Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
1.11
1.12
1.13
1.14
1.15
1.16
1.17
1.18
1.19
1.20
1.21
1.22
1.23
1.24
1.25
1.26
1.27
1.28
1.29
1.30
2.1
2.2
2.3
2.4
2.5
3.1
3.2
3.3
3.4
3.5
3.6
3.7
3.8

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

NZ_NDXL01000001.1 (Streptomyces kasugaensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | butyrolactone | 35,444 | 46,385 |  |
Region 1.2 | NRPS | 54,962 | 101,144 |  |
Region 1.3 | NRPS | 198,026 | 241,415 | Low | pyrroloformamide A/pyrroloformamide B/pyrroloformamide D/pyrroloformamide C | NRPS:Type I+other:other
Region 1.4 | NAPAA | 298,048 | 332,052 | High | γ-poly-L-2,4-diaminobutyric acid | NRPS:Type I
Region 1.5 | terpene,indole,T3PKS,butyrolactone | 356,475 | 426,695 | Low | rebeccamycin | other:other
Region 1.6 | NRPS,NRPS-like | 435,179 | 483,475 | High | antipain | NRPS:Type I
Region 1.7 | aureonuclemycin | 553,314 | 578,463 |  |
Region 1.8 | T1PKS | 581,025 | 701,297 | High | tetramycin B | PKS
Region 1.9 | redox-cofactor | 757,241 | 779,335 |  |
Region 1.10 | other | 807,085 | 848,464 |  |
Region 1.11 | T3PKS,NRP-metallophore,NRPS | 894,311 | 980,389 | High | paenibactin | NRPS:Type I
Region 1.12 | NRPS,NRPS-like | 1,250,044 | 1,330,145 | Low | TP-1161 | ribosomal:RiPP:Thiopeptide
Region 1.13 | triceptide | 1,581,049 | 1,602,273 |  |
Region 1.14 | NRPS-like,ranthipeptide,lassopeptide | 1,789,969 | 1,854,354 |  |
Region 1.15 | T2PKS,other,PKS-like | 1,980,946 | 2,053,419 | Low | cytorhodin | PKS
Region 1.16 | triceptide | 2,355,202 | 2,376,714 |
Region 1.17 | NI-siderophore | 3,065,827 | 3,098,710 |  |
Region 1.18 | T1PKS,butyrolactone | 3,183,500 | 3,233,372 |  |
Region 1.19 | lassopeptide | 3,297,917 | 3,320,448 |
Region 1.20 | RiPP-like | 3,321,521 | 3,332,336 |
Region 1.21 | butyrolactone,betalactone,lanthipeptide-class-i | 3,354,618 | 3,401,696 |  |
Region 1.22 | RiPP-like | 3,531,074 | 3,542,454 |  |
Region 1.23 | hydrogen-cyanide | 3,600,020 | 3,612,860 | Low | aborycin | ribosomal:RiPP
Region 1.24 | lanthipeptide-class-iii | 3,944,307 | 3,966,871 | Low | formicamycin A/formicamycin B/formicamycin C/formicamycin D/formicamycin E/formicamycin F/formicamycin G/formicamycin H/formicamycin I/formicamycin J/formicamycin K/formicamycin L/formicamycin M/fasamycin C/fasamycin D/fasamycin E | PKS:Type II aromatic
Region 1.25 | butyrolactone | 4,034,094 | 4,045,008 |  |
Region 1.26 | terpene | 4,306,394 | 4,332,995 | High | hopene | terpene
Region 1.27 | CDPS | 4,542,599 | 4,563,324 | Low | albonoursin | other:other
Region 1.28 | NRPS,NAPAA | 4,615,807 | 4,695,188 | Low | rimosamide | NRPS:Type I
Region 1.29 | hydrogen-cyanide | 4,719,931 | 4,732,909 |  |
Region 1.30 | NRPS-like,NRPS | 4,796,692 | 4,865,478 | Low | rotihibin A | NRPS:Type I

NZ_NDXL01000002.1 (Streptomyces kasugaensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | lassopeptide | 228,866 | 252,996 | Medium | ulleungdin | ribosomal:unmodified
Region 2.2 | terpene | 855,279 | 877,651 |  |
Region 2.3 | lanthipeptide-class-v | 1,312,055 | 1,354,198 | Medium | pristinin A3 | ribosomal:RiPP
Region 2.4 | lanthipeptide-class-i | 1,441,533 | 1,467,977 |
Region 2.5 | NI-siderophore | 1,634,044 | 1,665,591 |  |

NZ_NDXL01000003.1 (Streptomyces kasugaensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | NRPS-like,arylpolyene | 85,580 | 128,533 |  |
Region 3.2 | lanthipeptide-class-i,NRPS-like,T1PKS | 345,622 | 469,070 | Low | concanamycin A | PKS
Region 3.3 | T1PKS,NRPS-like,NRPS | 698,928 | 776,773 | High | rakicidin A/rakicidin B | NRPS:Type I+PKS:Type I
Region 3.4 | NAPAA | 795,226 | 838,006 | High | ε-Poly-L-lysine | NRPS:Type I
Region 3.5 | lanthipeptide-class-i | 1,676,560 | 1,701,561 |
Region 3.6 | lassopeptide | 1,841,461 | 1,863,807 |
Region 3.7 | aminopolycarboxylic-acid | 1,958,369 | 1,971,829 | High | Ethylenediaminesuccinic acid hydroxyarginine | other:other
Region 3.8 | ectoine | 2,347,678 | 2,358,082 | High | ectoine | other:ectoine

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | butyrolactone | 35,444 | 46,385 |  |
Region 1.2 | NRPS | 54,962 | 101,144 |  |
Region 1.3 | NRPS | 198,026 | 241,415 | Low | pyrroloformamide A/pyrroloformamide B/pyrroloformamide D/pyrroloformamide C | NRPS:Type I+other:other
Region 1.4 | NAPAA | 298,048 | 332,052 | High | γ-poly-L-2,4-diaminobutyric acid | NRPS:Type I
Region 1.5 | terpene,indole,T3PKS,butyrolactone | 356,475 | 426,695 | Low | rebeccamycin | other:other
Region 1.6 | NRPS,NRPS-like | 435,179 | 483,475 | High | antipain | NRPS:Type I
Region 1.7 | aureonuclemycin | 553,314 | 578,463 |  |
Region 1.8 | T1PKS | 581,025 | 701,297 | High | tetramycin B | PKS
Region 1.9 | redox-cofactor | 757,241 | 779,335 |  |
Region 1.10 | other | 807,085 | 848,464 |  |
Region 1.11 | T3PKS,NRP-metallophore,NRPS | 894,311 | 980,389 | High | paenibactin | NRPS:Type I
Region 1.12 | NRPS,NRPS-like | 1,250,044 | 1,330,145 | Low | TP-1161 | ribosomal:RiPP:Thiopeptide
Region 1.13 | triceptide | 1,581,049 | 1,602,273 |  |
Region 1.14 | NRPS-like,ranthipeptide,lassopeptide | 1,789,969 | 1,854,354 |  |
Region 1.15 | T2PKS,other,PKS-like | 1,980,946 | 2,053,419 | Low | cytorhodin | PKS
Region 1.16 | triceptide | 2,355,202 | 2,376,714 |
Region 1.17 | NI-siderophore | 3,065,827 | 3,098,710 |  |
Region 1.18 | T1PKS,butyrolactone | 3,183,500 | 3,233,372 |  |
Region 1.19 | lassopeptide | 3,297,917 | 3,320,448 |
Region 1.20 | RiPP-like | 3,321,521 | 3,332,336 |
Region 1.21 | butyrolactone,betalactone,lanthipeptide-class-i | 3,354,618 | 3,401,696 |  |
Region 1.22 | RiPP-like | 3,531,074 | 3,542,454 |  |
Region 1.23 | hydrogen-cyanide | 3,600,020 | 3,612,860 | Low | aborycin | ribosomal:RiPP
Region 1.24 | lanthipeptide-class-iii | 3,944,307 | 3,966,871 | Low | formicamycin A/formicamycin B/formicamycin C/formicamycin D/formicamycin E/formicamycin F/formicamycin G/formicamycin H/formicamycin I/formicamycin J/formicamycin K/formicamycin L/formicamycin M/fasamycin C/fasamycin D/fasamycin E | PKS:Type II aromatic
Region 1.25 | butyrolactone | 4,034,094 | 4,045,008 |  |
Region 1.26 | terpene | 4,306,394 | 4,332,995 | High | hopene | terpene
Region 1.27 | CDPS | 4,542,599 | 4,563,324 | Low | albonoursin | other:other
Region 1.28 | NRPS,NAPAA | 4,615,807 | 4,695,188 | Low | rimosamide | NRPS:Type I
Region 1.29 | hydrogen-cyanide | 4,719,931 | 4,732,909 |  |
Region 1.30 | NRPS-like,NRPS | 4,796,692 | 4,865,478 | Low | rotihibin A | NRPS:Type I
Region 2.1 | lassopeptide | 228,866 | 252,996 | Medium | ulleungdin | ribosomal:unmodified
Region 2.2 | terpene | 855,279 | 877,651 |  |
Region 2.3 | lanthipeptide-class-v | 1,312,055 | 1,354,198 | Medium | pristinin A3 | ribosomal:RiPP
Region 2.4 | lanthipeptide-class-i | 1,441,533 | 1,467,977 |
Region 2.5 | NI-siderophore | 1,634,044 | 1,665,591 |  |
Region 3.1 | NRPS-like,arylpolyene | 85,580 | 128,533 |  |
Region 3.2 | lanthipeptide-class-i,NRPS-like,T1PKS | 345,622 | 469,070 | Low | concanamycin A | PKS
Region 3.3 | T1PKS,NRPS-like,NRPS | 698,928 | 776,773 | High | rakicidin A/rakicidin B | NRPS:Type I+PKS:Type I
Region 3.4 | NAPAA | 795,226 | 838,006 | High | ε-Poly-L-lysine | NRPS:Type I
Region 3.5 | lanthipeptide-class-i | 1,676,560 | 1,701,561 |
Region 3.6 | lassopeptide | 1,841,461 | 1,863,807 |
Region 3.7 | aminopolycarboxylic-acid | 1,958,369 | 1,971,829 | High | Ethylenediaminesuccinic acid hydroxyarginine | other:other
Region 3.8 | ectoine | 2,347,678 | 2,358,082 | High | ectoine | other:ectoine

No secondary metabolite regions were found in these records:
  NZ_NDXL01000004.1 (Streptomyces kasugaensis)
  NZ_NDXL01000005.1 (Streptomyces kasugaensis)

Compact view
NZ_NDXL01000001.1 - Region 1 - butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 35,444 - 46,385 nt. (total: 10,942 nt) Show pHMM detection rules used
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: dehydratase
B7024_RS00165: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
B7024_RS00175: cysteine synthase

smcogs
  SMCOG1081: cysteine 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 | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.77 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.70 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.64 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.40 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002213.3 |  | 0.34 | PKS | HEx-pks16 polyketide | Punctularia strigosozonata HHB-11173 SS5
BGC0001469.5 |  | 0.31 | NRPS | marthiapeptide A | Brevibacillus sp. Leaf182
BGC0000914.5 |  | 0.31 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000943.5 |  | 0.30 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0001587.5 |  | 0.30 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001671.3 |  | 0.30 | NRPS | monobactam | Agrobacterium tumefaciens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.77 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.70 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.64 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.40 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002213.3 |  | 0.34 | PKS | HEx-pks16 polyketide | Punctularia strigosozonata HHB-11173 SS5
BGC0001469.5 |  | 0.31 | NRPS | marthiapeptide A | Brevibacillus sp. Leaf182
BGC0000914.5 |  | 0.31 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000943.5 |  | 0.30 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0001587.5 |  | 0.30 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001671.3 |  | 0.30 | NRPS | monobactam | Agrobacterium tumefaciens

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (5):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.79 out of 29.65
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.58 out of 18.57
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.27 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.89 out of 26.06
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.03 out of 25.88
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_NDXL01000001.1 - Region 2 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 54,962 - 101,144 nt. (total: 46,183 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase
B7024_RS00245: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

B7024_RS00250: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

B7024_RS00260: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

B7024_RS00285: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

B7024_RS00355: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS00365: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

B7024_RS00370: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS00400: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

B7024_RS00405: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

B7024_RS00410: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: halogenase methyltransferase
B7024_RS00320: methyltransferase

smcogs
  SMCOG1248: methyltransferase

B7024_RS00350: halogenase

smcogs
  SMCOG1119: halogenase

Hydrolases: esterase hydrolase
B7024_RS00290: HAD-superfamily hydrolase, subfamily IA, variant

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

B7024_RS00325: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
B7024_RS00235: 3-oxoacyl-(acyl carrier protein) synthase III

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

B7024_RS00330: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS00335: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000357.5 |  | 0.68 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001250.4 |  | 0.63 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000357.5 |  | 0.68 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001250.4 |  | 0.63 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  | 0.63 | 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:
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.98 out of 29.51
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.35 out of 18.57
Confidence: medium
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 22.40
Confidence: strong
Additional weak hits (19):
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.66 out of 29.72
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.83 out of 31.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 25.75
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.97 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.06 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.88 out of 31.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.51 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.70 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.25 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.28 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.40 out of 32.93
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.27 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.36 out of 18.57
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.62 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.33 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.74 out of 28.19
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 54961 - 101144:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B7024_RS00330: X - X
AMP-binding (12..379): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

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

AMP-binding (1063..1441): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    ADD-------DTTLVVSGEVHTYGGIEWGLAAAQ
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

B7024_RS00335: X
AMP-binding (7..391): 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:
    YAYGFDVTIDEPYIRTGGELNEYGPTETVAGAVF
  Nearest Stachelhaus code(s):
    4Me-Pro DVQYVGHAIK (44% 8Å match)
    Thr DGDYVRLAGK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
DosR | Hypoxia stress response regulator
HypR | L-hydroxyproline utilization repressor
ToxT | Regulator of MSHA biosynthesis

NZ_NDXL01000001.1 - Region 3 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 198,026 - 241,415 nt. (total: 43,390 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase reductase
B7024_RS00900: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

B7024_RS00930: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B7024_RS00995: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: aminotransferase methyltransferase
B7024_RS00925: aminotransferase

smcogs
  SMCOG1019: aminotransferase

B7024_RS00980: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase
B7024_RS00935: thioesterase

smcogs
  SMCOG1004: thioesterase

B7024_RS41085: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase lyase
B7024_RS00910: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

B7024_RS43045: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
B7024_RS00885: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS00895: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS00945: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B7024_RS42050: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002458.3 |  | 0.74 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002458.3 |  | 0.74 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0002135.2 |  | 0.63 | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (7):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.56 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.85 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.47 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.67 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.94 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 3, location 198025 - 241415:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).
B7024_RS00885: X
AMP-binding (12..422): 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:
    LVVVHARFYSALTQNATFDFQLYGQSETGPVAGG
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

B7024_RS00895: X
AMP-binding (67..451): 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:
    ITFPFTFGLGGVFTVSAGEIDGIGATELLHVFIA
  Nearest Stachelhaus code(s):
    Abu or Ival DMGFIAGVVK (32% 8Å match)
    Ala DVGFVAGVLK (29% 8Å match)
  Stachelhaus code match:
    60% (weak)

B7024_RS00945: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (538..938): 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:
    TDIAFDLSVYDGNSLLSGDTSLGGATEGSIWSVC
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

B7024_RS42050: X
AMP-binding (14..286): 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:
    MAAPFGAGVWENSLFLGGGHHLYGLAEATAVSTH
  Nearest Stachelhaus code(s):
    Leu DYWSFGLVVK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

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

NZ_NDXL01000001.1 - Region 4 - NAPAA
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: 298,048 - 332,052 nt. (total: 34,005 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
B7024_RS01290: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

B7024_RS01325: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase aminotransferase
B7024_RS01305: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

B7024_RS01350: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase
B7024_RS01345: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase
B7024_RS01300: 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 | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002535.2 |  | 0.92 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002174.2 |  | 0.74 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.63 | 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
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002535.2 |  | 0.92 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002174.2 |  | 0.74 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.63 | 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
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.46 out of 27.04
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.64 out of 24.78
Confidence: medium
Additional weak hits (9):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.36 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.68 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.99 out of 21.55
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.43 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.86 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 4, location 298047 - 332052:
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).
B7024_RS01300: X
AMP-binding (22..415): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FVVLFDFSIEEPCCLVSGELNAYGPTETTVTATC
  Nearest Stachelhaus code(s):
    Val DFESLAAVYK (62% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
LexA variant 2 | Repressor of DNA damage response

NZ_NDXL01000001.1 - Region 5 - T3PKS,butyrolactone,indole,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 356,475 - 426,695 nt. (total: 70,221 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
indole: (indsynth or dmat or indole_PTase)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
B7024_RS01505: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

B7024_RS01515: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS01550: Oxidation

MITE
  MITE0000070Oxidation (identity: 63.70%)
smcogs
  SMCOG1050: monooxygenase FAD-binding

B7024_RS01555: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS01655: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS01665: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS01670: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

B7024_RS01710: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase methyltransferase
B7024_RS01535: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

B7024_RS01690: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Lyases: cyclase
B7024_RS01510: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase
B7024_RS01650: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

Translocases: permease
B7024_RS01620: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

B7024_RS42070: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | terpene | indole | T3PKS | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000849.4 |  |  |  |  | 1.02 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  |  |  |  | 0.98 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  |  |  |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001223.5 |  |  |  |  | 0.66 | other (other) | hydroxysporine | uncultured bacterium
BGC0001336.5 |  |  |  |  | 0.58 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001310.5 |  |  |  |  | 0.56 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  |  |  |  | 0.56 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000660.5 |  |  |  |  | 0.49 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0002084.4 |  |  |  |  | 0.47 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002099.3 |  |  |  |  | 0.47 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.82 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0000849.4 |  | 0.79 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002127.3 |  | 0.71 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001223.5 |  | 0.69 | other (other) | hydroxysporine | uncultured bacterium
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001224.5 |  | 0.64 | other (other) | reductasporine | uncultured bacterium
BGC0001336.5 |  | 0.63 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
B7024_RS01510: T1TS
Domain 1 (4 - 311): Type 1 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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 25.31
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.33 out of 23.79
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.97 out of 30.22
Confidence: medium
Additional weak hits (29):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.07 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.02 out of 36.54
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.88 out of 33.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.83 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.20 out of 21.55
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.03 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.05 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.12 out of 27.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.42 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.03 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.86 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.48 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.01 out of 20.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.54 out of 36.54
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.50 out of 31.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.09 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.92 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.81 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.58 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.79 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.33 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.27 out of 20.01
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.37 out of 32.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.46 out of 33.14
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
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
--- | ---
CatR | H2O2-responsive repressor
ClgR | Caseinolytic protease gene regulator
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator

NZ_NDXL01000001.1 - Region 6 - NRPS,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: 435,179 - 483,475 nt. (total: 48,297 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B7024_RS01880: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Lyases: dehydratase
B7024_RS01895: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
B7024_RS01870: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B7024_RS01875: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS01885: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS01890: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | NRPS-like | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002051.2 |  |  |  | 1.38 | NRPS | antipain | Streptomyces sp.
BGC0001249.5 |  |  |  | 1.26 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  |  |  | 1.13 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  |  |  | 1.11 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  |  |  | 1.09 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  |  |  | 1.07 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  |  | 1.04 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  |  |  | 1.03 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 1.02 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  |  |  | 1.00 | NRPS | peramine | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002051.2 |  | 0.76 | NRPS | antipain | Streptomyces sp.
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.70 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  | 0.66 | NRPS | peramine | Epichloe festucae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
Additional weak hits (11):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.40 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.11 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.45 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.11 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.96 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.13 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.57 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.26 out of 29.65
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 10, location 435178 - 483475:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Arg) + (Phe) + (Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 11, location 435178 - 478307:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Arg) + (Phe) + (Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 12, location 439568 - 481470:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Arg) + (Phe) + (Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 441570 - 483475:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Arg) + (Phe) + (Val)

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).
B7024_RS01875: Arg
Search NORINE for peptide: strict or relaxed
AMP-binding (466..858): Arg
nrpys: Arg

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:
    HAAAFDVALEEPNLVLGGELNAYGVTEAAITTTV
  Nearest Stachelhaus code(s):
    Arg DVENVGAITK (74% 8Å match)
  Stachelhaus code match:
    100% (strong)

B7024_RS01885: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (34..443): Phe
nrpys: Phe

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    MGYVFDPHVKETVLVVGGDHNAYGPAEATVMSTM
  Nearest Stachelhaus code(s):
    Phe DPLVVGAVVK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

B7024_RS01890: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (2..407): 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:
    N/A
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LEPSFDAATFEAVLLVGGEVNGYGPTEATTFATA
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor

NZ_NDXL01000001.1 - Region 7 - aureonuclemycin
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: 553,314 - 578,463 nt. (total: 25,150 nt) Show pHMM detection rules used
aureonuclemycin: (her4 and her5 and her6 and her7)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
B7024_RS02410: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

B7024_RS02430: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: methyltransferase
B7024_RS02415: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

B7024_RS02425: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
B7024_RS02420: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

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 | aureonuclemycin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001592.5 |  | 0.44 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0000889.5 |  | 0.44 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0000249.5 |  | 0.44 | PKS | nogalamycin | Streptomyces nogalater
BGC0000217.5 |  | 0.43 | PKS | daunorubicin | Streptomyces sp.
BGC0000719.5 |  | 0.42 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0000218.5 |  | 0.41 | PKS | doxorubicin | Streptomyces peucetius
BGC0000720.3 |  | 0.41 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0001510.5 |  | 0.40 | other (other) | anisomycin | Streptomyces hygrospinosus
BGC0002443.3 |  | 0.40 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0002354.4 |  | 0.39 | other (other) | huimycin | Kutzneria albida DSM 43870

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001592.5 |  | 0.44 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0000889.5 |  | 0.44 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0000249.5 |  | 0.44 | PKS | nogalamycin | Streptomyces nogalater
BGC0000217.5 |  | 0.43 | PKS | daunorubicin | Streptomyces sp.
BGC0000719.5 |  | 0.42 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0000218.5 |  | 0.41 | PKS | doxorubicin | Streptomyces peucetius
BGC0000720.3 |  | 0.41 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0001510.5 |  | 0.40 | other (other) | anisomycin | Streptomyces hygrospinosus
BGC0002443.3 |  | 0.40 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0002354.4 |  | 0.39 | other (other) | huimycin | Kutzneria albida DSM 43870

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (6):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.19 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.97 out of 39.62
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.99 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.01 out of 27.55
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.95 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_NDXL01000001.1 - Region 8 - 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: 581,025 - 701,297 nt. (total: 120,273 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
B7024_RS02510: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS02525: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS02615: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS02625: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS02660: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: PPTase acetyltransferase acylase aminotransferase glycosyltransferase transferase
B7024_RS02560: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

B7024_RS02595: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B7024_RS02605: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

B7024_RS02610: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

B7024_RS02670: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

B7024_RS02680: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

B7024_RS02700: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

B7024_RS02710: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: esterase
B7024_RS02565: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
B7024_RS02640: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

B7024_RS02675: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
B7024_RS02590: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS02600: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS02630: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS02635: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS02690: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000018.5 |  | 0.73 | PKS | angolamycin | Streptomyces eurythermus
BGC0000016.4 |  | 0.66 | other (other) | amphotericin B | Streptomyces nodosus
BGC0001239.3 |  | 0.64 | other (other) | biotin | Aspergillus nidulans
BGC0000067.5 |  | 0.64 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0002154.2 |  | 0.64 | 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
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000018.5 |  | 0.73 | PKS | angolamycin | Streptomyces eurythermus
BGC0000016.4 |  | 0.66 | other (other) | amphotericin B | Streptomyces nodosus
BGC0001239.3 |  | 0.64 | other (other) | biotin | Aspergillus nidulans
BGC0000067.5 |  | 0.64 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0002154.2 |  | 0.64 | 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.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.97 out of 23.79
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.81 out of 29.51
Confidence: medium
Additional weak hits (30):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.41 out of 27.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.49 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.77 out of 26.85
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 19.26
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.20 out of 31.73
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.23 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.36 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.00 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.03 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.56 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.12 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.58 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.82 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.38 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.50 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.79 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.85 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.24 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.30 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.01 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.89 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.11 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.88 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.27 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.43 out of 29.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.95 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.33 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.32 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 15, location 581024 - 701297:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (Me-ohmal - Me-ohmal) + (ccmal - ccmal - ccmal - ccmal) + (ccmal - ohmal - Me-ohmal - ohmal - ohmal - ohmal) + (redmal - ccmal)
Non-colinear ordering:
  B7024_RS02600 + B7024_RS02595 + B7024_RS02590 + B7024_RS02635 + B7024_RS02630

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).
B7024_RS02590: mal - mal - mal - mal
PKS_AT (551..841): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 240.9
  inactive: 108.1
  Methoxymalonyl-CoA: 68.6
  Methylmalonyl-CoA: 63.3
  Propionyl-CoA: 41.2
  Ethylmalonyl-CoA: 32.8
  2-Methylbutyryl-CoA: 26.6
  Benzoyl-CoA: 23.1
  Isobutyryl-CoA: 21.8
  Acetyl-CoA: 20.4
  trans-1,2-CPDA: 15.3
  CHC-CoA: 12.9
  fatty_acid: 9.6
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2311..2601): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 232.2
  inactive: 111.5
  Methylmalonyl-CoA: 56.0
  Methoxymalonyl-CoA: 55.1
  Propionyl-CoA: 47.2
  Isobutyryl-CoA: 28.9
  Acetyl-CoA: 25.1
  Ethylmalonyl-CoA: 22.2
  2-Methylbutyryl-CoA: 21.4
  fatty_acid: 17.3
  Benzoyl-CoA: 16.7
  trans-1,2-CPDA: 8.5
  CHC-CoA: 7.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4040..4327): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 223.6
  inactive: 104.2
  Methylmalonyl-CoA: 59.9
  Methoxymalonyl-CoA: 56.4
  Propionyl-CoA: 46.0
  Isobutyryl-CoA: 26.3
  Ethylmalonyl-CoA: 25.4
  2-Methylbutyryl-CoA: 21.0
  Acetyl-CoA: 20.7
  Benzoyl-CoA: 18.3
  fatty_acid: 17.8
  CHC-CoA: 15.9
  trans-1,2-CPDA: 10.5
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5772..6064): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 224.3
  inactive: 105.1
  Methylmalonyl-CoA: 55.0
  Methoxymalonyl-CoA: 53.2
  Propionyl-CoA: 37.5
  Isobutyryl-CoA: 29.8
  2-Methylbutyryl-CoA: 23.2
  Acetyl-CoA: 20.1
  Ethylmalonyl-CoA: 16.8
  Benzoyl-CoA: 16.4
  CHC-CoA: 7.7
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

B7024_RS02595: mmal - mmal
PKS_AT (564..862): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 219.9
  Ethylmalonyl-CoA: 210.9
  Methoxymalonyl-CoA: 183.4
  2-Methylbutyryl-CoA: 136.1
  trans-1,2-CPDA: 127.6
  Propionyl-CoA: 111.7
  CHC-CoA: 105.7
  Malonyl-CoA: 96.2
  Isobutyryl-CoA: 83.9
  Benzoyl-CoA: 68.7
  3-Methylbutyryl-CoA: 42.5
  fatty_acid: 40.4
  Acetyl-CoA: 33.8
  inactive: 22.0

PKS_AT (2098..2398): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Malonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 209.3
  Ethylmalonyl-CoA: 193.7
  Methoxymalonyl-CoA: 171.1
  2-Methylbutyryl-CoA: 137.4
  trans-1,2-CPDA: 131.9
  CHC-CoA: 109.2
  Malonyl-CoA: 106.1
  Propionyl-CoA: 100.1
  Isobutyryl-CoA: 77.8
  Benzoyl-CoA: 75.0
  Acetyl-CoA: 41.7
  fatty_acid: 37.4
  3-Methylbutyryl-CoA: 34.5
  inactive: 23.2

B7024_RS02600: mal
PKS_AT (519..812): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 240.8
  inactive: 109.7
  Methoxymalonyl-CoA: 64.1
  Methylmalonyl-CoA: 57.0
  Ethylmalonyl-CoA: 36.6
  Propionyl-CoA: 35.0
  Isobutyryl-CoA: 30.6
  Acetyl-CoA: 23.0
  Benzoyl-CoA: 19.9
  2-Methylbutyryl-CoA: 15.9
  trans-1,2-CPDA: 11.4
  CHC-CoA: 9.5
  fatty_acid: 9.3
  3-Methylbutyryl-CoA: 0.0

B7024_RS02630: mal - mal
PKS_AT (565..856): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 224.4
  inactive: 111.7
  Methoxymalonyl-CoA: 66.7
  Methylmalonyl-CoA: 64.6
  Propionyl-CoA: 40.2
  Isobutyryl-CoA: 38.2
  Benzoyl-CoA: 23.2
  2-Methylbutyryl-CoA: 22.4
  Acetyl-CoA: 19.8
  Ethylmalonyl-CoA: 18.3
  trans-1,2-CPDA: 17.3
  CHC-CoA: 17.1
  fatty_acid: 12.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2619..2910): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 224.3
  inactive: 109.9
  Methylmalonyl-CoA: 67.6
  Methoxymalonyl-CoA: 62.9
  Propionyl-CoA: 43.6
  Isobutyryl-CoA: 33.0
  2-Methylbutyryl-CoA: 23.9
  Benzoyl-CoA: 22.0
  Ethylmalonyl-CoA: 21.6
  CHC-CoA: 19.5
  trans-1,2-CPDA: 16.7
  Acetyl-CoA: 16.5
  3-Methylbutyryl-CoA: 0.0
  fatty_acid: -1.7

B7024_RS02635: mal - mal - mmal - mal - mal - mal
PKS_AT (558..851): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 235.5
  inactive: 98.1
  Methoxymalonyl-CoA: 73.0
  Methylmalonyl-CoA: 65.6
  Propionyl-CoA: 41.5
  Ethylmalonyl-CoA: 33.8
  Isobutyryl-CoA: 33.4
  2-Methylbutyryl-CoA: 30.9
  Benzoyl-CoA: 30.4
  Acetyl-CoA: 29.3
  CHC-CoA: 22.0
  trans-1,2-CPDA: 18.1
  fatty_acid: 14.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2301..2597): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 229.2
  inactive: 113.2
  Methoxymalonyl-CoA: 64.4
  Methylmalonyl-CoA: 57.5
  Propionyl-CoA: 35.5
  Benzoyl-CoA: 20.2
  Acetyl-CoA: 19.5
  Ethylmalonyl-CoA: 17.9
  Isobutyryl-CoA: 16.2
  trans-1,2-CPDA: 15.1
  2-Methylbutyryl-CoA: 15.1
  fatty_acid: 13.9
  CHC-CoA: 8.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3834..4134): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 213.6
  Ethylmalonyl-CoA: 203.9
  Methoxymalonyl-CoA: 176.5
  2-Methylbutyryl-CoA: 131.4
  trans-1,2-CPDA: 129.1
  Propionyl-CoA: 116.2
  CHC-CoA: 98.2
  Malonyl-CoA: 98.1
  Isobutyryl-CoA: 81.2
  Benzoyl-CoA: 69.7
  3-Methylbutyryl-CoA: 48.7
  fatty_acid: 34.6
  Acetyl-CoA: 33.7
  inactive: 22.5

PKS_AT (5367..5664): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 236.6
  inactive: 126.0
  Methoxymalonyl-CoA: 68.2
  Methylmalonyl-CoA: 59.3
  Propionyl-CoA: 37.6
  Isobutyryl-CoA: 28.4
  2-Methylbutyryl-CoA: 21.2
  Acetyl-CoA: 20.7
  Benzoyl-CoA: 19.2
  Ethylmalonyl-CoA: 17.8
  fatty_acid: 14.1
  CHC-CoA: 11.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (6887..7184): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 233.9
  inactive: 113.4
  Methoxymalonyl-CoA: 59.6
  Methylmalonyl-CoA: 53.0
  Propionyl-CoA: 26.5
  Isobutyryl-CoA: 22.6
  Acetyl-CoA: 21.4
  Benzoyl-CoA: 18.0
  Ethylmalonyl-CoA: 17.7
  fatty_acid: 17.4
  trans-1,2-CPDA: 9.7
  2-Methylbutyryl-CoA: 9.5
  CHC-CoA: 8.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (8399..8686): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 207.0
  inactive: 83.6
  Methylmalonyl-CoA: 50.8
  Methoxymalonyl-CoA: 50.7
  Propionyl-CoA: 27.9
  Benzoyl-CoA: 20.4
  Acetyl-CoA: 19.3
  Ethylmalonyl-CoA: 14.5
  Isobutyryl-CoA: 12.8
  2-Methylbutyryl-CoA: 10.8
  trans-1,2-CPDA: 7.3
  CHC-CoA: 3.4
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_NDXL01000001.1 - Region 9 - redox-cofactor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 757,241 - 779,335 nt. (total: 22,095 nt) Show pHMM detection rules used
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
B7024_RS03005: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold 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 | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001100.5 |  | 0.35 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0000874.5 |  | 0.30 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0000905.5 |  | 0.30 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000906.3 |  | 0.29 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000453.5 |  | 0.28 | NRPS | valinomycin | Streptomyces tsusimaensis
BGC0000265.5 |  | 0.26 | PKS | rhodomycin | Streptomyces purpurascens
BGC0001976.3 |  | 0.24 | terpene | eupenifeldin | Phoma sp.
BGC0000982.5 |  | 0.24 | NRPS, PKS | cystothiazole A | Cystobacter fuscus
BGC0001827.3 |  | 0.24 | PKS | xenovulene A | Sarocladium sp. 'schorii'
BGC0000075.5 |  | 0.23 | PKS | hygrocin A, hygrocin B | Streptomyces sp. LZ35

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001100.5 |  | 0.35 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0000874.5 |  | 0.30 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0000905.5 |  | 0.30 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000906.3 |  | 0.29 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000453.5 |  | 0.28 | NRPS | valinomycin | Streptomyces tsusimaensis
BGC0000265.5 |  | 0.26 | PKS | rhodomycin | Streptomyces purpurascens
BGC0001976.3 |  | 0.24 | terpene | eupenifeldin | Phoma sp.
BGC0000982.5 |  | 0.24 | NRPS, PKS | cystothiazole A | Cystobacter fuscus
BGC0001827.3 |  | 0.24 | PKS | xenovulene A | Sarocladium sp. 'schorii'
BGC0000075.5 |  | 0.23 | PKS | hygrocin A, hygrocin B | Streptomyces sp. LZ35

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.13 out of 20.47
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (7):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.37 out of 31.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.90 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.15 out of 21.55
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.40 out of 29.38
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.03 out of 30.12
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (757240...779335)
B7024_RS03035
  RRE type: PqqD_RRE
  Location: 4 - 84
  Score: 66.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
VqsM | Regulator of quorum-sensing signalling systems

NZ_NDXL01000001.1 - Region 10 - other
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: 807,085 - 848,464 nt. (total: 41,380 nt) Show pHMM detection rules used
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
B7024_RS03240: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

B7024_RS03255: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

B7024_RS03280: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Lyases: decarboxylase
B7024_RS03340: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Translocases: permease
B7024_RS03335: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

B7024_RS03390: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | other | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002573.2 |  | 0.59 | other (other) | phosphoramidon | Streptomyces mozunensis
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001184.4 |  | 0.43 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0001778.5 |  | 0.43 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000883.5 |  | 0.43 | other (other) | arginomycin | Streptomyces arginensis
BGC0002482.2 |  | 0.42 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0000709.5 |  | 0.41 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0001458.4 |  | 0.41 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0001972.4 |  | 0.40 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis
BGC0000340.5 |  | 0.40 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002573.2 |  | 0.59 | other (other) | phosphoramidon | Streptomyces mozunensis
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001184.4 |  | 0.43 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0001778.5 |  | 0.43 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000883.5 |  | 0.43 | other (other) | arginomycin | Streptomyces arginensis
BGC0002482.2 |  | 0.42 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0000709.5 |  | 0.41 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0001458.4 |  | 0.41 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0001972.4 |  | 0.40 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis
BGC0000340.5 |  | 0.40 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35

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:
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.87 out of 25.75
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.08 out of 18.57
Confidence: medium
Additional weak hits (12):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.57 out of 26.85
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.67 out of 32.74
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.05 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.63 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.21 out of 18.57
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.01 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.70 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.09 out of 36.54
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.87 out of 30.98
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.95 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.87 out of 33.14
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.53 out of 27.04
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MatP | Cell cycle regulator
ToxT | Regulator of MSHA biosynthesis

NZ_NDXL01000001.1 - Region 11 - NRP-metallophore,NRPS,T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 894,311 - 980,389 nt. (total: 86,079 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
B7024_RS03675: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

B7024_RS03875: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase methyltransferase transferase
B7024_RS03645: methyltransferase

smcogs
  SMCOG1089: methyltransferase

B7024_RS03680: Methylation

MITE
  MITE0000155Methylation (identity: 76.40%)
smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

B7024_RS03815: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

B7024_RS03825: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

B7024_RS03890: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: esterase hydrolase peptidase
B7024_RS03650: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

B7024_RS03655: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

B7024_RS03780: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

B7024_RS03810: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

B7024_RS03870: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: dehydratase hydratase
B7024_RS03790: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

B7024_RS03830: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

B7024_RS03835: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: isomerase mutase
B7024_RS03795: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

B7024_RS03910: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase synthase
B7024_RS03685: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

B7024_RS03800: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS03860: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: permease
B7024_RS03700: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | T3PKS | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  |  |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  |  |  | 0.62 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002135.2 |  |  |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002493.3 |  |  |  | 0.61 | NRPS | parabactin | Paracoccus denitrificans PD1222

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.83 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  | 0.64 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002493.3 |  | 0.64 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0002135.2 |  | 0.64 | 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.
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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.64 out of 26.33
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 36.53 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.36 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.73 out of 36.53
Confidence: medium
Additional weak hits (27):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.04 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.89 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.75 out of 30.22
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.23 out of 27.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.73 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.72 out of 28.14
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.35 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.72 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.24 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.07 out of 29.65
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.69 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.68 out of 39.62
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.31 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.29 out of 35.63
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.78 out of 39.62
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.82 out of 30.98
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.93 out of 26.85
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.99 out of 36.53
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.17 out of 39.62
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.69 out of 36.53
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 18, location 894310 - 980389:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 20, location 918113 - 980389:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B7024_RS03800: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (32..443): diOH-Bz
nrpys: diOH-Bz

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
  Small clusters prediction:
    Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
  Single AA prediction:
    dhb (diOH-Bz)

Stachelhaus prediction details:
  Stachelhaus sequence:
    SGSLFPLSSPGGGVLVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPGLGVVNK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

B7024_RS03860: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (474..868): 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:
    RWMTFDVSVWEWHFFCSGEHNLYGPTEAAVDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (100% 8Å match)
    Ala or Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
DmdR1 | Iron(II)-dependent repressor

NZ_NDXL01000001.1 - Region 12 - NRPS,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: 1,250,044 - 1,330,145 nt. (total: 80,102 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
B7024_RS05355: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS05370: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS05375: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS05385: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: aminotransferase methyltransferase
B7024_RS05310: aminotransferase

smcogs
  SMCOG1019: aminotransferase

B7024_RS05330: methyltransferase

smcogs
  SMCOG1089: methyltransferase

B7024_RS05380: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: back translocase esterase
B7024_RS05360: thioesterase

smcogs
  SMCOG1004: thioesterase

B7024_RS05390: thioesterase

smcogs
  SMCOG1004: thioesterase

B7024_RS05410: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

B7024_RS05415: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Lyases: hydratase
B7024_RS05315: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
B7024_RS05300: 1-deoxy-D-xylulose-5-phosphate synthase

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

B7024_RS05335: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B7024_RS05340: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B7024_RS05345: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B7024_RS05365: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS42160: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  | 0.84 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001135.5 |  |  | 0.80 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  |  | 0.78 | NRPS | enniatin | Fusarium equiseti
BGC0001128.4 |  |  | 0.78 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.78 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.78 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  |  | 0.75 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  |  | 0.75 | NRPS | AM-toxin | Alternaria alternata
BGC0002135.2 |  |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.75 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000342.4 |  | 0.74 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.31 out of 18.57
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.29 out of 23.43
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.93 out of 30.25
Confidence: medium
Additional weak hits (9):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.15 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.85 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.82 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.99 out of 30.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.10 out of 26.06
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.41 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.52 out of 20.01
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 21, location 1250043 - 1330145:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-Thr - Val - X - Pro) + (Pro - X) + (NMe-Val - NMe-Tyr) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 22, location 1250043 - 1325683:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-Thr - Val - X - Pro) + (Pro - X) + (NMe-Val - NMe-Tyr) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 23, location 1288333 - 1330145:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro - X) + (NMe-Val - NMe-Tyr) + (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).
B7024_RS05330: Thr - Val - X
Search NORINE for peptide: strict or relaxed
AMP-binding (26..437): 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:
    LATHFDFSVWEGNQVFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1523..1941): 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:
    LDSSFDASTFEGWLVVGGDVNGYGPTEMTTFVSR
  Nearest Stachelhaus code(s):
    Val DAFWVGGTFK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2601..3002): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LETSFDPSTYESLILTGGDRSLYGPTEITLCTAQ
  Nearest Stachelhaus code(s):
    Hpg DAYHLGLLCK (68% 8Å match)
  Stachelhaus code match:
    80% (moderate)

B7024_RS42160: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (5..270): Pro
nrpys: 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:
    LWQTFDVLVQESFAAQAGEVNHYGPAETHVVTSF
  Nearest Stachelhaus code(s):
    Pro DVQFAAHVVK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

B7024_RS05340: Pro - X
Search NORINE for peptide: strict or relaxed
AMP-binding (1630..2060): Pro
nrpys: 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:
    LWQTFDVLVQESFAAQAGEVNHYGPAETHVVTSF
  Nearest Stachelhaus code(s):
    Pro DVQFAAHVVK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2723..3124): X
nrpys: Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VDQGFDMSVGDMVAVTAGEFNAYGPTETTVCATT
  Nearest Stachelhaus code(s):
    Ala DVWVVAAVIK (71% 8Å match)
    Tyr DASTVAAVCK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

B7024_RS05345: Val - Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (472..890): 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:
    LDSSFDASTFEGWLVVGGDVNGYGPTEMTTFVSR
  Nearest Stachelhaus code(s):
    Val DAFWVGGTFK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1952..2347): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VDQVFDMAVGDMVAVAAGEFNAYGPTETTICATT
  Nearest Stachelhaus code(s):
    bOH-Tyr DTSKVAAICK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

B7024_RS05365: X
AMP-binding (25..417): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    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:
    FDDAFDASIFESFAITGGDFAAYGPTEATVFTSL
  Nearest Stachelhaus code(s):
    Ile DAGFIGAVFK (56% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
ColR | Phenol-responsive regulator
ToxT | Regulator of MSHA biosynthesis

NZ_NDXL01000001.1 - Region 13 - triceptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,581,049 - 1,602,273 nt. (total: 21,225 nt) Show pHMM detection rules used
triceptide: ((cds(PF04055 and (TIGR04085 or SPASM)) and triceptide_precursor) or triceptide_rSAM)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
B7024_RS06755: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

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

Reference | triceptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000593.4 |  | 0.43 | ribosomal | microviridin J | Microcystis aeruginosa MRC
BGC0000592.5 |  | 0.41 | ribosomal | microviridin B | Microcystis aeruginosa NIES-298
BGC0000591.5 |  | 0.40 | ribosomal | marinostatin | Alteromonas sp. B-10-31
BGC0002049.3 |  | 0.39 | ribosomal | microviridin N9, microviridin N8, microviridin N7, microviridin N6, microviridin N5, microviridin N4, microviridin N3 | Nostoc punctiforme PCC 73102
BGC0000594.5 |  | 0.37 | ribosomal | microviridin K | Planktothrix agardhii NIVA-CYA 126/8
BGC0001768.4 |  | 0.36 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4
BGC0001796.5 |  | 0.35 | NRPS | tauramamide | Brevibacillus laterosporus DSM 25
BGC0002626.2 |  | 0.34 | ribosomal | microviridin 1688, microviridin 1739, microviridin 1748 | Nostoc sp. TH1S01
BGC0000700.5 |  | 0.32 | saccharide | istamycin | Streptomyces tenjimariensis
BGC0002439.3 |  | 0.32 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000593.4 |  | 0.43 | ribosomal | microviridin J | Microcystis aeruginosa MRC
BGC0000592.5 |  | 0.41 | ribosomal | microviridin B | Microcystis aeruginosa NIES-298
BGC0000591.5 |  | 0.40 | ribosomal | marinostatin | Alteromonas sp. B-10-31
BGC0002049.3 |  | 0.39 | ribosomal | microviridin N9, microviridin N8, microviridin N7, microviridin N6, microviridin N5, microviridin N4, microviridin N3 | Nostoc punctiforme PCC 73102
BGC0000594.5 |  | 0.37 | ribosomal | microviridin K | Planktothrix agardhii NIVA-CYA 126/8
BGC0001768.4 |  | 0.36 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4
BGC0001796.5 |  | 0.35 | NRPS | tauramamide | Brevibacillus laterosporus DSM 25
BGC0002626.2 |  | 0.34 | ribosomal | microviridin 1688, microviridin 1739, microviridin 1748 | Nostoc sp. TH1S01
BGC0000700.5 |  | 0.32 | saccharide | istamycin | Streptomyces tenjimariensis
BGC0002439.3 |  | 0.32 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.65 out of 18.46
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.31 out of 23.79
Confidence: medium
Additional weak hits (14):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.75 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.10 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.74 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.11 out of 29.38
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.65 out of 29.51
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.60 out of 32.93
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.97 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.20 out of 29.65
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.10 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.09 out of 35.63
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.96 out of 36.53
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.43 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_NDXL01000001.1 - Region 14 - NRPS-like,lassopeptide,ranthipeptide
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: 1,789,969 - 1,854,354 nt. (total: 64,386 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)
ranthipeptide: (TIGR03973 or SCIFF or (cds(PF04055 and (TIGR04085 or SPASM)) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]) and not (TIGR01716 or subtilosin or TIGR02111 or TIGR03966 or TIGR04103 or (YcaO or TIGR03604))))
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lasso peptides
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
B7024_RS07640: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

B7024_RS07845: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

B7024_RS07865: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
B7024_RS07920: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: hydrolase
B7024_RS07900: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: decarboxylase
B7024_RS07630: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

B7024_RS07635: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: ligase
B7024_RS07720: 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 | ranthipeptide | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001539.4 |  |  |  | 0.39 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001634.3 |  |  |  | 0.36 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0000856.3 |  |  |  | 0.32 | other (other) | ectoine | Methylophaga thalassica
BGC0000565.5 |  |  |  | 0.31 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000853.3 |  |  |  | 0.30 | other (other) | ectoine | Streptomyces anulatus
BGC0002318.2 |  |  |  | 0.30 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000866.5 |  |  |  | 0.30 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000716.5 |  |  |  | 0.29 | saccharide | spectinomycin | Streptomyces netropsis
BGC0001435.4 |  |  |  | 0.29 | NRPS, PKS | ikarugamycin | Streptomyces sp. ZJ306
BGC0001440.5 |  |  |  | 0.28 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001539.4 |  | 0.52 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001634.3 |  | 0.51 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0002318.2 |  | 0.47 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000866.5 |  | 0.47 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0000853.3 |  | 0.45 | other (other) | ectoine | Streptomyces anulatus
BGC0000843.5 |  | 0.45 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0000700.5 |  | 0.45 | saccharide | istamycin | Streptomyces tenjimariensis
BGC0000578.3 |  | 0.45 | ribosomal | SRO15-2005 | Streptomyces filamentosus NRRL 15998
BGC0001440.5 |  | 0.44 | other (other) | cystargolide A, cystargolide B | Kitasatospora cystarginea

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.37 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.94 out of 20.97
Confidence: medium
Additional weak hits (14):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.67 out of 25.88
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.48 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.72 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.05 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.70 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.94 out of 33.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.61 out of 33.14
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.08 out of 27.18
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.76 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
Lasso peptides
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 disulfide 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 25, location 1789968 - 1854354:
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 26, location 1789968 - 1833499:
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).
B7024_RS07720: X
AMP-binding (88..520): 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:
    FDFLHVMGRGAGWWWAVSALDGYGSTEAGVVSLD
  Nearest Stachelhaus code(s):
    Abu or Ival DCGWVVGVVK (26% 8Å match)
  Stachelhaus code match:
    70% (weak)

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

ranthipeptide protocluster (1814045...1852532)
B7024_RS07895
  RRE type: Stand_Alone_Lasso_RRE
  Location: 4 - 83
  Score: 42.4
lassopeptide protocluster (1831792...1854354)
B7024_RS07895
  RRE type: Stand_Alone_Lasso_RRE
  Location: 4 - 83
  Score: 42.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_NDXL01000001.1 - Region 15 - PKS-like,T2PKS,other
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: 1,980,946 - 2,053,419 nt. (total: 72,474 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)
PKS-like: (t2pks2 or ksIII)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxygenase
B7024_RS08605: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

B7024_RS08630: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

B7024_RS08645: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B7024_RS08670: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS08680: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS08705: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS08715: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS08765: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS08785: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acylase aminotransferase glycosyltransferase kinase methyltransferase transferase
B7024_RS08585: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

B7024_RS08660: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

B7024_RS08700: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

B7024_RS08740: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B7024_RS08745: methyltransferase

smcogs
  SMCOG1089: methyltransferase

B7024_RS08755: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

B7024_RS08770: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

B7024_RS08815: aminotransferase

smcogs
  SMCOG1019: aminotransferase

B7024_RS08835: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: amidase hydrolase
B7024_RS08760: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

B7024_RS08790: amidase

smcogs
  SMCOG1105: amidase

Lyases: cyclase dehydratase
B7024_RS08590: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

B7024_RS08655: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

B7024_RS08710: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Ligases: synthase
B7024_RS08725: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS08730: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

B7024_RS08735: 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 | T2PKS | other | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000217.5 |  |  |  | 1.80 | PKS | daunorubicin | Streptomyces sp.
BGC0000218.5 |  |  |  | 1.70 | PKS | doxorubicin | Streptomyces peucetius
BGC0000231.5 |  |  |  | 1.12 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001160.5 |  |  |  | 0.85 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  | 0.85 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000234.5 |  |  |  | 0.84 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001254.3 |  |  |  | 0.80 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001723.5 |  |  |  | 0.76 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000272.3 |  |  |  | 0.72 | PKS | spore pigment | Streptomyces collinus
BGC0002000.4 |  |  |  | 0.72 | PKS | setomimycin | Streptomyces aurantiacus JA 4570

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000217.5 |  | 0.84 | PKS | daunorubicin | Streptomyces sp.
BGC0000218.5 |  | 0.82 | PKS | doxorubicin | Streptomyces peucetius
BGC0000231.5 |  | 0.70 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000234.5 |  | 0.62 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001254.3 |  | 0.60 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001723.5 |  | 0.59 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002000.4 |  | 0.58 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0000235.5 |  | 0.57 | PKS | kiamycin | Streptomyces sp. W007

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 23.25 out of 25.31
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.17 out of 25.31
Confidence: medium
Additional weak hits (15):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.57 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.33 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.73 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.01 out of 32.74
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.26 out of 18.57
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.46 out of 27.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.99 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.14 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.16 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.94 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.71 out of 35.63
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.76 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.08 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.60 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
Type II PKS
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B7024_RS08740: mal
PKS_AT (8..297): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 66.7%
  inactive: 58.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 31.3
  Methoxymalonyl-CoA: 27.9
  Methylmalonyl-CoA: 27.3
  Propionyl-CoA: 25.8
  inactive: 11.8
  Ethylmalonyl-CoA: 8.3
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-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

Link to PARAS substrate predictor
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  1980945 to 2053419
Starter unit(s):
  propionyl-CoA (Score: 977.0; E-value: 0)
Malonyl elongations:
  8|9 (Score: 648.5; E-value: 8.1e-198)
Product class(es):
  anthracycline
Product molecular weight(s):
  propionyl-CoA_8: 725 Da
  propionyl-CoA_9: 767 Da

B7024_RS08605
  OXY (Score: 252.3; E-value: 2.3e-77)
B7024_RS08640
  CYC C5-C14/C3-C16 (Score: 435.3; E-value: 1.7e-133)
B7024_RS08680
  KR (Score: 68.2; E-value: 2e-21)
B7024_RS08685
  ACP (Score: 98.8; E-value: 3.2e-31)
B7024_RS08690
  CYC (Score: 13.5; E-value: 8.5e-05)
B7024_RS08700
  GT (Score: 454.1; E-value: 1.2e-138)
B7024_RS08705
  KR C17 (Score: 381.7; E-value: 3.4e-117)
B7024_RS08710
  CYC C7-C12 (Score: 439.5; E-value: 1.2e-134)
B7024_RS08715
  KR C9 (Score: 466.7; E-value: 4.5e-143)
B7024_RS08725
  KS (Score: 714.4; E-value: 9.7e-218)
B7024_RS08730
  CLF 8|9 (Score: 648.5; E-value: 8.1e-198)
B7024_RS08735
  KSIII (Score: 489.8; E-value: 9.4e-150)
  KSIII WP_100109100.1_Doxorubicin_propionyl-CoA (Score: 536.0; E-value: 0.0)
B7024_RS08740
  AT (Score: 438.2; E-value: 4.6e-134)
  AT AAA87621.1_Daunomycin_propionyl-CoA (Score: 441.0; E-value: 1.11e-159)
B7024_RS08745
  MET carboxy_O (Score: 356.2; E-value: 2e-109)
B7024_RS08750
  CYC C2-C19 (Score: 272.5; E-value: 1.4e-84)
B7024_RS08755
  MET (Score: 291.3; E-value: 2.2e-89)
B7024_RS08770
  GT (Score: 452.6; E-value: 3.6e-138)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_NDXL01000001.1 - Region 16 - triceptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,355,202 - 2,376,714 nt. (total: 21,513 nt) Show pHMM detection rules used
triceptide: ((cds(PF04055 and (TIGR04085 or SPASM)) and triceptide_precursor) or triceptide_rSAM)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
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 | triceptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002316.2 |  | 0.39 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000515.4 |  | 0.33 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.32 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000556.5 |  | 0.32 | ribosomal | streptin | Streptococcus pyogenes
BGC0001789.3 |  | 0.31 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000536.3 |  | 0.31 | ribosomal | nisin Q | Lactococcus lactis
BGC0000535.4 |  | 0.31 | ribosomal | nisin A | Lactococcus lactis subsp. lactis
BGC0000559.4 |  | 0.31 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000537.3 |  | 0.31 | ribosomal | nisin U | Streptococcus uberis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002316.2 |  | 0.39 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000515.4 |  | 0.33 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.32 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000556.5 |  | 0.32 | ribosomal | streptin | Streptococcus pyogenes
BGC0001789.3 |  | 0.31 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000536.3 |  | 0.31 | ribosomal | nisin Q | Lactococcus lactis
BGC0000535.4 |  | 0.31 | ribosomal | nisin A | Lactococcus lactis subsp. lactis
BGC0000559.4 |  | 0.31 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000537.3 |  | 0.31 | ribosomal | nisin U | Streptococcus uberis

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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
Additional weak hits (6):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.88 out of 26.85
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.33 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.19 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.97 out of 30.22
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.57 out of 27.04
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor

NZ_NDXL01000001.1 - Region 17 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,065,827 - 3,098,710 nt. (total: 32,884 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
B7024_RS13385: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
B7024_RS13325: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: amidase
B7024_RS13380: amidase

smcogs
  SMCOG1105: amidase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0002163.3 |  | 0.53 | other (other) | fusatin, fusatinic acid, 8-oxo-fusatin, 8-oxo-isopentenyladenine | Fusarium pseudograminearum CS3096
BGC0001713.5 |  | 0.53 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002683.2 |  | 0.51 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002470.2 |  | 0.51 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0001531.5 |  | 0.51 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002633.2 |  | 0.51 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0002163.3 |  | 0.53 | other (other) | fusatin, fusatinic acid, 8-oxo-fusatin, 8-oxo-isopentenyladenine | Fusarium pseudograminearum CS3096
BGC0001713.5 |  | 0.53 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002683.2 |  | 0.51 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002470.2 |  | 0.51 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0001531.5 |  | 0.51 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002633.2 |  | 0.51 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.37 out of 20.47
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 25.29 out of 27.18
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.83 out of 27.18
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72
Confidence: medium
Additional weak hits (7):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.42 out of 18.57
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.53 out of 31.73
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.05 out of 31.73
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.63 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.67 out of 25.75
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
LexA variant 2 | Repressor of DNA damage response
MexT | Global virulence regulator
NrdR | Represses ribonucleotide reductase encoding genes
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_NDXL01000001.1 - Region 18 - T1PKS,butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,183,500 - 3,233,372 nt. (total: 49,873 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))
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
B7024_RS13780: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS13810: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS13830: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

B7024_RS13840: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS13860: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: PPTase aminotransferase halogenase
B7024_RS13795: halogenase

smcogs
  SMCOG1119: halogenase

B7024_RS13845: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

B7024_RS13890: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: dehalogenase
B7024_RS13815: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: dehydratase
B7024_RS13835: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
B7024_RS13770: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS13800: 3-oxoacyl-(acyl carrier protein) synthase III

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

B7024_RS13805: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS13855: 3-oxoacyl-(acyl carrier protein) synthase III

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

B7024_RS13865: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS13875: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: permease
B7024_RS13745: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | T1PKS | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001164.3 |  |  | 0.53 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.53 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002174.2 |  |  | 0.48 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001273.3 |  |  | 0.43 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.42 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.42 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001162.3 |  |  | 0.35 | PKS | 1-heptadecene | Moorea producens JHB
BGC0001163.3 |  |  | 0.35 | PKS | 1-heptadecene | Moorea producens 3L
BGC0001161.5 |  |  | 0.35 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0000041.3 |  |  | 0.33 | PKS | oronofacic acid | Pseudomonas syringae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.66 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
Additional weak hits (15):
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.42 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.58 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.94 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.96 out of 36.54
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.48 out of 27.55
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.90 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.35 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.51 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.81 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.35 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.53 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.93 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 32, location 3183499 - 3233372:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-ccmal) + (mal)
Non-colinear ordering:
  B7024_RS13810 + B7024_RS13805

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).
B7024_RS13770: X
AMP-binding (22..429): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    QIILHDMGMF--AGVIGAEQPAYGMAEATLAVTG
  Nearest Stachelhaus code(s):
    Trp DAGIVGACAK (41% 8Å match)
    Arg DAEGVGAIAK (38% 8Å match)
    Cit DMEADGAVDK (35% 8Å match)
    Ala DVFFVGLVAK (29% 8Å match)
  Stachelhaus code match:
    60% (weak)

B7024_RS13805: mal
PKS_AT (569..863): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 200.0
  inactive: 98.4
  Methoxymalonyl-CoA: 61.0
  Methylmalonyl-CoA: 52.1
  Propionyl-CoA: 33.3
  Benzoyl-CoA: 28.7
  Isobutyryl-CoA: 23.0
  Acetyl-CoA: 19.2
  CHC-CoA: 18.8
  Ethylmalonyl-CoA: 12.1
  2-Methylbutyryl-CoA: 10.7
  trans-1,2-CPDA: 6.8
  fatty_acid: 6.6
  3-Methylbutyryl-CoA: 0.0

B7024_RS13810: mmal
PKS_AT (679..983): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Malonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 203.4
  Ethylmalonyl-CoA: 195.7
  Methoxymalonyl-CoA: 169.6
  2-Methylbutyryl-CoA: 155.9
  Propionyl-CoA: 129.9
  trans-1,2-CPDA: 126.3
  CHC-CoA: 125.2
  Malonyl-CoA: 107.5
  Isobutyryl-CoA: 77.6
  Benzoyl-CoA: 64.9
  Acetyl-CoA: 50.9
  fatty_acid: 47.1
  3-Methylbutyryl-CoA: 40.2
  inactive: 25.3

B7024_RS13865: X
AMP-binding (37..371): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNALYALVAQAAAVAVGGDYLTYGLTEATLAAHA
  Nearest Stachelhaus code(s):
    Suc ALQSTGTPRK (74% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
RpoN | Regulator of nitrogen assimilation and virulence

NZ_NDXL01000001.1 - Region 19 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,297,917 - 3,320,448 nt. (total: 22,532 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
B7024_RS14210: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001539.4 |  | 0.52 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001634.3 |  | 0.48 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001645.3 |  | 0.47 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0002318.2 |  | 0.46 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000277.5 |  | 0.40 | PKS | urdamycin | Streptomyces fradiae
BGC0000578.3 |  | 0.40 | ribosomal | SRO15-2005 | Streptomyces filamentosus NRRL 15998
BGC0002104.3 |  | 0.26 | NRPS, PKS | eurocidin D, eurocidin E | Streptomyces eurocidicus ATCC 27428
BGC0000722.5 |  | 0.24 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. jinggangensis
BGC0002293.2 |  | 0.24 | NRPS | ohmyungsamycin A, ohmyungsamycin B | Streptomyces sp.
BGC0000409.5 |  | 0.24 | NRPS | porothramycin A | Streptomyces albus subsp. albus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001539.4 |  | 0.52 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001634.3 |  | 0.48 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001645.3 |  | 0.47 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0002318.2 |  | 0.46 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000277.5 |  | 0.40 | PKS | urdamycin | Streptomyces fradiae
BGC0000578.3 |  | 0.40 | ribosomal | SRO15-2005 | Streptomyces filamentosus NRRL 15998
BGC0002104.3 |  | 0.26 | NRPS, PKS | eurocidin D, eurocidin E | Streptomyces eurocidicus ATCC 27428
BGC0000722.5 |  | 0.24 | other (cyclitol), saccharide | validamycin A | Streptomyces hygroscopicus subsp. jinggangensis
BGC0002293.2 |  | 0.24 | NRPS | ohmyungsamycin A, ohmyungsamycin B | Streptomyces sp.
BGC0000409.5 |  | 0.24 | NRPS | porothramycin A | Streptomyces albus subsp. albus

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.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lassopeptide(s) for B7024_RS41330

B7024_RS41330
Leader:
MEHTTQTPAYQAPIVLDAGDVVEVTL
Full core:
G T Q N F D T A D D T Q Y K N A
Putative macrolactam:
G T Q N F D T A D

#### antiSMASH-DB 4.0 matches for B7024_RS41330

100.0%
NZ_CP058556.1 and 1 other:
NZ_NDXL01000001.1 Lassopeptides: B7024_RS41330_lassopeptide
Lassopeptides: HXS80_RS05610_lassopeptide
1
G T Q N F D T A D D T Q Y K N A
16
G T Q N F D T A D D T Q Y K N A
1
G T Q N F D T A D D T Q Y K N A
16
93.8%
NZ_AP019620.1 and 8 others:
NZ_CP019458.1 Lassopeptides: BV401_RS42770_lassopeptide NZ_CP029823.1 Lassopeptides: DNK48_RS31710_lassopeptide NZ_CP054916.1 Lassopeptides: HUT19_RS28470_lassopeptide NZ_CP084681.1 Lassopeptides: KI385_RS02505_lassopeptide NZ_JANCLX010000011.1 Lassopeptides: NMK44_RS19060_lassopeptide NZ_LT907981.1 Lassopeptides: CPH93_RS35700_lassopeptide NZ_NNBP01000024.1 Lassopeptides: CG747_RS46950_lassopeptide NZ_VSKT01000018.1 Lassopeptides: allorf_84246_84536_lassopeptide
Lassopeptides: GYK45_RS31700_lassopeptide
1
G T Q N F D T A D D T Q Y K N A
16
G T N F D T A D D T Q Y K N A
1
G T N N F D T A D D T Q Y K N A
16
93.8%
NZ_LWLE01000015.1:
Lassopeptides: A6A29_RS44175_lassopeptide
1
G T Q N F D T A D D T Q Y K N A
16
G T Q F D T A D D T Q Y K N A
1
G T Q T F D T A D D T Q Y K N A
16
with 19 more sequence matches
Only the first 10 are displayed here.
93.8%
NZ_VEHK01000011.1:
Lassopeptides: FS984_RS26875_lassopeptide
1
G T Q N F D T A D D T Q Y K N A
16
G T+N F D T A D D T Q Y K N A
1
G T E N F D T A D D T Q Y K N A
16
87.5%
NZ_CP045178.1 and 1 other:
NZ_NDXL01000001.1 Lassopeptides: B7024_RS40605_lassopeptide
Lassopeptides: GBW32_RS37240_lassopeptide
1
G T Q N F D T A D D T Q Y K N A
16
G T N F D T A D D T+Y K N A
1
G T N N F D T A D D T E Y K N A
16
81.2%
NZ_CP042266.1:
Lassopeptides: FQU76_RS10490_lassopeptide
1
G T Q N F D T A D D T Q Y K N A
16
G T+ F D T A D D T+Y K N A
1
G T E T F D T A D D T E Y K N A
16
81.2%
NZ_CP118575.1:
Lassopeptides: PV796_RS40100_lassopeptide
1
G T Q N F D T A D D T Q Y K N A
16
G T N F D A D D T+Y K N A
1
G T N N F D H A D D T E Y K N A
16
81.2%
NZ_JABBGE010000005.1:
Lassopeptides: HHL19_RS16445_lassopeptide
1
G T Q N F D T A D D T Q Y K N
15
G T Q+F D T A D D T Q Y K+
1
G T Q S F D T A D D T Q Y K H
15
81.2%
NZ_SMSN01000051.1:
Lassopeptides: E2C11_RS23985_lassopeptide
1
G T Q N F D T A D D T Q Y K N A
16
G T F D T A D D T+Y K N A
1
G T N T F D T A D D T E Y K N A
16
81.2%
NZ_VEHK01000001.1:
Lassopeptides: FS984_RS39240_lassopeptide
1
G T Q N F D T A D D T Q Y K N A
16
G T +F D T A D D T+Y K N A
1
G T N S F D T A D D T E Y K N A
16
75.0%
NZ_BMNG01000026.1 and 1 other:
NZ_LT907981.1 Lassopeptides: CPH93_RS35415_lassopeptide
Lassopeptides: IEY91_RS39205_lassopeptide
1
G T Q N F D T A D D T Q Y K N
15
G T Q F D T A D D T+Y K+
1
G T Q P F D T A D D T E Y K H
15
70.6%
NZ_BMUT01000019.1 and 2 others:
NZ_JACHJF010000007.1 Lassopeptides: FHS36_RS14205_lassopeptide NZ_WPBY01000022.1 Lassopeptides: GO001_RS23565_lassopeptide
Lassopeptides: IE241_RS30965_lassopeptide
1
G T Q N F D T A D D T Q Y K
14
G Q N F D T D D T Q Y K
1
G N Q N F D T V D D T Q Y K
14
68.8%
NC_015951.1:
Lassopeptides: STRVI_RS44745_lassopeptide
1
G T Q N F D T A D D T Q Y K
14
G T Q D+A D D T Q Y K
1
G T Q Y Q D S A D D T Q Y K
14

#### 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:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.44 out of 36.53
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (2):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.29 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.89 out of 27.78
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

B7024_RS41330 - Class II
  Cleavage pHMM score: 0.80
  RODEO score: 20
  Monoisotopic mass: 1769.7 Da
  Molecular weight: 1770.8 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (3297916...3320448)
B7024_RS14205
  RRE type: Stand_Alone_Lasso_RRE
  Location: 2 - 81
  Score: 45.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_NDXL01000001.1 - Region 20 - 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: 3,321,521 - 3,332,336 nt. (total: 10,816 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: electron transfer
B7024_RS14275: flavodoxin

smcogs
  SMCOG1134: flavodoxin

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001882.3 |  | 0.28 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0000366.5 |  | 0.25 | NRPS | gobichelin A, gobichelin B | Streptomyces sp. NRRL F-4415
BGC0001830.3 |  | 0.23 | PKS | rosamicin, salinipyrone A, pacificanone A | Salinispora pacifica
BGC0000981.3 |  | 0.23 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E6
BGC0000031.5 |  | 0.21 | PKS | borrelidin | Streptomyces parvulus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001882.3 |  | 0.28 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0000366.5 |  | 0.25 | NRPS | gobichelin A, gobichelin B | Streptomyces sp. NRRL F-4415
BGC0001830.3 |  | 0.23 | PKS | rosamicin, salinipyrone A, pacificanone A | Salinispora pacifica
BGC0000981.3 |  | 0.23 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E6
BGC0000031.5 |  | 0.21 | PKS | borrelidin | Streptomyces parvulus

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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 25.31
Confidence: medium
Additional weak hits (6):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.99 out of 29.25
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.71 out of 20.01
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.14 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.97 out of 31.73
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.78 out of 27.18
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 out of 30.98
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor

NZ_NDXL01000001.1 - Region 21 - betalactone,butyrolactone,lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,354,618 - 3,401,696 nt. (total: 47,079 nt) Show pHMM detection rules used
butyrolactone: AfsA
betalactone: (HMGL-like and AMP-binding)
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
B7024_RS14405: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

B7024_RS14420: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

B7024_RS14450: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B7024_RS14475: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS14500: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

B7024_RS14505: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

B7024_RS14535: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS43125: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: methyltransferase
B7024_RS14540: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
B7024_RS14430: HAD-superfamily hydrolase, subfamily IA, variant

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

B7024_RS14480: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: cyclase dehydratase hydratase lyase
B7024_RS14400: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

B7024_RS14470: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

B7024_RS14550: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

B7024_RS14555: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: synthase
B7024_RS14485: 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 | butyrolactone | betalactone | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000848.5 |  |  |  | 0.96 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  |  |  | 0.70 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  |  |  | 0.58 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002576.2 |  |  |  | 0.44 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002578.2 |  |  |  | 0.34 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000243.4 |  |  |  | 0.30 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0000829.5 |  |  |  | 0.29 | other (other) | violacein | Chromobacterium violaceum
BGC0001985.4 |  |  |  | 0.28 | other (other) | Pyrazofurin | Streptomyces candidus
BGC0001302.5 |  |  |  | 0.27 | other (other) | lomofungin | Streptomyces lomondensis
BGC0001633.3 |  |  |  | 0.27 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.77 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0000849.4 |  | 0.68 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.63 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001289.5 |  | 0.54 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002578.2 |  | 0.53 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002635.2 |  | 0.52 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001985.4 |  | 0.49 | other (other) | Pyrazofurin | Streptomyces candidus
BGC0000544.4 |  | 0.48 | ribosomal | planosporicin | Planomonospora alba
BGC0001302.5 |  | 0.47 | other (other) | lomofungin | Streptomyces lomondensis

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 B7024_RS14545

B7024_RS14560
Leader:
MTTALLAAETDLDLDLADLDLDIQTAVTGGANAPLEPT
Core:
M F T F I T C D T G G A T G T S C A F T N G C N P M C C
Core with dehydrations:
M F Dhb F I Dhb Cys D Dhb G G A Dhb G Dhb Dha Cys A F Dhb N G Cys N P M Cys Cys

#### antiSMASH-DB 4.0 matches for B7024_RS14560

100.0%
NZ_NDXL01000001.1 and 1 other:
NZ_NDXL01000001.1 Lanthipeptides: B7024_RS14560_lanthipeptide
Lanthipeptides: B7024_RS14560_lanthipeptide
1
M F T F I T C D T G G A T G T S C A F T N G C N P M C C
28
M F T F I T C D T G G A T G T S C A F T N G C N P M C C
1
M F T F I T C D T G G A T G T S C A F T N G C N P M C C
28
74.2%
NZ_KB890946.1 and 1 other:
NZ_KB890946.1 Lanthipeptides: B053_RS0127015_lanthipeptide
Lanthipeptides: B053_RS0127015_lanthipeptide
1
M F T F I T C D T G G A T G T S C A F T N G C N P M C C
28
M F T F I T C+T G T G T S C F T+G C N P M C C
4
M F T F I T C E T T G T T G T S C G F T D G C N P M C C
31
51.6%
NZ_CP051486.1:
Lanthipeptides: allorf_1199788_1199997_lanthipeptide
2
F T F I T C D T G G A T G T S C A F T N G C N P M C C
28
+T+ +C G A T G T S C F T C N P+C C
5
W T Y G S C G C T G A T G T S C G F T E A C N P L C C
31
with 5 more sequence matches
39.3%
NZ_JALLPQ010000001.1:
Lanthipeptides: MWG58_RS11840_lanthipeptide
13
T G T S C A F T N G C N P M C C
28
+ T S C T N G C N P C C
13
S A T S C F A T N G C N P S C C
28
36.7%
NZ_CP034351.1 and 1 other:
NZ_CP034351.1 Lanthipeptides: D1J60_RS35670_lanthipeptide
Lanthipeptides: D1J60_RS35670_lanthipeptide
2
F T F I T C D T G G A T G T S C A F T N G C N P M C C
28
F T I T C + A T T + + P C C
3
F T K I T C G S K S A T S T I I S C V D E L G P T C C
29
21.4%
NZ_CP034550.1:
Lanthipeptides: EKG83_RS09715_lanthipeptide
17
C A F T N G C N P M C
27
C A +G C+P C
5
C A T D D G C D P T C
15
20.7%
NZ_CP036016.1:
Lanthipeptides: allorf_075467_075682_lanthipeptide
11
G A T G T S C A F T N G C N P M C
27
G G++C + C P C
12
G N D G S T C T L S V E C R P A C
28
17.9%
NZ_CP012752.1 and 1 other:
NZ_QQAU01000011.1 Lanthipeptides: DFR72_RS30360_lanthipeptide
Lanthipeptides: AOZ06_RS53910_lanthipeptide
14
G T S C A F T N G C N P M C
27
++C ++G C+P C
2
A S A C D T S D G C D P T C
15

#### MIBiG 4.0 matches for B7024_RS14560

14.3%
BGC0001155.5 (AGY49587.1):
Thiopeptide: GE2270
17
C A F T N G C N P
25
C F C+P
6
C G F C C S C S P
14

#### Lanthipeptide(s) for B7024_RS14555

B7024_RS14560
Leader:
MTTALLAAETDLDLDLADLDLDIQTAVTGGANAPLEPT
Core:
M F T F I T C D T G G A T G T S C A F T N G C N P M C C
Core with dehydrations:
M F Dhb F I Dhb Cys D Dhb G G A Dhb G Dhb Dha Cys A F Dhb N G Cys N P M Cys Cys

#### antiSMASH-DB 4.0 matches for B7024_RS14560

100.0%
NZ_NDXL01000001.1 and 1 other:
NZ_NDXL01000001.1 Lanthipeptides: B7024_RS14560_lanthipeptide
Lanthipeptides: B7024_RS14560_lanthipeptide
1
M F T F I T C D T G G A T G T S C A F T N G C N P M C C
28
M F T F I T C D T G G A T G T S C A F T N G C N P M C C
1
M F T F I T C D T G G A T G T S C A F T N G C N P M C C
28
74.2%
NZ_KB890946.1 and 1 other:
NZ_KB890946.1 Lanthipeptides: B053_RS0127015_lanthipeptide
Lanthipeptides: B053_RS0127015_lanthipeptide
1
M F T F I T C D T G G A T G T S C A F T N G C N P M C C
28
M F T F I T C+T G T G T S C F T+G C N P M C C
4
M F T F I T C E T T G T T G T S C G F T D G C N P M C C
31
51.6%
NZ_CP051486.1:
Lanthipeptides: allorf_1199788_1199997_lanthipeptide
2
F T F I T C D T G G A T G T S C A F T N G C N P M C C
28
+T+ +C G A T G T S C F T C N P+C C
5
W T Y G S C G C T G A T G T S C G F T E A C N P L C C
31
with 5 more sequence matches
39.3%
NZ_JALLPQ010000001.1:
Lanthipeptides: MWG58_RS11840_lanthipeptide
13
T G T S C A F T N G C N P M C C
28
+ T S C T N G C N P C C
13
S A T S C F A T N G C N P S C C
28
36.7%
NZ_CP034351.1 and 1 other:
NZ_CP034351.1 Lanthipeptides: D1J60_RS35670_lanthipeptide
Lanthipeptides: D1J60_RS35670_lanthipeptide
2
F T F I T C D T G G A T G T S C A F T N G C N P M C C
28
F T I T C + A T T + + P C C
3
F T K I T C G S K S A T S T I I S C V D E L G P T C C
29
21.4%
NZ_CP034550.1:
Lanthipeptides: EKG83_RS09715_lanthipeptide
17
C A F T N G C N P M C
27
C A +G C+P C
5
C A T D D G C D P T C
15
20.7%
NZ_CP036016.1:
Lanthipeptides: allorf_075467_075682_lanthipeptide
11
G A T G T S C A F T N G C N P M C
27
G G++C + C P C
12
G N D G S T C T L S V E C R P A C
28
17.9%
NZ_CP012752.1 and 1 other:
NZ_QQAU01000011.1 Lanthipeptides: DFR72_RS30360_lanthipeptide
Lanthipeptides: AOZ06_RS53910_lanthipeptide
14
G T S C A F T N G C N P M C
27
++C ++G C+P C
2
A S A C D T S D G C D P T C
15

#### MIBiG 4.0 matches for B7024_RS14560

14.3%
BGC0001155.5 (AGY49587.1):
Thiopeptide: GE2270
17
C A F T N G C N P
25
C F C+P
6
C G F C C S C S P
14

#### 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: 20.04 out of 23.79
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52
Confidence: strong
Additional weak hits (18):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.64 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.22 out of 30.22
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.77 out of 33.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.84 out of 30.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.03 out of 39.62
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.76 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.61 out of 26.06
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.11 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.45 out of 27.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.93 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.21 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.37 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.34 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 35.63
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.50 out of 24.78
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.90 out of 33.14
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

B7024_RS14560 - Class I
  Cleavage pHMM score: 0.40
  RODEO score: 16
  Monoisotopic mass: 2727.1 Da
  Molecular weight: 2729.1 Da
  Number of bridges: 5
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2747.2 Da N = 1
    2765.2 Da N = 2
B7024_RS14560 - Class I
  Cleavage pHMM score: 0.40
  RODEO score: 16
  Monoisotopic mass: 2727.1 Da
  Molecular weight: 2729.1 Da
  Number of bridges: 5
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2747.2 Da N = 1
    2765.2 Da N = 2

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (3376114...3401696)
B7024_RS14555
  RRE type: Lanthipeptide_LanB_RRE
  Location: 158 - 258
  Score: 54.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism

NZ_NDXL01000001.1 - Region 22 - 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: 3,531,074 - 3,542,454 nt. (total: 11,381 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
B7024_RS15190: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Hydrolases: hydrolase
B7024_RS15195: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000843.5 |  | 0.34 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0002007.2 |  | 0.33 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0002387.2 |  | 0.32 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0002788.2 |  | 0.31 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0001377.5 |  | 0.30 | PKS | uncialamycin | Streptomyces uncialis
BGC0001925.4 |  | 0.28 | other (other) | altemicidin, SB-203207, SB-203208 | Streptomyces sp.
BGC0001177.4 |  | 0.28 | PKS | mensacaricin | Streptomyces bottropensis
BGC0000232.5 |  | 0.28 | PKS | hatomarubigin A, hatomarubigin B, hatomarubigin C, hatomarubigin D | Streptomyces sp. 2238-SVT4
BGC0001564.4 |  | 0.27 | NRPS, PKS | cusperin | Cuspidothrix issatschenkoi CHARLIE-1
BGC0000274.5 |  | 0.27 | PKS | tetarimycin A, tetarimycin B | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000843.5 |  | 0.34 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0002007.2 |  | 0.33 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0002387.2 |  | 0.32 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0002788.2 |  | 0.31 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0001377.5 |  | 0.30 | PKS | uncialamycin | Streptomyces uncialis
BGC0001925.4 |  | 0.28 | other (other) | altemicidin, SB-203207, SB-203208 | Streptomyces sp.
BGC0001177.4 |  | 0.28 | PKS | mensacaricin | Streptomyces bottropensis
BGC0000232.5 |  | 0.28 | PKS | hatomarubigin A, hatomarubigin B, hatomarubigin C, hatomarubigin D | Streptomyces sp. 2238-SVT4
BGC0001564.4 |  | 0.27 | NRPS, PKS | cusperin | Cuspidothrix issatschenkoi CHARLIE-1
BGC0000274.5 |  | 0.27 | PKS | tetarimycin A, tetarimycin B | 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.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.61 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.20 out of 39.62
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_NDXL01000001.1 - Region 23 - hydrogen-cyanide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,600,020 - 3,612,860 nt. (total: 12,841 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase reductase
B7024_RS15495: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

B7024_RS15500: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

B7024_RS15510: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Hydrolases: deaminase
B7024_RS15530: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

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

Reference | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0000603.5 |  | 0.34 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0002285.2 |  | 0.33 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000339.5 |  | 0.29 | NRPS | echinomycin | Streptomyces lasaliensis
BGC0000595.3 |  | 0.29 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001649.3 |  | 0.26 | PKS | lavendiol | Streptomyces lavendulae
BGC0001001.5 |  | 0.24 | NRPS, PKS | jamaicamide A, jamaicamide B, jamaicamide C | Lyngbya majuscula
BGC0000135.5 |  | 0.23 | PKS | reveromycin A | Streptomyces sp. SN-593
BGC0000949.5 |  | 0.22 | NRPS | A-500359 A, A-500359 B | Streptomyces griseus
BGC0000291.5 |  | 0.22 | NRPS | A54145 | Streptomyces fradiae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0000603.5 |  | 0.34 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0002285.2 |  | 0.33 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000339.5 |  | 0.29 | NRPS | echinomycin | Streptomyces lasaliensis
BGC0000595.3 |  | 0.29 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001649.3 |  | 0.26 | PKS | lavendiol | Streptomyces lavendulae
BGC0001001.5 |  | 0.24 | NRPS, PKS | jamaicamide A, jamaicamide B, jamaicamide C | Lyngbya majuscula
BGC0000135.5 |  | 0.23 | PKS | reveromycin A | Streptomyces sp. SN-593
BGC0000949.5 |  | 0.22 | NRPS | A-500359 A, A-500359 B | Streptomyces griseus
BGC0000291.5 |  | 0.22 | NRPS | A54145 | Streptomyces fradiae

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:
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40
Confidence: strong
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.52 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.51 out of 30.22
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.52 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.60 out of 36.54
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.83 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.16 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
HypR | L-hydroxyproline utilization repressor

NZ_NDXL01000001.1 - Region 24 - lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,944,307 - 3,966,871 nt. (total: 22,565 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
B7024_RS17105: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold 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-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.55 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.54 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.53 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000501.3 |  | 0.53 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0002700.2 |  | 0.52 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000496.5 |  | 0.50 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000553.3 |  | 0.50 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002111.3 |  | 0.49 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000518.3 |  | 0.46 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002698.2 |  | 0.44 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.55 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.54 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.53 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000501.3 |  | 0.53 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0002700.2 |  | 0.52 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000496.5 |  | 0.50 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000553.3 |  | 0.50 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002111.3 |  | 0.49 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000518.3 |  | 0.46 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002698.2 |  | 0.44 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566

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 B7024_RS17095

B7024_RS17090
Leader:
MAILDLQTMEPPESEAAP
Core:
I D D V L A T G S S L S V L N C T V S T V S T L L C L
Core with dehydrations:
I D D V L A Dhb G Dha Dha L Dha V L N Cys Dhb V Dha Dhb V Dha Dhb L L Cys L

#### antiSMASH-DB 4.0 matches for B7024_RS17090

100.0%
NZ_NDXL01000001.1:
Lanthipeptides: B7024_RS17090_lanthipeptide
1
I D D V L A T G S S L S V L N C T V S T V S T L L C L
27
I D D V L A T G S S L S V L N C T V S T V S T L L C L
1
I D D V L A T G S S L S V L N C T V S T V S T L L C L
27
81.5%
NZ_CP054919.1 and 1 other:
NZ_JAGIYX010000006.1 Lanthipeptides: J5Y04_RS12150_lanthipeptide
Lanthipeptides: HUT16_RS18950_lanthipeptide
1
I D D V L A T G S S L S V L N C T V S T V S T L L C L
27
I D D L A+ S S L S V L N C S T V S T L L C L
1
I D D T L A S T S S L S V L N C G T S T V S T L L C L
27
63.0%
NZ_KK853997.1 and 1 other:
NZ_NNBO01000001.1 Lanthipeptides: CG736_RS00225_lanthipeptide
Lanthipeptides: KCH_RS42000_lanthipeptide
9
S S L S V L N C T V S T V S T L L C L
27
S S L S V+N C T S T V S T L L C L
4
S S L S V V N C T N S T V S T L L C L
22
with 42 more sequence matches
Only the first 10 are displayed here.
59.3%
NZ_BBYG01000014.1 and 13 others:
NZ_BMSI01000005.1 Lanthipeptides: IE189_RS14480_lanthipeptide NZ_BMSI01000005.1 Lanthipeptides: IE189_RS14480_lanthipeptide NZ_CP023689.1 Lanthipeptides: CP983_RS00340_lanthipeptide NZ_CP030772.1 Lanthipeptides: C9F11_RS46215_lanthipeptide NZ_CP045643.1 Lanthipeptides: GFH48_RS36070_lanthipeptide NZ_CP050975.1 Lanthipeptides: HEP85_RS04970_lanthipeptide NZ_CP056041.1 Lanthipeptides: HUT05_RS01780_lanthipeptide NZ_CP106795.1 Lanthipeptides: N8I86_RS01600_lanthipeptide NZ_KB911702.1 Lanthipeptides: H294_RS47360_lanthipeptide NZ_KQ948763.1 Lanthipeptides: AQJ64_RS47660_lanthipeptide NZ_KQ949024.1 Lanthipeptides: AQJ58_RS42360_lanthipeptide NZ_LIWA01000005.1 Lanthipeptides: AMK32_RS41535_lanthipeptide NZ_LMEQ01000030.1 Lanthipeptides: ASD48_RS43705_lanthipeptide
Lanthipeptides: AOQ37_RS39920_lanthipeptide
9
S S L S V L N C T V S T V S T L L C L
27
S S L S +N C T S T V S T L L C L
3
S S L S A V N C T N S T V S T L L C L
21
55.6%
NZ_CP048405.1:
Lanthipeptides: GXW83_RS16365_lanthipeptide
9
S S L S V L N C T V S T V S T L L C L
27
S+L S +N C T S T V S T L L C L
4
S T L S A V N C T N S T V S T L L C L
22
48.1%
NZ_AXVK01000021.1:
Lanthipeptides: K332_RS23900_lanthipeptide
8
G S S L S V L N C T V-S T V S T L L C
26
G S S+S V N C V S T+S L C
2
G S S V S V-N C K V I S T I S F F L C
20
48.1%
NZ_FKJI03000003.1:
Lanthipeptides: A7P67_RS08715_lanthipeptide
10
S L S V L N C T V S T V S T L L C L
27
+L S+L+C V S V S T L L C L
1
T L S L L S C-V S A V S T L L C L
17
48.1%
NZ_KV809437.1 and 2 others:
NZ_PNGL01000006.1 Lanthipeptides: CJ228_RS12250_lanthipeptide NZ_SPKT01000006.1 Lanthipeptides: E4A49_RS12090_lanthipeptide
Lanthipeptides: HMPREF2863_RS12160_lanthipeptide
8
G S S L S V L N C T V-S T V S T L L C
26
G S S L S V N C V S T+S +C
2
G S S L S V-N C K V I S T I S V A V C
20
48.1%
NZ_NUFU01000017.1 and 2 others:
NZ_NUFU01000017.1 Lanthipeptides: CN902_RS28885_lanthipeptide NZ_VEAZ01000013.1 Lanthipeptides: FS498_RS29425_lanthipeptide
Lanthipeptides: CN902_RS28890_lanthipeptide
8
G S S L S V L N C T V-S T V S T L L C
26
G S S L S V N C V S T+S +C
2
G S S L S V-N C K V V S T I S F A V C
20
44.4%
NC_013929.1 and 5 others:
NZ_CP043956.1 Lanthipeptides: F3K20_RS40780_lanthipeptide NZ_CP050692.1 Lanthipeptides: HCX60_RS01560_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS02035_lanthipeptide NZ_FWZW01000014.1 Lanthipeptides: B9O01_RS36545_lanthipeptide NZ_KL997500.1 Lanthipeptides: IQ61_RS45670_lanthipeptide
Lanthipeptides: SCAB_RS45825_lanthipeptide
15
N C T V S T V S T L L C L
27
N C T S T V S T L L C L
12
N C T N S T V S T L L C L
24
44.4%
NZ_CP031455.1:
Lanthipeptides: DXZ73_RS14610_lanthipeptide
9
S S L S V L N C T V S T V S T L L C L
27
S++S+L+C V S T S L L C L
5
S T V S L L S C-V S T A S I L L C L
22
44.4%
NZ_CP042266.1:
Lanthipeptides: FQU76_RS00910_lanthipeptide
7
T G S S L S V L N C-T V S T V S T L L C
26
T G S S L S+L+C S +S L C
1
T G S S L S L L S C G H H S N L S L L A C
21
44.4%
NZ_CP043661.1 and 1 other:
NZ_SOCE01000001.1 Lanthipeptides: EV138_RS20105_lanthipeptide
Lanthipeptides: F1D05_RS17325_lanthipeptide
6
A T G S S L S V L N C---T V S T V S T L L C
26
G S+L+V L C T S +S L L C
2
G G G S T L T V L G C A S H T P S N L S L L L C
25

#### MIBiG 4.0 matches for B7024_RS17090

37.0%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
7
T G S S L S V L N C T V S T V S T L L C
26
T G S +S+L C S++S +L C
1
T G S Q V S L L V C E Y S S L S V V L C
20
25.9%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
9
S S L S V L N C T
17
S S L S V+ C T
13
S S L S V V L C T
21

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.73 out of 23.79
Confidence: strong
Additional weak hits (6):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.95 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.07 out of 21.84
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.40 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.17 out of 28.19
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.

B7024_RS17090 - Class III
  Cleavage pHMM score: 12.20
  RODEO score: 0
  Monoisotopic mass: 2561.4 Da
  Molecular weight: 2563.0 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2581.0 Da N = 1
    2599.0 Da N = 2
    2617.0 Da N = 3
    2635.0 Da N = 4
    2653.1 Da N = 5
    2671.1 Da N = 6
    2689.1 Da N = 7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism

NZ_NDXL01000001.1 - Region 25 - butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,034,094 - 4,045,008 nt. (total: 10,915 nt) Show pHMM detection rules used
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase protease
B7024_RS17435: HAD-superfamily hydrolase, subfamily IA, variant

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

B7024_RS41890: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

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 | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.76 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.58 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.46 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000595.3 |  | 0.36 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000597.4 |  | 0.35 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000914.5 |  | 0.34 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000703.4 |  | 0.31 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0002571.2 |  | 0.31 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0000705.3 |  | 0.30 | saccharide | kanamycin | Streptomyces kanamyceticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.76 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.58 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.46 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000595.3 |  | 0.36 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000597.4 |  | 0.35 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000914.5 |  | 0.34 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000703.4 |  | 0.31 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0002571.2 |  | 0.31 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0000705.3 |  | 0.30 | saccharide | kanamycin | Streptomyces kanamyceticus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (4):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.82 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.53 out of 39.62
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_NDXL01000001.1 - Region 26 - 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: 4,306,394 - 4,332,995 nt. (total: 26,602 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B7024_RS18535: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase
B7024_RS18530: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

B7024_RS18605: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Ligases: synthase synthetase
B7024_RS18575: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

B7024_RS18600: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.76 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.58 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.51 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.76 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.58 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.51 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | 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.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

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

Genes with terpene domains:
B7024_RS18560: PT_phytoene_like
Domain 1 (6 - 275): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

B7024_RS18565: PT_phytoene_like
Domain 1 (17 - 301): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

B7024_RS18575: PT_FPPS_like
Domain 1 (58 - 352): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

B7024_RS18580: T2TS
Domain 1 (37 - 658): 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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 20.76 out of 21.84
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.90 out of 29.72
Confidence: medium
Additional weak hits (13):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.99 out of 26.85
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.45 out of 29.51
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.82 out of 36.54
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.59 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.42 out of 23.43
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.98 out of 29.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.04 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.95 out of 27.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.28 out of 29.25
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
MexT | Global virulence regulator
NtrC | Nitrogen regulatory protein C

NZ_NDXL01000001.1 - Region 27 - CDPS
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: 4,542,599 - 4,563,324 nt. (total: 20,726 nt) Show pHMM detection rules used
CDPS: CDPS

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
B7024_RS19530: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS19550: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

Hydrolases: hydrolase
B7024_RS19555: hydrolase

smcogs
  SMCOG1179: hydrolase

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 | CDPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000851.5 |  | 0.68 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0001986.3 |  | 0.60 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0002276.2 |  | 0.56 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000866.5 |  | 0.45 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002013.4 |  | 0.42 | ribosomal | curacozole | Streptomyces curacoi
BGC0002496.3 |  | 0.39 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000671.3 |  | 0.39 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0000218.5 |  | 0.37 | PKS | doxorubicin | Streptomyces peucetius
BGC0001575.4 |  | 0.36 | NRPS | PZN5, PZN6, PZN7, PZN9, PZN10, PZN11 | Ruminococcus sp. 5_1_39BFAA
BGC0001882.3 |  | 0.36 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000851.5 |  | 0.68 | other (other) | albonoursin | Streptomyces noursei ATCC 11455
BGC0001986.3 |  | 0.60 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0002276.2 |  | 0.56 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000866.5 |  | 0.45 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002013.4 |  | 0.42 | ribosomal | curacozole | Streptomyces curacoi
BGC0002496.3 |  | 0.39 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000671.3 |  | 0.39 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0000218.5 |  | 0.37 | PKS | doxorubicin | Streptomyces peucetius
BGC0001575.4 |  | 0.36 | NRPS | PZN5, PZN6, PZN7, PZN9, PZN10, PZN11 | Ruminococcus sp. 5_1_39BFAA
BGC0001882.3 |  | 0.36 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (5):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.65 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 30.25
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.82 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.04 out of 24.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.83 out of 26.12
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_NDXL01000001.1 - Region 28 - NAPAA,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,615,807 - 4,695,188 nt. (total: 79,382 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
B7024_RS19840: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

B7024_RS19935: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

B7024_RS19995: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: acyltransferase
B7024_RS19870: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: esterase hydrolase
B7024_RS19830: thioesterase

smcogs
  SMCOG1004: thioesterase

B7024_RS19855: thioesterase

smcogs
  SMCOG1004: thioesterase

B7024_RS19905: HAD-superfamily hydrolase, subfamily IA, variant

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

B7024_RS19980: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: hydratase
B7024_RS19990: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

B7024_RS20000: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
B7024_RS19860: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS19865: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS19875: 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 | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  | 0.69 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
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
BGC0002135.2 |  |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001251.4 |  |  | 0.62 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  |  | 0.62 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001878.2 |  | 0.76 | NRPS, PKS | detoxin N2, detoxin N3 | Streptomyces sp. NRRL B-1347
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000342.4 |  | 0.70 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.69 | 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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 22.87 out of 26.33
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.25 out of 27.04
Confidence: medium
Additional weak hits (11):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.20 out of 28.14
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.97 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.93 out of 26.06
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.82 out of 27.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.46 out of 28.19
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.93 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.41 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 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 46, location 4615806 - 4695188:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Gly) + (Pro - Cys) + (Val) + (Ile - Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 47, location 4615806 - 4680445:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Gly) + (Pro - Cys) + (Val) + (Ile - Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 48, location 4661201 - 4695188:
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).
B7024_RS19860: Ile - Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (22..418): 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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LPGSFDALSFEVFILVGGEHNVYGPTEATTFALC
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (65% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1081..1485): Pro
nrpys: 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:
    LWQAFDVSFQEGFMVTAGEFNHYGPTETHVVSAL
  Nearest Stachelhaus code(s):
    Pro DVQFVAHVVK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

B7024_RS19865: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (536..927): Val
nrpys: Val

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  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:
    LHWSFDVSVQELYLLVGVELNGYGPTETTVYSTG
  Nearest Stachelhaus code(s):
    Met DVFYLGGVFK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

B7024_RS19870: Pro - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (495..902): Pro
nrpys: 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:
    LWQAFDVSFQESFLVTAGEYNQYGPTETHVVSQH
  Nearest Stachelhaus code(s):
    Pro DVQFVAQVVK (88% 8Å match)
    Hpr DVQFVAQVVK (74% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1555..1954): 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:
    TDISFDLSVYDGNSMLSGDDSLGGATEASIWSIH
  Nearest Stachelhaus code(s):
    Cys DLYNMSLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

B7024_RS19875: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (458..832): 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:
    LAITFDISGLELQALTGGEVNVYGPTEATIWATS
  Nearest Stachelhaus code(s):
    Gly DILQLGVIWK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

B7024_RS19945: X
AMP-binding (20..416): 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:
    FIVMFDFSIEEPYCVVGGELNTYGPTETTVTATW
  Nearest Stachelhaus code(s):
    Lys DIESIGTVTK (62% 8Å match)
    Gln or Tyr DAESVGTVVK (59% 8Å match)
    Arg DVENVGAVTK (56% 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
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
DasR | N-acetylglucosamine dependent repressor

NZ_NDXL01000001.1 - Region 29 - hydrogen-cyanide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,719,931 - 4,732,909 nt. (total: 12,979 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase reductase
B7024_RS20140: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

B7024_RS20150: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Hydrolases: deaminase
B7024_RS20125: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: hydratase
B7024_RS20165: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

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

Reference | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002285.2 |  | 0.36 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001431.4 |  | 0.33 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca
BGC0001429.4 |  | 0.33 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca DW4/3-1
BGC0000131.5 |  | 0.32 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000529.5 |  | 0.31 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000821.5 |  | 0.31 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0001333.5 |  | 0.31 | other (other) | BE-54017 | uncultured bacterium AB1650
BGC0002443.3 |  | 0.31 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0000652.5 |  | 0.31 | terpene | napyradiomycin | Streptomyces sp. CNQ525
BGC0001079.5 |  | 0.31 | PKS, terpene | napyradiomycin A80915C, napyradiomycin 2, napyradiomycin 3, napyradiomycin 4 | Streptomyces aculeolatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002285.2 |  | 0.36 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001431.4 |  | 0.33 | NRPS, PKS | myxochromide S | Stigmatella aurantiaca
BGC0001429.4 |  | 0.33 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca DW4/3-1
BGC0000131.5 |  | 0.32 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000529.5 |  | 0.31 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000821.5 |  | 0.31 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0001333.5 |  | 0.31 | other (other) | BE-54017 | uncultured bacterium AB1650
BGC0002443.3 |  | 0.31 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0000652.5 |  | 0.31 | terpene | napyradiomycin | Streptomyces sp. CNQ525
BGC0001079.5 |  | 0.31 | PKS, terpene | napyradiomycin A80915C, napyradiomycin 2, napyradiomycin 3, napyradiomycin 4 | Streptomyces aculeolatus

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:
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 25.53 out of 29.51
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.44 out of 23.79
Confidence: medium
Additional weak hits (10):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.96 out of 26.33
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.50 out of 36.54
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.28 out of 29.38
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.00 out of 30.98
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.14 out of 22.40
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.30 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.14 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism

NZ_NDXL01000001.1 - Region 30 - NRPS,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: 4,796,692 - 4,865,478 nt. (total: 68,787 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
B7024_RS20550: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS20575: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acyltransferase carbamoyltransferase
B7024_RS20515: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

B7024_RS20565: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: esterase
B7024_RS20555: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase
B7024_RS20545: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS20580: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS20585: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS20590: 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 | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  | 0.90 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.90 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.90 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.89 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  |  | 0.88 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001135.5 |  |  | 0.86 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.86 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  |  | 0.86 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  |  | 0.84 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  | 0.84 | NRPS | AM-toxin | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001825.4 |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.86 out of 21.84
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.36 out of 20.97
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.07 out of 30.12
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (13):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.99 out of 29.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.30 out of 30.22
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.66 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.81 out of 20.01
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.88 out of 36.54
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.41 out of 18.57
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.18 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.52 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.04 out of 18.57
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.04 out of 20.01
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 50, location 4796691 - 4865478:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X) + (Thr - X) + (Leu - Val - X) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 51, location 4796691 - 4839574:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - X) + (Leu - Val - X) + (Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 52, location 4802583 - 4865478:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X) + (Thr - X) + (Leu - Val - X) + (Thr)

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).
B7024_RS20545: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (370..770): 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:
    LATHFDFSVWEGSQVFGGEVNMFGITETTVHTTA
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (97% 8Å match)
    aThr DFWSVGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

B7024_RS20565: Leu - Val - X
Search NORINE for peptide: strict or relaxed
AMP-binding (467..852): Leu
nrpys: Leu

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FDRSLDAAAYEVFLATGGGHHLYGPAGHATAATA
  Nearest Stachelhaus code(s):
    Leu DAWLAGLTAK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1519..1908): 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:
    LDRSFDAATYEVWLTTGGDANGYGPTETTTFATH
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2562..2948): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSLTFDMAVPELQALVGAETNLYGPTETTVWSTA
  Nearest Stachelhaus code(s):
    D-Ala DMPQLGMVWK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

B7024_RS20580: X
AMP-binding (17..398): 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:
    glu,gln (Glu, Gln)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGLAFDASVQQRDLFMGGEVNLYGPTECTVDATV
  Nearest Stachelhaus code(s):
    Ile DAQDLGVVDK (76% 8Å match)
    OH-Orn DAQEGGLVDK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

B7024_RS20585: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (459..863): 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:
    LSGHFDWTVWEGCLMLGGECNLYGITETTVHVTT
  Nearest Stachelhaus code(s):
    Ser DMWNTGLVHK (71% 8Å match)
    Thr DLWQLGLVHK (38% 8Å match)
  Stachelhaus code match:
    70% (weak)

B7024_RS20590: X - X
AMP-binding (10..379): 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:
    HAAAVDVAIEQTNLISGSDVNAYGPTETVITATA
  Nearest Stachelhaus code(s):
    Arg DVENVGAITK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (983..1379): X
nrpys: Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TAQSWDAFALEGQLFTGGEGNGYGPVESLGFTTC
  Nearest Stachelhaus code(s):
    Val DALWLGGVFK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CcpA | Catabolite control protein A
MexT | Global virulence regulator
OsdR | Development and stress management regulator

NZ_NDXL01000002.1 - Region 1 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 228,866 - 252,996 nt. (total: 24,131 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
B7024_RS22740: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002053.3 |  | 0.70 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001507.3 |  | 0.66 | ribosomal | anantin C | Streptomyces olindensis
BGC0001307.3 |  | 0.63 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0001552.3 |  | 0.62 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001550.3 |  | 0.61 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001506.5 |  | 0.60 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0001493.5 |  | 0.60 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001539.4 |  | 0.60 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001548.4 |  | 0.59 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001781.4 |  | 0.59 | ribosomal | sphaericin | Planomonospora sphaerica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002053.3 |  | 0.70 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001507.3 |  | 0.66 | ribosomal | anantin C | Streptomyces olindensis
BGC0001307.3 |  | 0.63 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0001552.3 |  | 0.62 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001550.3 |  | 0.61 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001506.5 |  | 0.60 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0001493.5 |  | 0.60 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001539.4 |  | 0.60 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001548.4 |  | 0.59 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001781.4 |  | 0.59 | ribosomal | sphaericin | Planomonospora sphaerica

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - 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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.25 out of 29.72
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
Additional weak hits (7):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.45 out of 27.78
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.17 out of 29.51
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.63 out of 27.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.32 out of 26.12
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.12 out of 27.55
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.42 out of 27.55
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.67 out of 24.78
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (228865...252996)
B7024_RS22725
  RRE type: Stand_Alone_Lasso_RRE
  Location: 0 - 85
  Score: 81.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C

NZ_NDXL01000002.1 - Region 2 - 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: 855,279 - 877,651 nt. (total: 22,373 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
B7024_RS25625: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B7024_RS25630: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: aminotransferase
B7024_RS25585: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: cyclase
B7024_RS25600: 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 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000902.4 |  | 0.45 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001224.5 |  | 0.45 | other (other) | reductasporine | uncultured bacterium
BGC0000285.5 |  | 0.41 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001485.4 |  | 0.40 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001483.4 |  | 0.39 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002382.3 |  | 0.39 | ribosomal | grimoviridin | Grimontia marina
BGC0001336.5 |  | 0.39 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001223.5 |  | 0.38 | other (other) | hydroxysporine | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000902.4 |  | 0.45 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001224.5 |  | 0.45 | other (other) | reductasporine | uncultured bacterium
BGC0000285.5 |  | 0.41 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001485.4 |  | 0.40 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001483.4 |  | 0.39 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002382.3 |  | 0.39 | ribosomal | grimoviridin | Grimontia marina
BGC0001336.5 |  | 0.39 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001223.5 |  | 0.38 | other (other) | hydroxysporine | 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.
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:
B7024_RS25600: T1TS + T1TS
Domain 1 (6 - 331): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (372 - 754): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.52 out of 23.79
Confidence: medium
Additional weak hits (7):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.41 out of 36.53
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.02 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.60 out of 24.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.75 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism

NZ_NDXL01000002.1 - Region 3 - 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: 1,312,055 - 1,354,198 nt. (total: 42,144 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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
B7024_RS27700: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: methyltransferase
B7024_RS27710: O-methyltransferase

smcogs
  SMCOG1042: O-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 | lanthipeptide-class-v | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002303.3 |  | 0.58 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002110.3 |  | 0.42 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908
BGC0001229.4 |  | 0.42 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0002130.3 |  | 0.42 | ribosomal | cacaoidin | Streptomyces cacaoi CA-170360
BGC0000504.5 |  | 0.41 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001896.4 |  | 0.41 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0000518.3 |  | 0.40 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000527.5 |  | 0.40 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001224.5 |  | 0.40 | other (other) | reductasporine | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002303.3 |  | 0.58 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002110.3 |  | 0.42 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908
BGC0001229.4 |  | 0.42 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0002130.3 |  | 0.42 | ribosomal | cacaoidin | Streptomyces cacaoi CA-170360
BGC0000504.5 |  | 0.41 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0001896.4 |  | 0.41 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0000518.3 |  | 0.40 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000527.5 |  | 0.40 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001224.5 |  | 0.40 | other (other) | reductasporine | 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.
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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.54 out of 23.79
Confidence: medium
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.98 out of 30.22
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.67 out of 20.97
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.81 out of 18.57
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.78 out of 35.63
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.80 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
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
--- | ---
IolR | Regulator of the inositol catabolism

NZ_NDXL01000002.1 - Region 4 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,441,533 - 1,467,977 nt. (total: 26,445 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
B7024_RS28295: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

B7024_RS28300: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: 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-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.47 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.46 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000542.3 |  | 0.46 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.46 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002316.2 |  | 0.45 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002120.3 |  | 0.45 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0001948.3 |  | 0.43 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000544.4 |  | 0.42 | ribosomal | planosporicin | Planomonospora alba
BGC0000549.3 |  | 0.40 | ribosomal | salivaricin D | Streptococcus salivarius

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.47 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.46 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000542.3 |  | 0.46 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.46 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002316.2 |  | 0.45 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0002120.3 |  | 0.45 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0001948.3 |  | 0.43 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000544.4 |  | 0.42 | ribosomal | planosporicin | Planomonospora alba
BGC0000549.3 |  | 0.40 | ribosomal | salivaricin D | Streptococcus salivarius

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 B7024_RS28295

B7024_RS28290
Leader:
MSPSITHATKASPQPAQAATDGFELDVTLVEVSDTA
Core:
G L I S L T N D G C G E T C G A C T T N V A
Core with dehydrations:
G L I Dha L Dhb N D G Cys G E Dhb Cys G A Cys Dhb Dhb N V A

#### antiSMASH-DB 4.0 matches for B7024_RS28290

100.0%
NZ_NDXL01000002.1:
Lanthipeptides: B7024_RS28290_lanthipeptide
1
G L I S L T N D G C G E T C G A C T T N V A
22
G L I S L T N D G C G E T C G A C T T N V A
1
G L I S L T N D G C G E T C G A C T T N V A
22
95.5%
NZ_CP028834.1 and 1 other:
NZ_CP074380.1 Lanthipeptides: KGS77_RS25025_lanthipeptide
Lanthipeptides: DBP13_RS26755_lanthipeptide
1
G L I S L T N D G C G E T C G A C T T N V A
22
G L I S L T+D G C G E T C G A C T T N V A
1
G L I S L T D D G C G E T C G A C T T N V A
22
86.4%
NZ_CP048882.1:
Lanthipeptides: G4Z16_RS00540_lanthipeptide
1
G L I S L T N D G C G E T C G A C T T N V A
22
G L+S+T N D G C G T C G A C T T N V A
1
G L V S I T N D G C G S T C G A C T T N V A
22
with 171 more sequence matches
Only the first 10 are displayed here.
81.8%
NZ_BCMN01000021.1:
Lanthipeptides: AV140_RS32375_lanthipeptide
1
G L I S L T N D G C G E T C G A C T T N V A
22
G L++L T+D G C G T C G A C T T N V A
1
G L V N L T D D G C G S T C G A C T T N V A
22
77.3%
NZ_AQRK01000088.1 and 27 others:
NZ_BMVQ01000014.1 Lanthipeptides: IE283_RS30975_lanthipeptide NZ_CP019724.1 Lanthipeptides: B1H29_RS19645_lanthipeptide NZ_CP019724.1 Lanthipeptides: B1H29_RS08000_lanthipeptide NZ_CP022438.1 Lanthipeptides: CGZ69_RS15030_lanthipeptide NZ_CP022438.1 Lanthipeptides: CGZ69_RS15030_lanthipeptide NZ_CP023202.1 Lanthipeptides: SXIN_RS04650_lanthipeptide NZ_CP023700.1 Lanthipeptides: CP969_RS17265_lanthipeptide NZ_CP023702.1 Lanthipeptides: CP967_RS19640_lanthipeptide NZ_CP033073.1 Lanthipeptides: D9753_RS20300_lanthipeptide NZ_CP063808.1 Lanthipeptides: IOD14_RS42650_lanthipeptide NZ_CP071872.1 Lanthipeptides: J4032_RS33705_lanthipeptide NZ_CP071872.1 Lanthipeptides: J4032_RS33705_lanthipeptide NZ_CP075691.1 Lanthipeptides: KKZ08_RS16460_lanthipeptide NZ_CP082362.1 Lanthipeptides: K4G22_RS18080_lanthipeptide NZ_CP094676.1 Lanthipeptides: L6J92_RS33095_lanthipeptide NZ_CP101138.1 Lanthipeptides: M6G08_RS35600_lanthipeptide NZ_CP117709.1 Lanthipeptides: PSQ21_RS13565_lanthipeptide NZ_CP117866.1 Lanthipeptides: PBV52_RS22590_lanthipeptide NZ_JAFIQY010000056.1 Lanthipeptides: JXZ78_RS36930_lanthipeptide NZ_JAJDST010000050.1 Lanthipeptides: LJC81_RS33260_lanthipeptide NZ_JAJDST010000050.1 Lanthipeptides: LJC81_RS33260_lanthipeptide NZ_JH993790.1 Lanthipeptides: STRVIR_RS0119395_lanthipeptide NZ_KB890926.1 Lanthipeptides: B053_RS0114140_lanthipeptide NZ_KB891987.1 Lanthipeptides: B079_RS0100320_lanthipeptide NZ_KB912961.1 Lanthipeptides: B065_RS0117615_lanthipeptide NZ_KQ947985.1 Lanthipeptides: AQI70_RS05650_lanthipeptide NZ_LIPF01000016.1 Lanthipeptides: AMK11_RS35705_lanthipeptide
Lanthipeptides: YUW_RS13695_lanthipeptide
1
G L I S L T N D G C G E T C G A C T T N V A
22
G L++L T+D C G T C G A C T T N V A
1
G L V N L T D D N C G S T C G A C T T N V A
22
77.3%
NZ_CP070379.1 and 1 other:
NZ_LFBV01000012.1 Lanthipeptides: AB852_RS38205_lanthipeptide
Lanthipeptides: JVE63_RS15825_lanthipeptide
1
G L I S L T N D G C G E T C G A C T T N V A
22
G L++L T+D C G T C G A C T T N V A
1
G L V N L T D D N C G T T C G A C T T N V A
22
72.7%
NZ_AP018365.1:
Lanthipeptides: RVR_RS08440_lanthipeptide
4
S L T N D G C G E T C G A C T T N V A
22
S L T+D C G T C G A C T T N V A
2
S L T D D N C G S T C G A C T T N V A
20
72.7%
NZ_BMSI01000021.1 and 1 other:
NZ_JAPTYM010000001.1 Lanthipeptides: O1M07_RS07535_lanthipeptide
Lanthipeptides: IE189_RS36010_lanthipeptide
5
L T N D G C G E T C G A C T T N V A
22
L T+D G C G T C G A C T T N V A
1
L T D D G C G S T C G A C T T N V A
18
68.2%
NC_021177.1 and 1 other:
NZ_BMUG01000006.1 Lanthipeptides: IE264_RS18330_lanthipeptide
Lanthipeptides: SFUL_RS28885_lanthipeptide
5
L T N D G C G E T C G A C T T N V A
22
L T+D C G T C G A C T T N V A
1
L T D D N C G S T C G A C T T N V A
18
68.2%
NZ_BBVA01000002.1 and 7 others:
NZ_CP030865.1 Lanthipeptides: MicB006_RS27820_lanthipeptide NZ_FMCS01000017.1 Lanthipeptides: GA0070214_RS30700_lanthipeptide NZ_JAGPXW010000015.1 Lanthipeptides: KBX71_RS18490_lanthipeptide NZ_JALJRJ010000030.1 Lanthipeptides: OC439_RS27920_lanthipeptide NZ_LT594324.1 Lanthipeptides: GA0070621_RS04875_lanthipeptide NZ_LT607410.1 Lanthipeptides: GA0074696_RS20405_lanthipeptide NZ_LT607753.1 Lanthipeptides: GA0070614_RS02740_lanthipeptide
Lanthipeptides: A4R25_RS30565_lanthipeptide
4
S L T N D G C G E T C G A C T T N V A
22
+L T+D G C G T C A C T T N V A
1
N L T D D G C G S T C T A C T T N V A
19
65.2%
NZ_JACHCX010000001.1:
Lanthipeptides: HDC93_RS03095_lanthipeptide
2
L I S L T N D G C G E T C-G A C T T N V A
22
L I+L T+D G C T C G+C T N V A
2
L I N L T D D G C K P T C K G S C A T N V A
23
63.6%
NZ_AP026073.1 and 13 others:
NZ_BBUY01000020.1 Lanthipeptides: AZE13_RS34600_lanthipeptide NZ_BMUN01000013.1 Lanthipeptides: IE238_RS22260_lanthipeptide NZ_CP009754.1 Lanthipeptides: NI25_RS06465_lanthipeptide NZ_CP015588.1 Lanthipeptides: A7J05_RS07195_lanthipeptide NZ_CP023697.1 Lanthipeptides: CP972_RS03610_lanthipeptide NZ_CP029192.1 Lanthipeptides: DEJ48_RS36690_lanthipeptide NZ_CP029192.1 Lanthipeptides: DEJ48_RS36690_lanthipeptide NZ_CP031194.1 Lanthipeptides: DVK44_RS04655_lanthipeptide NZ_CP039123.1 Lanthipeptides: E5N77_RS29900_lanthipeptide NZ_CP042324.1 Lanthipeptides: FQ762_RS35785_lanthipeptide NZ_CP042324.1 Lanthipeptides: FQ762_RS35780_lanthipeptide NZ_CP116257.1 Lanthipeptides: BJ961_RS11895_lanthipeptide NZ_ML123127.1 Lanthipeptides: EES47_RS19530_lanthipeptide
Lanthipeptides: HEK616_RS04845_lanthipeptide
3
I S L T N D G C G E T C G A-C T T N V A
22
I+L T+D G C G T C + C T N V A
1
I N L T D D G C G S T C S S P C A T N V A
21
63.6%
NZ_BBUY01000020.1:
Lanthipeptides: AZE13_RS28700_lanthipeptide
2
L I S L T N D G C G E T C-G A C T T N V A
22
L I+L T+D G C +C G+C T N V A
1
L I N L T D D G C K P S C Q G S C A T N V A
22

#### MIBiG 4.0 matches for B7024_RS28290

14.7%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
3
I S L T N D G C
10
I S L G C
4
I S L C T P G C
11

#### 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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 24.48 out of 29.72
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.64 out of 29.51
Confidence: medium
Additional weak hits (6):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.50 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.64 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.31 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.13 out of 28.19
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

B7024_RS28290 - Class I
  Cleavage pHMM score: -5.80
  RODEO score: 21
  Monoisotopic mass: 2008.9 Da
  Molecular weight: 2010.2 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2028.2 Da N = 1
    2046.2 Da N = 2

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (1441532...1467977)
B7024_RS28295
  RRE type: Lanthipeptide_LanB_RRE
  Location: 157 - 249
  Score: 65.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
DosR | Hypoxia stress response regulator
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_NDXL01000002.1 - Region 5 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,634,044 - 1,665,591 nt. (total: 31,548 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase
B7024_RS29100: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Lyases: decarboxylase
B7024_RS29180: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: synthase
B7024_RS29110: cysteine synthase

smcogs
  SMCOG1081: cysteine 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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.50 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000943.5 |  | 0.47 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000947.5 |  | 0.47 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0002471.3 |  | 0.44 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0002470.2 |  | 0.44 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0001587.5 |  | 0.43 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001226.4 |  | 0.43 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000563.4 |  | 0.42 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000866.5 |  | 0.42 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002635.2 |  | 0.41 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.50 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000943.5 |  | 0.47 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000947.5 |  | 0.47 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0002471.3 |  | 0.44 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0002470.2 |  | 0.44 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0001587.5 |  | 0.43 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001226.4 |  | 0.43 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000563.4 |  | 0.42 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0000866.5 |  | 0.42 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0002635.2 |  | 0.41 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (9):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.65 out of 27.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.57 out of 26.12
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.94 out of 19.26
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.58 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.33 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.82 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.66 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
VqsM | Regulator of quorum-sensing signalling systems

NZ_NDXL01000003.1 - Region 1 - NRPS-like,arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 85,580 - 128,533 nt. (total: 42,954 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)
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer oxidoreductase oxygenase
B7024_RS29990: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

B7024_RS29995: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

B7024_RS30000: flavodoxin

smcogs
  SMCOG1134: flavodoxin

B7024_RS30035: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS30045: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS30060: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS30085: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: hydrolase
B7024_RS29945: Amination

MITE
  MITE0000131Amination (identity: 61.50%)
smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Hydrolases: esterase hydrolase
B7024_RS29945: Amination

MITE
  MITE0000131Amination (identity: 61.50%)
smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

B7024_RS30005: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

B7024_RS30050: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
B7024_RS30055: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
B7024_RS30010: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS30015: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS30020: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS30025: 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 | NRPS-like | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002493.3 |  |  | 0.52 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0002274.2 |  |  | 0.51 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002474.2 |  |  | 0.48 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0001444.5 |  |  | 0.48 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0001850.4 |  |  | 0.43 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0001868.4 |  |  | 0.40 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0001987.2 |  |  | 0.39 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000866.5 |  |  | 0.38 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0001917.4 |  |  | 0.38 | PKS | 5aTHQ-9i, 5aTHQ-9n, 5aTHQ-10a, STAMs-9i, STAMs-9n | Streptomyces nigrescens
BGC0000936.5 |  |  | 0.38 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002493.3 |  | 0.60 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0002274.2 |  | 0.59 | NRPS | aspulvinone H, aspulvinone B1 | Aspergillus terreus NIH2624
BGC0002474.2 |  | 0.58 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0001444.5 |  | 0.57 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0001850.4 |  | 0.54 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0000866.5 |  | 0.53 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0001868.4 |  | 0.53 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0001987.2 |  | 0.52 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0001917.4 |  | 0.52 | PKS | 5aTHQ-9i, 5aTHQ-9n, 5aTHQ-10a, STAMs-9i, STAMs-9n | Streptomyces nigrescens
BGC0000867.3 |  | 0.51 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (15):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.87 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.60 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.62 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.72 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.92 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.23 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.95 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.22 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.39 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.09 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.55 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.10 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B7024_RS30010: X
AMP-binding (58..439): 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:
    GWRAHSSAIAYYLAQNTGDADG----ERLPGSVF
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

B7024_RS30015: X
AMP-binding (113..512): 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:
    MGFAFGGFGNACCSTTAGEVNCFGATELMHVVLL
  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
--- | ---

NZ_NDXL01000003.1 - Region 2 - NRPS-like,T1PKS,lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 345,622 - 469,070 nt. (total: 123,449 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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 oxidoreductase
B7024_RS31115: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

B7024_RS31200: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

B7024_RS31210: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B7024_RS31235: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS31255: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: PPTase acylase aminotransferase
B7024_RS31140: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

B7024_RS31165: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B7024_RS31185: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B7024_RS31190: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B7024_RS31220: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B7024_RS31275: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase phosphatase
B7024_RS31215: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

B7024_RS31225: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase dehydratase
B7024_RS31105: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

B7024_RS31110: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: ligase synthase
B7024_RS31150: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS31170: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

B7024_RS31175: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS31180: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS31195: 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 | lanthipeptide-class-i | NRPS-like | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002576.2 |  |  |  | 1.31 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002135.2 |  |  |  | 0.80 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  |  |  | 0.79 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001166.5 |  |  |  | 0.78 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001249.5 |  |  |  | 0.78 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0000357.5 |  |  |  | 0.78 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0000538.3 |  |  |  | 0.58 | ribosomal | nisin Z | Lactococcus lactis
BGC0000542.3 |  |  |  | 0.56 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  |  |  | 0.56 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002635.2 |  |  |  | 0.56 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.74 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0000041.3 |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002175.3 |  | 0.63 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0000067.5 |  | 0.62 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus

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.
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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
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 B7024_RS31110

B7024_RS31125
Leader:
MSDFDLDAKVVDNETGEPAPR
Core:
I T S W S L C T P G C V T A A G C T T S V C T Q G C H V S K
Core with dehydrations:
I Dhb Dha W Dha L Cys Dhb P G Cys V Dhb A A G Cys Dhb Dhb Dha V Cys Dhb Q G Cys H V Dha K

#### antiSMASH-DB 4.0 matches for B7024_RS31125

100.0%
NZ_NDXL01000003.1:
Lanthipeptides: B7024_RS31125_lanthipeptide
1
I T S W S L C T P G C V T A A G C T T S V C T Q G C H V S K
30
I T S W S L C T P G C V T A A G C T T S V C T Q G C H V S K
1
I T S W S L C T P G C V T A A G C T T S V C T Q G C H V S K
30
86.7%
NZ_CP034587.1:
Lanthipeptides: EKH77_RS16870_lanthipeptide
1
I T S W S L C T P G C V T A A G C T T S V C T Q G C H V S K
30
I T S S L C T P G C +A A G C T T S V C T Q G C H+S K
1
I T S I S L C T P G C P S A A G C T T S V C T Q G C H I S K
30
86.7%
NZ_CP086322.1:
Lanthipeptides: K9S39_RS23570_lanthipeptide
1
I T S W S L C T P G C V T A A G C T T S V C T Q G C H V S K
30
I T S S L C T P G C V T A A G C T T+ C T Q G C H+S K
1
I T S V S L C T P G C V T A A G C T T A K C T Q G C H I S K
30
with 110 more sequence matches
Only the first 10 are displayed here.
60.6%
NZ_CP085954.1:
Lanthipeptides: LK411_RS13585_lanthipeptide
1
I T S W S L C T P G C V T A A-G C T T S V C--T Q G C H V S K
30
I T S S L C T P G C T A G C T C T G C ++K
1
I T S K S L C T P G C P T G A L G C F T Q N C D P T N G C T I T K
33
58.8%
NC_013656.1 and 18 others:
NC_020450.1 Lanthipeptides: LILO_RS03015_lanthipeptide NZ_CP009472.1 Lanthipeptides: LG36_RS03420_lanthipeptide NZ_CP010050.1 Lanthipeptides: QI18_RS03300_lanthipeptide NZ_CP015903.1 Lanthipeptides: LLUC08_RS03255_lanthipeptide NZ_CP024954.1 Lanthipeptides: CV702_RS02990_lanthipeptide NZ_CP066300.1 Lanthipeptides: LacL0098_RS03205_lanthipeptide NZ_CP098790.1 Lanthipeptides: M5C73_RS03405_lanthipeptide NZ_JAALEQ010000006.1 Lanthipeptides: HFD15_RS10120_lanthipeptide NZ_JAJONJ010000005.1 Lanthipeptides: LSG16_RS07195_lanthipeptide NZ_JAQDWM010000007.1 Lanthipeptides: PGU01_RS08180_lanthipeptide NZ_JAQDXV010000018.1 Lanthipeptides: PGT80_RS11850_lanthipeptide NZ_JAQEIZ010000019.1 Lanthipeptides: PGX18_RS12025_lanthipeptide NZ_JAQEOU010000022.1 Lanthipeptides: PGV42_RS12330_lanthipeptide NZ_JAQEOV010000015.1 Lanthipeptides: PGW09_RS10765_lanthipeptide NZ_MTJP01000006.1 Lanthipeptides: BW151_RS03795_lanthipeptide NZ_MTJR01000005.1 Lanthipeptides: BW153_RS02980_lanthipeptide NZ_MTJS01000002.1 Lanthipeptides: BW154_RS09850_lanthipeptide NZ_RAGL01000022.1 Lanthipeptides: D6108_RS11395_lanthipeptide
Lanthipeptides: LLKF_RS13210_lanthipeptide
1
I T S W S L C T P G C V T A A--G C T--T S V C T Q G C H V S K
30
I T S S L C T P G C T A G C T+ C H V S K
1
I T S I S L C T P G C K T G A L M G C N M K T A T C N C S I H V S K
34
58.8%
NZ_CP065984.1 and 2 others:
NZ_CP095737.1 Lanthipeptides: MXM90_RS03205_lanthipeptide NZ_JAQDXJ010000021.1 Lanthipeptides: PGU19_RS11740_lanthipeptide
Lanthipeptides: I6I21_RS02785_lanthipeptide
1
I T S W S L C T P G C V T A A--G C T--T S V C T Q G C H V S K
30
I T S S L C T P G C T A G C T+ C H V S K
1
I T S I S L C T P G C K T G A L M G C N M K T A T C H C S I H V S K
34
55.9%
NZ_CP090412.1 and 3 others:
NZ_QSTB01000004.1 Lanthipeptides: DXC22_RS03785_lanthipeptide NZ_VSTZ01000009.1 Lanthipeptides: FYK98_RS07445_lanthipeptide NZ_VSTZ01000009.1 Lanthipeptides: FYK98_RS07445_lanthipeptide
Lanthipeptides: LZF92_RS09890_lanthipeptide
1
I T S W S L C T P G C V T A A--G C T T S V C T Q G C H V
28
I T S+S L C T P G C T A G C T + G C H V
1
I T S Y S L C T P G C K T G A L M G C T M K T A S C G C H V
30
55.9%
NZ_JAQDYA010000007.1 and 1 other:
NZ_JAQDYA010000007.1 Lanthipeptides: PGT72_RS09560_lanthipeptide
Lanthipeptides: PGT72_RS09560_lanthipeptide
1
I T S W S L C T P G C V T A A--G C T--T S V C T Q G C H V S K
30
I T S S L C T P G C T A G C T+ C H V S+
1
I T S I S L C T P G C K T G A L M G C N M K T A T C N C S I H V S R
34
53.1%
NZ_CP059471.1 and 3 others:
NZ_FNZW01000001.1 Lanthipeptides: BMZ61_RS02110_lanthipeptide NZ_FOYC01000001.1 Lanthipeptides: BMZ88_RS03370_lanthipeptide NZ_KE384124.1 Lanthipeptides: G597_RS0106700_lanthipeptide
Lanthipeptides: H1R75_RS06635_lanthipeptide
1
I T S W S L C T P G C V T A A--G C T T S V C T Q G C H V
28
I T S S L C T P G C T A C T G C H
1
I T S K S L C T P G C K T G A L M T C P I K T A T C G C H F
30
52.9%
NZ_FBTD01000003.1:
Lanthipeptides: PB1E_RS03075_lanthipeptide
1
I T S W S L C T P G C V T A A--G C T T S V C T Q G C H V
28
I T S S L C T P G C T A G C + G C H V
1
I T S V S L C T P G C K T G A L M G C N M K T A S C G C H V
30
52.9%
NZ_JALGRO010000002.1:
Lanthipeptides: MT346_RS01980_lanthipeptide
1
I T S W S L C T P G C V T A A-G C T T S V C T Q G C H V S K
30
I T S+S L C T P G C T C T+ C T G C +S
1
I T S F S L C T P G C P T G G F A C F T A A C T G G C T I S S
31
52.9%
NZ_LR793265.1:
Lanthipeptides: HV392_RS09825_lanthipeptide
1
I T S W S L C T P G C V T---------A A G C T T S V C T Q G C H V S K
30
I T S+S L C T P G C+T +A G C V H+S K
1
I T S Y S L C T P G C I T G R L M G C Q F Q S A G C N V H V-----H I S K
34
52.9%
NZ_LR793265.1:
Lanthipeptides: HV392_RS09830_lanthipeptide
1
I T S W S L C T P G C V T A A--G C--T T S V C T Q G C H V S K
30
I T S+S L C T P G C+T G C ++ C H V S K
1
I T S Y S L C T P G C I T G V L M G C Q F Q S A G C N V H V H V S K
34

#### MIBiG 4.0 matches for B7024_RS31125

58.8%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
1
I T S W S L C T P G C V T A A--G C T--T S V C T Q G C H V S K
30
I T S S L C T P G C T A G C T+ C H V S K
1
I T S I S L C T P G C K T G A L M G C N M K T A T C H C S I H V S K
34
21.6%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
12
V T A A G C T T S V C T Q G C
26
V+A A C T+ C T C
23
V S A A F C P T T K C T S R C
37
16.7%
BGC0002110.3 (QKV49894.1):
Lanthipeptide: birimositide
17
C T T S V C T Q G C
26
C T+ C T C
17
C P T T K C T S K C
26

#### 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.37 out of 23.43
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (21):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.22 out of 26.85
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.08 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.43 out of 21.55
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 30.11
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.17 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.26 out of 29.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.94 out of 36.54
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.42 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.80 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.72 out of 30.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.56 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.23 out of 30.25
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.03 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.75 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.12 out of 32.93
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.41 out of 30.98
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.45 out of 26.85
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.27 out of 30.12
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
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.

B7024_RS31125 - Class I
  Cleavage pHMM score: 5.00
  RODEO score: 31
  Monoisotopic mass: 2820.3 Da
  Molecular weight: 2822.2 Da
  Number of bridges: 5
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2840.3 Da N = 1
    2858.3 Da N = 2
    2876.3 Da N = 3
    2894.3 Da N = 4
    2912.3 Da N = 5

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 345621 - 469070:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 345781 - 388901:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 350614 - 469070:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Me-ohmal - Me-ohmal - Me-ohmal) + (ohmal - Me-ohmal) + (Me-ohmal - Me-ohmal) + (Me-ohmal - ohmal) + (Me-ohmal - Me-ohmal - Me-ohmal) + (Me-ohmal) + (Me-ohmal - Me-ccmal) + (Me-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).
B7024_RS31150: X
AMP-binding (445..838): 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:
    FWTTFDLAANALTLVVIGEVNTYGPTEATVMMTR
  Nearest Stachelhaus code(s):
    Ala DLMTMCTVAK (56% 8Å match)
    Dhpg DALSVGTVMK (50% 8Å match)
  Stachelhaus code match:
    60% (weak)

B7024_RS31165: mmal - mmal - mmal
PKS_AT (577..866): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 178.8
  Methoxymalonyl-CoA: 159.1
  Ethylmalonyl-CoA: 148.9
  2-Methylbutyryl-CoA: 123.9
  Propionyl-CoA: 101.7
  Malonyl-CoA: 98.8
  CHC-CoA: 94.7
  trans-1,2-CPDA: 87.4
  Isobutyryl-CoA: 54.5
  Benzoyl-CoA: 47.1
  3-Methylbutyryl-CoA: 44.7
  inactive: 40.0
  Acetyl-CoA: 26.3
  fatty_acid: 21.4

PKS_AT (2085..2382): mmal
ATSignature: Methoxymalonyl-CoA, Methylmalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 79.2%
  Methylmalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 169.3
  Ethylmalonyl-CoA: 160.5
  Methoxymalonyl-CoA: 152.2
  trans-1,2-CPDA: 97.9
  2-Methylbutyryl-CoA: 86.1
  Propionyl-CoA: 84.7
  Malonyl-CoA: 65.1
  CHC-CoA: 63.8
  Isobutyryl-CoA: 61.4
  3-Methylbutyryl-CoA: 59.4
  Acetyl-CoA: 44.0
  Benzoyl-CoA: 42.3
  inactive: 18.0
  fatty_acid: 11.6

PKS_AT (3605..3895): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 180.9
  Methoxymalonyl-CoA: 161.0
  Ethylmalonyl-CoA: 153.4
  2-Methylbutyryl-CoA: 118.3
  Propionyl-CoA: 100.5
  Malonyl-CoA: 91.2
  trans-1,2-CPDA: 89.1
  CHC-CoA: 75.9
  Isobutyryl-CoA: 57.4
  Benzoyl-CoA: 51.7
  3-Methylbutyryl-CoA: 40.3
  inactive: 30.4
  Acetyl-CoA: 30.4
  fatty_acid: 21.7

B7024_RS31170: mal - mmal
PKS_AT (568..856): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 140.9
  inactive: 69.9
  Methoxymalonyl-CoA: 63.5
  Methylmalonyl-CoA: 53.5
  Isobutyryl-CoA: 38.5
  fatty_acid: 35.6
  Propionyl-CoA: 26.9
  Acetyl-CoA: 24.4
  Benzoyl-CoA: 23.9
  Ethylmalonyl-CoA: 22.1
  trans-1,2-CPDA: 16.9
  2-Methylbutyryl-CoA: 16.2
  CHC-CoA: 12.3
  3-Methylbutyryl-CoA: 8.0

PKS_AT (2032..2321): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 176.6
  Methoxymalonyl-CoA: 155.2
  Ethylmalonyl-CoA: 147.6
  2-Methylbutyryl-CoA: 111.9
  Malonyl-CoA: 98.1
  CHC-CoA: 91.9
  Propionyl-CoA: 91.7
  trans-1,2-CPDA: 84.9
  Isobutyryl-CoA: 58.2
  Benzoyl-CoA: 50.7
  inactive: 40.8
  3-Methylbutyryl-CoA: 36.8
  fatty_acid: 28.4
  Acetyl-CoA: 27.3

B7024_RS31175: mmal - mmal
PKS_AT (587..882): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 180.5
  Methoxymalonyl-CoA: 159.6
  Ethylmalonyl-CoA: 152.4
  2-Methylbutyryl-CoA: 125.2
  Propionyl-CoA: 100.9
  Malonyl-CoA: 90.1
  trans-1,2-CPDA: 89.7
  CHC-CoA: 70.9
  Isobutyryl-CoA: 57.6
  Benzoyl-CoA: 50.3
  3-Methylbutyryl-CoA: 43.3
  inactive: 32.2
  Acetyl-CoA: 24.9
  fatty_acid: 21.7

PKS_AT (2072..2365): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 180.3
  Methoxymalonyl-CoA: 161.7
  Ethylmalonyl-CoA: 156.2
  2-Methylbutyryl-CoA: 108.7
  Propionyl-CoA: 96.5
  Malonyl-CoA: 93.8
  trans-1,2-CPDA: 91.5
  CHC-CoA: 71.0
  Isobutyryl-CoA: 55.9
  Benzoyl-CoA: 53.5
  3-Methylbutyryl-CoA: 44.5
  Acetyl-CoA: 37.2
  inactive: 34.8
  fatty_acid: 23.9

B7024_RS31180: mmal - mal
PKS_AT (576..866): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 181.5
  Methoxymalonyl-CoA: 160.8
  Ethylmalonyl-CoA: 157.5
  2-Methylbutyryl-CoA: 123.6
  Propionyl-CoA: 105.0
  trans-1,2-CPDA: 92.1
  Malonyl-CoA: 89.3
  CHC-CoA: 74.4
  Isobutyryl-CoA: 62.5
  Benzoyl-CoA: 50.5
  3-Methylbutyryl-CoA: 41.9
  inactive: 33.9
  Acetyl-CoA: 28.5
  fatty_acid: 23.9

PKS_AT (2060..2348): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 140.9
  inactive: 69.9
  Methoxymalonyl-CoA: 63.5
  Methylmalonyl-CoA: 53.5
  Isobutyryl-CoA: 38.5
  fatty_acid: 35.6
  Propionyl-CoA: 26.9
  Acetyl-CoA: 24.4
  Benzoyl-CoA: 23.9
  Ethylmalonyl-CoA: 22.1
  trans-1,2-CPDA: 16.9
  2-Methylbutyryl-CoA: 16.2
  CHC-CoA: 12.3
  3-Methylbutyryl-CoA: 8.0

B7024_RS31185: mmal - mmal - mmal
PKS_AT (583..872): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 175.2
  Methoxymalonyl-CoA: 156.8
  Ethylmalonyl-CoA: 147.7
  2-Methylbutyryl-CoA: 118.6
  Propionyl-CoA: 98.8
  Malonyl-CoA: 91.4
  trans-1,2-CPDA: 85.4
  CHC-CoA: 80.6
  Isobutyryl-CoA: 59.7
  Benzoyl-CoA: 48.8
  3-Methylbutyryl-CoA: 35.9
  inactive: 30.4
  Acetyl-CoA: 23.5
  fatty_acid: 22.9

PKS_AT (2069..2358): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 180.7
  Methoxymalonyl-CoA: 161.3
  Ethylmalonyl-CoA: 155.4
  2-Methylbutyryl-CoA: 121.6
  Propionyl-CoA: 102.5
  Malonyl-CoA: 90.4
  trans-1,2-CPDA: 89.0
  CHC-CoA: 82.9
  Isobutyryl-CoA: 59.8
  Benzoyl-CoA: 48.6
  3-Methylbutyryl-CoA: 41.3
  inactive: 28.9
  Acetyl-CoA: 28.0
  fatty_acid: 24.5

PKS_AT (3602..3895): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 183.4
  Methoxymalonyl-CoA: 162.0
  Ethylmalonyl-CoA: 157.4
  2-Methylbutyryl-CoA: 119.8
  Propionyl-CoA: 99.8
  Malonyl-CoA: 95.1
  trans-1,2-CPDA: 92.1
  CHC-CoA: 75.8
  Isobutyryl-CoA: 64.0
  Benzoyl-CoA: 54.7
  3-Methylbutyryl-CoA: 42.1
  inactive: 30.8
  Acetyl-CoA: 25.7
  fatty_acid: 25.2

B7024_RS31190: mmal
PKS_AT (587..877): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 182.4
  Methoxymalonyl-CoA: 161.4
  Ethylmalonyl-CoA: 157.2
  2-Methylbutyryl-CoA: 122.8
  Propionyl-CoA: 104.2
  trans-1,2-CPDA: 92.0
  Malonyl-CoA: 91.4
  CHC-CoA: 74.0
  Isobutyryl-CoA: 59.1
  Benzoyl-CoA: 52.2
  3-Methylbutyryl-CoA: 38.4
  inactive: 34.9
  Acetyl-CoA: 29.3
  fatty_acid: 23.4

B7024_RS31195: mmal - mmal
PKS_AT (593..883): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 180.5
  Methoxymalonyl-CoA: 161.1
  Ethylmalonyl-CoA: 149.3
  2-Methylbutyryl-CoA: 119.5
  Propionyl-CoA: 100.5
  Malonyl-CoA: 94.6
  trans-1,2-CPDA: 88.4
  CHC-CoA: 74.8
  Isobutyryl-CoA: 59.0
  Benzoyl-CoA: 48.1
  3-Methylbutyryl-CoA: 40.5
  inactive: 28.9
  Acetyl-CoA: 25.3
  fatty_acid: 22.1

PKS_AT (2098..2397): mmal
ATSignature: Methoxymalonyl-CoA, Methylmalonyl-CoA

Top 3 matches:
  Methoxymalonyl-CoA: 79.2%
  Methylmalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 173.5
  Ethylmalonyl-CoA: 159.8
  Methoxymalonyl-CoA: 152.7
  trans-1,2-CPDA: 97.1
  2-Methylbutyryl-CoA: 86.9
  Propionyl-CoA: 82.5
  Malonyl-CoA: 67.7
  CHC-CoA: 66.5
  Isobutyryl-CoA: 61.8
  3-Methylbutyryl-CoA: 56.7
  Acetyl-CoA: 44.3
  Benzoyl-CoA: 42.1
  inactive: 20.3
  fatty_acid: 11.4

B7024_RS31220: mmal
PKS_AT (538..815): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 177.3
  Methoxymalonyl-CoA: 155.9
  Ethylmalonyl-CoA: 142.7
  2-Methylbutyryl-CoA: 110.3
  Malonyl-CoA: 95.9
  Propionyl-CoA: 92.7
  trans-1,2-CPDA: 89.0
  CHC-CoA: 74.0
  Isobutyryl-CoA: 60.3
  Benzoyl-CoA: 52.9
  inactive: 39.6
  3-Methylbutyryl-CoA: 37.9
  Acetyl-CoA: 30.2
  fatty_acid: 28.0

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (345621...370059)
B7024_RS31110
  RRE type: Lanthipeptide_LanB_RRE
  Location: 154 - 244
  Score: 50.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_NDXL01000003.1 - Region 3 - NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 698,928 - 776,773 nt. (total: 77,846 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
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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
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 synthase
B7024_RS32445: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS32475: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

B7024_RS32500: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

B7024_RS32610: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

B7024_RS32620: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: glycosyltransferase methyltransferase
B7024_RS32490: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

B7024_RS42865: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase synthase
B7024_RS32475: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

B7024_RS32570: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
B7024_RS32515: 3-oxoacyl-(acyl carrier protein) synthase III

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

B7024_RS32525: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS32535: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS32540: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

B7024_RS32545: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS32550: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B7024_RS32560: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS32575: 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-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000342.4 |  |  |  | 1.39 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  |  |  | 1.27 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001327.5 |  |  |  | 1.27 | NRPS, PKS | rakicidin A, rakicidin B | Micromonospora purpureochromogenes
BGC0001160.5 |  |  |  | 1.20 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001833.4 |  |  |  | 1.19 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  |  | 1.19 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  |  | 1.18 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001164.3 |  |  |  | 1.18 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001261.3 |  |  |  | 1.17 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  |  |  | 1.16 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001327.5 |  | 0.78 | NRPS, PKS | rakicidin A, rakicidin B | Micromonospora purpureochromogenes
BGC0000342.4 |  | 0.76 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.72 | NRPS | AM-toxin | Alternaria alternata
BGC0001160.5 |  | 0.72 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.88 out of 20.97
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.23 out of 29.51
Confidence: medium
Additional weak hits (17):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.15 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.31 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.10 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.34 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.09 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.58 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.09 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.66 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.32 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.91 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.73 out of 31.73
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.12 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.75 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.00 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.35 out of 29.38
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.79 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.98 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 6, location 698927 - 776773:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Me-redmal) + (ohmal) + (Ser) + (ccmal) + (NMe-Gly) + (Glu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 698927 - 761682:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Me-redmal) + (ohmal) + (Ser) + (ccmal) + (NMe-Gly) + (Glu)

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).
B7024_RS32535: NH2 - mmal
CAL_domain (40..489): NH2
minowa: NH2

Prediction, score:
  NH2: 187.7
  Acetyl-CoA: 74.2
  fatty_acid: 26.7
  AHBA: 13.0
  shikimic_acid: 0.0

PKS_AT (1249..1548): mmal
ATSignature: Malonyl-CoA, Methylmalonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  Methylmalonyl-CoA: 75.0%
  Methoxymalonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 139.4
  Methoxymalonyl-CoA: 113.3
  Malonyl-CoA: 104.2
  Ethylmalonyl-CoA: 99.3
  Isobutyryl-CoA: 90.2
  Propionyl-CoA: 80.0
  2-Methylbutyryl-CoA: 76.1
  Benzoyl-CoA: 74.7
  3-Methylbutyryl-CoA: 60.4
  trans-1,2-CPDA: 54.4
  Acetyl-CoA: 51.6
  fatty_acid: 36.6
  CHC-CoA: 35.1
  inactive: 34.3

B7024_RS32540: mal
PKS_AT (566..862): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 62.5%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 180.9
  inactive: 110.8
  Methoxymalonyl-CoA: 79.5
  Methylmalonyl-CoA: 77.4
  Propionyl-CoA: 62.9
  Ethylmalonyl-CoA: 52.4
  2-Methylbutyryl-CoA: 45.7
  Isobutyryl-CoA: 45.6
  CHC-CoA: 39.9
  Acetyl-CoA: 39.8
  trans-1,2-CPDA: 21.7
  Benzoyl-CoA: 20.6
  fatty_acid: 17.3
  3-Methylbutyryl-CoA: 7.5

B7024_RS32545: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (500..900): 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:
    RWMTFDVSVWEWHFFCSGEHNLYGPTEAAIDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHFSLIDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

B7024_RS32550: mal
PKS_AT (564..862): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 156.7
  inactive: 94.6
  Methoxymalonyl-CoA: 66.4
  Methylmalonyl-CoA: 54.0
  Propionyl-CoA: 40.4
  Isobutyryl-CoA: 36.2
  CHC-CoA: 35.2
  Ethylmalonyl-CoA: 30.1
  2-Methylbutyryl-CoA: 26.4
  Benzoyl-CoA: 21.0
  fatty_acid: 20.4
  Acetyl-CoA: 18.8
  trans-1,2-CPDA: 11.5
  3-Methylbutyryl-CoA: 4.4

B7024_RS42865: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (504..897): 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:
    FSMTFDISLLELQALAGGEWNMYGPTETTIWSAA
  Nearest Stachelhaus code(s):
    Gly DILQLGMIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

B7024_RS32560: Glu
Search NORINE for peptide: strict or relaxed
AMP-binding (507..899): Glu
nrpys: Glu

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

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

B7024_RS32575: X
AMP-binding (515..917): X
nrpys: Asp, Asn

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    N/A
  Small clusters prediction:
    asp,asn (Asp, Asn)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWTSFDLGIPNAKMIAAGDATEYGPTEITIGNSG
  Nearest Stachelhaus code(s):
    Asn DLTKIGEVGK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
DosR | Hypoxia stress response regulator

NZ_NDXL01000003.1 - Region 4 - NAPAA
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: 795,226 - 838,006 nt. (total: 42,781 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B7024_RS32780: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS32785: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B7024_RS32805: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
B7024_RS32845: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: hydratase
B7024_RS32855: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
B7024_RS32765: 1-deoxy-D-xylulose-5-phosphate synthase

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

B7024_RS32815: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS32820: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS32830: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS32840: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B7024_RS32850: 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 | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.59 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.59 | 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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.19 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31
Confidence: medium
Additional weak hits (9):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.82 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.96 out of 21.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.37 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 39.62
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 20.94 out of 32.93
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.08 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.03 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.87 out of 30.25
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.84 out of 27.04
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 795225 - 838006:
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).
B7024_RS32815: X
AMP-binding (9..414): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSPA-------AHMIHGAAEEYYAASEGGGAFAT
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

B7024_RS32820: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (13..414): 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:
    ASALAQLHVF-PFAYYGASYNCFGQSEIGPLAMV
  Nearest Stachelhaus code(s):
    Ala DLFFCGGPLK (24% 8Å match)
  Stachelhaus code match:
    70% (weak)

B7024_RS32830: X
AMP-binding (93..339): 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:
    WVVIYGLFTGGGMVIFGAEVDIYGLSE-----LM
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

B7024_RS32840: X
AMP-binding (37..413): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAELFDASCEELSTIVGGEWNTYGPTETTVVACA
  Nearest Stachelhaus code(s):
    Lys DAEDIGTVVK (68% 8Å match)
    Gln or Tyr DAESVGTVVK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

B7024_RS32850: X
AMP-binding (8..440): X
nrpys: Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    SHPPHGTSTLTISLSSSGALNNFGSSESGFNGTA
  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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_NDXL01000003.1 - Region 5 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,676,560 - 1,701,561 nt. (total: 25,002 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
B7024_RS36430: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

B7024_RS36435: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: 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-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.52 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001727.3 |  | 0.42 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000514.5 |  | 0.38 | ribosomal | gallidermin | Staphylococcus gallinarum
BGC0000529.5 |  | 0.36 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0001707.5 |  | 0.34 | ribosomal | nosiheptide | Streptomyces sp.
BGC0002656.2 |  | 0.27 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49
BGC0002022.4 |  | 0.22 | PKS | armeniaspirol A, armeniaspirol B, armeniaspirol C | Streptomyces armeniacus
BGC0001396.5 |  | 0.21 | PKS | aldgamycin J, aldgamycin K, aldgamycin P, aldgamycin E | Streptomyces sp. A1(2016)

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.52 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001727.3 |  | 0.42 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000514.5 |  | 0.38 | ribosomal | gallidermin | Staphylococcus gallinarum
BGC0000529.5 |  | 0.36 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0001707.5 |  | 0.34 | ribosomal | nosiheptide | Streptomyces sp.
BGC0002656.2 |  | 0.27 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49
BGC0002022.4 |  | 0.22 | PKS | armeniaspirol A, armeniaspirol B, armeniaspirol C | Streptomyces armeniacus
BGC0001396.5 |  | 0.21 | PKS | aldgamycin J, aldgamycin K, aldgamycin P, aldgamycin E | Streptomyces sp. A1(2016)

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 B7024_RS36430

B7024_RS36425
Leader:
MTVQLERPVAPAQPVTEDRQEPGQADFDLDITIVEGGPAAD
Core:
Q L I R L T S D G C N S T C A T A C V S C P
Core with dehydrations:
Q L I R L Dhb Dha D G Cys N Dha Dhb Cys A Dhb A Cys V Dha Cys P

#### antiSMASH-DB 4.0 matches for B7024_RS36425

100.0%
NZ_NDXL01000003.1 and 1 other:
NZ_NDXL01000003.1 Lanthipeptides: B7024_RS36425_lanthipeptide
Lanthipeptides: B7024_RS36425_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T S D G C N S T C A T A C V S C P
1
Q L I R L T S D G C N S T C A T A C V S C P
22
95.5%
NC_016109.1 and 4 others:
NC_016109.1 Lanthipeptides: KSE_RS29105_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide
Lanthipeptides: KSE_RS29105_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T+D G C N S T C A T A C V S C P
1
Q L I R L T N D G C N S T C A T A C V S C P
22
95.5%
NZ_CP021121.1 and 1 other:
NZ_CP021121.1 Lanthipeptides: CAG99_RS19010_lanthipeptide
Lanthipeptides: CAG99_RS19010_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A T A C V S C P
1
Q L I R L T G D G C N S T C A T A C V S C P
22
with 174 more sequence matches
Only the first 10 are displayed here.
95.5%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS22650_lanthipeptide
Lanthipeptides: C7M71_RS22650_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A T A C V S C P
1
Q L I R L T D D G C N S T C A T A C V S C P
22
90.9%
NZ_JACERG010000017.1 and 1 other:
NZ_JACERG010000017.1 Lanthipeptides: H1X69_RS24645_lanthipeptide
Lanthipeptides: H1X69_RS24645_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T+D G C N S T C A+A C V S C P
1
Q L I R L T N D G C N S T C A S A C V S C P
22
86.4%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS16225_lanthipeptide
Lanthipeptides: GBF35_RS16225_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R+T D G C N S T C A T A C S C P
1
Q L I R M T D D G C N S T C A T A C N S C P
22
82.6%
NZ_BCBX01000061.1 and 1 other:
NZ_BCBX01000061.1 Lanthipeptides: AP234_RS35640_lanthipeptide
Lanthipeptides: AP234_RS35640_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C
21
Q L I R+T D G C N S T C A T A C V S C
1
Q L I R M T D D G C N S T C A T A C V S C
21
82.6%
NZ_CP119143.1 and 1 other:
NZ_CP119143.1 Lanthipeptides: PYR72_RS32440_lanthipeptide
Lanthipeptides: PYR72_RS32440_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R+T D G C N S T C A T A C S C P
1
Q L I R M T D D G C N S T C A T A C T S C P
22
78.3%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS37485_lanthipeptide
Lanthipeptides: GBF35_RS37485_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C
21
Q L I R+T D G C N S T C T A C V S C
1
Q L I R M T D D G C N S T C G T A C V S C
21
77.3%
NZ_CP026652.1 and 1 other:
NZ_CP026652.1 Lanthipeptides: C4B68_RS00400_lanthipeptide
Lanthipeptides: C4B68_RS00400_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T+D G C S T C +A C S C P
1
Q L I R L T N D G C G S T C Q S A C T S C P
22
60.9%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C-V S C P
22
+L I R+T D G C +T C T A C +C P
1
R L I R M T D D G C G T T C E T A C S T T C P
23
59.1%
NZ_AZVD01000043.1 and 3 others:
NZ_AZVD01000043.1 Lanthipeptides: K389_RS1000000127440_lanthipeptide NZ_KB898438.1 Lanthipeptides: D462_RS1000000129145_lanthipeptide NZ_KB898438.1 Lanthipeptides: D462_RS1000000129145_lanthipeptide
Lanthipeptides: K389_RS1000000127440_lanthipeptide
2
L I R L T S D G C N S T C A T A C V S C P
22
L+R T S D C T C A+A C S C
1
L L R S T S D N C G G T C A S A C T S C K
21
59.1%
NZ_CP061725.1 and 1 other:
NZ_CP061725.1 Lanthipeptides: ID554_RS13020_lanthipeptide
Lanthipeptides: ID554_RS13020_lanthipeptide
2
L I R L T S D G C N S T C A T A C V S C P
22
L+R T S D C T C A+A C S C
1
L M R S T S D N C G K T C A S A C T S C K
21

#### Lanthipeptide(s) for B7024_RS36440

B7024_RS36425
Leader:
MTVQLERPVAPAQPVTEDRQEPGQADFDLDITIVEGGPAAD
Core:
Q L I R L T S D G C N S T C A T A C V S C P
Core with dehydrations:
Q L I R L Dhb Dha D G Cys N Dha Dhb Cys A Dhb A Cys V Dha Cys P

#### antiSMASH-DB 4.0 matches for B7024_RS36425

100.0%
NZ_NDXL01000003.1 and 1 other:
NZ_NDXL01000003.1 Lanthipeptides: B7024_RS36425_lanthipeptide
Lanthipeptides: B7024_RS36425_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T S D G C N S T C A T A C V S C P
1
Q L I R L T S D G C N S T C A T A C V S C P
22
95.5%
NC_016109.1 and 4 others:
NC_016109.1 Lanthipeptides: KSE_RS29105_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide
Lanthipeptides: KSE_RS29105_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T+D G C N S T C A T A C V S C P
1
Q L I R L T N D G C N S T C A T A C V S C P
22
95.5%
NZ_CP021121.1 and 1 other:
NZ_CP021121.1 Lanthipeptides: CAG99_RS19010_lanthipeptide
Lanthipeptides: CAG99_RS19010_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A T A C V S C P
1
Q L I R L T G D G C N S T C A T A C V S C P
22
with 174 more sequence matches
Only the first 10 are displayed here.
95.5%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS22650_lanthipeptide
Lanthipeptides: C7M71_RS22650_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A T A C V S C P
1
Q L I R L T D D G C N S T C A T A C V S C P
22
90.9%
NZ_JACERG010000017.1 and 1 other:
NZ_JACERG010000017.1 Lanthipeptides: H1X69_RS24645_lanthipeptide
Lanthipeptides: H1X69_RS24645_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T+D G C N S T C A+A C V S C P
1
Q L I R L T N D G C N S T C A S A C V S C P
22
86.4%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS16225_lanthipeptide
Lanthipeptides: GBF35_RS16225_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R+T D G C N S T C A T A C S C P
1
Q L I R M T D D G C N S T C A T A C N S C P
22
82.6%
NZ_BCBX01000061.1 and 1 other:
NZ_BCBX01000061.1 Lanthipeptides: AP234_RS35640_lanthipeptide
Lanthipeptides: AP234_RS35640_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C
21
Q L I R+T D G C N S T C A T A C V S C
1
Q L I R M T D D G C N S T C A T A C V S C
21
82.6%
NZ_CP119143.1 and 1 other:
NZ_CP119143.1 Lanthipeptides: PYR72_RS32440_lanthipeptide
Lanthipeptides: PYR72_RS32440_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R+T D G C N S T C A T A C S C P
1
Q L I R M T D D G C N S T C A T A C T S C P
22
78.3%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS37485_lanthipeptide
Lanthipeptides: GBF35_RS37485_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C
21
Q L I R+T D G C N S T C T A C V S C
1
Q L I R M T D D G C N S T C G T A C V S C
21
77.3%
NZ_CP026652.1 and 1 other:
NZ_CP026652.1 Lanthipeptides: C4B68_RS00400_lanthipeptide
Lanthipeptides: C4B68_RS00400_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C V S C P
22
Q L I R L T+D G C S T C +A C S C P
1
Q L I R L T N D G C G S T C Q S A C T S C P
22
60.9%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
1
Q L I R L T S D G C N S T C A T A C-V S C P
22
+L I R+T D G C +T C T A C +C P
1
R L I R M T D D G C G T T C E T A C S T T C P
23
59.1%
NZ_AZVD01000043.1 and 3 others:
NZ_AZVD01000043.1 Lanthipeptides: K389_RS1000000127440_lanthipeptide NZ_KB898438.1 Lanthipeptides: D462_RS1000000129145_lanthipeptide NZ_KB898438.1 Lanthipeptides: D462_RS1000000129145_lanthipeptide
Lanthipeptides: K389_RS1000000127440_lanthipeptide
2
L I R L T S D G C N S T C A T A C V S C P
22
L+R T S D C T C A+A C S C
1
L L R S T S D N C G G T C A S A C T S C K
21
59.1%
NZ_CP061725.1 and 1 other:
NZ_CP061725.1 Lanthipeptides: ID554_RS13020_lanthipeptide
Lanthipeptides: ID554_RS13020_lanthipeptide
2
L I R L T S D G C N S T C A T A C V S C P
22
L+R T S D C T C A+A C S C
1
L M R S T S D N C G K T C A S A C T S C K
21

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (6):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.02 out of 30.97
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.00 out of 20.01
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.43 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
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.00 out of 23.43
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

B7024_RS36425 - Class I
  Cleavage pHMM score: -1.70
  RODEO score: 24
  Monoisotopic mass: 2134.0 Da
  Molecular weight: 2135.4 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2153.5 Da N = 1
    2171.5 Da N = 2
B7024_RS36425 - Class I
  Cleavage pHMM score: -1.70
  RODEO score: 24
  Monoisotopic mass: 2134.0 Da
  Molecular weight: 2135.4 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2153.5 Da N = 1
    2171.5 Da N = 2

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (1676559...1701561)
B7024_RS36430
  RRE type: Lanthipeptide_LanB_RRE
  Location: 153 - 242
  Score: 65.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_NDXL01000003.1 - Region 6 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,841,461 - 1,863,807 nt. (total: 22,347 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase
B7024_RS37170: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase
B7024_RS37180: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002006.2 |  | 0.56 | ribosomal | albusnodin | Streptomyces albus
BGC0001506.5 |  | 0.44 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0002053.3 |  | 0.44 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001493.5 |  | 0.43 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0002318.2 |  | 0.42 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0002064.2 |  | 0.39 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0000579.4 |  | 0.34 | ribosomal | SSV-2083 | Streptomyces sviceus ATCC 29083
BGC0001435.4 |  | 0.31 | NRPS, PKS | ikarugamycin | Streptomyces sp. ZJ306
BGC0002122.2 |  | 0.24 | NRPS | gramicidin S | Aneurinibacillus migulanus
BGC0000612.4 |  | 0.23 | ribosomal | thiocillin I | Bacillus cereus ATCC 14579

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002006.2 |  | 0.56 | ribosomal | albusnodin | Streptomyces albus
BGC0001506.5 |  | 0.44 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0002053.3 |  | 0.44 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001493.5 |  | 0.43 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0002318.2 |  | 0.42 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0002064.2 |  | 0.39 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0000579.4 |  | 0.34 | ribosomal | SSV-2083 | Streptomyces sviceus ATCC 29083
BGC0001435.4 |  | 0.31 | NRPS, PKS | ikarugamycin | Streptomyces sp. ZJ306
BGC0002122.2 |  | 0.24 | NRPS | gramicidin S | Aneurinibacillus migulanus
BGC0000612.4 |  | 0.23 | ribosomal | thiocillin I | Bacillus cereus ATCC 14579

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.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - 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.
No hits above weak threshold.
Weak hits (5):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.85 out of 26.12
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.23 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.86 out of 27.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.37 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.04 out of 28.19
Confidence: weak
Lasso peptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_NDXL01000003.1 - Region 7 - aminopolycarboxylic-acid
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: 1,958,369 - 1,971,829 nt. (total: 13,461 nt) Show pHMM detection rules used
aminopolycarboxylic-acid: (AesA and AesB and AesC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: deaminase
B7024_RS37700: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: decarboxylase
B7024_RS37705: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: synthase
B7024_RS37710: cysteine synthase

smcogs
  SMCOG1081: cysteine 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 | aminopolycarboxylic-acid | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001587.5 |  | 0.85 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002568.2 |  | 0.78 | other (other) | Ethylenediaminesuccinic acid hydroxyarginine | Streptomyces scabiei 87.22
BGC0002567.2 |  | 0.68 | other (other) | EDHA | Streptomyces sp. MA5143a
BGC0000943.5 |  | 0.42 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000932.5 |  | 0.36 | other (other) | tropodithietic acid, hydroxytropodithietic acid | Phaeobacter inhibens DSM 17395
BGC0002487.3 |  | 0.35 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0002213.3 |  | 0.33 | PKS | HEx-pks16 polyketide | Punctularia strigosozonata HHB-11173 SS5
BGC0001790.4 |  | 0.32 | NRPS | sulfazecin | Pseudomonas acidophila
BGC0000188.5 |  | 0.31 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0002656.2 |  | 0.29 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001587.5 |  | 0.85 | other (other) | ethylenediaminesuccinic acid hydroxyarginine (EDHA) | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002568.2 |  | 0.78 | other (other) | Ethylenediaminesuccinic acid hydroxyarginine | Streptomyces scabiei 87.22
BGC0002567.2 |  | 0.68 | other (other) | EDHA | Streptomyces sp. MA5143a
BGC0000943.5 |  | 0.42 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000932.5 |  | 0.36 | other (other) | tropodithietic acid, hydroxytropodithietic acid | Phaeobacter inhibens DSM 17395
BGC0002487.3 |  | 0.35 | other (other) | staphylopine | Staphylococcus aureus subsp. aureus Mu50
BGC0002213.3 |  | 0.33 | PKS | HEx-pks16 polyketide | Punctularia strigosozonata HHB-11173 SS5
BGC0001790.4 |  | 0.32 | NRPS | sulfazecin | Pseudomonas acidophila
BGC0000188.5 |  | 0.31 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0002656.2 |  | 0.29 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (6):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.72 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.04 out of 27.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.57 out of 36.53
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.49 out of 29.38
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.02 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.25 out of 36.53
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_NDXL01000003.1 - Region 8 - ectoine
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,347,678 - 2,358,082 nt. (total: 10,405 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
B7024_RS39335: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

B7024_RS39355: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-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 | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.88 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.86 | other (other) | ectoine | Streptomyces anulatus
BGC0000859.3 |  | 0.72 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000854.3 |  | 0.63 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000860.3 |  | 0.60 | other (other) | ectoine | Methylarcula marina

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.88 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.86 | other (other) | ectoine | Streptomyces anulatus
BGC0000859.3 |  | 0.72 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000854.3 |  | 0.63 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000860.3 |  | 0.60 | other (other) | ectoine | Methylarcula marina

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (4):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.79 out of 30.97
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.47 out of 21.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.04 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production