
  Methylmalonyl-CoA: 68.5
  Propionyl-CoA: 57.2
  Ethylmalonyl-CoA: 42.3
  2-Methylbutyryl-CoA: 35.4
  Isobutyryl-CoA: 34.0
  Benzoyl-CoA: 32.9
  CHC-CoA: 26.5
  Acetyl-CoA: 23.7
  fatty_acid: 16.0
  trans-1,2-CPDA: 11.6
  3-Methylbutyryl-CoA: 7.4

NPUN_RS17350: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (1120..1536): 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)

NPUN_RS17355: mal
PKS_AT (550..834): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 145.7
  inactive: 99.0
  Methoxymalonyl-CoA: 55.5
  Methylmalonyl-CoA: 55.4
  Propionyl-CoA: 40.1
  2-Methylbutyryl-CoA: 29.1
  Isobutyryl-CoA: 24.5
  CHC-CoA: 21.6
  Ethylmalonyl-CoA: 21.2
  Benzoyl-CoA: 16.9
  Acetyl-CoA: 12.9
  trans-1,2-CPDA: 9.4
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

NPUN_RS17360: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (460..868): Asp
nrpys: Asp

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:
    asp (Asp)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YGISADLGNTGAKIILGGEFNHYGPTEATVGVTT
  Nearest Stachelhaus code(s):
    Asp DLTKIGHVGK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

NPUN_RS17375: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (462..864): 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:
    YWCSFDLTITSSKIIIGGEVNEYGPTETVVGCCI
  Nearest Stachelhaus code(s):
    Asn DLTKIGEVGK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

NPUN_RS17420: mal
PKS_AT (552..872): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 129.1
  inactive: 82.9
  Methoxymalonyl-CoA: 72.9
  Methylmalonyl-CoA: 56.1
  Propionyl-CoA: 32.9
  Isobutyryl-CoA: 31.9
  Ethylmalonyl-CoA: 29.1
  Benzoyl-CoA: 26.9
  2-Methylbutyryl-CoA: 24.3
  Acetyl-CoA: 18.6
  3-Methylbutyryl-CoA: 13.5
  CHC-CoA: 12.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0

NPUN_RS17445: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (475..876): 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:
    YWCSFDLTITSSKLIIGGEVNEYGPTETVVGCCI
  Nearest Stachelhaus code(s):
    Asn DLTKIGEVGK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

NPUN_RS17455: fatty_acid
CAL_domain (48..487): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 36.2
  NH2: 32.1
  AHBA: 16.6
  Acetyl-CoA: 2.7
  shikimic_acid: 0.0

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-v protocluster (4214161...4256469)
NPUN_RS17170
  RRE type: PlpY_RRE
  Location: 14 - 64
  Score: 69.7
RRE-containing protocluster (4226482...4246683)
NPUN_RS17170
  RRE type: PlpY_RRE
  Location: 14 - 64
  Score: 69.7
spliceotide protocluster (4226684...4248620)
NPUN_RS17170
  RRE type: PlpY_RRE
  Location: 14 - 64
  Score: 69.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
ArcA | Repressor of carbon oxidation
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1 | Ferric Uptake Regulator
LexA variant 2 | Repressor of DNA damage response
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
SypG | Regulator of biofilm formation and host colonization
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NC_010628.1 - Region 15 - 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: 4,744,556 - 4,765,488 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
Ligases: synthetase
NPUN_RS19040: 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
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.48 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.45 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000640.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000641.3 |  | 0.35 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.34 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0001605.3 |  | 0.32 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000678.5 |  | 0.32 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000665.5 |  | 0.31 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.48 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.45 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000640.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000641.3 |  | 0.35 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.34 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0001605.3 |  | 0.32 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000678.5 |  | 0.32 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000665.5 |  | 0.31 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576

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:
NPUN_RS19040: 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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.62 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.38 out of 26.06
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.90 out of 32.93
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.07 out of 25.31
Confidence: medium
Additional weak hits (6):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 27.31 out of 31.73
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.78 out of 26.12
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.25 out of 30.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.91 out of 30.22
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.05 out of 33.14
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.46 out of 20.01
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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes

NC_010628.1 - Region 16 - 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: 4,829,312 - 4,850,283 nt. (total: 20,972 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
NPUN_RS19350: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Lyases: cyclase
NPUN_RS19355: 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
--- | --- | --- | --- | --- | ---
BGC0002043.3 |  | 0.48 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0002707.2 |  | 0.45 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
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 |  | 0.39 | NRPS | N-Acetyltryptophan | Aspergillus nidulans FGSC A4
BGC0002339.3 |  | 0.38 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000528.5 |  | 0.36 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002394.2 |  | 0.34 | terpene | taxa-4(5),11(12)-diene, taxa-4(20),11(12)-diene | Taxus chinensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002043.3 |  | 0.48 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0002707.2 |  | 0.45 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
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 |  | 0.39 | NRPS | N-Acetyltryptophan | Aspergillus nidulans FGSC A4
BGC0002339.3 |  | 0.38 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000528.5 |  | 0.36 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002394.2 |  | 0.34 | terpene | taxa-4(5),11(12)-diene, taxa-4(20),11(12)-diene | Taxus chinensis

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:
NPUN_RS19355: 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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.69 out of 26.06
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.48 out of 20.97
Confidence: medium
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 24.80 out of 29.25
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
--- | ---
CcpA | Catabolite control protein A
MogR | Repressor of flagellar motility genes
SypG | Regulator of biofilm formation and host colonization

NC_010628.1 - Region 17 - 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: 6,241,419 - 6,264,724 nt. (total: 23,306 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
Lyases: cyclase
NPUN_RS25520: 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 |  | 0.60 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001210.5 |  | 0.54 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000554.4 |  | 0.51 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000516.4 |  | 0.51 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0002005.2 |  | 0.50 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0002698.2 |  | 0.50 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0001579.4 |  | 0.49 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002699.2 |  | 0.60 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001210.5 |  | 0.54 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000554.4 |  | 0.51 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000516.4 |  | 0.51 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0002005.2 |  | 0.50 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0002698.2 |  | 0.50 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0001579.4 |  | 0.49 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli

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 NPUN_RS25520

allorf_6250196_6250426
Leader:
MALLNSGMKMILRDFKNLVETLQCNVSTPRSIYLISNAKKFFCYCNYLPYFSPILLYIQIRRAENTA
Core:
Q N K C R I S A V
Core with dehydrations:
Q N K Cys R I Dha A V

#### antiSMASH-DB 4.0 matches for allorf_6250196_6250426

100.0%
NC_010628.1:
Lanthipeptides: allorf_6250196_6250426_lanthipeptide
1
Q N K C R I S A V
9
Q N K C R I S A V
1
Q N K C R I S A V
9
allorf_6262847_6262939
Leader:
MIAYCLIPTTIIYA
Core:
H L L R F I Q F V C G G N Q S P
Core with dehydrations:
H L L R F I Q F V Cys G G N Q Dha P

#### antiSMASH-DB 4.0 matches for allorf_6262847_6262939

100.0%
NC_010628.1:
Lanthipeptides: allorf_6262847_6262939_lanthipeptide
1
H L L R F I Q F V C G G N Q S P
16
H L L R F I Q F V C G G N Q S P
1
H L L R F I Q F V C G G N Q S P
16
18.2%
NZ_JACSPZ010000014.1:
Lanthipeptides: H9635_RS18395_lanthipeptide
7
Q F V C G G N Q S P
16
Q F C G G+ P
24
Q F K C G G D N K P
33

#### MIBiG 4.0 matches for allorf_6262847_6262939

26.3%
BGC0000503.5 (cinA):
Lanthipeptide: cinnamycin
8
F V C G G N
13
F V C G N
12
F V C D G N
17

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.55 out of 18.46
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 20.10 out of 21.84
Confidence: medium
Additional weak hits (1):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.94 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_6250196_6250426 - Class II
  Cleavage pHMM score: -7.30
  RODEO score: 0
  Monoisotopic mass: 999.5 Da
  Molecular weight: 1000.2 Da
  Number of bridges: 1
allorf_6262847_6262939 - Class II
  Cleavage pHMM score: -4.90
  RODEO score: 0
  Monoisotopic mass: 1796.9 Da
  Molecular weight: 1798.1 Da
  Number of bridges: 1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MexT | Global virulence regulator
RpoN | Regulator of nitrogen assimilation and virulence

NC_010628.1 - Region 18 - 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: 6,769,638 - 6,812,394 nt. (total: 42,757 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: dehydrogenase oxidoreductase
NPUN_RS27815: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

NPUN_RS27850: nucleotide sugar dehydrogenase

smcogs
  SMCOG1152: nucleotide sugar dehydrogenase

Transferases: glycosyltransferase
NPUN_RS27825: sugar transferase

smcogs
  SMCOG1146: sugar transferase

NPUN_RS27835: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

NPUN_RS27845: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

NPUN_RS27855: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Ligases: ligase
NPUN_RS27820: 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
--- | --- | --- | --- | --- | ---
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002277.2 |  | 0.62 | NRPS | atromentin | Suillus grevillei
BGC0002135.2 |  | 0.62 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.62 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002277.2 |  | 0.62 | NRPS | atromentin | Suillus grevillei
BGC0002135.2 |  | 0.62 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.62 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.28 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
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.18 out of 28.19
Confidence: medium
Additional weak hits (6):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.55 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.74 out of 32.74
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.70 out of 33.14
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.29 out of 27.04
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 36, location 6769637 - 6812394:
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).
NPUN_RS27820: X
AMP-binding (47..449): 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:
    QWRIFDPSVWQWALTCGGEYNCYGPTEASIDTTF
  Nearest Stachelhaus code(s):
    ohdmTyr DPWGLGLIDK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
MexT | Global virulence regulator
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
ZuR variant 1 | Zinc-responsive repressor

NC_010628.1 - Region 19 - 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: 6,889,563 - 6,934,355 nt. (total: 44,793 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
NPUN_RS28240: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

NPUN_RS28370: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: methyltransferase
NPUN_RS28335: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: dehalogenase
NPUN_RS28350: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: hydratase
NPUN_RS28255: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Ligases: synthase
NPUN_RS28330: 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
BGC0001615.3 |  | 0.53 | NRPS | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000701.5 |  | 0.47 | saccharide | jinggangmycin | Streptomyces hygroscopicus subsp. yingchengensis
BGC0000779.3 |  | 0.43 | saccharide | lipopolysaccharide | Aeromonas piscicola
BGC0001441.5 |  | 0.43 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0001633.3 |  | 0.43 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001440.5 |  | 0.43 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0000762.3 |  | 0.42 | saccharide | exopolysaccharide | Rhizobium leguminosarum bv. viciae
BGC0001610.5 |  | 0.41 | other (other) | gougerotin | Streptomyces ahygroscopicus subsp. wuzhouensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000427.5 |  | 0.59 | NRPS | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0001615.3 |  | 0.53 | NRPS | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000701.5 |  | 0.47 | saccharide | jinggangmycin | Streptomyces hygroscopicus subsp. yingchengensis
BGC0000779.3 |  | 0.43 | saccharide | lipopolysaccharide | Aeromonas piscicola
BGC0001441.5 |  | 0.43 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0001633.3 |  | 0.43 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001440.5 |  | 0.43 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea
BGC0000762.3 |  | 0.42 | saccharide | exopolysaccharide | Rhizobium leguminosarum bv. viciae
BGC0001610.5 |  | 0.41 | other (other) | gougerotin | Streptomyces ahygroscopicus subsp. wuzhouensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.53 out of 20.97
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.47 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.88 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.21 out of 27.78
Confidence: medium
Additional weak hits (8):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.09 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.28 out of 30.25
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.11 out of 23.43
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.92 out of 26.06
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.36 out of 32.93
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.69 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.88 out of 31.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.35 out of 26.85
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
--- | ---
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ToxT | Regulator of MSHA biosynthesis

NC_010628.1 - 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: 7,714,881 - 7,736,797 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
NPUN_RS31685: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

NPUN_RS31755: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

NPUN_RS31760: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

NPUN_RS31765: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

NPUN_RS31775: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
NPUN_RS31780: 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
BGC0001267.3 |  | 0.39 | terpene | elymoclavine, Agroclavine I | Claviceps fusiformis
BGC0002362.3 |  | 0.39 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0002496.3 |  | 0.38 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000811.3 |  | 0.38 | other (other) | fumigaclavine C | Aspergillus fumigatus Af293
BGC0000348.4 |  | 0.36 | NRPS | ergovaline | Epichloe festucae var. lolii
BGC0001304.3 |  | 0.36 | PKS | aflavarin | Aspergillus flavus NRRL3357
BGC0000663.5 |  | 0.35 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0001927.4 |  | 0.35 | other (other) | A-94964 | Streptomyces sp.
BGC0000847.4 |  | 0.35 | other (non-nrp beta-lactam) | thienamycin | Streptomyces cattleya

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
BGC0001267.3 |  | 0.39 | terpene | elymoclavine, Agroclavine I | Claviceps fusiformis
BGC0002362.3 |  | 0.39 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0002496.3 |  | 0.38 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000811.3 |  | 0.38 | other (other) | fumigaclavine C | Aspergillus fumigatus Af293
BGC0000348.4 |  | 0.36 | NRPS | ergovaline | Epichloe festucae var. lolii
BGC0001304.3 |  | 0.36 | PKS | aflavarin | Aspergillus flavus NRRL3357
BGC0000663.5 |  | 0.35 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0001927.4 |  | 0.35 | other (other) | A-94964 | Streptomyces sp.
BGC0000847.4 |  | 0.35 | other (non-nrp beta-lactam) | thienamycin | Streptomyces cattleya

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

No significant matches found.

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

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

Genes with terpene domains:
NPUN_RS31725: T2TS
Domain 1 (4 - 636): 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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.34 out of 20.97
Confidence: medium
Additional weak hits (4):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.00 out of 32.74
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.98 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.04 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.82 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

NC_010628.1 - Region 21 - 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: 7,804,661 - 7,847,765 nt. (total: 43,105 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: oxygenase
NPUN_RS32125: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: methyltransferase sulfotransferase
NPUN_RS32100: glutathione S-transferase

smcogs
  SMCOG1193: glutathione S-transferase

NPUN_RS32205: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: phosphatase
NPUN_RS32105: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

Ligases: ligase
NPUN_RS32195: 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
BGC0002391.2 |  | 0.52 | terpene | zealexin B3, zealexin C2 | Zea mays
BGC0002482.2 |  | 0.47 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0002721.2 |  | 0.46 | saccharide | α-hydroxynitrile glucoside, β-hydroxynitrile glucoside, γ-hydroxynitrile glucoside | Hordeum vulgare subsp. vulgare
BGC0002171.2 |  | 0.45 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger ATCC 1015
BGC0002275.2 |  | 0.45 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger CBS 101883
BGC0001168.5 |  | 0.44 | NRPS | Livipeptin | Streptomyces lividans 1326
BGC0000817.4 |  | 0.43 | other (other) | methylarcyriarubin | uncultured bacterium
BGC0001317.3 |  | 0.43 | terpene | lupeol | Lotus japonicus
BGC0001336.5 |  | 0.43 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.59 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002391.2 |  | 0.52 | terpene | zealexin B3, zealexin C2 | Zea mays
BGC0002482.2 |  | 0.47 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0002721.2 |  | 0.46 | saccharide | α-hydroxynitrile glucoside, β-hydroxynitrile glucoside, γ-hydroxynitrile glucoside | Hordeum vulgare subsp. vulgare
BGC0002171.2 |  | 0.45 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger ATCC 1015
BGC0002275.2 |  | 0.45 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger CBS 101883
BGC0001168.5 |  | 0.44 | NRPS | Livipeptin | Streptomyces lividans 1326
BGC0000817.4 |  | 0.43 | other (other) | methylarcyriarubin | uncultured bacterium
BGC0001317.3 |  | 0.43 | terpene | lupeol | Lotus japonicus
BGC0001336.5 |  | 0.43 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium

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:
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 24.24 out of 29.25
Confidence: medium
Additional weak hits (5):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.29 out of 29.38
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.25 out of 30.97
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.62 out of 35.63
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.73 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
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 7804660 - 7847765:
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).
NPUN_RS32195: X
AMP-binding (28..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:
    NQFLHAYGLVMYHITSGAAKQAYGTTE-TFVTTY
  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
--- | ---
SypG | Regulator of biofilm formation and host colonization

NC_010628.1 - Region 22 - 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: 8,130,738 - 8,187,006 nt. (total: 56,269 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
Oxidoreductases: dehydrogenase
NPUN_RS33465: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase
NPUN_RS33535: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Ligases: ligase synthase
NPUN_RS33525: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS33530: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS33540: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

NPUN_RS40215: 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 |  |  |  | 1.33 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  |  |  | 1.27 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  |  |  | 1.26 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  | 1.25 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  |  |  | 1.24 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5 |  |  |  | 1.24 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001135.5 |  |  |  | 1.21 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  |  |  | 1.18 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  |  |  | 1.18 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
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
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.73 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.71 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.09 out of 29.72
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.99 out of 27.55
Confidence: medium
Additional weak hits (8):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.07 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.06 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.72 out of 29.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.79 out of 30.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.35 out of 25.75
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.28 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.13 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 40, location 8130737 - 8187006:
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 41, location 8130737 - 8178305:
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 42, location 8140055 - 8184972:
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 43, location 8144975 - 8187006:
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).
NPUN_RS33525: 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:
    HAIPCDTFIESPNIMVGGELNAYGALETTLTATV
  Nearest Stachelhaus code(s):
    Arg DVENVGAITK (59% 8Å match)
    bLys DTENVGTLVK (44% 8Å match)
  Stachelhaus code match:
    70% (weak)

NPUN_RS33530: 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:
    LETSFDASTFEGWLLAGGDINGYGPTESTTFTCC
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

NPUN_RS33540: 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: 165.0
  inactive: 118.6
  Methoxymalonyl-CoA: 78.6
  Methylmalonyl-CoA: 70.1
  Propionyl-CoA: 50.4
  Ethylmalonyl-CoA: 45.3
  Isobutyryl-CoA: 35.1
  2-Methylbutyryl-CoA: 28.6
  Benzoyl-CoA: 25.3
  CHC-CoA: 24.6
  fatty_acid: 20.9
  3-Methylbutyryl-CoA: 18.0
  Acetyl-CoA: 17.9
  trans-1,2-CPDA: 17.3

NPUN_RS40215: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (67..466): 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
--- | ---
GnfM | Regulator of nitrogen-fixation genes
NtrC | Nitrogen regulatory protein C

NC_010631.1 - Region 1 - 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: 84,655 - 108,005 nt. (total: 23,351 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
Lyases: cyclase
NPUN_RS34130: 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 |  | 1.00 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000554.4 |  | 0.51 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0002698.2 |  | 0.49 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001210.5 |  | 0.48 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000527.5 |  | 0.47 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0002704.2 |  | 0.46 | ribosomal | archalan β | Halorussus salinus
BGC0002674.2 |  | 0.46 | ribosomal | enterocin F4-9 | Enterococcus faecalis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002699.2 |  | 1.00 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001555.4 |  | 0.52 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000554.4 |  | 0.51 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002703.2 |  | 0.49 | ribosomal | archalan α | Halorussus salinus
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0002698.2 |  | 0.49 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001210.5 |  | 0.48 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000527.5 |  | 0.47 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0002704.2 |  | 0.46 | ribosomal | archalan β | Halorussus salinus
BGC0002674.2 |  | 0.46 | ribosomal | enterocin F4-9 | Enterococcus faecalis

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 NPUN_RS34130

allorf_104115_104270
Leader:
MSSEELVVRQGN
Core:
N A K V V S P K G R G E R T R H I E L S S A P L H L C L P P P N I F G L A D Y
Core with dehydrations:
N A K V V Dha P K G R G E R Dhb R H I E L Dha Dha A P L H L Cys L P P P N I F G L A D Y

#### antiSMASH-DB 4.0 matches for allorf_104115_104270

100.0%
NC_010631.1:
Lanthipeptides: allorf_104115_104270_lanthipeptide
1
N A K V V S P K G R G E R T R H I E L S S A P L H L C L P P P N I F G L A D Y
39
N A K V V S P K G R G E R T R H I E L S S A P L H L C L P P P N I F G L A D Y
1
N A K V V S P K G R G E R T R H I E L S S A P L H L C L P P P N I F G L A D Y
39
20.5%
NZ_RCOL01000001.1:
Lanthipeptides: allorf_2499994_2500137_lanthipeptide
7
P K G R G E R T R H I E L S S A P
23
P+ R G R T R S+P
10
P R A R G P R T R P W R A W S S P
26
14.0%
NZ_JALGBX010000020.1 and 1 other:
NZ_JANAVF010000016.1 Lanthipeptides: NLX94_RS30150_lanthipeptide
Lanthipeptides: MTF69_RS28785_lanthipeptide
29
P P P N I F G L A D
38
P P P+I G+A
5
P P P S I S G I A T
14
allorf_107318_107491
Leader:
MRQQGCRGAGEKEEVLGI
Core:
C V R I F R N F A L L P C P S A I L T L H T L Q L N L V P F D L E V H I A E N
Core with dehydrations:
Cys V R I F R N F A L L P Cys P Dha A I L Dhb L H Dhb L Q L N L V P F D L E V H I A E N

#### antiSMASH-DB 4.0 matches for allorf_107318_107491

100.0%
NC_010631.1:
Lanthipeptides: allorf_107318_107491_lanthipeptide
1
C V R I F R N F A L L P C P S A I L T L H T L Q L N L V P F D L E V H I A E N
39
C V R I F R N F A L L P C P S A I L T L H T L Q L N L V P F D L E V H I A E N
1
C V R I F R N F A L L P C P S A I L T L H T L Q L N L V P F D L E V H I A E N
39
allorf_107755_107880
Leader:
MWRCAIEITASIFM
Core:
Y L Q V L R R V C K N S G L L N L V S F A K A R K V T
Core with dehydrations:
Y L Q V L R R V Cys K N Dha G L L N L V Dha F A K A R K V Dhb

#### antiSMASH-DB 4.0 matches for allorf_107755_107880

100.0%
NC_010631.1:
Lanthipeptides: allorf_107755_107880_lanthipeptide
1
Y L Q V L R R V C K N S G L L N L V S F A K A R K V T
27
Y L Q V L R R V C K N S G L L N L V S F A K A R K V T
1
Y L Q V L R R V C K N S G L L N L V S F A K A R K V T
27

#### 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:
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.77 out of 32.93
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
Additional weak hits (2):
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 15.78 out of 18.46
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.46 out of 23.43
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_104115_104270 - Class II
  Cleavage pHMM score: -7.20
  RODEO score: 0
  Monoisotopic mass: 4180.3 Da
  Molecular weight: 4182.8 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4200.8 Da N = 1
    4218.8 Da N = 2
    4236.9 Da N = 3
allorf_107318_107491 - Class II
  Cleavage pHMM score: -3.90
  RODEO score: 0
  Monoisotopic mass: 4375.4 Da
  Molecular weight: 4378.2 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4396.2 Da N = 1
allorf_107755_107880 - Class II
  Cleavage pHMM score: -5.50
  RODEO score: 0
  Monoisotopic mass: 3021.8 Da
  Molecular weight: 3023.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3041.7 Da N = 1
    3059.7 Da N = 2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
LexA variant 3 | Repressor of DNA damage response
MexT | Global virulence regulator
RpoN | Regulator of nitrogen assimilation and virulence

NC_010632.1 - 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: 113,694 - 134,341 nt. (total: 20,648 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
NPUN_RS35870: 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
--- | --- | --- | --- | --- | ---
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000506.4 |  | 0.30 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0001727.3 |  | 0.28 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0002007.2 |  | 0.26 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000310.5 |  | 0.26 | NRPS | bacitracin | Bacillus licheniformis
BGC0001701.4 |  | 0.24 | ribosomal | nisin O | Blautia obeum
BGC0000260.3 |  | 0.23 | PKS | prodigiosin | Hahella chejuensis KCTC 2396
BGC0000997.4 |  | 0.22 | NRPS, PKS | glidobactin, glidobactin B, glidobactin C | [Polyangium] brachysporum
BGC0000845.5 |  | 0.22 | other (non-nrp beta-lactam) | clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0002288.2 |  | 0.20 | NRPS | ashimide A, ashimide B | Streptomyces sp. NA03103

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000506.4 |  | 0.30 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0001727.3 |  | 0.28 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0002007.2 |  | 0.26 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000310.5 |  | 0.26 | NRPS | bacitracin | Bacillus licheniformis
BGC0001701.4 |  | 0.24 | ribosomal | nisin O | Blautia obeum
BGC0000260.3 |  | 0.23 | PKS | prodigiosin | Hahella chejuensis KCTC 2396
BGC0000997.4 |  | 0.22 | NRPS, PKS | glidobactin, glidobactin B, glidobactin C | [Polyangium] brachysporum
BGC0000845.5 |  | 0.22 | other (non-nrp beta-lactam) | clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0002288.2 |  | 0.20 | NRPS | ashimide A, ashimide B | Streptomyces sp. NA03103

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:
NPUN_RS35860: TS_Pyr4
Domain 1 (4 - 209): 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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.70 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.20 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.17 out of 27.78
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.54 out of 26.33
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
Additional weak hits (4):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.14 out of 25.88
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.97 out of 32.74
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.12 out of 31.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.90 out of 35.63
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
--- | ---
ANR | Anaerobic transcriptional regulator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria

NC_010630.1 - Region 1 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 62,034 - 3,789 nt. (total: 64,784 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
NPUN_RS36795: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: ligase
NPUN_RS36790: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

NPUN_RS38145: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.87 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  | 0.87 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.86 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  |  | 0.86 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  | 0.84 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.83 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  | 0.82 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  | 0.81 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  | 0.79 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  |  | 0.79 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.74 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.72 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.71 | 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.

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: 23.72 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 24.20 out of 27.78
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.63 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.19 out of 27.78
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.99 out of 27.55
Confidence: medium
Additional weak hits (6):
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.01 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.75 out of 30.11
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.45 out of 32.74
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.25 out of 31.73
Confidence: weak
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.03 out of 20.47
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.65 out of 29.25
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 62033 - 3789:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Cys) + (ccmal) + (Cys - Ala - Thr - 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).
NPUN_RS36790: Cys - Ala - Thr - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (538..939): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNTLLSGDVSLGGATEASIWSIC
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1622..2022): 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)

AMP-binding (2684..3088): 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 (3750..4150): 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)

NPUN_RS36795: mal
PKS_AT (540..836): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.7
  inactive: 170.2
  Methoxymalonyl-CoA: 68.8
  Methylmalonyl-CoA: 60.9
  Propionyl-CoA: 49.9
  Isobutyryl-CoA: 40.3
  2-Methylbutyryl-CoA: 22.8
  Acetyl-CoA: 22.5
  Ethylmalonyl-CoA: 20.2
  CHC-CoA: 17.0
  Benzoyl-CoA: 16.2
  trans-1,2-CPDA: 14.2
  fatty_acid: 11.3
  3-Methylbutyryl-CoA: 0.0

NPUN_RS38145: NH2 - Cys
Search NORINE for peptide: strict or relaxed
CAL_domain (46..478): NH2
minowa: NH2

Prediction, score:
  NH2: 24.5
  fatty_acid: 23.6
  AHBA: 8.6
  Acetyl-CoA: 5.7
  shikimic_acid: 0.0

AMP-binding (1168..1569): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNSLMSGDVSVGGPTETSIWNIC
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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
GnfM | Regulator of nitrogen-fixation genes
MogR | Repressor of flagellar motility genes

NC_010629.1 - Region 1 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 18,867 - 2,675 nt. (total: 10,228 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

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

No matches found.

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

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: 24.04 out of 30.25
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.85 out of 20.97
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 24.60 out of 30.25
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.50 out of 28.19
Confidence: medium
Additional weak hits (7):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.79 out of 26.06
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.46 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.29 out of 32.74
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.78 out of 30.22
Confidence: weak
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: 24.43 out of 30.98
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.56 out of 27.04
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
ColR | Phenol-responsive regulator
ZuR variant 1 | Zinc-responsive repressor