Select genomic region:
Overview
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### Identified secondary metabolite regions using strictness 'relaxed'

NZ_CP031264.1 (Peterkaempfera bronchialis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | butyrolactone | 337,755 | 348,693 |
Region 2 | azole-containing-RiPP,RRE-containing | 568,031 | 611,631 |  |
Region 3 | terpene | 632,880 | 658,575 | High | isorenieratene | terpene
Region 4 | terpene | 889,137 | 910,177 |
Region 5 | terpene,NRPS,NRPS-like,betalactone | 933,924 | 999,816 | High | hopene | terpene
Region 6 | terpene-precursor | 1,430,107 | 1,451,237 |  |
Region 7 | HR-T2PKS,butyrolactone,furan | 1,647,081 | 1,688,256 | Low | colabomycin E | PKS:Type II
Region 8 | terpene | 1,762,058 | 1,784,325 | High | geosmin | terpene:Sesquiterpene
Region 9 | lanthipeptide-class-i | 1,913,336 | 1,938,691 |
Region 10 | terpene-precursor | 2,949,009 | 2,970,049 |  |
Region 11 | triceptide,phosphonate | 3,399,919 | 3,421,802 |
Region 12 | t3nrps-iterative,NRPS,NRPS-like,T1PKS | 3,791,593 | 3,867,609 |  |
Region 13 | lanthipeptide-class-i | 3,972,237 | 3,997,435 |  |
Region 14 | NI-siderophore | 5,027,690 | 5,060,365 |  |
Region 15 | lanthipeptide-class-i | 5,090,990 | 5,115,983 |
Region 16 | RiPP-like | 5,258,636 | 5,270,001 |  |
Region 17 | NRPS,T1PKS | 5,548,259 | 5,638,062 | Medium | neocarzilin A/neocarzilin B | PKS
Region 18 | NRP-metallophore,NRPS | 5,710,134 | 5,768,654 | High | coelichelin | NRPS:Type I
Region 19 | T1PKS | 5,778,290 | 5,829,279 | Low | abyssomicin M/abyssomicin N/abyssomicin O/abyssomicin P/abyssomicin Q/abyssomicin R/abyssomicin S/abyssomicin T/abyssomicin U/abyssomicin V/abyssomicin W/abyssomicin X | PKS
Region 20 | T3PKS,T1PKS | 5,852,092 | 6,035,626 | Low | caniferolide A/caniferolide B/caniferolide C/caniferolide D | PKS:Type I
Region 21 | NRPS | 6,227,093 | 6,291,077 |  |
Region 22 | hglE-KS | 6,585,150 | 6,638,960 |  |
Region 23 | T2PKS,RiPP-like | 6,722,194 | 6,794,700 | Medium | spore pigment | PKS

NZ_CP031264.1 - 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: 337,755 - 348,693 nt. (total: 10,939 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
C7M71_RS01455: HAD-superfamily hydrolase, subfamily IA, variant

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

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 |  | 0.77 | 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 |  | 0.51 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.44 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000914.5 |  | 0.35 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0002390.2 |  | 0.31 | terpene | zealexin A1 | Zea mays
BGC0002657.2 |  | 0.27 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0001771.4 |  | 0.27 | NRPS | scleric acid | Streptomyces sclerotialus
BGC0000038.5 |  | 0.26 | PKS | coelimycin P1 | Streptomyces coelicolor A3(2)
BGC0000760.5 |  | 0.26 | saccharide | emulsan | Acinetobacter venetianus RAG-1 = CIP 110063

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.77 | 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 |  | 0.51 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.44 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000914.5 |  | 0.35 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0002390.2 |  | 0.31 | terpene | zealexin A1 | Zea mays
BGC0002657.2 |  | 0.27 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0001771.4 |  | 0.27 | NRPS | scleric acid | Streptomyces sclerotialus
BGC0000038.5 |  | 0.26 | PKS | coelimycin P1 | Streptomyces coelicolor A3(2)
BGC0000760.5 |  | 0.26 | saccharide | emulsan | Acinetobacter venetianus RAG-1 = CIP 110063

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.
No hits above weak threshold.
Weak hits (2):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.84 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.19 out of 27.78
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP031264.1 - Region 2 - RRE-containing,azole-containing-RiPP
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: 568,031 - 611,631 nt. (total: 43,601 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Azole RiPPs
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
C7M71_RS02710: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Translocases: transporter
C7M71_RS02555: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | azole-containing-RiPP | RRE-containing | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000563.4 |  |  |  | 0.42 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  |  |  | 0.40 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0002635.2 |  |  |  | 0.39 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001579.4 |  |  |  | 0.38 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0002303.3 |  |  |  | 0.38 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0000605.5 |  |  |  | 0.38 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0001779.5 |  |  |  | 0.37 | ribosomal | siamycin | Streptomyces nodosus
BGC0001660.3 |  |  |  | 0.36 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0001655.3 |  |  |  | 0.35 | ribosomal | LP2006 | Nocardiopsis alba DSM 43377
BGC0001364.3 |  |  |  | 0.34 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.50 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0001146.5 |  | 0.49 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000606.5 |  | 0.49 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0002303.3 |  | 0.47 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0002311.3 |  | 0.47 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001145.5 |  | 0.46 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5 |  | 0.45 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0002144.3 |  | 0.44 | ribosomal | phazolicin | Rhizobium sp. Pop5
BGC0000605.5 |  | 0.43 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0000563.4 |  | 0.43 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712

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

No significant matches found.

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: 18.37 out of 20.47
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
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
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 (15):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.12 out of 26.85
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.10 out of 20.01
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.82 out of 20.01
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.22 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.10 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.90 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.07 out of 32.74
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.79 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
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.79 out of 20.97
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.66 out of 27.18
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.39 out of 24.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (568030...596820)
C7M71_RS32465
  RRE type: Thiopeptide_F_RRE
  Location: 0 - 82
  Score: 39.5
RRE-containing protocluster (576816...598550)
C7M71_RS32465
  RRE type: Thiopeptide_F_RRE
  Location: 0 - 82
  Score: 39.5
RRE-containing protocluster (589927...611631)
C7M71_RS02680
  RRE type: Thiopeptide_F_RRE
  Location: 0 - 80
  Score: 32.8

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
VqsM | Regulator of quorum-sensing signalling systems

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_CP031264.1 - Region 3 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 632,880 - 658,575 nt. (total: 25,696 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
C7M71_RS02895: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

C7M71_RS02910: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
C7M71_RS02890: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: lyase
C7M71_RS02955: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.73 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.68 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.64 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.63 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.63 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000645.3 |  | 0.53 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.47 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.46 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000650.3 |  | 0.45 | terpene | carotenoid | Algoriphagus sp. KK10202C

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.73 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.68 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.64 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.63 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.63 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000645.3 |  | 0.53 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.47 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.46 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000650.3 |  | 0.45 | terpene | carotenoid | Algoriphagus sp. KK10202C

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
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
C7M71_RS02885: Lycopene_cycl
Domain 1 (6 - 377): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

C7M71_RS02905: PT_phytoene_like
Domain 1 (16 - 307): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.56 out of 20.47
Confidence: medium
Additional weak hits (5):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 27.04
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.36 out of 21.84
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.61 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP031264.1 - Region 4 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 889,137 - 910,177 nt. (total: 21,041 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
C7M71_RS03940: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: aminotransferase
C7M71_RS03915: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Lyases: cyclase
C7M71_RS03935: 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
--- | --- | --- | --- | --- | ---
BGC0000709.5 |  | 0.35 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000889.5 |  | 0.35 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001965.4 |  | 0.35 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus
BGC0000711.5 |  | 0.34 | saccharide | neomycin | Streptomyces fradiae
BGC0002222.2 |  | 0.34 | PKS | zopfiellin | Diffractella curvata
BGC0000897.5 |  | 0.34 | other (other) | dehydrophos | Streptomyces luridus
BGC0001302.5 |  | 0.34 | other (other) | lomofungin | Streptomyces lomondensis
BGC0000194.5 |  | 0.33 | PKS | actinorhodin | Streptomyces coelicolor A3(2)
BGC0001336.5 |  | 0.33 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001366.5 |  | 0.33 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000709.5 |  | 0.35 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000889.5 |  | 0.35 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001965.4 |  | 0.35 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus
BGC0000711.5 |  | 0.34 | saccharide | neomycin | Streptomyces fradiae
BGC0002222.2 |  | 0.34 | PKS | zopfiellin | Diffractella curvata
BGC0000897.5 |  | 0.34 | other (other) | dehydrophos | Streptomyces luridus
BGC0001302.5 |  | 0.34 | other (other) | lomofungin | Streptomyces lomondensis
BGC0000194.5 |  | 0.33 | PKS | actinorhodin | Streptomyces coelicolor A3(2)
BGC0001336.5 |  | 0.33 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001366.5 |  | 0.33 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2

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

No significant matches found.

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
C7M71_RS03935: T1TS
Domain 1 (6 - 320): 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
Additional weak hits (4):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.16 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.15 out of 18.57
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.65 out of 26.12
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.22 out of 39.62
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP031264.1 - Region 5 - NRPS,NRPS-like,betalactone,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: 933,924 - 999,816 nt. (total: 65,893 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)
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)
betalactone: (HMGL-like and AMP-binding)

#### 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 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
C7M71_RS04150: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

C7M71_RS04185: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

C7M71_RS04240: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

C7M71_RS04340: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase transferase
C7M71_RS04115: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

C7M71_RS04190: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: esterase hydrolase
C7M71_RS04290: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

C7M71_RS04295: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: hydratase lyase
C7M71_RS04305: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

C7M71_RS04315: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

C7M71_RS04320: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Ligases: ligase synthase synthetase
C7M71_RS04120: 1-deoxy-D-xylulose-5-phosphate synthase

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

C7M71_RS04145: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

C7M71_RS04260: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

C7M71_RS04275: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

C7M71_RS04285: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | terpene | NRPS | NRPS-like | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000342.4 |  |  |  |  | 1.09 | NRPS | enniatin | Fusarium equiseti
BGC0001833.4 |  |  |  |  | 1.05 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  |  |  | 1.04 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002135.2 |  |  |  |  | 1.02 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  |  |  |  | 1.02 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  |  |  | 1.01 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  |  |  |  | 1.01 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  |  |  | 1.01 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  |  |  |  | 1.00 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  |  |  | 1.00 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.73 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
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:
C7M71_RS04140: T2TS
Domain 1 (3 - 619): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

C7M71_RS04145: PT_FPPS_like
Domain 1 (63 - 344): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

C7M71_RS04155: PT_phytoene_like
Domain 1 (2 - 279): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

C7M71_RS04160: PT_phytoene_like
Domain 1 (23 - 319): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 19.46 out of 20.01
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (17):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.83 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.37 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.97 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.06 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.39 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.46 out of 27.04
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.74 out of 23.43
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.03 out of 26.06
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.72 out of 27.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.33 out of 26.85
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.17 out of 27.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.70 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.49 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.98 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.37 out of 29.38
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 7, location 933923 - 999816:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 948530 - 999816:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Asp)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
C7M71_RS04260: X
AMP-binding (479..874): 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:
    FSYAFDMSQGEACMMAGGEINCYGPTEAAVGCTS
  Nearest Stachelhaus code(s):
    Leu or Ile DMGWMGGVIK (44% 8Å match)
  Stachelhaus code match:
    70% (weak)

C7M71_RS04285: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (10..394): Asp
nrpys: Asp

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

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

Link to PARAS substrate predictor
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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
ArgR | Regulator of arginine biosynthesis genes

NZ_CP031264.1 - Region 6 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,430,107 - 1,451,237 nt. (total: 21,131 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
C7M71_RS06285: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

C7M71_RS06310: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: phosphorylase
C7M71_RS06275: thiamine-phosphate pyrophosphorylase

smcogs
  SMCOG1280: thiamine-phosphate pyrophosphorylase

Ligases: synthetase
C7M71_RS06270: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Translocases: transporter
C7M71_RS06290: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.43 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000664.5 |  | 0.41 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001227.3 |  | 0.40 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000649.3 |  | 0.40 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002345.2 |  | 0.40 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0000633.3 |  | 0.40 | terpene | carotenoid | Streptomyces avermitilis
BGC0000678.5 |  | 0.40 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001456.3 |  | 0.39 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.43 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000664.5 |  | 0.41 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001227.3 |  | 0.40 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000649.3 |  | 0.40 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002345.2 |  | 0.40 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0000633.3 |  | 0.40 | terpene | carotenoid | Streptomyces avermitilis
BGC0000678.5 |  | 0.40 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001456.3 |  | 0.39 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
C7M71_RS06270: PT_FPPS_like
Domain 1 (57 - 374): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
Additional weak hits (11):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.81 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.15 out of 20.97
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.38 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.25 out of 30.25
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.64 out of 27.04
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.68 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.21 out of 18.57
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.29 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP031264.1 - Region 7 - HR-T2PKS,butyrolactone,furan
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: 1,647,081 - 1,688,256 nt. (total: 41,176 nt) Show pHMM detection rules used
HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-synt))
butyrolactone: AfsA
furan: (mmyO or AvrD)

#### 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 oxygenase
C7M71_RS07205: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

C7M71_RS07225: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

C7M71_RS07305: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

C7M71_RS07310: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

C7M71_RS07340: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

C7M71_RS07355: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

C7M71_RS07370: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase
C7M71_RS07325: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Hydrolases: esterase
C7M71_RS07260: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

Lyases: hydratase
C7M71_RS07360: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

C7M71_RS07365: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
C7M71_RS07245: 1-deoxy-D-xylulose-5-phosphate synthase

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

C7M71_RS07270: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS07290: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C7M71_RS07345: 3-oxoacyl-(acyl carrier protein) synthase III

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

C7M71_RS07350: 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 | HR-T2PKS | butyrolactone | furan | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001535.3 |  |  |  | 0.56 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0000706.3 |  |  |  | 0.45 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001534.3 |  |  |  | 0.43 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0000914.5 |  |  |  | 0.41 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000850.5 |  |  |  | 0.41 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000194.5 |  |  |  | 0.38 | PKS | actinorhodin | Streptomyces coelicolor A3(2)
BGC0001625.5 |  |  |  | 0.38 | PKS | Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F | Streptomyces sp. CB01883
BGC0002578.2 |  |  |  | 0.37 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002826.2 |  |  |  | 0.36 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0001386.5 |  |  |  | 0.36 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001535.3 |  | 0.65 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001534.3 |  | 0.57 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0000850.5 |  | 0.54 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.53 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002711.2 |  | 0.50 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000889.5 |  | 0.50 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0002826.2 |  | 0.50 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0001295.5 |  | 0.49 | other (other) | cremeomycin | Streptomyces cremeus
BGC0000662.5 |  | 0.49 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001592.5 |  | 0.49 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 21.84 out of 23.79
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.77 out of 23.79
Confidence: medium
Additional weak hits (9):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.59 out of 31.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.71 out of 25.88
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.54 out of 29.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.26 out of 32.74
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.34 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.66 out of 33.14
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.98 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 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).
C7M71_RS07290: X
AMP-binding (12..371): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    ESFNFGLIGG-HFGVSGGEGQAYGMTETGIIATD
  Nearest Stachelhaus code(s):
    nohBza GLGLVGAIIK (91% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

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

NZ_CP031264.1 - Region 8 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,762,058 - 1,784,325 nt. (total: 22,268 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
Transferases: PPTase
C7M71_RS07730: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Lyases: cyclase
C7M71_RS07765: Terpene synthase/cyclase metal-binding domain protein

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

C7M71_RS07775: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: ligase
C7M71_RS07800: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.75 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.40 | other (other) | melanin | Streptomyces avermitilis
BGC0000676.5 |  | 0.40 | terpene | aphidicolin, aphidicolan-16β-ol, 3-deoxyaphidicolin, 17-deoxyaphidicolin | Phoma betae
BGC0000688.4 |  | 0.39 | terpene | copalyl diphosphate | Diaporthe amygdali
BGC0001336.5 |  | 0.38 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0002227.3 |  | 0.36 | NRPS | AKML B, AKML D, AKML A, AKML C | Aspergillus luchuensis IFO 4308
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001888.2 |  | 0.36 | other (other) | mannosylerythritol lipid A, mannosylerythritol lipid B, mannosylerythritol lipid C | Ustilago maydis 521

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.75 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.40 | other (other) | melanin | Streptomyces avermitilis
BGC0000676.5 |  | 0.40 | terpene | aphidicolin, aphidicolan-16β-ol, 3-deoxyaphidicolin, 17-deoxyaphidicolin | Phoma betae
BGC0000688.4 |  | 0.39 | terpene | copalyl diphosphate | Diaporthe amygdali
BGC0001336.5 |  | 0.38 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0002227.3 |  | 0.36 | NRPS | AKML B, AKML D, AKML A, AKML C | Aspergillus luchuensis IFO 4308
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001888.2 |  | 0.36 | other (other) | mannosylerythritol lipid A, mannosylerythritol lipid B, mannosylerythritol lipid C | Ustilago maydis 521

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:
C7M71_RS07765: T1TS + T1TS
Domain 1 (2 - 327): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (343 - 714): 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.
No hits above weak threshold.
Weak hits (7):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.97 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.75 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.29 out of 35.63
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.30 out of 28.14
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.80 out of 27.04
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
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
--- | ---

NZ_CP031264.1 - Region 9 - 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: 1,913,336 - 1,938,691 nt. (total: 25,356 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
Oxidoreductases: oxidoreductase
C7M71_RS08440: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acetyltransferase
C7M71_RS08520: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Lyases: cyclase decarboxylase dehydratase
C7M71_RS08455: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

C7M71_RS08480: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

C7M71_RS08485: 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.
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0000538.3 |  | 0.48 | ribosomal | nisin Z | Lactococcus lactis
BGC0000584.5 |  | 0.48 | ribosomal | colicin V | Escherichia coli
BGC0000560.5 |  | 0.47 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000537.3 |  | 0.47 | ribosomal | nisin U | Streptococcus uberis
BGC0001229.4 |  | 0.45 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000554.4 |  | 0.45 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002323.2 |  | 0.44 | ribosomal | nisin J | Staphylococcus capitis
BGC0000533.3 |  | 0.44 | ribosomal | mutacin III | Streptococcus mutans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0000538.3 |  | 0.48 | ribosomal | nisin Z | Lactococcus lactis
BGC0000584.5 |  | 0.48 | ribosomal | colicin V | Escherichia coli
BGC0000560.5 |  | 0.47 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000537.3 |  | 0.47 | ribosomal | nisin U | Streptococcus uberis
BGC0001229.4 |  | 0.45 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000554.4 |  | 0.45 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002323.2 |  | 0.44 | ribosomal | nisin J | Staphylococcus capitis
BGC0000533.3 |  | 0.44 | ribosomal | mutacin III | Streptococcus mutans

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 C7M71_RS08480

C7M71_RS08475
Leader:
MADTRVSGGATALAERPAADGAFADEFSLDVRVVVAAHPNGKLACS
Core:
T S D G C G S S C S G S A C T S F T D D P V
Core with dehydrations:
Dhb Dha D G Cys G Dha Dha Cys Dha G Dha A Cys Dhb Dha F Dhb D D P V

#### antiSMASH-DB 4.0 matches for C7M71_RS08475

100.0%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS08475_lanthipeptide
Lanthipeptides: C7M71_RS08475_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D G C G S S C S G S A C T S F T D D P V
1
T S D G C G S S C S G S A C T S F T D D P V
22
67.9%
NZ_KB905816.1 and 1 other:
NZ_KB905816.1 Lanthipeptides: F603_RS35860_lanthipeptide
Lanthipeptides: F603_RS35860_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D G C G S+C S G S A C S F T D D P
7
T S D G C G S T C S G S A C N S F T D D P A
28
63.6%
NZ_BMXL01000030.1:
Lanthipeptides: IE143_RS19675_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D
20
T D G C G S S C S A C T+ T D
4
T D D G C G S S C P-S A C T T S T S D
22
with 169 more sequence matches
Only the first 10 are displayed here.
63.6%
NZ_CP099837.1:
Lanthipeptides: NE857_RS26275_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D
20
T D G C G S S C S A C T+ T D
4
T D D G C G S S C P-S A C T T S T A D
22
63.0%
NC_015957.1 and 1 other:
NC_015957.1 Lanthipeptides: STRVI_RS47470_lanthipeptide
Lanthipeptides: STRVI_RS47470_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D C G S S C S G+A C T S F D P
6
T S D N C G S S C S G T A C T S F V G D P A
27
62.5%
NZ_CP020563.1 and 9 others:
NZ_CP020563.1 Lanthipeptides: B7C62_RS17025_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS19590_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS19590_lanthipeptide NZ_CP047144.1 Lanthipeptides: GR129_RS18590_lanthipeptide NZ_CP047144.1 Lanthipeptides: GR129_RS18590_lanthipeptide NZ_CP094483.1 Lanthipeptides: ME763_RS16680_lanthipeptide NZ_CP094483.1 Lanthipeptides: ME763_RS16680_lanthipeptide NZ_PDER01000003.1 Lanthipeptides: CQW39_RS06845_lanthipeptide NZ_PDER01000003.1 Lanthipeptides: CQW39_RS06845_lanthipeptide
Lanthipeptides: B7C62_RS17025_lanthipeptide
1
T S D G C G S S C S--G S A C T S F T D D P V
22
T D G C G S+C+ S A C S F T+D P
1
T G D G C G S T C A T G A S A C G S F T E D P A
24
60.7%
NZ_KB895870.1 and 1 other:
NZ_KB895870.1 Lanthipeptides: C569_RS0127950_lanthipeptide
Lanthipeptides: C569_RS0127950_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D G C G S S C S S A C T+ + D P V
7
T S D G C G S S C S T S A C T T K S C D P V
28
59.3%
NC_013929.1 and 11 others:
NC_013929.1 Lanthipeptides: SCAB_RS44850_lanthipeptide NZ_CP024989.1 Lanthipeptides: CVT30_RS13845_lanthipeptide NZ_CP024989.1 Lanthipeptides: CVT30_RS13845_lanthipeptide NZ_CP024989.1 Lanthipeptides: CVT30_RS13845_lanthipeptide NZ_CP043956.1 Lanthipeptides: F3K20_RS28980_lanthipeptide NZ_CP043956.1 Lanthipeptides: F3K20_RS28980_lanthipeptide NZ_CP119182.1 Lanthipeptides: IHE65_RS14995_lanthipeptide NZ_CP119182.1 Lanthipeptides: IHE65_RS14995_lanthipeptide NZ_JABXWH010000012.1 Lanthipeptides: HW845_RS28550_lanthipeptide NZ_JABXWH010000012.1 Lanthipeptides: HW845_RS28550_lanthipeptide NZ_KL997517.1 Lanthipeptides: IQ61_RS45045_lanthipeptide
Lanthipeptides: SCAB_RS44850_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D C G S+C S G+A C S F T D P
6
T S D N C G S T C S G T A C A S F T G D P A
27
59.1%
NZ_JAPZVP010000006.1 and 1 other:
NZ_JAPZVP010000006.1 Lanthipeptides: O1R50_RS08905_lanthipeptide
Lanthipeptides: O1R50_RS08905_lanthipeptide
1
T S D G C G S S C S G S A C T S
16
T S D G C G S+C+ S A C T S
6
T S D G C G S T C A-S A C T S
20
57.7%
NZ_ATYW01000025.1 and 1 other:
NZ_ATYW01000025.1 Lanthipeptides: YWW_RS32370_lanthipeptide
Lanthipeptides: YWW_RS32370_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D G C G++C S A C+S F T++P V
5
T S D G C G N T C Q T S A C S S F T N N P V
26
57.7%
NZ_PGGV01000032.1 and 1 other:
NZ_PGGV01000032.1 Lanthipeptides: CUT39_RS12965_lanthipeptide
Lanthipeptides: CUT39_RS12965_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T D G C G++C G S A C S F T++P V
5
T D D G C G N T C Q G S A C A S F T N N P V
26
57.1%
NZ_JAGPXX010000003.1 and 1 other:
NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS04145_lanthipeptide
Lanthipeptides: KBZ10_RS04145_lanthipeptide
1
T S D G C G S S C S--G S A C T S F T D D P V
22
T S D G C G++C+ S A C S F T D D P
5
T S D G C G N T C A N G A S A C N S F T D D P A
28
56.5%
NZ_VWVW01000031.1:
Lanthipeptides: FYW96_RS22360_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D
20
T D G C G S S C S A C T+ D
5
T D D G C G S S C P-S A C T T S A S D
23

#### Lanthipeptide(s) for C7M71_RS08490

C7M71_RS08475
Leader:
MADTRVSGGATALAERPAADGAFADEFSLDVRVVVAAHPNGKLACS
Core:
T S D G C G S S C S G S A C T S F T D D P V
Core with dehydrations:
Dhb Dha D G Cys G Dha Dha Cys Dha G Dha A Cys Dhb Dha F Dhb D D P V

#### antiSMASH-DB 4.0 matches for C7M71_RS08475

100.0%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS08475_lanthipeptide
Lanthipeptides: C7M71_RS08475_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D G C G S S C S G S A C T S F T D D P V
1
T S D G C G S S C S G S A C T S F T D D P V
22
67.9%
NZ_KB905816.1 and 1 other:
NZ_KB905816.1 Lanthipeptides: F603_RS35860_lanthipeptide
Lanthipeptides: F603_RS35860_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D G C G S+C S G S A C S F T D D P
7
T S D G C G S T C S G S A C N S F T D D P A
28
63.6%
NZ_BMXL01000030.1:
Lanthipeptides: IE143_RS19675_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D
20
T D G C G S S C S A C T+ T D
4
T D D G C G S S C P-S A C T T S T S D
22
with 169 more sequence matches
Only the first 10 are displayed here.
63.6%
NZ_CP099837.1:
Lanthipeptides: NE857_RS26275_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D
20
T D G C G S S C S A C T+ T D
4
T D D G C G S S C P-S A C T T S T A D
22
63.0%
NC_015957.1 and 1 other:
NC_015957.1 Lanthipeptides: STRVI_RS47470_lanthipeptide
Lanthipeptides: STRVI_RS47470_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D C G S S C S G+A C T S F D P
6
T S D N C G S S C S G T A C T S F V G D P A
27
62.5%
NZ_CP020563.1 and 9 others:
NZ_CP020563.1 Lanthipeptides: B7C62_RS17025_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS19590_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS19590_lanthipeptide NZ_CP047144.1 Lanthipeptides: GR129_RS18590_lanthipeptide NZ_CP047144.1 Lanthipeptides: GR129_RS18590_lanthipeptide NZ_CP094483.1 Lanthipeptides: ME763_RS16680_lanthipeptide NZ_CP094483.1 Lanthipeptides: ME763_RS16680_lanthipeptide NZ_PDER01000003.1 Lanthipeptides: CQW39_RS06845_lanthipeptide NZ_PDER01000003.1 Lanthipeptides: CQW39_RS06845_lanthipeptide
Lanthipeptides: B7C62_RS17025_lanthipeptide
1
T S D G C G S S C S--G S A C T S F T D D P V
22
T D G C G S+C+ S A C S F T+D P
1
T G D G C G S T C A T G A S A C G S F T E D P A
24
60.7%
NZ_KB895870.1 and 1 other:
NZ_KB895870.1 Lanthipeptides: C569_RS0127950_lanthipeptide
Lanthipeptides: C569_RS0127950_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D G C G S S C S S A C T+ + D P V
7
T S D G C G S S C S T S A C T T K S C D P V
28
59.3%
NC_013929.1 and 11 others:
NC_013929.1 Lanthipeptides: SCAB_RS44850_lanthipeptide NZ_CP024989.1 Lanthipeptides: CVT30_RS13845_lanthipeptide NZ_CP024989.1 Lanthipeptides: CVT30_RS13845_lanthipeptide NZ_CP024989.1 Lanthipeptides: CVT30_RS13845_lanthipeptide NZ_CP043956.1 Lanthipeptides: F3K20_RS28980_lanthipeptide NZ_CP043956.1 Lanthipeptides: F3K20_RS28980_lanthipeptide NZ_CP119182.1 Lanthipeptides: IHE65_RS14995_lanthipeptide NZ_CP119182.1 Lanthipeptides: IHE65_RS14995_lanthipeptide NZ_JABXWH010000012.1 Lanthipeptides: HW845_RS28550_lanthipeptide NZ_JABXWH010000012.1 Lanthipeptides: HW845_RS28550_lanthipeptide NZ_KL997517.1 Lanthipeptides: IQ61_RS45045_lanthipeptide
Lanthipeptides: SCAB_RS44850_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D C G S+C S G+A C S F T D P
6
T S D N C G S T C S G T A C A S F T G D P A
27
59.1%
NZ_JAPZVP010000006.1 and 1 other:
NZ_JAPZVP010000006.1 Lanthipeptides: O1R50_RS08905_lanthipeptide
Lanthipeptides: O1R50_RS08905_lanthipeptide
1
T S D G C G S S C S G S A C T S
16
T S D G C G S+C+ S A C T S
6
T S D G C G S T C A-S A C T S
20
57.7%
NZ_ATYW01000025.1 and 1 other:
NZ_ATYW01000025.1 Lanthipeptides: YWW_RS32370_lanthipeptide
Lanthipeptides: YWW_RS32370_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T S D G C G++C S A C+S F T++P V
5
T S D G C G N T C Q T S A C S S F T N N P V
26
57.7%
NZ_PGGV01000032.1 and 1 other:
NZ_PGGV01000032.1 Lanthipeptides: CUT39_RS12965_lanthipeptide
Lanthipeptides: CUT39_RS12965_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D P V
22
T D G C G++C G S A C S F T++P V
5
T D D G C G N T C Q G S A C A S F T N N P V
26
57.1%
NZ_JAGPXX010000003.1 and 1 other:
NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS04145_lanthipeptide
Lanthipeptides: KBZ10_RS04145_lanthipeptide
1
T S D G C G S S C S--G S A C T S F T D D P V
22
T S D G C G++C+ S A C S F T D D P
5
T S D G C G N T C A N G A S A C N S F T D D P A
28
56.5%
NZ_VWVW01000031.1:
Lanthipeptides: FYW96_RS22360_lanthipeptide
1
T S D G C G S S C S G S A C T S F T D D
20
T D G C G S S C S A C T+ D
5
T D D G C G S S C P-S A C T T S A S D
23

#### 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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (2):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.60 out of 23.43
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.69 out of 30.97
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.

C7M71_RS08475 - Class I
  Cleavage pHMM score: -4.00
  RODEO score: 23
  Monoisotopic mass: 1920.7 Da
  Molecular weight: 1922.0 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1940.0 Da N = 1
    1958.0 Da N = 2
    1976.0 Da N = 3
    1994.0 Da N = 4
    2012.1 Da N = 5
    2030.1 Da N = 6
C7M71_RS08475 - Class I
  Cleavage pHMM score: -4.00
  RODEO score: 23
  Monoisotopic mass: 1920.7 Da
  Molecular weight: 1922.0 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1940.0 Da N = 1
    1958.0 Da N = 2
    1976.0 Da N = 3
    1994.0 Da N = 4
    2012.1 Da N = 5
    2030.1 Da N = 6

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (1913335...1938691)
C7M71_RS08480
  RRE type: Lanthipeptide_LanB_RRE
  Location: 158 - 251
  Score: 60.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP031264.1 - Region 10 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,949,009 - 2,970,049 nt. (total: 21,041 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
C7M71_RS13005: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: PPTase
C7M71_RS13025: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Lyases: cyclase
C7M71_RS13000: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Ligases: synthetase
C7M71_RS13045: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001294.5 |  | 0.39 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000678.5 |  | 0.37 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000664.5 |  | 0.37 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001294.5 |  | 0.39 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000678.5 |  | 0.37 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000664.5 |  | 0.37 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
C7M71_RS13045: PT_FPPS_like
Domain 1 (60 - 344): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.99 out of 20.47
Confidence: medium
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.62 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.19 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.77 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.88 out of 28.14
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.91 out of 32.74
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.93 out of 32.93
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP031264.1 - Region 11 - phosphonate,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: 3,399,919 - 3,421,802 nt. (total: 21,884 nt) Show pHMM detection rules used
triceptide: ((cds(PF04055 and (TIGR04085 or SPASM)) and triceptide_precursor) or triceptide_rSAM)
phosphonate: (phosphonates and minimum(1, [2-Hacid_dh_C, Aldedh, Aminotran_1_2, Aminotran_5, AurF, CTP_transf_like, DUF4992, Fe-ADH, HMGL-like, Metallophos_2, NTP_transf_3, NTP_transf_5, PALP, PEP_mutase, TPP_enzyme_C, TPP_enzyme_N, phosphonates]) and not (phosphonatesHydrolase or phosphonatesMeIsocitrateLyase))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
C7M71_RS15090: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

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 | phosphonate | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001859.4 |  |  | 0.28 | other (phosphonate) | fosfomycin | Pseudomonas syringae
BGC0000904.5 |  |  | 0.28 | other (other) | FR-900098 | Streptomyces rubellomurinus
BGC0000897.5 |  |  | 0.18 | other (other) | dehydrophos | Streptomyces luridus
BGC0000926.5 |  |  | 0.17 | other (other) | rhizocticin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000075.5 |  |  | 0.10 | PKS | hygrocin A, hygrocin B | Streptomyces sp. LZ35
BGC0000106.5 |  |  | 0.10 | PKS | naphthomycin A | Streptomyces sp. CS
BGC0000998.5 |  |  | 0.10 | NRPS, PKS | guadinomine, guadinomine B, guadinomic acid | Streptomyces sp. K01-0509
BGC0000084.5 |  |  | 0.09 | PKS | laidlomycin | Streptomyces sp. CS684
BGC0001500.3 |  |  | 0.09 | PKS | allocyclinone A, allocyclinone B, allocyclinone C, allocyclinone D | Actinoallomurus sp. ID145698
BGC0000188.5 |  |  | 0.08 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001859.4 |  | 0.44 | other (phosphonate) | fosfomycin | Pseudomonas syringae
BGC0000904.5 |  | 0.43 | other (other) | FR-900098 | Streptomyces rubellomurinus
BGC0000897.5 |  | 0.34 | other (other) | dehydrophos | Streptomyces luridus
BGC0000926.5 |  | 0.34 | other (other) | rhizocticin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000188.5 |  | 0.32 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0000253.4 |  | 0.29 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001357.3 |  | 0.29 | PKS | carbamidocyclophane A, carbamidocyclophane B, carbamidocyclophane C, carbamidocyclophane D, carbamidocyclophane E, carbamidocyclophane F, carbamidocyclophane H, carbamidocyclophane M, carbamidocyclophane N, carbamidocyclophane O, carbamidocyclophane P, carbamidocyclophane Q, carbamidocyclophane R, carbamidocyclophane S, carbamidocyclophane T, carbamidocyclophane U | Nostoc sp. CAVN2
BGC0002813.2 |  | 0.28 | NRPS, PKS | phorbactazole A, phorbactazole B, phorbactazole C, phorbactazole D, phorbactazole E, phorbactazole F | Acanthopleuribacter pedis KCTC 12899
BGC0001488.3 |  | 0.28 | other (other) | 4-formylaminooxyvinylglycine | Pseudomonas fluorescens WH6
BGC0000834.5 |  | 0.26 | other (aminocoumarin), saccharide | cathomycin | Streptomyces niveus

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (2):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.92 out of 30.22
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.44 out of 20.01
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP031264.1 - Region 12 - NRPS,NRPS-like,T1PKS,t3nrps-iterative
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,791,593 - 3,867,609 nt. (total: 76,017 nt) Show pHMM detection rules used
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
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)
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
C7M71_RS16925: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

C7M71_RS16965: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

C7M71_RS17000: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

C7M71_RS17035: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

C7M71_RS17050: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

Transferases: acetyltransferase acylase aminotransferase
C7M71_RS16940: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

C7M71_RS16955: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

C7M71_RS16980: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
C7M71_RS17055: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: decarboxylase hydratase
C7M71_RS17020: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

C7M71_RS17060: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
C7M71_RS16930: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C7M71_RS16990: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

C7M71_RS16995: 3-oxoacyl-(acyl carrier protein) synthase III

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

C7M71_RS17015: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

C7M71_RS17025: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

C7M71_RS17040: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C7M71_RS30715: 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 | t3nrps-iterative | NRPS | NRPS-like | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  |  |  |  | 2.05 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001132.4 |  |  |  |  |  | 1.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  |  |  |  |  | 1.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  |  |  |  |  | 1.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  |  |  | 1.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  |  |  |  |  | 1.58 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  |  |  |  |  | 1.55 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001825.4 |  |  |  |  |  | 1.53 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001273.3 |  |  |  |  |  | 1.50 | PKS | asperlactone | Aspergillus ochraceus
BGC0001758.4 |  |  |  |  |  | 1.50 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
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
BGC0001261.3 |  | 0.67 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.65 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001833.4 |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.84 out of 30.12
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
Additional weak hits (6):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.32 out of 26.85
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.90 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.66 out of 27.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.51 out of 32.93
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.24 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 19, location 3791592 - 3867609:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Gly) + (ohmal) + (X) + (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).
C7M71_RS16930: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (583..988): 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:
    TDLSFDLSVFDANSMLSGDVVMGGATEASIWSNI
  Nearest Stachelhaus code(s):
    Cys DLYNMSMIWK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

C7M71_RS30715: X
AMP-binding (31..413): 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:
    HVWSWDSAVQDAHSALGGDAGAYGSTECSCALLR
  Nearest Stachelhaus code(s):
    Phe DAGALGACAK (38% 8Å match)
    Leu DALHSGAVAK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

C7M71_RS16980: mal
PKS_AT (551..847): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 83.3%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 154.6
  inactive: 85.6
  Methoxymalonyl-CoA: 75.1
  Methylmalonyl-CoA: 67.5
  Propionyl-CoA: 64.2
  Ethylmalonyl-CoA: 44.7
  2-Methylbutyryl-CoA: 43.6
  Isobutyryl-CoA: 32.5
  CHC-CoA: 26.5
  trans-1,2-CPDA: 20.7
  Benzoyl-CoA: 19.6
  Acetyl-CoA: 15.0
  fatty_acid: 8.7
  3-Methylbutyryl-CoA: 0.0

C7M71_RS17015: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (424..820): 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:
    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:
    TAVSFDLSVYDGNSLLSGDISLGGATEGSIWSIH
  Nearest Stachelhaus code(s):
    Gly DLYNLSLIWK (94% 8Å match)
    Cys DLYNLSLIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

C7M71_RS17025: X
AMP-binding (15..409): 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:
    FWFTFDPSLRESFLFFAGEVNLYGMTEGTLAQLY
  Nearest Stachelhaus code(s):
    Asp DPRHLALLAK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

C7M71_RS17040: X
AMP-binding (9..387): 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:
    RLWLHGIDVL-PSGISGSARQVYGLSEIAVICFD
  Nearest Stachelhaus code(s):
    Hpg DALSIGAVIK (32% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP031264.1 - Region 13 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,972,237 - 3,997,435 nt. (total: 25,199 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
Transferases: transferase
C7M71_RS17690: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Lyases: cyclase dehydratase
C7M71_RS17725: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

C7M71_RS17730: 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
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.52 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0002316.2 |  | 0.49 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000506.4 |  | 0.43 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000544.4 |  | 0.42 | ribosomal | planosporicin | Planomonospora alba
BGC0000559.4 |  | 0.41 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0001701.4 |  | 0.40 | ribosomal | nisin O | Blautia obeum
BGC0000511.5 |  | 0.40 | ribosomal | ericin S | Bacillus subtilis
BGC0002120.3 |  | 0.39 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.52 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0002316.2 |  | 0.49 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000506.4 |  | 0.43 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000544.4 |  | 0.42 | ribosomal | planosporicin | Planomonospora alba
BGC0000559.4 |  | 0.41 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0001701.4 |  | 0.40 | ribosomal | nisin O | Blautia obeum
BGC0000511.5 |  | 0.40 | ribosomal | ericin S | Bacillus subtilis
BGC0002120.3 |  | 0.39 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706

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 C7M71_RS17725

C7M71_RS17720
Leader:
MAPQSSTLKAATDFSGEGMSDFDLSIETVASAPIVPG
Core:
L L N D T G D G C G S T C Q S A C S N S T C I S G
Core with dehydrations:
L L N D Dhb G D G Cys G Dha Dhb Cys Q Dha A Cys Dha N Dha Dhb Cys I Dha G

#### antiSMASH-DB 4.0 matches for C7M71_RS17720

100.0%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS17720_lanthipeptide
Lanthipeptides: C7M71_RS17720_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T G D G C G S T C Q S A C S N S T C I S G
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
92.3%
NZ_CP029188.1 and 1 other:
NZ_CP029188.1 Lanthipeptides: DDW44_RS30840_lanthipeptide
Lanthipeptides: DDW44_RS30840_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T G D G C G S T C Q S A C S N S T C I G
2
L L N D T G D G C G S T C Q S A C S N S T C I G G
26
92.0%
NZ_CP045096.1 and 1 other:
NZ_CP045096.1 Lanthipeptides: F9278_RS23695_lanthipeptide
Lanthipeptides: F9278_RS23695_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T G D G C G+T C Q S A C S N S T C I G
1
L L N D T G D G C G A T C Q S A C S N S T C I G G
25
with 175 more sequence matches
Only the first 10 are displayed here.
88.5%
NZ_AP024135.1 and 3 others:
NZ_AP024135.1 Lanthipeptides: K6K39_RS04810_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide
Lanthipeptides: K6K39_RS04810_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T G D G C G S T C Q S A C+N S T C I G
2
L L N D T G D G C G S T C Q S A C A N S T C I G G
26
84.0%
NZ_CP045031.1 and 2 others:
NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide
Lanthipeptides: F9V55_RS07565_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C I S G
25
L N D T D C G S T C Q S A C S N S T C I G
1
L N D T S D N C G S T C Q S A C S N S T C I G G
24
84.0%
NZ_FOLM01000004.1 and 1 other:
NZ_FOLM01000004.1 Lanthipeptides: BM242_RS10130_lanthipeptide
Lanthipeptides: BM242_RS10130_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T D C S T C Q S A C S N S T C I G
1
L L N D T D D N C T S T C Q S A C S N S T C I G G
25
82.1%
NZ_CP084541.1 and 1 other:
NZ_CP084541.1 Lanthipeptides: LC193_RS13810_lanthipeptide
Lanthipeptides: LC193_RS13810_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T G D G C S T C Q S A C S N S T C I G
4
L L N D T G D G C T S T C Q S A C S N S T C I G G
28
80.0%
NZ_BBUZ01000023.1 and 5 others:
NZ_BBUZ01000023.1 Lanthipeptides: ASC60_RS09240_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide
Lanthipeptides: ASC60_RS09240_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C
22
L L N D T G D G C +T C Q S A C S N S T C
1
L L N D T G D G C T A T C Q S A C S N S T C
22
80.0%
NZ_BBYG01000008.1 and 3 others:
NZ_BBYG01000008.1 Lanthipeptides: AOQ37_RS04295_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide
Lanthipeptides: AOQ37_RS04295_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C
22
L N D T G D G C S T C Q S A C S N S T C
1
L N D T G D G C T S T C Q S A C S N S T C
21
80.0%
NZ_KQ257877.1 and 1 other:
NZ_KQ257877.1 Lanthipeptides: IQ64_RS44800_lanthipeptide
Lanthipeptides: IQ64_RS44800_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C
22
L N D T G D G C G T C Q S A C S N S T C
1
L N D T G D G C G Q T C Q S A C S N S T C
21
80.0%
NZ_VEHK01000015.1 and 1 other:
NZ_VEHK01000015.1 Lanthipeptides: FS984_RS32600_lanthipeptide
Lanthipeptides: FS984_RS32600_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C I
23
L N D T D G C S T C Q S A C S N S T C I
1
L N D T S D G C T S T C Q S A C S N S T C I
22
76.0%
NZ_BMSX01000001.1 and 10 others:
NZ_BMSX01000001.1 Lanthipeptides: IE263_RS00615_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide
Lanthipeptides: IE263_RS00615_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C I S G
25
L N D T D C S T C Q S A C+N S T C I G
1
L N D T S D N C T S T C Q S A C T N S T C I G G
24
76.0%
NZ_CP030771.1 and 4 others:
NZ_CP030771.1 Lanthipeptides: C9F11_RS21100_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide
Lanthipeptides: C9F11_RS21100_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C I S G
25
L N D T D C S T C S A C S N S T C I G
1
L N D T S D N C T S T C A S A C S N S T C I G G
24

#### Lanthipeptide(s) for C7M71_RS17735

C7M71_RS17720
Leader:
MAPQSSTLKAATDFSGEGMSDFDLSIETVASAPIVPG
Core:
L L N D T G D G C G S T C Q S A C S N S T C I S G
Core with dehydrations:
L L N D Dhb G D G Cys G Dha Dhb Cys Q Dha A Cys Dha N Dha Dhb Cys I Dha G

#### antiSMASH-DB 4.0 matches for C7M71_RS17720

100.0%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS17720_lanthipeptide
Lanthipeptides: C7M71_RS17720_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T G D G C G S T C Q S A C S N S T C I S G
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
92.3%
NZ_CP029188.1 and 1 other:
NZ_CP029188.1 Lanthipeptides: DDW44_RS30840_lanthipeptide
Lanthipeptides: DDW44_RS30840_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T G D G C G S T C Q S A C S N S T C I G
2
L L N D T G D G C G S T C Q S A C S N S T C I G G
26
92.0%
NZ_CP045096.1 and 1 other:
NZ_CP045096.1 Lanthipeptides: F9278_RS23695_lanthipeptide
Lanthipeptides: F9278_RS23695_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T G D G C G+T C Q S A C S N S T C I G
1
L L N D T G D G C G A T C Q S A C S N S T C I G G
25
with 175 more sequence matches
Only the first 10 are displayed here.
88.5%
NZ_AP024135.1 and 3 others:
NZ_AP024135.1 Lanthipeptides: K6K39_RS04810_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide NZ_CP084203.1 Lanthipeptides: KBP30_RS00925_lanthipeptide
Lanthipeptides: K6K39_RS04810_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T G D G C G S T C Q S A C+N S T C I G
2
L L N D T G D G C G S T C Q S A C A N S T C I G G
26
84.0%
NZ_CP045031.1 and 2 others:
NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide
Lanthipeptides: F9V55_RS07565_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C I S G
25
L N D T D C G S T C Q S A C S N S T C I G
1
L N D T S D N C G S T C Q S A C S N S T C I G G
24
84.0%
NZ_FOLM01000004.1 and 1 other:
NZ_FOLM01000004.1 Lanthipeptides: BM242_RS10130_lanthipeptide
Lanthipeptides: BM242_RS10130_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T D C S T C Q S A C S N S T C I G
1
L L N D T D D N C T S T C Q S A C S N S T C I G G
25
82.1%
NZ_CP084541.1 and 1 other:
NZ_CP084541.1 Lanthipeptides: LC193_RS13810_lanthipeptide
Lanthipeptides: LC193_RS13810_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C I S G
25
L L N D T G D G C S T C Q S A C S N S T C I G
4
L L N D T G D G C T S T C Q S A C S N S T C I G G
28
80.0%
NZ_BBUZ01000023.1 and 5 others:
NZ_BBUZ01000023.1 Lanthipeptides: ASC60_RS09240_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP025018.1 Lanthipeptides: CFP59_RS29940_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide NZ_CP029823.1 Lanthipeptides: DNK48_RS29795_lanthipeptide
Lanthipeptides: ASC60_RS09240_lanthipeptide
1
L L N D T G D G C G S T C Q S A C S N S T C
22
L L N D T G D G C +T C Q S A C S N S T C
1
L L N D T G D G C T A T C Q S A C S N S T C
22
80.0%
NZ_BBYG01000008.1 and 3 others:
NZ_BBYG01000008.1 Lanthipeptides: AOQ37_RS04295_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide NZ_CP045178.1 Lanthipeptides: GBW32_RS17875_lanthipeptide
Lanthipeptides: AOQ37_RS04295_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C
22
L N D T G D G C S T C Q S A C S N S T C
1
L N D T G D G C T S T C Q S A C S N S T C
21
80.0%
NZ_KQ257877.1 and 1 other:
NZ_KQ257877.1 Lanthipeptides: IQ64_RS44800_lanthipeptide
Lanthipeptides: IQ64_RS44800_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C
22
L N D T G D G C G T C Q S A C S N S T C
1
L N D T G D G C G Q T C Q S A C S N S T C
21
80.0%
NZ_VEHK01000015.1 and 1 other:
NZ_VEHK01000015.1 Lanthipeptides: FS984_RS32600_lanthipeptide
Lanthipeptides: FS984_RS32600_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C I
23
L N D T D G C S T C Q S A C S N S T C I
1
L N D T S D G C T S T C Q S A C S N S T C I
22
76.0%
NZ_BMSX01000001.1 and 10 others:
NZ_BMSX01000001.1 Lanthipeptides: IE263_RS00615_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP080647.1 Lanthipeptides: K1J60_RS22740_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP102512.1 Lanthipeptides: JIX56_RS21495_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_CP119143.1 Lanthipeptides: PYR72_RS23045_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide NZ_KL997427.1 Lanthipeptides: IQ62_RS25015_lanthipeptide
Lanthipeptides: IE263_RS00615_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C I S G
25
L N D T D C S T C Q S A C+N S T C I G
1
L N D T S D N C T S T C Q S A C T N S T C I G G
24
76.0%
NZ_CP030771.1 and 4 others:
NZ_CP030771.1 Lanthipeptides: C9F11_RS21100_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide NZ_FNIE01000002.1 Lanthipeptides: BLR33_RS05585_lanthipeptide
Lanthipeptides: C9F11_RS21100_lanthipeptide
2
L N D T G D G C G S T C Q S A C S N S T C I S G
25
L N D T D C S T C S A C S N S T C I G
1
L N D T S D N C T S T C A S A C S N S T C I G G
24

#### 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: 19.00 out of 20.47
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 25.31
Confidence: medium
Additional weak hits (5):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.90 out of 33.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.74 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.41 out of 24.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
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.

C7M71_RS17720 - Class I
  Cleavage pHMM score: -7.70
  RODEO score: 24
  Monoisotopic mass: 2248.9 Da
  Molecular weight: 2250.4 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2268.4 Da N = 1
    2286.4 Da N = 2
    2304.5 Da N = 3
    2322.5 Da N = 4
C7M71_RS17720 - Class I
  Cleavage pHMM score: -7.70
  RODEO score: 24
  Monoisotopic mass: 2248.9 Da
  Molecular weight: 2250.4 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2268.4 Da N = 1
    2286.4 Da N = 2
    2304.5 Da N = 3
    2322.5 Da N = 4

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (3972236...3997435)
C7M71_RS17725
  RRE type: Lanthipeptide_LanB_RRE
  Location: 153 - 241
  Score: 64.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP031264.1 - Region 14 - 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: 5,027,690 - 5,060,365 nt. (total: 32,676 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
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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001713.5 |  | 0.54 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002692.2 |  | 0.53 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0001572.3 |  | 0.52 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000295.5 |  | 0.52 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0000941.3 |  | 0.52 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001499.5 |  | 0.51 | other (other) | aerobactin | Pantoea ananatis
BGC0000942.4 |  | 0.48 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0002471.3 |  | 0.47 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0002683.2 |  | 0.47 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001713.5 |  | 0.54 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002692.2 |  | 0.53 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0001572.3 |  | 0.52 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000295.5 |  | 0.52 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0000941.3 |  | 0.52 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001499.5 |  | 0.51 | other (other) | aerobactin | Pantoea ananatis
BGC0000942.4 |  | 0.48 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0002471.3 |  | 0.47 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0002683.2 |  | 0.47 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.51 out of 23.79
Confidence: medium
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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 26.88 out of 27.18
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.09 out of 27.18
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (8):
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: 17.51 out of 21.84
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.74 out of 23.43
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.28 out of 36.53
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.46 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.06 out of 29.65
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
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes

NZ_CP031264.1 - Region 15 - 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: 5,090,990 - 5,115,983 nt. (total: 24,994 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
Oxidoreductases: dehydrogenase
C7M71_RS22710: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: cyclase dehydratase
C7M71_RS22640: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

C7M71_RS22645: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0001289.5 |  | 0.52 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000542.3 |  | 0.48 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0002635.2 |  | 0.48 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000541.5 |  | 0.48 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0001727.3 |  | 0.43 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000529.5 |  | 0.40 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000603.5 |  | 0.39 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0000637.3 |  | 0.38 | terpene | carotenoid | Corynebacterium glutamicum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002640.2 |  | 0.56 | ribosomal | thalassomonasin A, thalassomonasin B | Thalassomonas actiniarum
BGC0001289.5 |  | 0.52 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000542.3 |  | 0.48 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0002635.2 |  | 0.48 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000541.5 |  | 0.48 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0001727.3 |  | 0.43 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0000529.5 |  | 0.40 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000603.5 |  | 0.39 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0000637.3 |  | 0.38 | terpene | carotenoid | Corynebacterium glutamicum

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 C7M71_RS22635

C7M71_RS22650
Leader:
MTVQMEPPVAPAQPTAEQQDLTGFDLDITIVEGGPAAD
Core:
Q L I R L T D D G C N S T C A T A C V S C P
Core with dehydrations:
Q L I R L Dhb D D G Cys N Dha Dhb Cys A Dhb A Cys V Dha Cys P

#### antiSMASH-DB 4.0 matches for C7M71_RS22650

100.0%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS22650_lanthipeptide
Lanthipeptides: C7M71_RS22650_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C V S C P
22
Q L I R L T D 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
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 D 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 D 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 181 more sequence matches
Only the first 10 are displayed here.
95.5%
NZ_NDXL01000003.1 and 1 other:
NZ_NDXL01000003.1 Lanthipeptides: B7024_RS36425_lanthipeptide
Lanthipeptides: B7024_RS36425_lanthipeptide
1
Q L I R L T D 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 S D G C N S T C A T A C V S C P
22
90.9%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS16225_lanthipeptide
Lanthipeptides: GBF35_RS16225_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C V S C P
22
Q L I R+T D 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
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 D 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
87.0%
NZ_BCBX01000061.1 and 1 other:
NZ_BCBX01000061.1 Lanthipeptides: AP234_RS35640_lanthipeptide
Lanthipeptides: AP234_RS35640_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C V S C
21
Q L I R+T D 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
87.0%
NZ_CP119143.1 and 1 other:
NZ_CP119143.1 Lanthipeptides: PYR72_RS32440_lanthipeptide
Lanthipeptides: PYR72_RS32440_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C V S C P
22
Q L I R+T D 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
82.6%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS37485_lanthipeptide
Lanthipeptides: GBF35_RS37485_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C V S C
21
Q L I R+T D 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 D 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
65.2%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C-V S C P
22
+L I R+T D 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
63.6%
NZ_KL997433.1 and 1 other:
NZ_KL997433.1 Lanthipeptides: IQ62_RS26155_lanthipeptide
Lanthipeptides: IQ62_RS26155_lanthipeptide
5
L T D D G C N S T C A T A C V S C
21
L T D D G C S T C A+A C S C
1
L T D D G C G S T C A S A C T S C
17
63.6%
NZ_LN850107.1 and 1 other:
NZ_LN850107.1 Lanthipeptides: BN1701_RS34270_lanthipeptide
Lanthipeptides: BN1701_RS34270_lanthipeptide
3
I R L T D D G C N S T C A T A C V S C P
22
+R L T D D G C +T C +A C S C P
1
L R L T D D G C G A T C E S A C N S C P
20

#### Lanthipeptide(s) for C7M71_RS22645

C7M71_RS22650
Leader:
MTVQMEPPVAPAQPTAEQQDLTGFDLDITIVEGGPAAD
Core:
Q L I R L T D D G C N S T C A T A C V S C P
Core with dehydrations:
Q L I R L Dhb D D G Cys N Dha Dhb Cys A Dhb A Cys V Dha Cys P

#### antiSMASH-DB 4.0 matches for C7M71_RS22650

100.0%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS22650_lanthipeptide
Lanthipeptides: C7M71_RS22650_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C V S C P
22
Q L I R L T D 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
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 D 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 D 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 181 more sequence matches
Only the first 10 are displayed here.
95.5%
NZ_NDXL01000003.1 and 1 other:
NZ_NDXL01000003.1 Lanthipeptides: B7024_RS36425_lanthipeptide
Lanthipeptides: B7024_RS36425_lanthipeptide
1
Q L I R L T D 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 S D G C N S T C A T A C V S C P
22
90.9%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS16225_lanthipeptide
Lanthipeptides: GBF35_RS16225_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C V S C P
22
Q L I R+T D 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
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 D 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
87.0%
NZ_BCBX01000061.1 and 1 other:
NZ_BCBX01000061.1 Lanthipeptides: AP234_RS35640_lanthipeptide
Lanthipeptides: AP234_RS35640_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C V S C
21
Q L I R+T D 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
87.0%
NZ_CP119143.1 and 1 other:
NZ_CP119143.1 Lanthipeptides: PYR72_RS32440_lanthipeptide
Lanthipeptides: PYR72_RS32440_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C V S C P
22
Q L I R+T D 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
82.6%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS37485_lanthipeptide
Lanthipeptides: GBF35_RS37485_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C V S C
21
Q L I R+T D 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 D 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
65.2%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
1
Q L I R L T D D G C N S T C A T A C-V S C P
22
+L I R+T D 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
63.6%
NZ_KL997433.1 and 1 other:
NZ_KL997433.1 Lanthipeptides: IQ62_RS26155_lanthipeptide
Lanthipeptides: IQ62_RS26155_lanthipeptide
5
L T D D G C N S T C A T A C V S C
21
L T D D G C S T C A+A C S C
1
L T D D G C G S T C A S A C T S C
17
63.6%
NZ_LN850107.1 and 1 other:
NZ_LN850107.1 Lanthipeptides: BN1701_RS34270_lanthipeptide
Lanthipeptides: BN1701_RS34270_lanthipeptide
3
I R L T D D G C N S T C A T A C V S C P
22
+R L T D D G C +T C +A C S C P
1
L R L T D D G C G A T C E S A C N S C P
20

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.14 out of 23.79
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.39 out of 25.31
Confidence: medium
Additional weak hits (9):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.78 out of 23.43
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.28 out of 27.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.07 out of 26.85
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.09 out of 30.22
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.13 out of 36.53
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.01 out of 31.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.01 out of 32.74
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.13 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.72 out of 24.78
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.

C7M71_RS22650 - Class I
  Cleavage pHMM score: -1.70
  RODEO score: 21
  Monoisotopic mass: 2180.0 Da
  Molecular weight: 2181.5 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2199.5 Da N = 1
C7M71_RS22650 - Class I
  Cleavage pHMM score: -1.70
  RODEO score: 21
  Monoisotopic mass: 2180.0 Da
  Molecular weight: 2181.5 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2199.5 Da N = 1

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (5090989...5115983)
C7M71_RS22645
  RRE type: Lanthipeptide_LanB_RRE
  Location: 153 - 242
  Score: 65.2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
IolR | Regulator of the inositol catabolism

NZ_CP031264.1 - Region 16 - 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: 5,258,636 - 5,270,001 nt. (total: 11,366 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: dehydrogenase
C7M71_RS23310: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

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
--- | --- | --- | --- | --- | ---
BGC0002788.2 |  | 0.27 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000241.5 |  | 0.21 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440
BGC0001693.3 |  | 0.20 | PKS | nenestatin | Micromonospora echinospora
BGC0000240.5 |  | 0.20 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora pacifica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002788.2 |  | 0.27 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0000241.5 |  | 0.21 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440
BGC0001693.3 |  | 0.20 | PKS | nenestatin | Micromonospora echinospora
BGC0000240.5 |  | 0.20 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora pacifica

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 (2):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.25 out of 33.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.65 out of 29.38
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP031264.1 - Region 17 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,548,259 - 5,638,062 nt. (total: 89,804 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidase oxidoreductase oxygenase
C7M71_RS24555: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

C7M71_RS24605: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

C7M71_RS24655: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: acylase halogenase methyltransferase
C7M71_RS24550: methyltransferase

smcogs
  SMCOG1089: methyltransferase

C7M71_RS24590: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

C7M71_RS24620: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

C7M71_RS24630: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

Hydrolases: esterase
C7M71_RS24565: thioesterase

smcogs
  SMCOG1004: thioesterase

C7M71_RS24650: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
C7M71_RS24530: Pseudouridine synthase

smcogs
  SMCOG1154: Pseudouridine synthase

C7M71_RS24560: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C7M71_RS24575: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C7M71_RS24580: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C7M71_RS24585: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS24635: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

C7M71_RS24640: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS24645: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS24660: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport
C7M71_RS24680: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002341.2 |  |  | 0.93 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001275.3 |  |  | 0.91 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  |  | 0.91 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  | 0.89 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001825.4 |  |  | 0.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002192.3 |  |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0002191.2 |  |  | 0.61 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001758.4 |  |  | 0.61 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.77 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.77 | PKS | asperlactone | Aspergillus ochraceus
BGC0002341.2 |  | 0.76 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000111.5 |  | 0.68 | PKS | neocarzilin A, neocarzilin B | Streptomyces carzinostaticus
BGC0001276.3 |  | 0.68 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001825.4 |  | 0.65 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001128.4 |  | 0.64 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.65 out of 18.46
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.09 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.92 out of 23.79
Confidence: medium
Additional weak hits (13):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.39 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.23 out of 21.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.19 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.95 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.98 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.76 out of 31.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.07 out of 20.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.59 out of 27.55
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.98 out of 35.63
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.23 out of 23.43
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 26.85
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 24, location 5548258 - 5638062:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal) + (Me-redmal) + (pk) + (ccmal) + (Cys) + (Cys) + (Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 25, location 5548258 - 5602235:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (ccmal) + (Cys) + (Cys) + (Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 26, location 5562338 - 5638062:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal) + (Me-redmal) + (pk) + (ccmal) + (Cys) + (Cys) + (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).
C7M71_RS24560: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (482..881): 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:
    TDVSFDLSVWDGNSLMSGDIAMGGATEASIWSNI
  Nearest Stachelhaus code(s):
    Cys DLWNLSLIWK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

C7M71_RS24575: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (538..935): 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:
    TDVSFDLSVYDGNSLLSGDVSLGGATEASIWSVC
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

C7M71_RS24580: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (533..941): 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:
    TEVSFDLSVYDGNSLLSGDVSLGGATEASIWSIC
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

C7M71_RS24585: mal
PKS_AT (552..848): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 190.1
  inactive: 88.9
  Methoxymalonyl-CoA: 48.4
  Methylmalonyl-CoA: 32.1
  Propionyl-CoA: 26.7
  Acetyl-CoA: 16.1
  Isobutyryl-CoA: 11.2
  Ethylmalonyl-CoA: 8.7
  2-Methylbutyryl-CoA: 6.2
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

C7M71_RS24590: pk
PKS_AT (536..822): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 223.6
  Methylmalonyl-CoA: 218.9
  Methoxymalonyl-CoA: 183.8
  2-Methylbutyryl-CoA: 150.1
  trans-1,2-CPDA: 140.7
  Propionyl-CoA: 124.3
  Malonyl-CoA: 111.9
  CHC-CoA: 106.5
  Isobutyryl-CoA: 69.3
  Benzoyl-CoA: 67.2
  Acetyl-CoA: 47.9
  fatty_acid: 35.9
  3-Methylbutyryl-CoA: 31.8
  inactive: 23.4

C7M71_RS24635: mmal
PKS_AT (537..834): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Malonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 146.7
  Methoxymalonyl-CoA: 111.8
  Ethylmalonyl-CoA: 108.3
  Malonyl-CoA: 91.3
  Isobutyryl-CoA: 73.1
  Benzoyl-CoA: 71.4
  2-Methylbutyryl-CoA: 65.7
  Propionyl-CoA: 65.4
  CHC-CoA: 61.3
  trans-1,2-CPDA: 61.2
  Acetyl-CoA: 44.2
  3-Methylbutyryl-CoA: 35.8
  inactive: 31.6
  fatty_acid: 10.4

C7M71_RS24640: mal
PKS_AT (1755..2030): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 175.6
  inactive: 124.7
  Methoxymalonyl-CoA: 68.2
  Methylmalonyl-CoA: 62.9
  Propionyl-CoA: 53.4
  Ethylmalonyl-CoA: 39.6
  Isobutyryl-CoA: 38.8
  2-Methylbutyryl-CoA: 31.0
  Benzoyl-CoA: 24.1
  fatty_acid: 19.9
  Acetyl-CoA: 14.5
  CHC-CoA: 12.5
  3-Methylbutyryl-CoA: 12.3
  trans-1,2-CPDA: 11.6

C7M71_RS24660: X
AMP-binding (35..416): 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:
    SARG--RTISAWVFVLVGGRAEFAPAGGAMPWTA
  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
--- | ---
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP031264.1 - Region 18 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,710,134 - 5,768,654 nt. (total: 58,521 nt) Show pHMM detection rules used
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: oxidoreductase oxygenase
C7M71_RS25060: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

C7M71_RS25065: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

C7M71_RS25115: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: formyltransferase
C7M71_RS25110: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: esterase hydrolase phosphatase
C7M71_RS25155: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

C7M71_RS25175: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

C7M71_RS25205: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Ligases: ligase
C7M71_RS25145: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: transporter
C7M71_RS25105: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000325.5 |  |  | 1.10 | NRPS | coelichelin | Streptomyces coelicolor A3(2)
BGC0000357.5 |  |  | 0.69 | 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
BGC0001825.4 |  |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001240.4 |  |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001261.3 |  |  | 0.58 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  |  | 0.57 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001833.4 |  |  | 0.56 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001164.3 |  |  | 0.49 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002476.2 |  |  | 0.42 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0002073.3 |  |  | 0.38 | NRPS | dehydroxynocardamine | Corynebacterium propinquum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000325.5 |  | 0.81 | NRPS | coelichelin | Streptomyces coelicolor A3(2)
BGC0000357.5 |  | 0.67 | 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
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001261.3 |  | 0.62 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001833.4 |  | 0.62 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001164.3 |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002476.2 |  | 0.54 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0002073.3 |  | 0.51 | NRPS | dehydroxynocardamine | Corynebacterium propinquum

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: 22.05 out of 22.40
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.03 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 35.53 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.90 out of 36.53
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: 17.92 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
Additional weak hits (9):
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
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.67 out of 27.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.39 out of 26.85
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 39.62
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.39 out of 36.53
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
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
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 27, location 5710133 - 5768654:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Fo-OH-Orn - D-Thr - OH-Orn)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
C7M71_RS25145: Fo-OH-Orn - Thr - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (144..542): Fo-OH-Orn
nrpys: Fo-OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWQAFDISINELYLWCGGEYHGYGPAETTIGVSH
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DINYWGGIGK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1629..2046): 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:
    LNTHFDFAVWEGNQIFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3064..3464): OH-Orn
nrpys: OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MNHVFDMSWEEWNVLLGGEYNLYGPTEYTINTLG
  Nearest Stachelhaus code(s):
    OH-Orn DMENLGLINK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

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

NZ_CP031264.1 - Region 19 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,778,290 - 5,829,279 nt. (total: 50,990 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: oxidoreductase oxygenase
C7M71_RS25270: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

C7M71_RS25290: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

C7M71_RS25340: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: acylase acyltransferase
C7M71_RS25275: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

C7M71_RS32190: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase hydrolase
C7M71_RS25230: thioesterase

smcogs
  SMCOG1004: thioesterase

C7M71_RS25365: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: cyclase
C7M71_RS25295: Diels-Alderase cyclase

extras
  DA_cyclase: Diels-Alderase cyclase

Ligases: synthase
C7M71_RS25300: 3-oxoacyl-(acyl carrier protein) synthase III

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

C7M71_RS25305: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS25325: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.65 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
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
BGC0001258.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001275.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002175.3 |  | 0.63 | PKS | YWA1 | Aspergillus oryzae RIB40

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.65 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
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
BGC0001258.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001275.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002175.3 |  | 0.63 | PKS | YWA1 | Aspergillus oryzae RIB40

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: 18.37 out of 20.47
Confidence: medium
Additional weak hits (9):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.82 out of 30.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.47 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.56 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.29 out of 30.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.65 out of 32.93
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 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 28, location 5778289 - 5829279:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal) + (mal)
Non-colinear ordering:
  C7M71_RS32190 + C7M71_RS25325

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).
C7M71_RS32190: mmal
PKS_AT (989..1282): 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: 192.6
  Ethylmalonyl-CoA: 181.1
  Methoxymalonyl-CoA: 142.9
  2-Methylbutyryl-CoA: 121.9
  trans-1,2-CPDA: 105.9
  Propionyl-CoA: 96.8
  CHC-CoA: 81.9
  Malonyl-CoA: 72.4
  Isobutyryl-CoA: 59.7
  Benzoyl-CoA: 59.3
  3-Methylbutyryl-CoA: 34.0
  Acetyl-CoA: 32.5
  inactive: 23.7
  fatty_acid: 20.1

C7M71_RS25325: mal
PKS_AT (566..855): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 187.0
  inactive: 87.4
  Methoxymalonyl-CoA: 71.4
  Methylmalonyl-CoA: 45.8
  Propionyl-CoA: 31.3
  Isobutyryl-CoA: 23.4
  Acetyl-CoA: 18.0
  2-Methylbutyryl-CoA: 17.2
  Ethylmalonyl-CoA: 16.0
  CHC-CoA: 13.8
  fatty_acid: 9.8
  Benzoyl-CoA: 8.2
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

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_CP031264.1 - Region 20 - T1PKS,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: 5,852,092 - 6,035,626 nt. (total: 183,535 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
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
C7M71_RS25550: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

C7M71_RS25595: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

C7M71_RS25650: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

C7M71_RS25655: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

C7M71_RS25660: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

C7M71_RS25690: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

C7M71_RS25755: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

C7M71_RS25860: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

C7M71_RS25865: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: glycosyltransferase transferase
C7M71_RS25600: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

C7M71_RS25710: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

C7M71_RS25880: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: esterase
C7M71_RS25785: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
C7M71_RS25605: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

C7M71_RS25885: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: racemase
C7M71_RS25610: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: synthase
C7M71_RS25590: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

C7M71_RS25700: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS25705: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS25725: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS25740: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS25820: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS32770: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS33300: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
C7M71_RS25615: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

C7M71_RS25670: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | T3PKS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
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)
BGC0000143.5 |  |  | 0.50 | PKS | salinomycin | Streptomyces albus
BGC0001273.3 |  |  | 0.42 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  | 0.42 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002631.2 |  |  | 0.42 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001276.3 |  |  | 0.42 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.42 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  |  | 0.36 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001948.3 |  |  | 0.35 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.82 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000143.5 |  | 0.73 | PKS | salinomycin | Streptomyces albus
BGC0002127.3 |  | 0.71 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000041.3 |  | 0.69 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000016.4 |  | 0.65 | other (other) | amphotericin B | Streptomyces nodosus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.10 out of 23.79
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 24.94 out of 29.65
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.55 out of 26.85
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 out of 25.31
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.33 out of 27.04
Confidence: medium
Additional weak hits (20):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.71 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.00 out of 28.14
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.10 out of 25.88
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.61 out of 30.97
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.83 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.57 out of 27.78
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.80 out of 23.43
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.94 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 30.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.45 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.16 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.17 out of 31.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.33 out of 30.22
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.66 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.74 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.46 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.34 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.61 out of 23.43
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 29, location 5852091 - 6035626:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-ohmal - Me-ohmal) + (Me-ohmal - Me-ohmal - ccmal) + (ohmal - ohmal - mal) + (Me-ohmal - redmal) + (Me-ohmal - ccmal) + (ohmal - ohmal) + (ccmal - ohmal) + (ccmal)
Non-colinear ordering:
  C7M71_RS25700 + C7M71_RS25705 + C7M71_RS25720 + C7M71_RS33295 + C7M71_RS25725 + C7M71_RS25740 + C7M71_RS32770 + C7M71_RS25820 + C7M71_RS25755

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 31, location 5878144 - 6035626:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-ohmal - Me-ohmal) + (Me-ohmal - Me-ohmal - ccmal) + (ohmal - ohmal - mal) + (Me-ohmal - redmal) + (Me-ohmal - ccmal) + (ohmal - ohmal) + (ccmal - ohmal) + (ccmal)
Non-colinear ordering:
  C7M71_RS25700 + C7M71_RS25705 + C7M71_RS25720 + C7M71_RS33295 + C7M71_RS25725 + C7M71_RS25740 + C7M71_RS32770 + C7M71_RS25820 + C7M71_RS25755

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).
C7M71_RS25700: mmal - mmal - mmal
PKS_AT (528..825): 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: 220.9
  Ethylmalonyl-CoA: 214.0
  Methoxymalonyl-CoA: 178.7
  2-Methylbutyryl-CoA: 148.9
  trans-1,2-CPDA: 145.5
  Propionyl-CoA: 119.3
  CHC-CoA: 110.5
  Malonyl-CoA: 104.9
  Isobutyryl-CoA: 76.0
  Benzoyl-CoA: 66.1
  Acetyl-CoA: 47.1
  fatty_acid: 33.9
  inactive: 30.4
  3-Methylbutyryl-CoA: 30.4

PKS_AT (1495..1792): 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: 220.2
  Ethylmalonyl-CoA: 214.8
  Methoxymalonyl-CoA: 180.3
  2-Methylbutyryl-CoA: 150.8
  trans-1,2-CPDA: 142.5
  Propionyl-CoA: 115.3
  CHC-CoA: 113.8
  Malonyl-CoA: 103.7
  Isobutyryl-CoA: 79.4
  Benzoyl-CoA: 67.8
  Acetyl-CoA: 49.4
  3-Methylbutyryl-CoA: 33.6
  fatty_acid: 33.4
  inactive: 31.9

PKS_AT (3011..3308): 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: 222.5
  Ethylmalonyl-CoA: 217.6
  Methoxymalonyl-CoA: 182.2
  2-Methylbutyryl-CoA: 154.5
  trans-1,2-CPDA: 142.6
  Propionyl-CoA: 116.6
  CHC-CoA: 114.8
  Malonyl-CoA: 105.2
  Isobutyryl-CoA: 80.3
  Benzoyl-CoA: 68.9
  Acetyl-CoA: 49.8
  3-Methylbutyryl-CoA: 34.4
  fatty_acid: 33.4
  inactive: 32.0

C7M71_RS25705: mmal - mmal - mal
PKS_AT (573..870): 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: 224.9
  Ethylmalonyl-CoA: 223.0
  Methoxymalonyl-CoA: 182.6
  2-Methylbutyryl-CoA: 151.1
  trans-1,2-CPDA: 150.7
  Propionyl-CoA: 121.1
  Malonyl-CoA: 108.2
  CHC-CoA: 104.0
  Isobutyryl-CoA: 67.0
  Benzoyl-CoA: 63.8
  Acetyl-CoA: 51.1
  fatty_acid: 47.3
  inactive: 29.6
  3-Methylbutyryl-CoA: 28.9

PKS_AT (2091..2388): 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: 224.3
  Ethylmalonyl-CoA: 218.7
  Methoxymalonyl-CoA: 183.7
  2-Methylbutyryl-CoA: 154.9
  trans-1,2-CPDA: 150.7
  Propionyl-CoA: 125.1
  CHC-CoA: 118.3
  Malonyl-CoA: 104.6
  Isobutyryl-CoA: 85.5
  Benzoyl-CoA: 71.3
  Acetyl-CoA: 56.2
  3-Methylbutyryl-CoA: 43.1
  fatty_acid: 40.7
  inactive: 32.9

PKS_AT (3627..3926): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 225.8
  inactive: 117.1
  Methoxymalonyl-CoA: 70.6
  Methylmalonyl-CoA: 53.7
  Propionyl-CoA: 39.6
  Isobutyryl-CoA: 29.6
  Benzoyl-CoA: 26.6
  Ethylmalonyl-CoA: 26.0
  fatty_acid: 25.6
  Acetyl-CoA: 22.2
  2-Methylbutyryl-CoA: 20.2
  trans-1,2-CPDA: 12.4
  CHC-CoA: 11.7
  3-Methylbutyryl-CoA: 0.0

C7M71_RS25720: mal - mal - mal
PKS_AT (565..858): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 224.2
  inactive: 101.7
  Methoxymalonyl-CoA: 59.8
  Methylmalonyl-CoA: 52.3
  Acetyl-CoA: 30.1
  Isobutyryl-CoA: 27.5
  Propionyl-CoA: 23.9
  Ethylmalonyl-CoA: 22.6
  Benzoyl-CoA: 20.4
  fatty_acid: 17.0
  CHC-CoA: 16.0
  2-Methylbutyryl-CoA: 15.8
  trans-1,2-CPDA: 12.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2047..2341): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 229.3
  inactive: 107.4
  Methoxymalonyl-CoA: 63.4
  Methylmalonyl-CoA: 56.2
  Acetyl-CoA: 26.6
  Propionyl-CoA: 26.2
  Isobutyryl-CoA: 25.9
  Ethylmalonyl-CoA: 25.4
  Benzoyl-CoA: 24.1
  trans-1,2-CPDA: 18.7
  CHC-CoA: 18.5
  2-Methylbutyryl-CoA: 17.3
  fatty_acid: 16.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3561..3854): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 219.3
  inactive: 95.4
  Methoxymalonyl-CoA: 65.3
  Methylmalonyl-CoA: 57.7
  Propionyl-CoA: 34.9
  Isobutyryl-CoA: 34.8
  Acetyl-CoA: 33.0
  Benzoyl-CoA: 29.2
  Ethylmalonyl-CoA: 22.7
  trans-1,2-CPDA: 22.1
  fatty_acid: 20.5
  CHC-CoA: 19.6
  2-Methylbutyryl-CoA: 17.3
  3-Methylbutyryl-CoA: 0.0

C7M71_RS25725: mmal - mal
PKS_AT (539..836): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 213.8
  Ethylmalonyl-CoA: 204.9
  Methoxymalonyl-CoA: 172.5
  2-Methylbutyryl-CoA: 161.3
  trans-1,2-CPDA: 143.8
  Propionyl-CoA: 114.3
  CHC-CoA: 92.6
  Malonyl-CoA: 86.8
  Isobutyryl-CoA: 66.6
  Benzoyl-CoA: 54.5
  3-Methylbutyryl-CoA: 48.4
  Acetyl-CoA: 33.5
  fatty_acid: 32.5
  inactive: 23.1

PKS_AT (2119..2413): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 228.5
  inactive: 107.0
  Methoxymalonyl-CoA: 63.0
  Methylmalonyl-CoA: 61.7
  Isobutyryl-CoA: 34.5
  Ethylmalonyl-CoA: 31.8
  Propionyl-CoA: 31.7
  Benzoyl-CoA: 30.1
  Acetyl-CoA: 28.7
  2-Methylbutyryl-CoA: 18.9
  fatty_acid: 17.9
  CHC-CoA: 16.7
  trans-1,2-CPDA: 15.0
  3-Methylbutyryl-CoA: 0.0

C7M71_RS33300: mal
PKS_AT (571..864): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 219.1
  inactive: 99.6
  Methoxymalonyl-CoA: 64.8
  Methylmalonyl-CoA: 59.2
  Propionyl-CoA: 28.6
  Isobutyryl-CoA: 26.5
  Ethylmalonyl-CoA: 25.5
  Acetyl-CoA: 20.4
  Benzoyl-CoA: 19.2
  2-Methylbutyryl-CoA: 15.0
  CHC-CoA: 13.8
  fatty_acid: 12.7
  trans-1,2-CPDA: 12.3
  3-Methylbutyryl-CoA: 0.0

C7M71_RS25740: mmal - mal
PKS_AT (566..863): 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: 224.0
  Ethylmalonyl-CoA: 219.9
  Methoxymalonyl-CoA: 183.0
  trans-1,2-CPDA: 152.3
  2-Methylbutyryl-CoA: 151.4
  Propionyl-CoA: 125.0
  CHC-CoA: 109.1
  Malonyl-CoA: 104.5
  Isobutyryl-CoA: 78.1
  Benzoyl-CoA: 68.9
  Acetyl-CoA: 54.4
  fatty_acid: 43.9
  3-Methylbutyryl-CoA: 39.1
  inactive: 31.3

PKS_AT (2116..2405): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 212.2
  inactive: 96.4
  Methoxymalonyl-CoA: 59.6
  Methylmalonyl-CoA: 47.9
  Isobutyryl-CoA: 31.4
  Ethylmalonyl-CoA: 20.8
  Acetyl-CoA: 20.2
  Propionyl-CoA: 17.4
  Benzoyl-CoA: 15.7
  2-Methylbutyryl-CoA: 9.5
  trans-1,2-CPDA: 9.2
  CHC-CoA: 5.1
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

C7M71_RS25745: X
AMP-binding (166..306): 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:
    -WIN------D-RTYLGGT--------GVIGATY
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

C7M71_RS25750: AHBA
CAL_domain (34..442): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 330.3
  shikimic_acid: 282.5
  fatty_acid: 0.0
  NH2: 0.0
  Acetyl-CoA: 0.0

C7M71_RS25755: mal
PKS_AT (599..886): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 91.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 213.2
  inactive: 115.6
  Methoxymalonyl-CoA: 66.9
  Methylmalonyl-CoA: 61.9
  Propionyl-CoA: 35.4
  Ethylmalonyl-CoA: 25.3
  Isobutyryl-CoA: 22.0
  Acetyl-CoA: 19.4
  2-Methylbutyryl-CoA: 14.5
  Benzoyl-CoA: 10.9
  CHC-CoA: 10.7
  trans-1,2-CPDA: 8.0
  fatty_acid: 7.9
  3-Methylbutyryl-CoA: 0.0

C7M71_RS25820: mal - mal
PKS_AT (570..865): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 221.3
  inactive: 106.4
  Methoxymalonyl-CoA: 59.1
  Methylmalonyl-CoA: 48.7
  Propionyl-CoA: 25.3
  Isobutyryl-CoA: 24.8
  Benzoyl-CoA: 22.6
  Acetyl-CoA: 21.5
  Ethylmalonyl-CoA: 20.3
  2-Methylbutyryl-CoA: 19.9
  fatty_acid: 16.9
  CHC-CoA: 14.3
  trans-1,2-CPDA: 12.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2332..2626): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 228.8
  inactive: 106.6
  Methoxymalonyl-CoA: 59.0
  Methylmalonyl-CoA: 53.8
  Acetyl-CoA: 27.7
  Propionyl-CoA: 24.5
  Benzoyl-CoA: 24.1
  Ethylmalonyl-CoA: 24.0
  Isobutyryl-CoA: 23.9
  trans-1,2-CPDA: 17.9
  2-Methylbutyryl-CoA: 17.1
  CHC-CoA: 15.7
  fatty_acid: 15.2
  3-Methylbutyryl-CoA: 0.0

C7M71_RS32770: mal - mal
PKS_AT (562..856): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 233.3
  inactive: 109.5
  Methoxymalonyl-CoA: 68.2
  Methylmalonyl-CoA: 61.3
  Isobutyryl-CoA: 33.2
  Ethylmalonyl-CoA: 31.4
  Propionyl-CoA: 30.7
  Benzoyl-CoA: 26.5
  Acetyl-CoA: 23.9
  2-Methylbutyryl-CoA: 20.1
  CHC-CoA: 18.8
  fatty_acid: 16.5
  trans-1,2-CPDA: 15.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2078..2372): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 232.2
  inactive: 109.1
  Methoxymalonyl-CoA: 64.5
  Methylmalonyl-CoA: 59.8
  Isobutyryl-CoA: 31.3
  Ethylmalonyl-CoA: 29.6
  Propionyl-CoA: 28.6
  Benzoyl-CoA: 26.7
  Acetyl-CoA: 24.9
  2-Methylbutyryl-CoA: 19.2
  CHC-CoA: 17.7
  fatty_acid: 15.3
  trans-1,2-CPDA: 14.6
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CatR | H2O2-responsive repressor
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
LexA variant 1 | Repressor of DNA damage response
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP031264.1 - Region 21 - 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: 6,227,093 - 6,291,077 nt. (total: 63,985 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 oxidoreductase oxygenase
C7M71_RS26720: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

C7M71_RS26770: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

C7M71_RS26810: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

C7M71_RS26855: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: acetyltransferase sulfhydrylase
C7M71_RS26825: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

C7M71_RS26850: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: phosphatase
C7M71_RS26795: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

Ligases: ligase
C7M71_RS26705: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C7M71_RS26760: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  | 0.70 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000307.4 |  | 0.70 | NRPS | AbT1 | Aureobasidium pullulans

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.92 out of 23.43
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.77 out of 29.51
Confidence: medium
Additional weak hits (7):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.82 out of 26.33
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.66 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.41 out of 33.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.12 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.77 out of 23.43
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.82 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 32, location 6227092 - 6291077:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Thr - Ala - Pro - Phe - NMe-Tyr - 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).
C7M71_RS26705: X
AMP-binding (24..477): 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:
    ETLLYGLMVQ-CWGQVAAE--------SHAEATE
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

C7M71_RS26760: X - Thr - Ala - Pro - Phe - Tyr - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (463..867): 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:
    LALTFDASWNQAEAAAGGEVNLYGPSECTVNSVV
  Nearest Stachelhaus code(s):
    OH-Orn DAQEGGLVDK (59% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1521..1925): 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:
    LTTHFDFSVWEGNQVFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2582..2952): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MEQSFDVSLWDGTVTVAGEVNAYGPTETTVIATM
  Nearest Stachelhaus code(s):
    Ala DVWCTAAVIK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3612..3999): 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:
    LWHTFDVSVQESFAAQAGEHNHYGPAETHVITAY
  Nearest Stachelhaus code(s):
    Pro DVQFAAHVVK (91% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4659..5045): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASFWDSTLVVAGEINAYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5703..6089): 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:
    LAQAFDASVSETTVVVAGEINAYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Tyr DASTVAAVCK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (7159..7540): 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:
    LTPSFDLSTYEVWLWTGGDVNGYGPTEATTLATC
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (82% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

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

NZ_CP031264.1 - Region 22 - hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,585,150 - 6,638,960 nt. (total: 53,811 nt) Show pHMM detection rules used
hglE-KS: (hglE or hglD)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acylase glycosyltransferase
C7M71_RS28210: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

C7M71_RS28255: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: dehalogenase
C7M71_RS28185: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: dehydratase
C7M71_RS28205: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
C7M71_RS28195: 3-oxoacyl-(acyl carrier protein) synthase III

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

C7M71_RS28200: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C7M71_RS28215: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS28220: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001268.4 |  | 0.60 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  | 0.58 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.58 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000869.5 |  | 0.54 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001872.3 |  | 0.54 | PKS | fabclavine-polyamine | Xenorhabdus bovienii SS-2004
BGC0000861.5 |  | 0.54 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0002648.2 |  | 0.54 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000862.3 |  | 0.53 | other (other) | eicosapentaenoic acid | Shewanella pneumatophori
BGC0000863.3 |  | 0.52 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001268.4 |  | 0.60 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  | 0.58 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.58 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000869.5 |  | 0.54 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001872.3 |  | 0.54 | PKS | fabclavine-polyamine | Xenorhabdus bovienii SS-2004
BGC0000861.5 |  | 0.54 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0002648.2 |  | 0.54 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000862.3 |  | 0.53 | other (other) | eicosapentaenoic acid | Shewanella pneumatophori
BGC0000863.3 |  | 0.52 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 22.87 out of 23.79
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 22.87 out of 26.33
Confidence: medium
Additional weak hits (8):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.85 out of 30.97
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 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
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.06 out of 23.43
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.81 out of 32.74
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.54 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 33, location 6585149 - 6638960:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
C7M71_RS30860: mxmal
PKS_AT (450..761): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 31.7
  Methylmalonyl-CoA: 30.6
  inactive: 16.4
  Malonyl-CoA: 16.2
  Acetyl-CoA: 10.6
  Ethylmalonyl-CoA: 10.0
  Propionyl-CoA: 9.9
  2-Methylbutyryl-CoA: 8.5
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

C7M71_RS28200: X
AMP-binding (30..456): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    QLAP-----FAGFGTSAGAHSAYGATECLPLSVI
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

C7M71_RS28215: mal
PKS_AT (584..879): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 70.8%
  inactive: 62.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 97.1
  inactive: 38.5
  Methoxymalonyl-CoA: 34.5
  Methylmalonyl-CoA: 32.0
  CHC-CoA: 13.4
  Ethylmalonyl-CoA: 12.4
  Isobutyryl-CoA: 11.8
  2-Methylbutyryl-CoA: 10.0
  Propionyl-CoA: 9.2
  Benzoyl-CoA: 5.8
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

C7M71_RS28220: mmal
PKS_AT (890..1181): mmal
ATSignature: (unknown)
No matches above 50%
minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 34.8
  Methoxymalonyl-CoA: 27.3
  Ethylmalonyl-CoA: 21.2
  Propionyl-CoA: 20.1
  2-Methylbutyryl-CoA: 14.6
  Benzoyl-CoA: 12.0
  inactive: 9.2
  Isobutyryl-CoA: 8.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  Malonyl-CoA: -3.3

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
IolR | Regulator of the inositol catabolism

NZ_CP031264.1 - Region 23 - RiPP-like,T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,722,194 - 6,794,700 nt. (total: 72,507 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)
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
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
C7M71_RS28755: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

C7M71_RS28835: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

C7M71_RS28885: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

C7M71_RS28925: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase methyltransferase
C7M71_RS28735: aminotransferase

smcogs
  SMCOG1019: aminotransferase

C7M71_RS28875: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: deacetylase phosphatase
C7M71_RS28930: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

C7M71_RS32340: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

Lyases: cyclase
C7M71_RS28865: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

C7M71_RS28870: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

Ligases: synthase
C7M71_RS28705: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

C7M71_RS28850: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

C7M71_RS28855: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | T2PKS | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000271.5 |  |  | 0.46 | PKS | spore pigment | Streptomyces avermitilis
BGC0000215.5 |  |  | 0.40 | PKS | curamycin | Streptomyces cyaneus
BGC0000272.3 |  |  | 0.34 | PKS | spore pigment | Streptomyces collinus
BGC0000231.5 |  |  | 0.27 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001513.3 |  |  | 0.25 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000275.4 |  |  | 0.24 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0000234.5 |  |  | 0.23 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001197.5 |  |  | 0.23 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002276.2 |  |  | 0.23 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000204.5 |  |  | 0.21 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000271.5 |  | 0.76 | PKS | spore pigment | Streptomyces avermitilis
BGC0000215.5 |  | 0.72 | PKS | curamycin | Streptomyces cyaneus
BGC0000272.3 |  | 0.67 | PKS | spore pigment | Streptomyces collinus
BGC0000231.5 |  | 0.60 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001513.3 |  | 0.59 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000275.4 |  | 0.58 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0000234.5 |  | 0.57 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002276.2 |  | 0.56 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000204.5 |  | 0.53 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200

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: 16.52 out of 19.26
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.66 out of 23.79
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.20 out of 27.04
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 25.31
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.44 out of 27.18
Confidence: medium
Additional weak hits (11):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.20 out of 23.43
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.96 out of 30.22
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.83 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.66 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.67 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.85 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.67 out of 30.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.57 out of 24.78
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.34 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.78 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
Type II PKS
TFBS Finder
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:
  6722193 to 6794700
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

C7M71_RS28835
  OXY (Score: 283.8; E-value: 6.4e-87)
C7M71_RS28845
  CYC C5-C18 (Score: 216.3; E-value: 2.5e-67)
C7M71_RS28850
  KS (Score: 719.5; E-value: 2.8e-219)
C7M71_RS28855
  CLF (Score: 556.0; E-value: 1.1e-169)
C7M71_RS28860
  ACP (Score: 58.9; E-value: 8.9e-19)
C7M71_RS28865
  CYC C9-C14 (Score: 246.4; E-value: 2e-76)
C7M71_RS28870
  CYC C4-C21/C2-C23|C2-C19 (Score: 148.9; E-value: 1e-46)
C7M71_RS28875
  MET C6|C8 (Score: 546.0; E-value: 6.3e-167)
C7M71_RS28925
  KR (Score: 107.7; E-value: 1.8e-33)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems