Select genomic region:
Overview
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1.34
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1.37

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

NZ_LT907981.1 (Streptomyces sp. 2323.1)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | melanin | 216,025 | 226,492 |
Region 2 | NRPS-like,benzoxazole,T1PKS,oligosaccharide,butyrolactone | 248,183 | 441,764 | High | cyphomycin | PKS
Region 3 | terpene | 502,303 | 527,185 | Medium | isorenieratene | terpene
Region 4 | other,NRPS,NRPS-like | 538,417 | 596,077 | High | antipain | NRPS:Type I
Region 5 | butyrolactone | 665,690 | 676,670 |  |
Region 6 | T1PKS,t3nrps-iterative | 723,328 | 828,632 | High | tripartilactam/niizalactam C | PKS
Region 7 | butyrolactone | 957,922 | 968,842 |  |
Region 8 | T3PKS | 1,060,809 | 1,101,993 |  |
Region 9 | T1PKS,hglE-KS | 1,132,520 | 1,184,439 |  |
Region 10 | terpene | 1,270,946 | 1,297,648 | Medium | hopene | terpene
Region 11 | NI-siderophore | 1,579,898 | 1,611,251 |  |
Region 12 | T2PKS,lassopeptide | 1,656,398 | 1,728,931 | High | lysolipin I | PKS
Region 13 | RiPP-like | 1,809,529 | 1,820,906 |  |
Region 14 | butyrolactone | 1,880,308 | 1,891,285 |
Region 15 | lassopeptide,HR-T2PKS | 1,891,724 | 1,933,922 | High | citrulassin D | ribosomal:RiPP
Region 16 | crocagin | 1,939,493 | 1,967,807 |
Region 17 | NI-siderophore | 2,084,530 | 2,117,221 | Low | kinamycin | PKS
Region 18 | triceptide | 2,651,679 | 2,673,238 |
Region 19 | linaridin | 3,549,767 | 3,570,658 | Medium | legonaridin | ribosomal:RiPP
Region 20 | lassopeptide | 3,637,117 | 3,659,735 |
Region 21 | lassopeptide | 3,713,989 | 3,736,506 | High | ulleungdin | ribosomal:unmodified
Region 22 | terpene | 3,743,167 | 3,765,410 |  |
Region 23 | terpene,azole-containing-RiPP | 4,171,898 | 4,220,142 | High | siomycin A | ribosomal:RiPP:Thiopeptide
Region 24 | T1PKS | 5,236,629 | 5,282,976 |  |
Region 25 | butyrolactone | 5,289,292 | 5,300,227 |  |
Region 26 | ectoine | 6,216,600 | 6,227,016 | High | ectoine | other:ectoine
Region 27 | NI-siderophore | 6,306,873 | 6,336,678 | High | legonoxamine A/desferrioxamine B/legonoxamine B | other:other
Region 28 | hglE-KS,T1PKS | 6,895,471 | 6,946,967 |  |
Region 29 | NI-siderophore | 7,084,158 | 7,117,027 | Low | peucechelin | NRPS:Type I
Region 30 | T2PKS | 7,235,314 | 7,307,829 | Medium | spore pigment | PKS
Region 31 | RiPP-like | 7,324,050 | 7,334,277 |  |
Region 32 | hydrogen-cyanide | 7,435,880 | 7,448,860 | Low | aborycin | ribosomal:RiPP
Region 33 | T3PKS | 7,480,060 | 7,521,124 | High | naringenin | PKS:Type III
Region 34 | RiPP-like | 7,544,116 | 7,556,047 |
Region 35 | NRPS,NRPS-like | 7,565,485 | 7,666,430 | Low | lipstatin | NRPS:Type I
Region 36 | transAT-PKS | 7,666,570 | 7,752,414 | High | iso-migrastatin/migrastatin/dorrigocin A/dorrigocin B/13-epi-dorrigocin A | PKS:Type I
Region 37 | T1PKS | 8,086,666 | 8,177,506 | High | phoslactomycin B | PKS

NZ_LT907981.1 - Region 1 - melanin
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: 216,025 - 226,492 nt. (total: 10,468 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase
CPH93_RS00975: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

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 | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000911.3 |  | 0.80 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000912.3 |  | 0.79 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.78 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.63 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.57 | other (other) | melanin | Streptomyces avermitilis
BGC0000662.5 |  | 0.35 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.34 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.34 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.33 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0000627.4 |  | 0.29 | ribosomal | ustiloxin B | Aspergillus flavus NRRL3357

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000911.3 |  | 0.80 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000912.3 |  | 0.79 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.78 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.63 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.57 | other (other) | melanin | Streptomyces avermitilis
BGC0000662.5 |  | 0.35 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.34 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.34 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.33 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0000627.4 |  | 0.29 | ribosomal | ustiloxin B | Aspergillus flavus NRRL3357

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 (3):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.64 out of 33.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.66 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LT907981.1 - Region 2 - NRPS-like,T1PKS,benzoxazole,butyrolactone,oligosaccharide
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: 248,183 - 441,764 nt. (total: 193,582 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
benzoxazole: (ksIII and AMP-binding and PP-binding and Amidohydro_1)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CPH93_RS01150: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

CPH93_RS01250: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS01305: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: PPTase acylase aminotransferase glycosyltransferase sulfotransferase transferase
CPH93_RS01080: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

CPH93_RS01090: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

CPH93_RS01200: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CPH93_RS01215: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CPH93_RS01220: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CPH93_RS01225: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CPH93_RS01240: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

CPH93_RS01245: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CPH93_RS01320: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CPH93_RS01355: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Hydrolases: hydrolase
CPH93_RS01070: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: dehydratase
CPH93_RS01110: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

CPH93_RS01165: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

CPH93_RS01230: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

CPH93_RS01235: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
CPH93_RS01065: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CPH93_RS01210: 3-oxoacyl-(acyl carrier protein) synthase III

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

CPH93_RS01260: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS01265: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS01285: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS01290: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CPH93_RS01315: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS36590: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | NRPS-like | benzoxazole | T1PKS | NRPS-like | oligosaccharide | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001276.3 |  |  |  |  |  |  | 1.70 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001877.4 |  |  |  |  |  |  | 1.59 | PKS | cyphomycin | Streptomyces sp. ISID311
BGC0001273.3 |  |  |  |  |  |  | 1.34 | PKS | asperlactone | Aspergillus ochraceus
BGC0001160.5 |  |  |  |  |  |  | 1.33 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  |  |  |  | 1.32 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001458.4 |  |  |  |  |  |  | 1.26 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0000850.5 |  |  |  |  |  |  | 1.21 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002191.2 |  |  |  |  |  |  | 1.18 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002192.3 |  |  |  |  |  |  | 1.10 | PKS | FR901512 | fungal sp. No.14919
BGC0000037.4 |  |  |  |  |  |  | 1.04 | PKS | cichorine | Aspergillus nidulans FGSC A4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001877.4 |  | 0.85 | PKS | cyphomycin | Streptomyces sp. ISID311
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.75 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  | 0.67 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.67 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000041.3 |  | 0.66 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001856.4 |  | 0.65 | PKS | caniferolide A, caniferolide B, caniferolide C, caniferolide D | Streptomyces caniferus
BGC0002276.2 |  | 0.64 | NRPS | choline | Aspergillus nidulans FGSC A4

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.81 out of 23.79
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.03 out of 36.53
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.16 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.35 out of 27.55
Confidence: medium
Additional weak hits (17):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.56 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.43 out of 26.85
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.91 out of 21.55
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.13 out of 29.51
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.83 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.70 out of 26.06
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.05 out of 19.26
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.85 out of 32.74
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.98 out of 35.63
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.39 out of 36.53
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.93 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.32 out of 26.12
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 248182 - 441764:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-ohmal - Me-ohmal) + (pk - Me-ohmal - ccmal) + (ccmal - redmal) + (ohmal - redmal - ohmal) + (ohmal - ohmal - mal - Me-ohmal - redmal) + (ohmal - redmal - ohmal) + (Me-ohmal - ccmal) + (AHBA - pk) + (Gln) + (Asn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 248182 - 291974:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Asn) + (Gln)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 272803 - 441764:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (AHBA - pk) + (Me-mal - Me-ohmal - Me-ohmal) + (pk - Me-ohmal - ccmal) + (ccmal - redmal) + (ohmal - redmal - ohmal) + (ohmal - ohmal - mal - Me-ohmal - redmal) + (ohmal - redmal - ohmal) + (Me-ohmal - ccmal)
Non-colinear ordering:
  CPH93_RS01215 + CPH93_RS01320 + CPH93_RS01315 + CPH93_RS01290 + CPH93_RS01285 + CPH93_RS36590 + CPH93_RS01265 + CPH93_RS01260

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).
CPH93_RS01065: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (415..819): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWATFDVSGTSLNLIVIGEVNEYGPTEATIGCTA
  Nearest Stachelhaus code(s):
    Asn DGTKIGEIGK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

CPH93_RS01125: Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (11..409): Gln
nrpys: Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    QWITFDAAQWEAQCFSGGEVNLYGPTECTINATA
  Nearest Stachelhaus code(s):
    Gln DAWQFGLINK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

CPH93_RS01215: AHBA - pk
CAL_domain (37..445): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 323.1
  shikimic_acid: 254.6
  Acetyl-CoA: 16.7
  NH2: 0.1
  fatty_acid: 0.0

PKS_AT (1182..1477): pk
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 83.3%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 204.4
  Methylmalonyl-CoA: 194.5
  Methoxymalonyl-CoA: 159.8
  2-Methylbutyryl-CoA: 138.1
  trans-1,2-CPDA: 127.2
  Propionyl-CoA: 110.8
  CHC-CoA: 105.9
  Malonyl-CoA: 86.8
  Benzoyl-CoA: 49.4
  Isobutyryl-CoA: 47.8
  3-Methylbutyryl-CoA: 37.2
  Acetyl-CoA: 34.1
  fatty_acid: 31.5
  inactive: 17.8

CPH93_RS01260: mmal - mal
PKS_AT (569..866): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 219.2
  Ethylmalonyl-CoA: 213.2
  Methoxymalonyl-CoA: 177.8
  2-Methylbutyryl-CoA: 165.6
  trans-1,2-CPDA: 141.7
  Propionyl-CoA: 123.8
  Malonyl-CoA: 109.6
  CHC-CoA: 100.0
  Isobutyryl-CoA: 81.5
  Benzoyl-CoA: 68.7
  Acetyl-CoA: 58.0
  3-Methylbutyryl-CoA: 39.9
  fatty_acid: 33.3
  inactive: 31.4

PKS_AT (2116..2410): 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: 235.5
  inactive: 129.6
  Methoxymalonyl-CoA: 63.2
  Methylmalonyl-CoA: 55.8
  Propionyl-CoA: 39.8
  Isobutyryl-CoA: 33.0
  Ethylmalonyl-CoA: 27.6
  Benzoyl-CoA: 26.3
  Acetyl-CoA: 26.3
  CHC-CoA: 16.2
  2-Methylbutyryl-CoA: 14.9
  fatty_acid: 13.1
  trans-1,2-CPDA: 8.8
  3-Methylbutyryl-CoA: 0.0

CPH93_RS01265: mal - mal - mal
PKS_AT (564..862): 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: 224.5
  inactive: 114.6
  Methoxymalonyl-CoA: 55.0
  Methylmalonyl-CoA: 44.1
  Propionyl-CoA: 30.5
  Isobutyryl-CoA: 28.3
  Acetyl-CoA: 24.3
  Benzoyl-CoA: 18.4
  Ethylmalonyl-CoA: 12.0
  CHC-CoA: 11.2
  fatty_acid: 7.6
  2-Methylbutyryl-CoA: 6.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2036..2333): 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: 231.1
  inactive: 117.3
  Methoxymalonyl-CoA: 59.2
  Methylmalonyl-CoA: 51.5
  Propionyl-CoA: 31.7
  Isobutyryl-CoA: 27.1
  Ethylmalonyl-CoA: 25.2
  Acetyl-CoA: 24.8
  Benzoyl-CoA: 23.1
  CHC-CoA: 13.8
  fatty_acid: 12.5
  2-Methylbutyryl-CoA: 12.1
  trans-1,2-CPDA: 9.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4159..4460): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.7
  inactive: 99.8
  Methoxymalonyl-CoA: 64.5
  Methylmalonyl-CoA: 40.9
  Isobutyryl-CoA: 33.3
  Propionyl-CoA: 32.6
  Benzoyl-CoA: 24.6
  Ethylmalonyl-CoA: 22.4
  Acetyl-CoA: 20.7
  2-Methylbutyryl-CoA: 14.7
  fatty_acid: 12.6
  CHC-CoA: 4.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

CPH93_RS36590: mal - mal - mal - mmal - mal
PKS_AT (572..868): 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: 225.7
  inactive: 118.6
  Methoxymalonyl-CoA: 58.0
  Methylmalonyl-CoA: 48.0
  Propionyl-CoA: 31.4
  Isobutyryl-CoA: 29.4
  Acetyl-CoA: 22.3
  Benzoyl-CoA: 21.4
  Ethylmalonyl-CoA: 21.1
  2-Methylbutyryl-CoA: 11.4
  CHC-CoA: 10.3
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2095..2386): 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: 228.4
  inactive: 115.0
  Methoxymalonyl-CoA: 58.9
  Methylmalonyl-CoA: 47.3
  Propionyl-CoA: 39.1
  Isobutyryl-CoA: 23.6
  Acetyl-CoA: 21.1
  Benzoyl-CoA: 17.7
  Ethylmalonyl-CoA: 15.1
  CHC-CoA: 12.4
  2-Methylbutyryl-CoA: 10.8
  fatty_acid: 9.9
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3554..3850): 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: 235.0
  inactive: 128.3
  Methoxymalonyl-CoA: 62.8
  Methylmalonyl-CoA: 55.5
  Propionyl-CoA: 39.3
  Isobutyryl-CoA: 31.9
  Benzoyl-CoA: 25.3
  Acetyl-CoA: 24.4
  Ethylmalonyl-CoA: 20.3
  CHC-CoA: 16.2
  2-Methylbutyryl-CoA: 13.1
  fatty_acid: 11.6
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5262..5559): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 95.8%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 217.1
  Ethylmalonyl-CoA: 209.0
  2-Methylbutyryl-CoA: 174.1
  Methoxymalonyl-CoA: 174.0
  trans-1,2-CPDA: 150.3
  Propionyl-CoA: 120.0
  CHC-CoA: 99.7
  Malonyl-CoA: 92.8
  Isobutyryl-CoA: 77.3
  Benzoyl-CoA: 55.7
  Acetyl-CoA: 50.4
  3-Methylbutyryl-CoA: 37.2
  fatty_acid: 29.3
  inactive: 20.1

PKS_AT (6834..7137): 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: 236.0
  inactive: 130.8
  Methoxymalonyl-CoA: 66.5
  Methylmalonyl-CoA: 57.9
  Isobutyryl-CoA: 37.6
  Propionyl-CoA: 36.0
  Benzoyl-CoA: 24.6
  Acetyl-CoA: 22.2
  Ethylmalonyl-CoA: 20.7
  CHC-CoA: 15.9
  2-Methylbutyryl-CoA: 14.6
  fatty_acid: 13.2
  trans-1,2-CPDA: 9.1
  3-Methylbutyryl-CoA: 0.0

CPH93_RS01285: mal - mal - mal
PKS_AT (577..871): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.0
  inactive: 113.9
  Methoxymalonyl-CoA: 69.3
  Methylmalonyl-CoA: 58.5
  Propionyl-CoA: 35.6
  Isobutyryl-CoA: 23.4
  Acetyl-CoA: 23.0
  Benzoyl-CoA: 17.5
  fatty_acid: 14.5
  Ethylmalonyl-CoA: 13.8
  CHC-CoA: 12.8
  2-Methylbutyryl-CoA: 10.4
  trans-1,2-CPDA: 8.3
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2121..2418): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 229.6
  inactive: 124.1
  Methoxymalonyl-CoA: 67.3
  Methylmalonyl-CoA: 59.2
  Propionyl-CoA: 40.7
  Ethylmalonyl-CoA: 28.8
  Acetyl-CoA: 28.1
  Isobutyryl-CoA: 27.6
  Benzoyl-CoA: 23.3
  CHC-CoA: 18.5
  fatty_acid: 15.1
  2-Methylbutyryl-CoA: 12.6
  trans-1,2-CPDA: 9.5
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4191..4485): 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: 238.2
  inactive: 120.5
  Methoxymalonyl-CoA: 60.8
  Methylmalonyl-CoA: 51.8
  Propionyl-CoA: 30.2
  Isobutyryl-CoA: 24.3
  Acetyl-CoA: 22.2
  Benzoyl-CoA: 17.3
  Ethylmalonyl-CoA: 15.6
  CHC-CoA: 11.6
  2-Methylbutyryl-CoA: 8.8
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

CPH93_RS01290: mal - mal
PKS_AT (585..881): 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: 215.6
  inactive: 108.8
  Methoxymalonyl-CoA: 64.7
  Methylmalonyl-CoA: 59.6
  Propionyl-CoA: 37.3
  2-Methylbutyryl-CoA: 31.5
  Isobutyryl-CoA: 30.1
  Ethylmalonyl-CoA: 29.3
  Benzoyl-CoA: 26.6
  Acetyl-CoA: 21.4
  fatty_acid: 17.3
  CHC-CoA: 16.9
  trans-1,2-CPDA: 14.5
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2356..2649): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 215.0
  inactive: 113.5
  Methoxymalonyl-CoA: 63.2
  Methylmalonyl-CoA: 43.1
  Propionyl-CoA: 35.3
  Isobutyryl-CoA: 22.7
  Acetyl-CoA: 20.7
  Ethylmalonyl-CoA: 11.1
  Benzoyl-CoA: 8.7
  2-Methylbutyryl-CoA: 7.4
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CPH93_RS01315: pk - mmal - mal
PKS_AT (574..870): 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: 233.4
  Methylmalonyl-CoA: 233.2
  Methoxymalonyl-CoA: 189.8
  2-Methylbutyryl-CoA: 164.7
  trans-1,2-CPDA: 154.9
  CHC-CoA: 123.2
  Propionyl-CoA: 118.1
  Malonyl-CoA: 112.5
  Isobutyryl-CoA: 82.8
  Benzoyl-CoA: 73.7
  Acetyl-CoA: 53.2
  3-Methylbutyryl-CoA: 44.0
  fatty_acid: 34.8
  inactive: 27.8

PKS_AT (2126..2423): 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: 231.5
  Ethylmalonyl-CoA: 231.0
  Methoxymalonyl-CoA: 187.0
  2-Methylbutyryl-CoA: 162.6
  trans-1,2-CPDA: 157.5
  CHC-CoA: 120.8
  Propionyl-CoA: 115.9
  Malonyl-CoA: 109.2
  Isobutyryl-CoA: 85.6
  Benzoyl-CoA: 73.5
  Acetyl-CoA: 52.8
  3-Methylbutyryl-CoA: 44.1
  fatty_acid: 34.4
  inactive: 26.9

PKS_AT (3670..3964): 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: 233.0
  inactive: 118.8
  Methoxymalonyl-CoA: 66.8
  Methylmalonyl-CoA: 55.7
  Propionyl-CoA: 38.0
  2-Methylbutyryl-CoA: 26.2
  Isobutyryl-CoA: 23.0
  Ethylmalonyl-CoA: 22.5
  Acetyl-CoA: 19.0
  fatty_acid: 18.4
  Benzoyl-CoA: 15.9
  CHC-CoA: 9.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

CPH93_RS01320: mmal - mmal - mmal
PKS_AT (551..848): 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: 218.4
  Ethylmalonyl-CoA: 215.7
  Methoxymalonyl-CoA: 172.2
  2-Methylbutyryl-CoA: 159.4
  trans-1,2-CPDA: 134.9
  Propionyl-CoA: 117.2
  CHC-CoA: 111.5
  Malonyl-CoA: 107.7
  Isobutyryl-CoA: 64.7
  Benzoyl-CoA: 55.2
  Acetyl-CoA: 51.2
  fatty_acid: 24.4
  inactive: 23.8
  3-Methylbutyryl-CoA: 15.4

PKS_AT (1577..1874): 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: 229.2
  Ethylmalonyl-CoA: 225.3
  Methoxymalonyl-CoA: 185.5
  2-Methylbutyryl-CoA: 158.9
  trans-1,2-CPDA: 146.6
  CHC-CoA: 119.2
  Malonyl-CoA: 111.3
  Propionyl-CoA: 110.1
  Isobutyryl-CoA: 78.7
  Benzoyl-CoA: 70.2
  Acetyl-CoA: 55.9
  3-Methylbutyryl-CoA: 30.5
  fatty_acid: 29.4
  inactive: 27.1

PKS_AT (3156..3453): 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: 231.3
  Ethylmalonyl-CoA: 230.0
  Methoxymalonyl-CoA: 185.5
  2-Methylbutyryl-CoA: 163.7
  trans-1,2-CPDA: 138.8
  CHC-CoA: 121.3
  Malonyl-CoA: 113.3
  Propionyl-CoA: 113.1
  Isobutyryl-CoA: 81.7
  Benzoyl-CoA: 68.1
  Acetyl-CoA: 57.6
  fatty_acid: 38.2
  3-Methylbutyryl-CoA: 31.0
  inactive: 24.0

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
DmdR1 | Iron(II)-dependent repressor
GnfM | Regulator of nitrogen-fixation genes
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_LT907981.1 - 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: 502,303 - 527,185 nt. (total: 24,883 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
CPH93_RS01675: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

CPH93_RS01735: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: esterase
CPH93_RS01755: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: synthase
CPH93_RS01740: 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002725.3 |  | 0.74 | ribosomal | prunipeptin | Streptomyces prunicolor NBRC 13075
BGC0000664.5 |  | 0.67 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.62 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.58 | terpene | carotenoid | Streptomyces avermitilis
BGC0001456.3 |  | 0.58 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001227.3 |  | 0.58 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000650.3 |  | 0.48 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000645.3 |  | 0.48 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.47 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002725.3 |  | 0.74 | ribosomal | prunipeptin | Streptomyces prunicolor NBRC 13075
BGC0000664.5 |  | 0.67 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.62 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.58 | terpene | carotenoid | Streptomyces avermitilis
BGC0001456.3 |  | 0.58 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001227.3 |  | 0.58 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000650.3 |  | 0.48 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000645.3 |  | 0.48 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.47 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium

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

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:
CPH93_RS01715: Lycopene_cycl
Domain 1 (5 - 382): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

CPH93_RS01730: PT_phytoene_like
Domain 1 (16 - 315): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.13 out of 18.57
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (13):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.18 out of 27.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.68 out of 20.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.83 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.45 out of 26.06
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.63 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.12 out of 30.98
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 25.23 out of 32.38
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 26.30 out of 32.93
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.07 out of 32.38
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
--- | ---
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_LT907981.1 - Region 4 - NRPS,NRPS-like,other
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 538,417 - 596,077 nt. (total: 57,661 nt) Show pHMM detection rules used
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CPH93_RS01975: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS01990: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS02020: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: acetyltransferase acyltransferase glycosyltransferase methyltransferase
CPH93_RS01835: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

CPH93_RS01840: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

CPH93_RS01845: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

CPH93_RS01925: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CPH93_RS01965: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Lyases: dehydratase
CPH93_RS01825: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

CPH93_RS01830: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
CPH93_RS01945: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CPH93_RS01950: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CPH93_RS01955: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CPH93_RS01960: 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 | other | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002051.2 |  |  |  | 1.75 | NRPS | antipain | Streptomyces sp.
BGC0001249.5 |  |  |  | 1.25 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  |  |  | 1.14 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  |  |  | 1.10 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000342.4 |  |  |  | 1.09 | NRPS | enniatin | Fusarium equiseti
BGC0001570.5 |  |  |  | 1.07 | NRPS | deimino-antipain | Streptomyces albulus
BGC0002135.2 |  |  |  | 1.05 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002164.2 |  |  |  | 1.01 | NRPS | peramine | Epichloe festucae
BGC0002286.3 |  |  |  | 1.00 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  |  | 1.00 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002051.2 |  | 0.83 | NRPS | antipain | Streptomyces sp.
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001570.5 |  | 0.69 | NRPS | deimino-antipain | Streptomyces albulus
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002164.2 |  | 0.67 | NRPS | peramine | Epichloe festucae
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.66 | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.00 out of 20.47
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.66 out of 30.12
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
Additional weak hits (19):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.04 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.40 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.07 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.82 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.06 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.94 out of 27.04
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.32 out of 27.04
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.91 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.85 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.27 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.99 out of 39.62
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.21 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.19 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.91 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 7, location 538416 - 596077:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 549054 - 592243:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 554160 - 596077:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CPH93_RS01950: Arg
Search NORINE for peptide: strict or relaxed
AMP-binding (468..857): Arg
nrpys: Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HGAAFDVALEEPNLVLGGELNVYGVTEAAISSTV
  Nearest Stachelhaus code(s):
    Arg DVENVGVISK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

CPH93_RS01955: Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (39..444): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MWYIFDPHLMEAVAMVGGDHNAYGPAEATVASTV
  Nearest Stachelhaus code(s):
    Phe DPLVMGAVIK (82% 8Å match)
  Stachelhaus code match:
    80% (moderate)

CPH93_RS01960: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (53..442): 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:
    LDPSFDASTFEGFFIVGGEVNGYGPTEAATFTTA
  Nearest Stachelhaus code(s):
    Val DAFFIGGTFK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_LT907981.1 - Region 5 - 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: 665,690 - 676,670 nt. (total: 10,981 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
Oxidoreductases: dehydrogenase
CPH93_RS02375: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

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 |  | 0.79 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.65 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000908.3 |  | 0.41 | other (other) | melanin | Streptomyces avermitilis
BGC0002313.3 |  | 0.39 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0001928.2 |  | 0.36 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001906.2 |  | 0.34 | PKS | 2-acetyl-1,3,6,8-tetrahydroxynaphthalene, 1,3,6,8-tetrahydroxynaphthalene | Daldinia eschscholzii IFB-TL01
BGC0002462.3 |  | 0.31 | saccharide | coformycin | Streptomyces kaniharaensis
BGC0002719.2 |  | 0.30 | NRPS | thanafactin A | Pseudomonas fluorescens
BGC0000384.6 |  | 0.30 | NRPS | lyngbyatoxin | Lyngbya majuscula

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.79 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.65 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000908.3 |  | 0.41 | other (other) | melanin | Streptomyces avermitilis
BGC0002313.3 |  | 0.39 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0001928.2 |  | 0.36 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001906.2 |  | 0.34 | PKS | 2-acetyl-1,3,6,8-tetrahydroxynaphthalene, 1,3,6,8-tetrahydroxynaphthalene | Daldinia eschscholzii IFB-TL01
BGC0002462.3 |  | 0.31 | saccharide | coformycin | Streptomyces kaniharaensis
BGC0002719.2 |  | 0.30 | NRPS | thanafactin A | Pseudomonas fluorescens
BGC0000384.6 |  | 0.30 | NRPS | lyngbyatoxin | Lyngbya majuscula

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.36 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.67 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.30 out of 26.06
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LT907981.1 - Region 6 - 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: 723,328 - 828,632 nt. (total: 105,305 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))
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CPH93_RS02675: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS02730: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acetyltransferase acylase glycosyltransferase transferase
CPH93_RS02670: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

CPH93_RS02700: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CPH93_RS02715: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CPH93_RS02740: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CPH93_RS02820: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

CPH93_RS02865: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

Hydrolases: esterase hydrolase
CPH93_RS02725: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CPH93_RS02810: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: decarboxylase
CPH93_RS02760: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
CPH93_RS02705: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS02710: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS02720: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS02750: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CPH93_RS02755: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CPH93_RS02780: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CPH93_RS37190: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: permease
CPH93_RS02830: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | T1PKS | t3nrps-iterative | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.85 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  | 0.85 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  |  | 0.85 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  | 0.83 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002154.2 |  |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000107.3 |  |  | 0.59 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  | 0.64 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4

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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 18.25 out of 18.46
Confidence: strong
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.59 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (8):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.69 out of 36.54
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.26 out of 32.93
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.09 out of 29.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.06 out of 29.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.79 out of 30.22
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.67 out of 32.74
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 12, location 723327 - 828632:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - ccmal) + (pk - ccmal) + (ccmal) + (ohmal) + (ccmal - ccmal - ccmal) + (mal)
Non-colinear ordering:
  CPH93_RS37190 + CPH93_RS02780 + CPH93_RS02720 + CPH93_RS02715 + CPH93_RS02710 + CPH93_RS02705

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).
CPH93_RS02705: mal
PKS_AT (610..935): 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: 210.0
  inactive: 110.2
  Methoxymalonyl-CoA: 62.1
  Methylmalonyl-CoA: 54.2
  Propionyl-CoA: 46.1
  Isobutyryl-CoA: 24.8
  2-Methylbutyryl-CoA: 20.8
  Acetyl-CoA: 15.5
  CHC-CoA: 14.1
  Benzoyl-CoA: 12.5
  fatty_acid: 12.2
  trans-1,2-CPDA: 9.9
  Ethylmalonyl-CoA: 9.0
  3-Methylbutyryl-CoA: 8.4

CPH93_RS02710: mal - mal - mal
PKS_AT (574..874): 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: 219.2
  inactive: 119.1
  Methoxymalonyl-CoA: 58.7
  Methylmalonyl-CoA: 54.9
  Propionyl-CoA: 47.3
  2-Methylbutyryl-CoA: 20.2
  Isobutyryl-CoA: 18.3
  Acetyl-CoA: 15.3
  fatty_acid: 12.3
  CHC-CoA: 11.4
  Benzoyl-CoA: 11.4
  Ethylmalonyl-CoA: 6.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2331..2648): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 227.1
  inactive: 109.7
  Methoxymalonyl-CoA: 70.4
  Methylmalonyl-CoA: 66.3
  Propionyl-CoA: 42.0
  Isobutyryl-CoA: 28.3
  2-Methylbutyryl-CoA: 23.4
  CHC-CoA: 20.1
  Benzoyl-CoA: 20.0
  Ethylmalonyl-CoA: 19.9
  Acetyl-CoA: 18.8
  trans-1,2-CPDA: 14.8
  fatty_acid: 13.6
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4129..4428): 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: 204.3
  inactive: 115.7
  Methoxymalonyl-CoA: 57.8
  Methylmalonyl-CoA: 49.7
  Propionyl-CoA: 42.1
  Isobutyryl-CoA: 18.3
  Acetyl-CoA: 15.1
  Benzoyl-CoA: 13.3
  2-Methylbutyryl-CoA: 12.4
  CHC-CoA: 9.1
  fatty_acid: 7.7
  Ethylmalonyl-CoA: 5.5
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

CPH93_RS02715: mal
PKS_AT (586..897): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 223.6
  inactive: 96.9
  Methoxymalonyl-CoA: 66.4
  Methylmalonyl-CoA: 56.8
  Propionyl-CoA: 33.8
  Ethylmalonyl-CoA: 31.1
  Isobutyryl-CoA: 27.5
  Benzoyl-CoA: 21.0
  2-Methylbutyryl-CoA: 18.6
  Acetyl-CoA: 15.0
  CHC-CoA: 14.7
  fatty_acid: 11.9
  trans-1,2-CPDA: 7.9
  3-Methylbutyryl-CoA: 0.0

CPH93_RS02720: mal
PKS_AT (563..862): 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: 219.4
  inactive: 125.2
  Methoxymalonyl-CoA: 60.1
  Methylmalonyl-CoA: 52.6
  Propionyl-CoA: 45.2
  Isobutyryl-CoA: 21.5
  2-Methylbutyryl-CoA: 20.4
  Acetyl-CoA: 15.0
  CHC-CoA: 12.0
  fatty_acid: 11.7
  Benzoyl-CoA: 10.7
  trans-1,2-CPDA: 4.8
  Ethylmalonyl-CoA: 4.1
  3-Methylbutyryl-CoA: 0.0

CPH93_RS02740: pk
PKS_AT (38..280): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

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

CPH93_RS02750: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (18..435): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YLQFFDCAMFDCFAFFAGEENLYGPTELTITIAA
  Nearest Stachelhaus code(s):
    Ala DCFFFALITK (91% 8Å match)
    bMe-Asp DCFFFALITK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

CPH93_RS02755: X
AMP-binding (14..412): 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:
    ASMFWDYGLYKMPITNTGAVRQFGQTECKRVSIM
  Nearest Stachelhaus code(s):
    3S-Abu DYYPTTQRIK (79% 8Å match)
    Asp DYYPTTMRVK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

CPH93_RS37190: mal - mal
PKS_AT (687..986): 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: 219.6
  inactive: 124.5
  Methoxymalonyl-CoA: 63.0
  Methylmalonyl-CoA: 53.4
  Propionyl-CoA: 44.1
  Isobutyryl-CoA: 23.8
  2-Methylbutyryl-CoA: 18.2
  Acetyl-CoA: 14.9
  CHC-CoA: 13.1
  Benzoyl-CoA: 12.0
  Ethylmalonyl-CoA: 9.6
  fatty_acid: 8.3
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2450..2750): 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: 215.3
  inactive: 119.6
  Methoxymalonyl-CoA: 58.1
  Methylmalonyl-CoA: 54.8
  Propionyl-CoA: 42.0
  2-Methylbutyryl-CoA: 25.2
  Isobutyryl-CoA: 24.8
  Acetyl-CoA: 15.1
  Benzoyl-CoA: 13.7
  fatty_acid: 12.6
  CHC-CoA: 9.4
  trans-1,2-CPDA: 6.1
  Ethylmalonyl-CoA: 3.5
  3-Methylbutyryl-CoA: 0.0

CPH93_RS02780: pk - mal
PKS_AT (577..875): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 232.0
  Methylmalonyl-CoA: 225.3
  Methoxymalonyl-CoA: 189.5
  2-Methylbutyryl-CoA: 169.4
  trans-1,2-CPDA: 151.7
  Propionyl-CoA: 118.7
  CHC-CoA: 116.5
  Malonyl-CoA: 108.4
  Isobutyryl-CoA: 85.6
  Benzoyl-CoA: 67.6
  Acetyl-CoA: 53.4
  3-Methylbutyryl-CoA: 51.0
  fatty_acid: 35.1
  inactive: 33.8

PKS_AT (2361..2661): 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: 215.8
  inactive: 117.3
  Methoxymalonyl-CoA: 57.3
  Methylmalonyl-CoA: 54.3
  Propionyl-CoA: 44.9
  2-Methylbutyryl-CoA: 28.4
  Isobutyryl-CoA: 20.2
  fatty_acid: 12.8
  Acetyl-CoA: 12.8
  Benzoyl-CoA: 12.7
  CHC-CoA: 9.5
  trans-1,2-CPDA: 8.5
  3-Methylbutyryl-CoA: 6.3
  Ethylmalonyl-CoA: 3.2

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
RpoN | Regulator of nitrogen assimilation and virulence
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_LT907981.1 - Region 7 - 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: 957,922 - 968,842 nt. (total: 10,921 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
CPH93_RS03510: 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 |  | 0.76 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.54 | 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 |  | 0.33 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0002571.2 |  | 0.31 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0000874.5 |  | 0.30 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0002657.2 |  | 0.26 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0001771.4 |  | 0.25 | NRPS | scleric acid | Streptomyces sclerotialus
BGC0001967.4 |  | 0.25 | NRPS, PKS | acyldepsipeptide 1 | Streptomyces hawaiiensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.76 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.54 | 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 |  | 0.33 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0002571.2 |  | 0.31 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0000874.5 |  | 0.30 | other (other) | blasticidin S | Streptomyces griseochromogenes
BGC0002657.2 |  | 0.26 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0001771.4 |  | 0.25 | NRPS | scleric acid | Streptomyces sclerotialus
BGC0001967.4 |  | 0.25 | NRPS, PKS | acyldepsipeptide 1 | Streptomyces hawaiiensis

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 (4):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.99 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.74 out of 29.65
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.18 out of 25.75
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LT907981.1 - Region 8 - 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: 1,060,809 - 1,101,993 nt. (total: 41,185 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
CPH93_RS04015: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

Hydrolases: glucosidase
CPH93_RS04195: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Ligases: synthase
CPH93_RS04110: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.89 | other (other) | germicidin | Streptomyces argillaceus
BGC0001810.3 |  | 0.45 | PKS | trehangelin | Polymorphospora rubra
BGC0000484.5 |  | 0.43 | ribosomal | glycocin F | Lactobacillus plantarum
BGC0001483.4 |  | 0.42 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0001387.5 |  | 0.42 | other (other) | nucleocidin | Streptomyces calvus
BGC0000501.3 |  | 0.42 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0001197.5 |  | 0.41 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000519.4 |  | 0.41 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.89 | other (other) | germicidin | Streptomyces argillaceus
BGC0001810.3 |  | 0.45 | PKS | trehangelin | Polymorphospora rubra
BGC0000484.5 |  | 0.43 | ribosomal | glycocin F | Lactobacillus plantarum
BGC0001483.4 |  | 0.42 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0001387.5 |  | 0.42 | other (other) | nucleocidin | Streptomyces calvus
BGC0000501.3 |  | 0.42 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0001197.5 |  | 0.41 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000519.4 |  | 0.41 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.80 out of 23.79
Confidence: medium
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 (13):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.77 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.64 out of 27.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.32 out of 29.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.75 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.80 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.23 out of 36.54
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.81 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.98 out of 21.55
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.42 out of 29.65
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator

NZ_LT907981.1 - Region 9 - T1PKS,hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,132,520 - 1,184,439 nt. (total: 51,920 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
hglE-KS: (hglE or hglD)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
CPH93_RS04435: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CPH93_RS04440: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CPH93_RS04445: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: glycosyltransferase halogenase kinase
CPH93_RS04320: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

CPH93_RS04380: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CPH93_RS04405: halogenase

smcogs
  SMCOG1119: halogenase

Hydrolases: hydrolase
CPH93_RS04385: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: synthase
CPH93_RS04395: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS04400: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001244.3 |  |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001273.3 |  |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.57 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  |  | 0.56 | PKS | FR901512 | fungal sp. No.14919
BGC0001284.4 |  |  | 0.56 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0000041.3 |  |  | 0.54 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000056.3 |  |  | 0.36 | PKS | esperamicin | Actinomadura verrucosospora

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001244.3 |  | 0.65 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001273.3 |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0000041.3 |  | 0.61 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000056.3 |  | 0.50 | PKS | esperamicin | Actinomadura verrucosospora

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.57 out of 25.31
Confidence: medium
Additional weak hits (13):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.60 out of 30.22
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 12.92 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.15 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.55 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.74 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.96 out of 32.74
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.61 out of 29.65
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.71 out of 29.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.52 out of 36.53
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.50 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 15, location 1132519 - 1184439:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal)
Non-colinear ordering:
  CPH93_RS04395 + CPH93_RS04390

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).
CPH93_RS04395: mal
PKS_AT (644..856): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 7.9
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

CPH93_RS04400: mal
PKS_AT (1291..1580): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 85.3
  Methoxymalonyl-CoA: 42.0
  Propionyl-CoA: 36.0
  Methylmalonyl-CoA: 35.1
  Ethylmalonyl-CoA: 19.8
  trans-1,2-CPDA: 16.3
  inactive: 13.5
  2-Methylbutyryl-CoA: 11.6
  fatty_acid: 7.2
  CHC-CoA: 3.1
  Isobutyryl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

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

NZ_LT907981.1 - Region 10 - 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: 1,270,946 - 1,297,648 nt. (total: 26,703 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
CPH93_RS04960: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase
CPH93_RS04895: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

CPH93_RS04965: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Ligases: synthase synthetase
CPH93_RS04900: 1-deoxy-D-xylulose-5-phosphate synthase

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

CPH93_RS04920: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.71 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0001361.3 |  | 0.50 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.50 | terpene | sodorifen | Serratia plymuthica
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002736.2 |  | 0.49 | terpene | preaspterpenacid I | Aspergillus terreus NIH2624
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.71 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0001361.3 |  | 0.50 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.50 | terpene | sodorifen | Serratia plymuthica
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002736.2 |  | 0.49 | terpene | preaspterpenacid I | Aspergillus terreus NIH2624
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

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

No significant matches found.

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

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

Genes with terpene domains:
CPH93_RS04915: T2TS
Domain 1 (29 - 662): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

CPH93_RS04920: PT_FPPS_like
Domain 1 (58 - 352): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

CPH93_RS04930: PT_phytoene_like
Domain 1 (17 - 300): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

CPH93_RS04935: PT_phytoene_like
Domain 1 (6 - 286): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (8):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.42 out of 27.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.55 out of 26.12
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.98 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.82 out of 36.54
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LT907981.1 - Region 11 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,579,898 - 1,611,251 nt. (total: 31,354 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase
CPH93_RS06215: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

CPH93_RS06315: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

Lyases: decarboxylase
CPH93_RS06280: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.62 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002527.2 |  | 0.60 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001408.5 |  | 0.60 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0000947.5 |  | 0.51 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000944.5 |  | 0.51 | other (non-nrp siderophore) | staphyloferrin A | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000942.4 |  | 0.47 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001972.4 |  | 0.44 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis
BGC0000943.5 |  | 0.43 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002471.3 |  | 0.43 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0001701.4 |  | 0.38 | ribosomal | nisin O | Blautia obeum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.62 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002527.2 |  | 0.60 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001408.5 |  | 0.60 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0000947.5 |  | 0.51 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000944.5 |  | 0.51 | other (non-nrp siderophore) | staphyloferrin A | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0000942.4 |  | 0.47 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001972.4 |  | 0.44 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis
BGC0000943.5 |  | 0.43 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002471.3 |  | 0.43 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0001701.4 |  | 0.38 | ribosomal | nisin O | Blautia obeum

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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.48 out of 20.97
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.49 out of 25.31
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.93 out of 30.25
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.38 out of 23.79
Confidence: medium
Additional weak hits (10):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.09 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.33 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.95 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.12 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.96 out of 26.33
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.30 out of 36.53
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.55 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.81 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.06 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.98 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
CcpA | Catabolite control protein A
ColR | Phenol-responsive regulator
IolR | Regulator of the inositol catabolism

NZ_LT907981.1 - Region 12 - T2PKS,lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,656,398 - 1,728,931 nt. (total: 72,534 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lasso peptides
TFBS Finder
NRPS/PKS 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
CPH93_RS06535: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CPH93_RS06550: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CPH93_RS06670: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS06710: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS06730: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS06790: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS06800: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS06810: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CPH93_RS06825: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CPH93_RS06835: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

CPH93_RS06845: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS06860: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase halogenase methyltransferase
CPH93_RS06795: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CPH93_RS06805: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CPH93_RS06815: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CPH93_RS06830: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CPH93_RS06850: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
MITE
  MITE0000024Halogenation (identity: 70.70%)
smcogs
  SMCOG1119: halogenase

CPH93_RS06865: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CPH93_RS37225: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: back translocase glucosidase hydrolase
CPH93_RS06590: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

CPH93_RS06615: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

CPH93_RS06720: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

CPH93_RS06750: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: cyclase dehydratase
CPH93_RS06520: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

CPH93_RS06680: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

CPH93_RS06705: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

Ligases: synthase
CPH93_RS06690: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CPH93_RS06695: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
CPH93_RS06630: 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 | T2PKS | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000242.5 |  |  | 0.76 | PKS | lysolipin I | Streptomyces tendae
BGC0000234.5 |  |  | 0.61 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000231.5 |  |  | 0.60 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001197.5 |  |  | 0.56 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000275.4 |  |  | 0.55 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0001723.5 |  |  | 0.53 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001513.3 |  |  | 0.51 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000217.5 |  |  | 0.48 | PKS | daunorubicin | Streptomyces sp.
BGC0002608.2 |  |  | 0.47 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0000215.5 |  |  | 0.47 | PKS | curamycin | Streptomyces cyaneus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002608.2 |  | 0.77 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0000242.5 |  | 0.77 | PKS | lysolipin I | Streptomyces tendae
BGC0000234.5 |  | 0.64 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000231.5 |  | 0.64 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002285.2 |  | 0.62 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001197.5 |  | 0.61 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001513.3 |  | 0.58 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0001723.5 |  | 0.58 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001512.5 |  | 0.58 | PKS | BE-24566B | Streptomyces sp.

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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
Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lassopeptide(s) for CPH93_RS35700

CPH93_RS35700
Leader:
MEQTTKPVYSAPVVLDAGDVAEVTL
Full core:
G T N N F D T A D D T Q Y K N A
Putative macrolactam:
G T N N F D T A D

#### antiSMASH-DB 4.0 matches for CPH93_RS35700

100.0%
NZ_AP019620.1 and 8 others:
NZ_CP019458.1 Lassopeptides: BV401_RS42770_lassopeptide NZ_CP029823.1 Lassopeptides: DNK48_RS31710_lassopeptide NZ_CP054916.1 Lassopeptides: HUT19_RS28470_lassopeptide NZ_CP084681.1 Lassopeptides: KI385_RS02505_lassopeptide NZ_JANCLX010000011.1 Lassopeptides: NMK44_RS19060_lassopeptide NZ_LT907981.1 Lassopeptides: CPH93_RS35700_lassopeptide NZ_NNBP01000024.1 Lassopeptides: CG747_RS46950_lassopeptide NZ_VSKT01000018.1 Lassopeptides: allorf_84246_84536_lassopeptide
Lassopeptides: GYK45_RS31700_lassopeptide
1
G T N N F D T A D D T Q Y K N A
16
G T N N F D T A D D T Q Y K N A
1
G T N N F D T A D D T Q Y K N A
16
93.8%
NZ_CP045178.1 and 1 other:
NZ_NDXL01000001.1 Lassopeptides: B7024_RS40605_lassopeptide
Lassopeptides: GBW32_RS37240_lassopeptide
1
G T N N F D T A D D T Q Y K N A
16
G T N N F D T A D D T+Y K N A
1
G T N N F D T A D D T E Y K N A
16
93.8%
NZ_CP058556.1 and 1 other:
NZ_NDXL01000001.1 Lassopeptides: B7024_RS41330_lassopeptide
Lassopeptides: HXS80_RS05610_lassopeptide
1
G T N N F D T A D D T Q Y K N A
16
G T N F D T A D D T Q Y K N A
1
G T Q N F D T A D D T Q Y K N A
16
with 17 more sequence matches
Only the first 10 are displayed here.
93.8%
NZ_VEHK01000011.1:
Lassopeptides: FS984_RS26875_lassopeptide
1
G T N N F D T A D D T Q Y K N A
16
G T N F D T A D D T Q Y K N A
1
G T E N F D T A D D T Q Y K N A
16
87.5%
NZ_CP118575.1:
Lassopeptides: PV796_RS40100_lassopeptide
1
G T N N F D T A D D T Q Y K N A
16
G T N N F D A D D T+Y K N A
1
G T N N F D H A D D T E Y K N A
16
87.5%
NZ_LWLE01000015.1:
Lassopeptides: A6A29_RS44175_lassopeptide
1
G T N N F D T A D D T Q Y K N A
16
G T F D T A D D T Q Y K N A
1
G T Q T F D T A D D T Q Y K N A
16
87.5%
NZ_SMSN01000051.1:
Lassopeptides: E2C11_RS23985_lassopeptide
1
G T N N F D T A D D T Q Y K N A
16
G T N F D T A D D T+Y K N A
1
G T N T F D T A D D T E Y K N A
16
87.5%
NZ_VEHK01000001.1:
Lassopeptides: FS984_RS39240_lassopeptide
1
G T N N F D T A D D T Q Y K N A
16
G T N+F D T A D D T+Y K N A
1
G T N S F D T A D D T E Y K N A
16
81.2%
NZ_CP042266.1:
Lassopeptides: FQU76_RS10490_lassopeptide
1
G T N N F D T A D D T Q Y K N A
16
G T F D T A D D T+Y K N A
1
G T E T F D T A D D T E Y K N A
16
75.0%
NZ_CP031455.1:
Lassopeptides: allorf_0788132_0788335_lassopeptide
1
G T N N F D T A D D T Q Y K N
15
G T N F D T A D D T+Y K+
1
G T N T F D T A D D T E Y K D
15
75.0%
NZ_JABBGE010000005.1:
Lassopeptides: HHL19_RS16445_lassopeptide
1
G T N N F D T A D D T Q Y K N
15
G T +F D T A D D T Q Y K+
1
G T Q S F D T A D D T Q Y K H
15
68.8%
NZ_BMNG01000026.1 and 1 other:
NZ_LT907981.1 Lassopeptides: CPH93_RS35415_lassopeptide
Lassopeptides: IEY91_RS39205_lassopeptide
1
G T N N F D T A D D T Q Y K N
15
G T F D T A D D T+Y K+
1
G T Q P F D T A D D T E Y K H
15
64.7%
NZ_BMUT01000019.1 and 2 others:
NZ_JACHJF010000007.1 Lassopeptides: FHS36_RS14205_lassopeptide NZ_WPBY01000022.1 Lassopeptides: GO001_RS23565_lassopeptide
Lassopeptides: IE241_RS30965_lassopeptide
1
G T N N F D T A D D T Q Y K N A
16
G N F D T D D T Q Y K
1
G N Q N F D T V D D T Q Y K Q G
16

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
Additional weak hits (13):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.76 out of 32.74
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.26 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.90 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.75 out of 36.54
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.74 out of 30.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.04 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.99 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.90 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.99 out of 27.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.44 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.41 out of 35.63
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
Lasso peptides
RREFinder
Type II PKS
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

CPH93_RS35700 - Class II
  Cleavage pHMM score: 1.40
  RODEO score: 21
  Monoisotopic mass: 1755.7 Da
  Molecular weight: 1756.7 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (1686851...1715810)
CPH93_RS06755
  RRE type: Stand_Alone_Lasso_RRE
  Location: 2 - 83
  Score: 49.0

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:
  1656397 to 1728931
Starter unit(s):
  malonamyl-CoA (Score: 979.0; E-value: 0)
Malonyl elongations:
  11|12 (Score: 684.5; E-value: 9.1e-209)
Product class(es):
  pentangular polyphenol
Product molecular weight(s):
  malonamyl-CoA_11: 831 Da
  malonamyl-CoA_12: 873 Da

CPH93_RS06655
  OXY (Score: 22.6; E-value: 1.1e-07)
CPH93_RS06670
  KR C19 (Score: 420.9; E-value: 3.7e-129)
CPH93_RS06680
  CYC C9-C14 (Score: 230.2; E-value: 1.8e-71)
CPH93_RS06685
  ACP (Score: 97.9; E-value: 6.1e-31)
CPH93_RS06690
  CLF 11|12 (Score: 684.5; E-value: 9.1e-209)
CPH93_RS06695
  KS (Score: 746.4; E-value: 1.8e-227)
CPH93_RS06700
  CYC C5-C18 (Score: 216.2; E-value: 2.8e-67)
CPH93_RS06705
  CYC C4-C21/C2-C23|C2-C19 (Score: 174.8; E-value: 9.2e-55)
CPH93_RS06710
  KR (Score: 114.2; E-value: 1.9e-35)
CPH93_RS06720
  AMID (Score: 1024.2; E-value: 0.0)
  AMID CAM34350.1_Lysolipin_malonamyl-CoA (Score: 979.0; E-value: 0.0)
CPH93_RS06775
  OXY (Score: 45.6; E-value: 1.1e-14)
CPH93_RS06795
  MET C11O (Score: 492.0; E-value: 1.8e-150)
CPH93_RS06805
  MET C13O|C17O (Score: 482.2; E-value: 1.6e-147)
CPH93_RS06810
  OXY (Score: 327.6; E-value: 3.4e-100)
CPH93_RS06815
  MET C13O|C17O (Score: 475.5; E-value: 1.8e-145)
CPH93_RS06830
  MET C13O|C17O (Score: 440.9; E-value: 5.6e-135)
CPH93_RS06845
  KR C11 (Score: 431.0; E-value: 2.9e-132)
CPH93_RS06850
  HAL (Score: 666.4; E-value: 4.7e-203)
CPH93_RS06860
  KR (Score: 173.8; E-value: 1.2e-53)
CPH93_RS06865
  MET (Score: 69.5; E-value: 6.3e-22)
CPH93_RS37225
  GT (Score: 354.7; E-value: 1.9e-108)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LT907981.1 - Region 13 - 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: 1,809,529 - 1,820,906 nt. (total: 11,378 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
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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001267.3 |  | 0.29 | terpene | elymoclavine, Agroclavine I | Claviceps fusiformis
BGC0002387.2 |  | 0.27 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0002788.2 |  | 0.24 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0001377.5 |  | 0.24 | PKS | uncialamycin | Streptomyces uncialis
BGC0001060.5 |  | 0.22 | PKS | dynemicin A | Micromonospora chersina
BGC0000221.5 |  | 0.21 | PKS | erdacin | uncultured soil bacterium V167
BGC0001984.3 |  | 0.20 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0001293.5 |  | 0.20 | PKS | cyclizidine | Streptomyces sp. NCIB 11649
BGC0000241.5 |  | 0.19 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440
BGC0001693.3 |  | 0.18 | PKS | nenestatin | Micromonospora echinospora

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001267.3 |  | 0.29 | terpene | elymoclavine, Agroclavine I | Claviceps fusiformis
BGC0002387.2 |  | 0.27 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0002788.2 |  | 0.24 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0001377.5 |  | 0.24 | PKS | uncialamycin | Streptomyces uncialis
BGC0001060.5 |  | 0.22 | PKS | dynemicin A | Micromonospora chersina
BGC0000221.5 |  | 0.21 | PKS | erdacin | uncultured soil bacterium V167
BGC0001984.3 |  | 0.20 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0001293.5 |  | 0.20 | PKS | cyclizidine | Streptomyces sp. NCIB 11649
BGC0000241.5 |  | 0.19 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440
BGC0001693.3 |  | 0.18 | PKS | nenestatin | Micromonospora echinospora

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.77 out of 29.72
Confidence: medium
Additional weak hits (1):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.79 out of 30.97
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C

NZ_LT907981.1 - Region 14 - 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: 1,880,308 - 1,891,285 nt. (total: 10,978 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
Oxidoreductases: dehydrogenase oxygenase
CPH93_RS07500: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CPH93_RS07515: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Hydrolases: hydrolase
CPH93_RS07490: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: hydratase
CPH93_RS07520: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

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

Reference | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.77 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.68 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.63 | 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
BGC0001633.3 |  | 0.41 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001302.5 |  | 0.37 | other (other) | lomofungin | Streptomyces lomondensis
BGC0001726.4 |  | 0.36 | NRPS, PKS | pactamide A, pactamide B, pactamide C, pactamide D, pactamide E, pactamide F | Streptomyces pactum
BGC0000996.5 |  | 0.36 | NRPS, PKS | frontalamide B, frontalamide A | Streptomyces sp. SPB78
BGC0001304.3 |  | 0.36 | PKS | aflavarin | Aspergillus flavus NRRL3357
BGC0000999.4 |  | 0.36 | NRPS, PKS | heat-stable antifungal factor | Lysobacter enzymogenes

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.77 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.68 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.63 | 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
BGC0001633.3 |  | 0.41 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001302.5 |  | 0.37 | other (other) | lomofungin | Streptomyces lomondensis
BGC0001726.4 |  | 0.36 | NRPS, PKS | pactamide A, pactamide B, pactamide C, pactamide D, pactamide E, pactamide F | Streptomyces pactum
BGC0000996.5 |  | 0.36 | NRPS, PKS | frontalamide B, frontalamide A | Streptomyces sp. SPB78
BGC0001304.3 |  | 0.36 | PKS | aflavarin | Aspergillus flavus NRRL3357
BGC0000999.4 |  | 0.36 | NRPS, PKS | heat-stable antifungal factor | Lysobacter enzymogenes

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: 18.76 out of 23.05
Confidence: medium
Additional weak hits (3):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.97 out of 30.22
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.44 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LT907981.1 - Region 15 - HR-T2PKS,lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,891,724 - 1,933,922 nt. (total: 42,199 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)
HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-synt))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lasso peptides
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
CPH93_RS07615: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase aminotransferase carbamoyltransferase methyltransferase
CPH93_RS07535: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

CPH93_RS07655: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

CPH93_RS07690: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CPH93_RS07695: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: hydrolase
CPH93_RS07580: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Isomerases: isomerase
CPH93_RS07665: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
CPH93_RS07640: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS07660: 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 | lassopeptide | HR-T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001550.3 |  |  | 1.26 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001552.3 |  |  | 1.21 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001549.3 |  |  | 1.18 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001551.4 |  |  | 1.07 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001548.4 |  |  | 0.94 | ribosomal | citrulassin A | Streptomyces albulus
BGC0000575.5 |  |  | 0.56 | ribosomal | lariatin | Rhodococcus jostii
BGC0001889.2 |  |  | 0.54 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0001655.3 |  |  | 0.53 | ribosomal | LP2006 | Nocardiopsis alba DSM 43377
BGC0001506.5 |  |  | 0.51 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0001539.4 |  |  | 0.51 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001550.3 |  | 0.85 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001552.3 |  | 0.84 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001549.3 |  | 0.84 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001551.4 |  | 0.81 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001548.4 |  | 0.77 | ribosomal | citrulassin A | Streptomyces albulus
BGC0000575.5 |  | 0.61 | ribosomal | lariatin | Rhodococcus jostii
BGC0001889.2 |  | 0.61 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0001506.5 |  | 0.59 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0001539.4 |  | 0.59 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001781.4 |  | 0.59 | ribosomal | sphaericin | Planomonospora sphaerica

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (7):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.59 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.30 out of 31.73
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.22 out of 25.88
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.26 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.41 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
Lasso peptides
NRPS/PKS substrates
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
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).
CPH93_RS07660: X
AMP-binding (48..384): 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:
    ERYLWGL-VGGHLGMTAGGSQCYGMTETGMITMD
  Nearest Stachelhaus code(s):
    nohBza GLGLVGAIIK (56% 8Å match)
  Stachelhaus code match:
    60% (weak)

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (1891723...1914304)
CPH93_RS07585
  RRE type: Stand_Alone_Lasso_RRE
  Location: 1 - 83
  Score: 78.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LT907981.1 - Region 16 - crocagin
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: 1,939,493 - 1,967,807 nt. (total: 28,315 nt) Show pHMM detection rules used
crocagin: (PhyH and Carbam_trans_N)

#### 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: reductase
CPH93_RS07835: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: methyltransferase
CPH93_RS07815: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: ligase
CPH93_RS07875: 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 | crocagin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000820.5 |  | 0.48 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0001488.3 |  | 0.45 | other (other) | 4-formylaminooxyvinylglycine | Pseudomonas fluorescens WH6
BGC0002659.2 |  | 0.45 | ribosomal | TvgA-RiPP | Halomonas anticariensis FP35 = DSM 16096
BGC0000188.5 |  | 0.43 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0000662.5 |  | 0.42 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000719.5 |  | 0.41 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0001050.5 |  | 0.40 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0000720.3 |  | 0.40 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0002071.2 |  | 0.40 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000820.5 |  | 0.48 | other (other) | physostigmine | Streptomyces griseofuscus
BGC0001488.3 |  | 0.45 | other (other) | 4-formylaminooxyvinylglycine | Pseudomonas fluorescens WH6
BGC0002659.2 |  | 0.45 | ribosomal | TvgA-RiPP | Halomonas anticariensis FP35 = DSM 16096
BGC0000188.5 |  | 0.43 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0000662.5 |  | 0.42 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000719.5 |  | 0.41 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0001050.5 |  | 0.40 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0000720.3 |  | 0.40 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0002071.2 |  | 0.40 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 21.56 out of 23.79
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
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
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.45 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.17 out of 23.79
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.51 out of 24.78
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
Additional weak hits (6):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.21 out of 20.01
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.62 out of 18.57
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.70 out of 32.74
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.40 out of 26.12
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.47 out of 36.54
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.87 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
OsdR | Development and stress management regulator

NZ_LT907981.1 - Region 17 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,084,530 - 2,117,221 nt. (total: 32,692 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CPH93_RS08365: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
CPH93_RS08410: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
CPH93_RS08355: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.55 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.52 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002683.2 |  | 0.51 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002470.2 |  | 0.51 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002633.2 |  | 0.51 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0001531.5 |  | 0.51 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.55 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.52 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002683.2 |  | 0.51 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002470.2 |  | 0.51 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002633.2 |  | 0.51 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0001531.5 |  | 0.51 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii

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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.40 out of 20.97
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.70 out of 29.51
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.60 out of 27.18
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
Additional weak hits (9):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.68 out of 20.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.85 out of 28.19
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.42 out of 27.18
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
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 23.43
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.06 out of 29.25
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.18 out of 23.43
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
DosR | Hypoxia stress response regulator
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes

NZ_LT907981.1 - Region 18 - triceptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,651,679 - 2,673,238 nt. (total: 21,560 nt) Show pHMM detection rules used
triceptide: ((cds(PF04055 and (TIGR04085 or SPASM)) and triceptide_precursor) or triceptide_rSAM)

#### Legend:

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

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

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

Reference | triceptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002316.2 |  | 0.39 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000043.5 |  | 0.37 | PKS | curacin A | Moorea producens 19L
BGC0000515.4 |  | 0.33 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.32 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000556.5 |  | 0.32 | ribosomal | streptin | Streptococcus pyogenes
BGC0001789.3 |  | 0.31 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000536.3 |  | 0.31 | ribosomal | nisin Q | Lactococcus lactis
BGC0000535.4 |  | 0.31 | ribosomal | nisin A | Lactococcus lactis subsp. lactis
BGC0000559.4 |  | 0.31 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000537.3 |  | 0.31 | ribosomal | nisin U | Streptococcus uberis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002316.2 |  | 0.39 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000043.5 |  | 0.37 | PKS | curacin A | Moorea producens 19L
BGC0000515.4 |  | 0.33 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.32 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000556.5 |  | 0.32 | ribosomal | streptin | Streptococcus pyogenes
BGC0001789.3 |  | 0.31 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000536.3 |  | 0.31 | ribosomal | nisin Q | Lactococcus lactis
BGC0000535.4 |  | 0.31 | ribosomal | nisin A | Lactococcus lactis subsp. lactis
BGC0000559.4 |  | 0.31 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000537.3 |  | 0.31 | ribosomal | nisin U | Streptococcus uberis

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (5):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.13 out of 26.85
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.77 out of 35.63
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.13 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.17 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LT907981.1 - Region 19 - linaridin
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: 3,549,767 - 3,570,658 nt. (total: 20,892 nt) Show pHMM detection rules used
linaridin: (cypemycin or cypI)

#### 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
CPH93_RS14900: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
CPH93_RS14895: methyltransferase

smcogs
  SMCOG1248: methyltransferase

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

Reference | linaridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001188.3 |  | 0.62 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0002319.3 |  | 0.48 | ribosomal | salinipeptin A, salinipeptin B, salinipeptin C, salinipeptin D | Streptomyces sp.
BGC0001735.5 |  | 0.47 | other (other) | pentostatine, vidarabine | Streptomyces antibioticus
BGC0000582.4 |  | 0.47 | ribosomal | cypemycin | Streptomyces sp. OH-4156
BGC0000583.5 |  | 0.44 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0000571.3 |  | 0.42 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0002312.2 |  | 0.42 | ribosomal | ubonodin | Burkholderia ubonensis
BGC0001229.4 |  | 0.42 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001188.3 |  | 0.62 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0002319.3 |  | 0.48 | ribosomal | salinipeptin A, salinipeptin B, salinipeptin C, salinipeptin D | Streptomyces sp.
BGC0001735.5 |  | 0.47 | other (other) | pentostatine, vidarabine | Streptomyces antibioticus
BGC0000582.4 |  | 0.47 | ribosomal | cypemycin | Streptomyces sp. OH-4156
BGC0000583.5 |  | 0.44 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0000571.3 |  | 0.42 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0002312.2 |  | 0.42 | ribosomal | ubonodin | Burkholderia ubonensis
BGC0001229.4 |  | 0.42 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.37 out of 20.47
Confidence: strong
Additional weak hits (10):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.86 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.07 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.39 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.10 out of 23.43
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.33 out of 28.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LT907981.1 - Region 20 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,637,117 - 3,659,735 nt. (total: 22,619 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
CPH93_RS15335: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001539.4 |  | 0.52 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001634.3 |  | 0.48 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001645.3 |  | 0.48 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0002318.2 |  | 0.44 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000578.3 |  | 0.40 | ribosomal | SRO15-2005 | Streptomyces filamentosus NRRL 15998
BGC0000565.5 |  | 0.34 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0001707.5 |  | 0.30 | ribosomal | nosiheptide | Streptomyces sp.
BGC0000957.5 |  | 0.26 | NRPS, PKS | mycotrienin I | Streptomyces sp. XZQH13
BGC0000806.5 |  | 0.25 | saccharide | phosphonoglycans | Glycomyces sp. NRRL B-16210
BGC0000700.5 |  | 0.25 | saccharide | istamycin | Streptomyces tenjimariensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001539.4 |  | 0.52 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001634.3 |  | 0.48 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001645.3 |  | 0.48 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0002318.2 |  | 0.44 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000578.3 |  | 0.40 | ribosomal | SRO15-2005 | Streptomyces filamentosus NRRL 15998
BGC0000565.5 |  | 0.34 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0001707.5 |  | 0.30 | ribosomal | nosiheptide | Streptomyces sp.
BGC0000957.5 |  | 0.26 | NRPS, PKS | mycotrienin I | Streptomyces sp. XZQH13
BGC0000806.5 |  | 0.25 | saccharide | phosphonoglycans | Glycomyces sp. NRRL B-16210
BGC0000700.5 |  | 0.25 | saccharide | istamycin | Streptomyces tenjimariensis

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

No significant matches found.

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.21 out of 20.97
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.88 out of 20.97
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (5):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.31 out of 26.85
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.74 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.39 out of 21.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 out of 28.19
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (3637116...3659735)
CPH93_RS15330
  RRE type: Stand_Alone_Lasso_RRE
  Location: 2 - 83
  Score: 41.1

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
CcpA | Catabolite control protein A

NZ_LT907981.1 - Region 21 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,713,989 - 3,736,506 nt. (total: 22,518 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
CPH93_RS15665: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Translocases: permease
CPH93_RS15715: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002053.3 |  | 0.82 | ribosomal | ulleungdin | Streptomyces sp.
BGC0002074.2 |  | 0.81 | ribosomal | huascopeptin | Streptomyces huasconensis
BGC0001507.3 |  | 0.73 | ribosomal | anantin C | Streptomyces olindensis
BGC0001307.3 |  | 0.65 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0001493.5 |  | 0.62 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001506.5 |  | 0.62 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0001552.3 |  | 0.62 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002318.2 |  | 0.60 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0001539.4 |  | 0.60 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001548.4 |  | 0.60 | ribosomal | citrulassin A | Streptomyces albulus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002053.3 |  | 0.82 | ribosomal | ulleungdin | Streptomyces sp.
BGC0002074.2 |  | 0.81 | ribosomal | huascopeptin | Streptomyces huasconensis
BGC0001507.3 |  | 0.73 | ribosomal | anantin C | Streptomyces olindensis
BGC0001307.3 |  | 0.65 | ribosomal | chaxapeptin | Streptomyces leeuwenhoekii
BGC0001493.5 |  | 0.62 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001506.5 |  | 0.62 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0001552.3 |  | 0.62 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002318.2 |  | 0.60 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0001539.4 |  | 0.60 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001548.4 |  | 0.60 | ribosomal | citrulassin A | Streptomyces albulus

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

No significant matches found.

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

#### Lassopeptide(s) for CPH93_RS35425

CPH93_RS35425
Leader:
MTEQSEQTPTEYIPPMLVEVGEFTEDTL
Full core:
G N W H G T S P D W F F N Y Y W
Putative macrolactam:
G N W H G T S P D

#### antiSMASH-DB 4.0 matches for CPH93_RS35425

100.0%
NZ_CP072931.1 and 3 others:
NZ_CP082945.1 Lassopeptides: K7396_RS10945_lassopeptide NZ_CP104317.1 Lassopeptides: NW605_RS09530_lassopeptide NZ_LT907981.1 Lassopeptides: CPH93_RS35425_lassopeptide
Lassopeptides: SU9_RS18360_lassopeptide
1
G N W H G T S P D W F F N Y Y W
16
G N W H G T S P D W F F N Y Y W
1
G N W H G T S P D W F F N Y Y W
16
56.2%
NZ_FOAZ01000040.1 and 1 other:
NZ_JADPRT010000002.1 Lassopeptides: I2501_RS04910_lassopeptide
Lassopeptides: BMY61_RS45675_lassopeptide
5
G T S P D W F F N Y Y W
16
G T P D W F F N W
4
G T V P D W F F N M N W
15

#### MIBiG 4.0 matches for CPH93_RS35425

16.7%
BGC0002289.2 (CQR60041.1):
Lasso peptide: Leepeptin
9
D W F F N Y
14
+W F+Y
11
N W H F D Y
16

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (5):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.16 out of 20.97
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.05 out of 19.26
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.83 out of 26.06
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.08 out of 18.57
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

CPH93_RS35425 - Class II
  Cleavage pHMM score: 4.50
  RODEO score: 20
  Monoisotopic mass: 2057.8 Da
  Molecular weight: 2059.1 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (3713988...3736506)
CPH93_RS15670
  RRE type: Stand_Alone_Lasso_RRE
  Location: 0 - 81
  Score: 85.8
  RRE type: Lasso_Fused_RRE
  Location: 0 - 59
  Score: 29.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LT907981.1 - Region 22 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,743,167 - 3,765,410 nt. (total: 22,244 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: aminotransferase methyltransferase
CPH93_RS15825: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

CPH93_RS15830: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: amidase
CPH93_RS15780: amidase

smcogs
  SMCOG1105: amidase

Lyases: cyclase
CPH93_RS15800: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.83 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002382.3 |  | 0.42 | ribosomal | grimoviridin | Grimontia marina
BGC0000842.5 |  | 0.42 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0000905.5 |  | 0.40 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000906.3 |  | 0.40 | other (other) | heme D1 | Heliophilum fasciatum
BGC0002633.2 |  | 0.39 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002683.2 |  | 0.38 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002535.2 |  | 0.37 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0001151.5 |  | 0.36 | other (non-nrp beta-lactam) | valclavam, (-)-2-(2-hydroxyethyl)clavam | Streptomyces antibioticus
BGC0000720.3 |  | 0.36 | saccharide | tobramycin | Streptoalloteichus tenebrarius

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.83 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002382.3 |  | 0.42 | ribosomal | grimoviridin | Grimontia marina
BGC0000842.5 |  | 0.42 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0000905.5 |  | 0.40 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000906.3 |  | 0.40 | other (other) | heme D1 | Heliophilum fasciatum
BGC0002633.2 |  | 0.39 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002683.2 |  | 0.38 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002535.2 |  | 0.37 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0001151.5 |  | 0.36 | other (non-nrp beta-lactam) | valclavam, (-)-2-(2-hydroxyethyl)clavam | Streptomyces antibioticus
BGC0000720.3 |  | 0.36 | saccharide | tobramycin | Streptoalloteichus tenebrarius

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:
CPH93_RS15800: T1TS + T1TS
Domain 1 (1 - 327): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (345 - 709): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.56 out of 23.79
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.48 out of 24.78
Confidence: medium
Additional weak hits (6):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.18 out of 29.38
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.24 out of 26.12
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.99 out of 36.54
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.02 out of 24.78
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response

NZ_LT907981.1 - Region 23 - azole-containing-RiPP,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,171,898 - 4,220,142 nt. (total: 48,245 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)
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)

#### 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
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 oxygenase
CPH93_RS17850: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

CPH93_RS17910: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS17930: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS35450: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: aminotransferase
CPH93_RS17830: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: dehalogenase esterase hydrolase
CPH93_RS17805: putative esterase

smcogs
  SMCOG1104: putative esterase

CPH93_RS17835: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

CPH93_RS17840: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: dehydratase
CPH93_RS17880: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

CPH93_RS17920: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: ligase
CPH93_RS17915: 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000611.5 |  |  | 0.96 | ribosomal | siomycin A | Streptomyces sioyaensis
BGC0000614.5 |  |  | 0.83 | ribosomal | thiostrepton | Streptomyces laurentii
BGC0001474.4 |  |  | 0.53 | ribosomal | thiopeptin | Streptomyces tateyamensis
BGC0001471.5 |  |  | 0.52 | ribosomal | saalfelduracin | Amycolatopsis saalfeldensis
BGC0002584.2 |  |  | 0.35 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0001896.4 |  |  | 0.33 | other (other) | carbazomycin B | Streptomyces luteoverticillatus
BGC0000885.3 |  |  | 0.31 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0001206.5 |  |  | 0.30 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0000846.5 |  |  | 0.30 | other (other) | tabtoxin | Pseudomonas syringae
BGC0001880.3 |  |  | 0.30 | ribosomal | scytodecamide | Scytonema sp. UIC 10036

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000611.5 |  | 0.88 | ribosomal | siomycin A | Streptomyces sioyaensis
BGC0000614.5 |  | 0.84 | ribosomal | thiostrepton | Streptomyces laurentii
BGC0001474.4 |  | 0.69 | ribosomal | thiopeptin | Streptomyces tateyamensis
BGC0001471.5 |  | 0.69 | ribosomal | saalfelduracin | Amycolatopsis saalfeldensis
BGC0001145.5 |  | 0.54 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0002584.2 |  | 0.54 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0001472.5 |  | 0.53 | ribosomal | berninamycin A | Streptomyces bernensis
BGC0000603.5 |  | 0.52 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0002311.3 |  | 0.52 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001640.3 |  | 0.51 | ribosomal | kocurin | Kocuria rosea

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

No significant matches found.

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

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

Genes with terpene domains:
CPH93_RS17825: PT_phytoene_like
Domain 1 (18 - 258): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.81 out of 23.79
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 25.31
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.23 out of 29.72
Confidence: medium
Additional weak hits (11):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.65 out of 26.12
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.71 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.12 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.94 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.80 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.46 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.65 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.58 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.01 out of 29.65
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
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.

#### (Thi)azol(in)e containing peptide(s)

CPH93_RS17865
Leader:
MSTAAIVGQEIGVEGLTGLDVDALEISEYMDETLLDGEDLSVTM
Core:
V S S A S C T T C I C T C S C S S
Core with dehydrations:
V Dha Dha A Dha Cys Dhb Dhb Cys I Cys Dhb Cys Dha Cys Dha Dha

#### antiSMASH-DB 4.0 matches for CPH93_RS17865

100.0%
NZ_LT907981.1:
Thiopeptides: CPH93_RS17865_thiopeptide
1
V S S A S C T T C I C T C S C S S
17
V S S A S C T T C I C T C S C S S
1
V S S A S C T T C I C T C S C S S
17
70.6%
NZ_LT907981.1:
Thiopeptides: CPH93_RS17870_thiopeptide
2
S S A S C T T C I C T C S C S S
17
S S S C T T C I C+ C S S
1
S S V S C T T C I C S G R C S S
16
47.1%
NZ_QQBC01000004.1:
Thiopeptides: DFR76_RS13815_thiopeptide
5
S C T T C I C T C S C
15
S C T+C+C C S C
1
S C T S C V C I C S C
11
with 10 more sequence matches
42.9%
NZ_CP036100.1 and 1 other:
NZ_CP072062.1 Lanthipeptides: J5V93_RS29680_lanthipeptide
Lanthipeptides: EXW47_RS29590_lanthipeptide
1
V S S A S C T T--C I C T C S C S S
17
V S A C T C I C T S C S+
8
V S R A V C K T G T C I C T T S C S N
26
42.9%
NZ_MOOT01000054.1 and 1 other:
NZ_MOOT01000054.1 Lanthipeptides: BK765_RS17680_lanthipeptide
Lanthipeptides: BK765_RS17685_lanthipeptide
1
V S S A S C T T--C I C T C S C S S
17
V S A C T C I C T S C S+
8
V S K A V C K T G T C I C T T S C S N
26
42.9%
NZ_QNRN01000010.1:
Lanthipeptides: DET63_RS17955_lanthipeptide
1
V S S A S C T T--C I C T C S C S S
17
V S A C T C I C T S C S+
8
V S K A I C K T G T C I C T T S C S N
26
40.0%
NZ_CP023711.1 and 11 others:
NZ_CP034141.1 Lanthipeptides: EGM68_RS25880_lanthipeptide NZ_CP040829.1 Lanthipeptides: FGY93_RS26165_lanthipeptide NZ_CP049598.1 Lanthipeptides: G7L40_RS03920_lanthipeptide NZ_CP071875.1 Lanthipeptides: J4I02_RS05145_lanthipeptide NZ_CP086373.1 Lanthipeptides: LMH85_RS04795_lanthipeptide NZ_CP092831.1 Lanthipeptides: MLD56_RS04795_lanthipeptide NZ_CP102865.1 Lanthipeptides: NWS42_RS17805_lanthipeptide NZ_JAFJXZ010000012.1 Lanthipeptides: JYU28_RS03620_lanthipeptide NZ_JAKVDC010000009.1 Lanthipeptides: MKN04_RS18550_lanthipeptide NZ_JWJJ01000002.1 Lanthipeptides: U707_RS25810_lanthipeptide NZ_POVT01000017.1 Lanthipeptides: C1T20_RS25545_lanthipeptide
Lanthipeptides: CPY53_RS19275_lanthipeptide
1
V S S A S C T T--C I C T C S C S S
17
V S A C T C I C T S C S+
10
V S K A V C K T L T C I C T G S C S N
28
39.3%
NZ_KB976165.1 and 1 other:
NZ_MOOT01000054.1 Lanthipeptides: BK765_RS17675_lanthipeptide
Lanthipeptides: ICC_RS37095_lanthipeptide
1
V S S A S C T--T C I C T C S C S S
17
V S A C T C+C T S C S+
8
V S R A P C K S G T C L C T T S C S N
26
30.8%
NZ_CP036100.1 and 5 others:
NZ_CP036100.1 Lanthipeptides: EXW47_RS29575_lanthipeptide NZ_CP036100.1 Lanthipeptides: EXW47_RS29570_lanthipeptide NZ_CP072062.1 Lanthipeptides: J5V93_RS29670_lanthipeptide NZ_CP072062.1 Lanthipeptides: J5V93_RS29665_lanthipeptide NZ_CP072062.1 Lanthipeptides: J5V93_RS29660_lanthipeptide
Lanthipeptides: EXW47_RS29580_lanthipeptide
8
T C I C T C S C S S
17
T C I C T S C S+
15
T C I C T T S C S N
24
30.8%
NZ_KB976165.1 and 1 other:
NZ_MOOT01000054.1 Lanthipeptides: BK765_RS17665_lanthipeptide
Lanthipeptides: ICC_RS25590_lanthipeptide
8
T C I C T C S C S S
17
T C I C T S C S+
15
T C I C T I S C S N
24
26.7%
NZ_CP034587.1:
Lanthipeptides: EKH77_RS16870_lanthipeptide
2
S S A S C T T C I C T C S C
15
S+A C T T +C T C
13
S A A G C T T S V C T Q G C
26
26.7%
NZ_NDXL01000003.1:
Lanthipeptides: B7024_RS31125_lanthipeptide
1
V S S A S C T T C I C T C S C
15
V++A C T T +C T C
12
V T A A G C T T S V C T Q G C
26
18.9%
NZ_KB913021.1:
Lanthipeptides: NATTI_RS0124330_lanthipeptide
1
V S S A S C T-T C I C T C S C S
16
+S A T T C I C T C C+
34
I S E A K Y T F T C I C T C K C T
50

#### MIBiG 4.0 matches for CPH93_RS17865

21.7%
BGC0002130.3 (QKI29070.1):
Lanthipeptide: cacaoidin
2
S S A S C T
7
S S A C T
1
S S A P C T
6
21.6%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
1
V S S A S C T T C I C T C S C
15
V S+A C T C T C
23
V S A A F C P T T K C T S R C
37
11.8%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
12
T C S C S
16
T C C S
25
T C H C S
29
CPH93_RS17870
Leader:
MSTVAAVGQDVGVEGLTGLDAGALEISETRTRRCSTARAAVTLI
Core:
S S V S C T T C I C S G R C S S
Core with dehydrations:
Dha Dha V Dha Cys Dhb Dhb Cys I Cys Dha G R Cys Dha Dha

#### antiSMASH-DB 4.0 matches for CPH93_RS17870

100.0%
NZ_LT907981.1:
Thiopeptides: CPH93_RS17870_thiopeptide
1
S S V S C T T C I C S G R C S S
16
S S V S C T T C I C S G R C S S
1
S S V S C T T C I C S G R C S S
16
23.3%
NZ_CP023711.1 and 11 others:
NZ_CP034141.1 Lanthipeptides: EGM68_RS25880_lanthipeptide NZ_CP040829.1 Lanthipeptides: FGY93_RS26165_lanthipeptide NZ_CP049598.1 Lanthipeptides: G7L40_RS03920_lanthipeptide NZ_CP071875.1 Lanthipeptides: J4I02_RS05145_lanthipeptide NZ_CP086373.1 Lanthipeptides: LMH85_RS04795_lanthipeptide NZ_CP092831.1 Lanthipeptides: MLD56_RS04795_lanthipeptide NZ_CP102865.1 Lanthipeptides: NWS42_RS17805_lanthipeptide NZ_JAFJXZ010000012.1 Lanthipeptides: JYU28_RS03620_lanthipeptide NZ_JAKVDC010000009.1 Lanthipeptides: MKN04_RS18550_lanthipeptide NZ_JWJJ01000002.1 Lanthipeptides: U707_RS25810_lanthipeptide NZ_POVT01000017.1 Lanthipeptides: C1T20_RS25545_lanthipeptide
Lanthipeptides: CPY53_RS19275_lanthipeptide
7
T C I C S G R C S S
16
T C I C+G C S+
19
T C I C T G S C S N
28
18.8%
NZ_KZ859514.1 and 1 other:
NZ_KZ859514.1 Lanthipeptides: DPQ64_RS19150_lanthipeptide
Lanthipeptides: DPQ64_RS19155_lanthipeptide
2
S V S C T-T C I C S G R C S
15
S+S C T +C+C S G C+
28
S L S C T D S C L C S G D C N
42
with 1 more sequence matches
14.0%
NZ_CP064030.1:
Lanthipeptides: ISN74_RS08625_lanthipeptide
9
I C S G R C S S
16
+C S G R C S
25
V C S G R C G S
32

#### MIBiG 4.0 matches for CPH93_RS17870

18.2%
BGC0000563.4 (AEA03263.1):
Lanthipeptide: venezuelin
7
T C I C S G
12
T C C G
2
T C E C V G
7
16.2%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
1
S S V S C T T C I C S G R C
14
S+ C T C+ R C
24
S A A F C P T T K C T S R C
37
15.4%
BGC0002110.3 (QKV49894.1):
Lanthipeptide: birimositide
5
C T T C I C S G R C
14
C T C+ +C
17
C P T T K C T S K C
26

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

#### Types:

Type I: Featuring genes encoding indolic acid side ring (series e)
Type II: Featuring the gene coding for quinaldic acid moiety formation (series a, b, and c)
Type III: No genes for synthesizing L-Trp derivatives (series d)
RREFinder
Terpene
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (4176724...4220142)
CPH93_RS17900
  RRE type: Thiopeptide_F_RRE
  Location: 0 - 83
  Score: 99.0
  RRE type: Heterocycloanthracin_C_RRE
  Location: 3 - 56
  Score: 30.6

Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C

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.

CPH93_RS17865
  Putative Type II
  Cleavage pHMM score: 21.40
  RODEO score: 33
  Monoisotopic mass: 1641.6 Da
  Molecular weight: 1642.9 Da
  Predicted peptide features:
  Central ring: piperidine; second macrocycle containing a quinaldic acid moiety
  Macrocycle: 26-member
Considering maturation reactions
  Monoisotopic mass: 1629.4 Da
  Molecular weight: 1630.7 Da
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1660.9 Da N = 1
    1678.9 Da N = 2
    1696.9 Da N = 3
    1715.0 Da N = 4
    1733.0 Da N = 5
    1751.0 Da N = 6
    1769.0 Da N = 7
    1787.0 Da N = 8
    1805.1 Da N = 9
CPH93_RS17870
  Putative Type II
  Cleavage pHMM score: 9.20
  RODEO score: 30
  Monoisotopic mass: 1579.6 Da
  Molecular weight: 1580.8 Da
  Predicted peptide features:
  Central ring: piperidine; second macrocycle containing a quinaldic acid moiety
Considering maturation reactions
  Monoisotopic mass: 1605.5 Da
  Molecular weight: 1606.6 Da
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1598.8 Da N = 1
    1616.8 Da N = 2
    1634.8 Da N = 3
    1652.9 Da N = 4
    1670.9 Da N = 5
    1688.9 Da N = 6
    1706.9 Da N = 7
    1724.9 Da N = 8

NZ_LT907981.1 - Region 24 - 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: 5,236,629 - 5,282,976 nt. (total: 46,348 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CPH93_RS22605: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CPH93_RS22655: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS22665: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Hydrolases: esterase hydrolase
CPH93_RS22530: putative esterase

smcogs
  SMCOG1104: putative esterase

CPH93_RS22560: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: synthase
CPH93_RS22600: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: permease
CPH93_RS22675: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000037.4 |  | 0.60 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0000037.4 |  | 0.60 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 21.15 out of 23.79
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.17 out of 23.79
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
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.86 out of 18.57
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.31 out of 23.79
Confidence: medium
Additional weak hits (16):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.49 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.37 out of 27.04
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 27.04
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.49 out of 36.54
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.53 out of 25.88
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.91 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.84 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.97 out of 29.38
Confidence: weak
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: 20.84 out of 29.38
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.87 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.41 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.19 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.34 out of 33.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.43 out of 32.93
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 35, location 5236628 - 5282976:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal)

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).
CPH93_RS22605: mmal
PKS_AT (550..843): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Malonyl-CoA: 70.8%
  Ethylmalonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 148.5
  Ethylmalonyl-CoA: 134.9
  Methoxymalonyl-CoA: 120.8
  Malonyl-CoA: 102.4
  Propionyl-CoA: 83.2
  Isobutyryl-CoA: 78.3
  2-Methylbutyryl-CoA: 77.3
  trans-1,2-CPDA: 75.8
  Acetyl-CoA: 57.2
  CHC-CoA: 44.4
  fatty_acid: 42.9
  inactive: 29.2
  Benzoyl-CoA: 20.0
  3-Methylbutyryl-CoA: 18.7

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
IolR | Regulator of the inositol catabolism
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_LT907981.1 - Region 25 - butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,289,292 - 5,300,227 nt. (total: 10,936 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
Oxidoreductases: dehydrogenase oxygenase
CPH93_RS22730: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CPH93_RS22745: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: synthase
CPH93_RS22720: 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 | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001723.5 |  | 0.46 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000231.5 |  | 0.45 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.44 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002711.2 |  | 0.43 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000275.4 |  | 0.43 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0001197.5 |  | 0.42 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000219.4 |  | 0.42 | PKS, saccharide | elloramycin | Streptomyces olivaceus
BGC0000272.3 |  | 0.42 | PKS | spore pigment | Streptomyces collinus
BGC0002510.2 |  | 0.42 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0001366.5 |  | 0.41 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001723.5 |  | 0.46 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000231.5 |  | 0.45 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.44 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002711.2 |  | 0.43 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000275.4 |  | 0.43 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0001197.5 |  | 0.42 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000219.4 |  | 0.42 | PKS, saccharide | elloramycin | Streptomyces olivaceus
BGC0000272.3 |  | 0.42 | PKS | spore pigment | Streptomyces collinus
BGC0002510.2 |  | 0.42 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0001366.5 |  | 0.41 | 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.
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):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.39 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LT907981.1 - Region 26 - ectoine
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,216,600 - 6,227,016 nt. (total: 10,417 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
CPH93_RS26775: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: aminotransferase methyltransferase
CPH93_RS26760: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CPH93_RS26770: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

CPH93_RS26790: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

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

Reference | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.92 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.85 | other (other) | ectoine | Streptomyces anulatus
BGC0000856.3 |  | 0.72 | other (other) | ectoine | Methylophaga thalassica
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.59 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.92 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.85 | other (other) | ectoine | Streptomyces anulatus
BGC0000856.3 |  | 0.72 | other (other) | ectoine | Methylophaga thalassica
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.59 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

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: 18.25 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.52 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
TFBS Finder
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

NZ_LT907981.1 - Region 27 - 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: 6,306,873 - 6,336,678 nt. (total: 29,806 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CPH93_RS27260: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Lyases: decarboxylase
CPH93_RS27265: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

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
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.87 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.80 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000941.3 |  | 0.80 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  | 0.72 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.72 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.61 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002073.3 |  | 0.60 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002690.2 |  | 0.54 | other (other) | FW0622 | Verrucosispora sp. FIM060022

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.87 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.80 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000941.3 |  | 0.80 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  | 0.72 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.72 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.61 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002073.3 |  | 0.60 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002690.2 |  | 0.54 | other (other) | FW0622 | Verrucosispora sp. FIM060022

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:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 25.31
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.03 out of 36.53
Confidence: medium
Additional weak hits (25):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.97 out of 31.73
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.93 out of 19.26
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.25 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.44 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 out of 30.98
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.23 out of 27.04
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.92 out of 27.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.27 out of 32.74
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.22 out of 39.62
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.67 out of 31.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.08 out of 32.93
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.92 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.67 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.10 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.03 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.96 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.29 out of 32.93
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.63 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.51 out of 26.06
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.67 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
DmdR1 | Iron(II)-dependent repressor

NZ_LT907981.1 - Region 28 - T1PKS,hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,895,471 - 6,946,967 nt. (total: 51,497 nt) Show pHMM detection rules used
hglE-KS: (hglE or hglD)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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: glycosyltransferase
CPH93_RS29905: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: hydrolase
CPH93_RS29870: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

CPH93_RS29900: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CPH93_RS29975: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: synthase
CPH93_RS29885: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CPH93_RS29890: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | hglE-KS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.59 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.58 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  |  | 0.58 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  |  | 0.57 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  |  | 0.53 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.53 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001254.3 |  |  | 0.51 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  |  | 0.51 | PKS | FR901512 | fungal sp. No.14919
BGC0000041.3 |  |  | 0.49 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000863.3 |  |  | 0.42 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.63 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.62 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001254.3 |  | 0.59 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  | 0.59 | PKS | FR901512 | fungal sp. No.14919
BGC0000041.3 |  | 0.58 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000863.3 |  | 0.54 | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 26.63 out of 29.51
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.70 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.56 out of 23.79
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.86 out of 18.57
Confidence: medium
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.55 out of 30.22
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.91 out of 23.79
Confidence: medium
Additional weak hits (18):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.15 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.89 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.40 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.57 out of 29.65
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.14 out of 32.93
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.90 out of 20.01
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.45 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.87 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.65 out of 32.93
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.12 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.37 out of 30.22
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.50 out of 25.75
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.96 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.13 out of 35.63
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.25 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.57 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 39, location 6895470 - 6946967:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk)
Non-colinear ordering:
  CPH93_RS29890 + CPH93_RS29895

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 40, location 6895470 - 6942412:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk)
Non-colinear ordering:
  CPH93_RS29890 + CPH93_RS29895

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 41, location 6902413 - 6946967:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk)
Non-colinear ordering:
  CPH93_RS29890 + CPH93_RS29895

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).
CPH93_RS29885: mal
PKS_AT (1232..1523): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 58.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 75.2
  Methoxymalonyl-CoA: 35.0
  Methylmalonyl-CoA: 31.7
  inactive: 31.4
  Propionyl-CoA: 24.7
  CHC-CoA: 17.6
  Ethylmalonyl-CoA: 17.0
  trans-1,2-CPDA: 13.4
  2-Methylbutyryl-CoA: 10.4
  fatty_acid: 9.3
  Isobutyryl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CPH93_RS29890: pk
PKS_AT (630..831): pk
ATSignature: (unknown)
No matches above 50%
minowa: Propionyl-CoA

Prediction, score:
  Propionyl-CoA: 10.6
  inactive: 7.0
  Malonyl-CoA: 5.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Methylmalonyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
ClgR | Caseinolytic protease gene regulator
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_LT907981.1 - Region 29 - 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: 7,084,158 - 7,117,027 nt. (total: 32,870 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CPH93_RS30765: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Lyases: decarboxylase lyase
CPH93_RS30705: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

CPH93_RS30725: 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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.77 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0001408.5 |  | 0.70 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002527.2 |  | 0.63 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000947.5 |  | 0.58 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0002073.3 |  | 0.58 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002682.2 |  | 0.55 | other (other) | aerobactin | Vibrio mimicus
BGC0001870.3 |  | 0.55 | other (other) | putrebactin, avaroferrin | Xenorhabdus budapestensis
BGC0002683.2 |  | 0.51 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002681.3 |  | 0.50 | other (other) | rhizoferrin | Francisella tularensis subsp. tularensis SCHU S4
BGC0000939.5 |  | 0.50 | other (other) | aerobactin | Grimontia hollisae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000946.5 |  | 0.77 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0001408.5 |  | 0.70 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002527.2 |  | 0.63 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0000947.5 |  | 0.58 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0002073.3 |  | 0.58 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002682.2 |  | 0.55 | other (other) | aerobactin | Vibrio mimicus
BGC0001870.3 |  | 0.55 | other (other) | putrebactin, avaroferrin | Xenorhabdus budapestensis
BGC0002683.2 |  | 0.51 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002681.3 |  | 0.50 | other (other) | rhizoferrin | Francisella tularensis subsp. tularensis SCHU S4
BGC0000939.5 |  | 0.50 | other (other) | aerobactin | Grimontia hollisae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.35 out of 23.79
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.90 out of 36.53
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
Additional weak hits (8):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.12 out of 29.25
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.04 out of 18.57
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.86 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.26 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism

NZ_LT907981.1 - Region 30 - 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: 7,235,314 - 7,307,829 nt. (total: 72,516 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)

#### 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 synthase
CPH93_RS31345: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CPH93_RS31360: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS31365: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS31380: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

CPH93_RS31475: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CPH93_RS37060: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Transferases: aminotransferase glycosyltransferase methyltransferase transferase
CPH93_RS31280: aminotransferase

smcogs
  SMCOG1019: aminotransferase

CPH93_RS31295: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

CPH93_RS31450: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CPH93_RS31485: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: hydrolase synthase
CPH93_RS31310: isochorismatase

smcogs
  SMCOG1027: isochorismatase

CPH93_RS31545: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

CPH93_RS37060: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Lyases: cyclase hydratase
CPH93_RS31385: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

CPH93_RS31440: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

CPH93_RS31445: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

Isomerases: mutase
CPH93_RS31525: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase synthase
CPH93_RS31300: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CPH93_RS31425: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS31430: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000272.3 |  | 0.76 | PKS | spore pigment | Streptomyces collinus
BGC0000271.5 |  | 0.73 | PKS | spore pigment | Streptomyces avermitilis
BGC0000215.5 |  | 0.69 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.63 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001197.5 |  | 0.61 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002276.2 |  | 0.61 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000234.5 |  | 0.61 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.60 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002277.2 |  | 0.59 | NRPS | atromentin | Suillus grevillei
BGC0001273.3 |  | 0.59 | PKS | asperlactone | Aspergillus ochraceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000272.3 |  | 0.76 | PKS | spore pigment | Streptomyces collinus
BGC0000271.5 |  | 0.73 | PKS | spore pigment | Streptomyces avermitilis
BGC0000215.5 |  | 0.69 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.63 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001197.5 |  | 0.61 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002276.2 |  | 0.61 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000234.5 |  | 0.61 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.60 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002277.2 |  | 0.59 | NRPS | atromentin | Suillus grevillei
BGC0001273.3 |  | 0.59 | PKS | asperlactone | Aspergillus ochraceus

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: 19.89 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.24 out of 19.26
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.25 out of 24.78
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
Additional weak hits (19):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.60 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.55 out of 28.14
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.74 out of 27.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.83 out of 26.85
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.52 out of 30.22
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.70 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.04 out of 21.84
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.63 out of 30.22
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.58 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.77 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.15 out of 29.65
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.05 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.74 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
Type II PKS
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CPH93_RS31300: X
AMP-binding (12..389): 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:
    TALLHGLILG-GFGVSGSAIERYGMTETLMNTSV
  Nearest Stachelhaus code(s):
    nohBza GLGLVGAIIK (44% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Cluster section:
  7235313 to 7307829
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

CPH93_RS31360
  KR (Score: 178.3; E-value: 5.2e-55)
CPH93_RS31365
  KR (Score: 153.2; E-value: 2.3e-47)
CPH93_RS31420
  CYC C5-C18 (Score: 214.3; E-value: 1.1e-66)
CPH93_RS31425
  KS (Score: 727.9; E-value: 7.6e-222)
CPH93_RS31430
  CLF (Score: 547.2; E-value: 5e-167)
CPH93_RS31435
  ACP (Score: 64.6; E-value: 1.5e-20)
CPH93_RS31440
  CYC C9-C14 (Score: 244.5; E-value: 7.6e-76)
CPH93_RS31445
  CYC C4-C21/C2-C23|C2-C19 (Score: 157.0; E-value: 3e-49)
CPH93_RS31450
  MET C6|C8 (Score: 529.5; E-value: 6.4e-162)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator

NZ_LT907981.1 - Region 31 - 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: 7,324,050 - 7,334,277 nt. (total: 10,228 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001555.4 |  | 0.47 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.46 | ribosomal | microcin N | Escherichia coli
BGC0000588.5 |  | 0.45 | ribosomal | microcin L | Escherichia coli
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000518.3 |  | 0.42 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002698.2 |  | 0.41 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0000484.5 |  | 0.39 | ribosomal | glycocin F | Lactobacillus plantarum
BGC0000504.5 |  | 0.39 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000500.5 |  | 0.38 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001555.4 |  | 0.47 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.46 | ribosomal | microcin N | Escherichia coli
BGC0000588.5 |  | 0.45 | ribosomal | microcin L | Escherichia coli
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000518.3 |  | 0.42 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002698.2 |  | 0.41 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0000484.5 |  | 0.39 | ribosomal | glycocin F | Lactobacillus plantarum
BGC0000504.5 |  | 0.39 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000500.5 |  | 0.38 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum

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 (7):
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.76 out of 29.38
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.07 out of 26.06
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.50 out of 25.75
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.98 out of 29.38
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LT907981.1 - Region 32 - hydrogen-cyanide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,435,880 - 7,448,860 nt. (total: 12,981 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase reductase
CPH93_RS32180: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS32185: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS32200: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CPH93_RS32210: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Hydrolases: peptidase
CPH93_RS32230: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: hydratase
CPH93_RS32175: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

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

Reference | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0000888.5 |  | 0.44 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000231.5 |  | 0.44 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000218.5 |  | 0.42 | PKS | doxorubicin | Streptomyces peucetius
BGC0002218.2 |  | 0.41 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0000217.5 |  | 0.41 | PKS | daunorubicin | Streptomyces sp.
BGC0000234.5 |  | 0.40 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002161.2 |  | 0.39 | PKS | scytalone, T3HN | Pestalotiopsis fici W106-1
BGC0000384.6 |  | 0.38 | NRPS | lyngbyatoxin | Lyngbya majuscula

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0000888.5 |  | 0.44 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000231.5 |  | 0.44 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000218.5 |  | 0.42 | PKS | doxorubicin | Streptomyces peucetius
BGC0002218.2 |  | 0.41 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0000217.5 |  | 0.41 | PKS | daunorubicin | Streptomyces sp.
BGC0000234.5 |  | 0.40 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002161.2 |  | 0.39 | PKS | scytalone, T3HN | Pestalotiopsis fici W106-1
BGC0000384.6 |  | 0.38 | NRPS | lyngbyatoxin | Lyngbya majuscula

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 (13):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.89 out of 25.88
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.96 out of 25.88
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.58 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.04 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.31 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.96 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.45 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.68 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.02 out of 23.43
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 22.40
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.29 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LT907981.1 - Region 33 - 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: 7,480,060 - 7,521,124 nt. (total: 41,065 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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 oxygenase
CPH93_RS32435: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS32525: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: aminotransferase
CPH93_RS32390: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Ligases: synthase
CPH93_RS32430: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.85 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.72 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001948.3 |  | 0.49 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000844.5 |  | 0.48 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000280.5 |  | 0.48 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.47 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0001485.4 |  | 0.45 | other (other) | chuangxinmycin | Actinoplanes tsinanensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.85 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.72 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001948.3 |  | 0.49 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0000844.5 |  | 0.48 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000280.5 |  | 0.48 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.47 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0001485.4 |  | 0.45 | other (other) | chuangxinmycin | Actinoplanes tsinanensis

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: 18.25 out of 20.47
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.96 out of 29.72
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.63 out of 18.46
Confidence: medium
Additional weak hits (13):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.75 out of 27.04
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 30.11
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.28 out of 27.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.78 out of 39.62
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.03 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.06 out of 31.73
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.48 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.24 out of 26.12
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.00 out of 35.63
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.22 out of 28.14
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
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_LT907981.1 - Region 34 - 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: 7,544,116 - 7,556,047 nt. (total: 11,932 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
Transferases: methyltransferase
CPH93_RS32630: methyltransferase

smcogs
  SMCOG1248: methyltransferase

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.42 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000468.5 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000470.6 |  | 0.40 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000469.6 |  | 0.38 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000518.3 |  | 0.35 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000598.5 |  | 0.35 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0001334.5 |  | 0.33 | other (other) | caldoniamide A, cladoniamide B, cladoniamide C7, cladoniamide D, cladoniamide E, cladoniamide F, cladoniamide G | Streptomyces uncialis
BGC0000633.3 |  | 0.32 | terpene | carotenoid | Streptomyces avermitilis
BGC0001753.3 |  | 0.30 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.42 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000468.5 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000470.6 |  | 0.40 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000469.6 |  | 0.38 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000518.3 |  | 0.35 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000598.5 |  | 0.35 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0001334.5 |  | 0.33 | other (other) | caldoniamide A, cladoniamide B, cladoniamide C7, cladoniamide D, cladoniamide E, cladoniamide F, cladoniamide G | Streptomyces uncialis
BGC0000633.3 |  | 0.32 | terpene | carotenoid | Streptomyces avermitilis
BGC0001753.3 |  | 0.30 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus

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):
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.43 out of 27.18
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.76 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LT907981.1 - Region 35 - NRPS,NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,565,485 - 7,666,430 nt. (total: 100,946 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CPH93_RS32760: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS32790: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS32795: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: acetyltransferase glycosyltransferase
CPH93_RS32685: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CPH93_RS32785: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

CPH93_RS32810: Glycosylation

MITE
  MITE0000033Glycosylation (identity: 61.10%)
smcogs
  SMCOG1102: glycosyltransferase

Hydrolases: esterase hydrolase
CPH93_RS32765: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

CPH93_RS32840: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
CPH93_RS32860: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
CPH93_RS32750: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

CPH93_RS32770: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CPH93_RS32775: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CPH93_RS32815: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

CPH93_RS32845: 3-oxoacyl-(acyl carrier protein) synthase III

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

CPH93_RS32850: 3-oxoacyl-(acyl carrier protein) synthase III

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

CPH93_RS32855: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CPH93_RS32865: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  | 0.70 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000307.4 |  |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  |  | 0.63 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000357.5 |  |  | 0.54 | 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
BGC0001250.4 |  |  | 0.54 | NRPS | epichloenin A | Epichloe festucae
BGC0002071.2 |  |  | 0.47 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  | 0.72 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.80 out of 23.43
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.45 out of 28.19
Confidence: medium
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
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: 22.50 out of 26.85
Confidence: medium
Additional weak hits (16):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.55 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.76 out of 29.38
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.31 out of 29.51
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.88 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.46 out of 32.74
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.84 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.04 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.62 out of 29.38
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.52 out of 29.65
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.56 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.27 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.69 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.81 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 48, location 7565484 - 7666430:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - D-Ala - D-Val - D-Ala - Leu) + (D-Orn - Thr - D-Orn - Val - D-Leu) + (Asn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 49, location 7565484 - 7644186:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu - D-Ala - D-Val - D-Ala - Leu) + (D-Orn - Thr - D-Orn - Val - D-Leu) + (Asn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 50, location 7623367 - 7666430:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Orn - Thr - D-Orn - Val - D-Leu) + (Asn)

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).
CPH93_RS32770: Leu - Ala - Val - Ala - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (40..422): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAASFDAAVLEILIIVGAEINSYGPTEATVVASW
  Nearest Stachelhaus code(s):
    Leu DALLIGAVVK (79% 8Å match)
    Leu or 3OH-Leu DALLIGAVVK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1079..1480): Ala
nrpys: Ala

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

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

AMP-binding (2592..2996): 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:
    LDRSFDAATYEVWLWTGGEVDGYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4114..4514): Ala
nrpys: Ala

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

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

AMP-binding (5633..6018): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAEAFDASVLEMLLIVGADINSYGPTETTVVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (74% 8Å match)
    Leu DALLIGAVVK (62% 8Å match)
  Stachelhaus code match:
    90% (moderate)

CPH93_RS32775: Orn - Thr - Orn - Val - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (519..906): Orn
nrpys: Orn

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:
    LGHAFDTSLEGLDLMLGGEYNFYGPTECTVDALA
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2041..2453): 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:
    LRTHFDFSVWEGNQIFGGEVNMYGITETTVHVSY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3112..3503): Orn
nrpys: Orn

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:
    LDHGFDTSWEGMDVMVGGEYNVYGPTECTVDAVY
  Nearest Stachelhaus code(s):
    Orn DTEDMGYVDK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4621..5002): 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:
    LDSSFDAATFEAWLWTGGDVDGYGPTETTTFATS
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (5658..6039): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAAAFDASYLEILIIVGAEINSYGPTEATVVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (68% 8Å match)
    Leu DALLIGAVVK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

CPH93_RS32855: X
AMP-binding (19..464): 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:
    TGIL----LYGDFAVSGGAHTTYGATEALPISSL
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CPH93_RS32865: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (420..810): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWATFDLTGTTAKLVVGGEVNEYGPTEATIGCIV
  Nearest Stachelhaus code(s):
    Asn DLTKVGEVGK (82% 8Å match)
    Asp DLTKVGHIGK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
BldD | Development and antibiotic global regulator
CRP | Cyclic AMP receptor protein
HypR | L-hydroxyproline utilization repressor
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_LT907981.1 - Region 36 - transAT-PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,666,570 - 7,752,414 nt. (total: 85,845 nt) Show pHMM detection rules used
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-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
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CPH93_RS33045: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS33050: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS33065: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CPH93_RS33075: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acylase methyltransferase
CPH93_RS33060: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CPH93_RS33070: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CPH93_RS35955: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase
CPH93_RS33040: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: decarboxylase dehydratase
CPH93_RS33010: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

CPH93_RS33125: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: synthase
CPH93_RS33055: 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 | transAT-PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000177.5 |  | 0.89 | PKS | iso-migrastatin, migrastatin, dorrigocin A, dorrigocin B, 13-epi-dorrigocin A | Streptomyces platensis subsp. rosaceus
BGC0000083.5 |  | 0.72 | PKS | lactimidomycin, 8,9-dihydrolactimidomycin, 8-hydroxy-8,9-dihydrolactidomycin, 17-hydroxy-8-desmethoxy-isomigrastatin | Streptomyces amphibiosporus
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002175.3 |  | 0.63 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000177.5 |  | 0.89 | PKS | iso-migrastatin, migrastatin, dorrigocin A, dorrigocin B, 13-epi-dorrigocin A | Streptomyces platensis subsp. rosaceus
BGC0000083.5 |  | 0.72 | PKS | lactimidomycin, 8,9-dihydrolactimidomycin, 8-hydroxy-8,9-dihydrolactidomycin, 17-hydroxy-8-desmethoxy-isomigrastatin | Streptomyces amphibiosporus
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002175.3 |  | 0.63 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0000107.3 |  | 0.63 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002099.3 |  | 0.57 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  | 0.57 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291

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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (22):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.46 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.08 out of 27.78
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.51 out of 39.62
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.05 out of 32.74
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.50 out of 26.33
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.13 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.82 out of 20.01
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.24 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.24 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.10 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.36 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.05 out of 32.74
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.04 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.69 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.33 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.68 out of 24.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.91 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.77 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.26 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 51, location 7666569 - 7752414:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - mal - ohmal) + (mal - Me-ccmal - Me-ohmal - mal - ccmal - mal) + (ccmal)
Non-colinear ordering:
  CPH93_RS33045 + CPH93_RS33050 + CPH93_RS33055

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).
CPH93_RS35955: mal
PKS_AT (4..282): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 115.3
  inactive: 40.9
  Methoxymalonyl-CoA: 36.3
  Methylmalonyl-CoA: 30.6
  Propionyl-CoA: 20.6
  Isobutyryl-CoA: 13.7
  Ethylmalonyl-CoA: 12.8
  2-Methylbutyryl-CoA: 11.1
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CPH93_RS33060: mal
PKS_AT (4..279): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 125.8
  inactive: 55.9
  Methoxymalonyl-CoA: 36.4
  Methylmalonyl-CoA: 35.0
  Propionyl-CoA: 28.1
  Isobutyryl-CoA: 27.4
  2-Methylbutyryl-CoA: 22.6
  CHC-CoA: 20.6
  Ethylmalonyl-CoA: 10.6
  Benzoyl-CoA: 7.9
  trans-1,2-CPDA: 6.8
  fatty_acid: 0.0
  Acetyl-CoA: 0.0
  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

NZ_LT907981.1 - Region 37 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,086,666 - 8,177,506 nt. (total: 90,841 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CPH93_RS34855: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS34880: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CPH93_RS34885: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS34890: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CPH93_RS34905: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CPH93_RS34930: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CPH93_RS34945: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CPH93_RS34950: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: acylase aminotransferase
CPH93_RS34900: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CPH93_RS34910: aminotransferase

smcogs
  SMCOG1019: aminotransferase

CPH93_RS34965: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase
CPH93_RS34985: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
CPH93_RS34895: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CPH93_RS34955: 3-oxoacyl-(acyl carrier protein) synthase III

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

CPH93_RS34960: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CPH93_RS34970: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CPH93_RS34975: 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
--- | --- | --- | --- | --- | ---
BGC0000123.5 |  | 0.86 | PKS | phoslactomycin B | Streptomyces sp. HK803
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.69 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
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
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000123.5 |  | 0.86 | PKS | phoslactomycin B | Streptomyces sp. HK803
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.69 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
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
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: 18.37 out of 20.47
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.29 out of 23.79
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.35 out of 27.18
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
Additional weak hits (22):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.67 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.26 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.42 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.83 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.96 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.56 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.33 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.28 out of 23.43
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.26 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.20 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.02 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.47 out of 36.54
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.45 out of 31.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.87 out of 20.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.57 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 52, location 8086665 - 8177506:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk - ccmal) + (ccmal - ohmal) + (ohemal) + (ccmal) + (ohemal) + (ohmal)
Non-colinear ordering:
  CPH93_RS34905 + CPH93_RS34900 + CPH93_RS34975 + CPH93_RS34970 + CPH93_RS34965 + CPH93_RS34960

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).
CPH93_RS34895: X
AMP-binding (466..896): X
nrpys: Asp, Asn, Glu, Gln, Aad

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  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:
    AMESHTGFLYGLQAVATGACGAFGTTETCLAALS
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CPH93_RS34900: mal - mal
PKS_AT (560..831): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 189.4
  inactive: 97.4
  Methoxymalonyl-CoA: 81.6
  Methylmalonyl-CoA: 79.1
  Propionyl-CoA: 49.6
  Ethylmalonyl-CoA: 46.8
  CHC-CoA: 35.7
  2-Methylbutyryl-CoA: 34.2
  Isobutyryl-CoA: 27.9
  trans-1,2-CPDA: 27.8
  Benzoyl-CoA: 24.6
  Acetyl-CoA: 24.1
  fatty_acid: 17.6
  3-Methylbutyryl-CoA: 8.8

PKS_AT (2304..2574): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 188.4
  inactive: 89.2
  Methylmalonyl-CoA: 76.1
  Methoxymalonyl-CoA: 76.1
  Propionyl-CoA: 47.5
  Ethylmalonyl-CoA: 46.4
  CHC-CoA: 42.1
  2-Methylbutyryl-CoA: 38.2
  trans-1,2-CPDA: 33.4
  Acetyl-CoA: 32.2
  Benzoyl-CoA: 31.7
  Isobutyryl-CoA: 21.7
  fatty_acid: 20.3
  3-Methylbutyryl-CoA: 11.4

CPH93_RS34905: pk - mal
PKS_AT (238..531): pk
ATSignature: CHC-CoA

Top 3 matches:
  CHC-CoA: 100.0%
  Propionyl-CoA: 66.7%
  Methylmalonyl-CoA: 66.7%

minowa: CHC-CoA

Prediction, score:
  CHC-CoA: 259.3
  Methylmalonyl-CoA: 143.7
  Ethylmalonyl-CoA: 131.5
  2-Methylbutyryl-CoA: 116.6
  Methoxymalonyl-CoA: 116.3
  Propionyl-CoA: 100.0
  trans-1,2-CPDA: 99.5
  Malonyl-CoA: 63.2
  Isobutyryl-CoA: 53.6
  Benzoyl-CoA: 41.7
  fatty_acid: 25.5
  Acetyl-CoA: 24.4
  inactive: 15.2
  3-Methylbutyryl-CoA: 11.4

PKS_AT (1225..1497): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 188.8
  Methoxymalonyl-CoA: 84.1
  Methylmalonyl-CoA: 81.5
  inactive: 80.8
  Ethylmalonyl-CoA: 52.9
  Propionyl-CoA: 45.7
  CHC-CoA: 43.1
  Isobutyryl-CoA: 41.9
  2-Methylbutyryl-CoA: 38.2
  Acetyl-CoA: 36.7
  trans-1,2-CPDA: 34.2
  Benzoyl-CoA: 33.4
  fatty_acid: 22.2
  3-Methylbutyryl-CoA: 14.2

CPH93_RS34960: mal
PKS_AT (561..833): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 186.7
  inactive: 87.8
  Methylmalonyl-CoA: 81.0
  Methoxymalonyl-CoA: 78.9
  Ethylmalonyl-CoA: 54.1
  Propionyl-CoA: 46.1
  2-Methylbutyryl-CoA: 41.3
  CHC-CoA: 38.2
  trans-1,2-CPDA: 34.5
  Acetyl-CoA: 31.0
  Benzoyl-CoA: 30.2
  fatty_acid: 24.9
  Isobutyryl-CoA: 21.1
  3-Methylbutyryl-CoA: 12.8

CPH93_RS34965: emal
PKS_AT (597..894): emal
ATSignature: Ethylmalonyl-CoA

Top 3 matches:
  Ethylmalonyl-CoA: 100.0%
  Methylmalonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 83.3%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 234.5
  Methylmalonyl-CoA: 178.3
  Methoxymalonyl-CoA: 154.9
  trans-1,2-CPDA: 120.1
  2-Methylbutyryl-CoA: 115.2
  CHC-CoA: 106.8
  Propionyl-CoA: 103.9
  Malonyl-CoA: 84.8
  Benzoyl-CoA: 80.2
  Isobutyryl-CoA: 74.4
  Acetyl-CoA: 53.1
  3-Methylbutyryl-CoA: 31.5
  fatty_acid: 25.7
  inactive: 25.0

CPH93_RS34970: mal
PKS_AT (566..866): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 184.6
  inactive: 107.5
  Methoxymalonyl-CoA: 50.3
  Methylmalonyl-CoA: 39.2
  Propionyl-CoA: 34.5
  Acetyl-CoA: 19.2
  Isobutyryl-CoA: 17.4
  Benzoyl-CoA: 16.7
  2-Methylbutyryl-CoA: 14.5
  fatty_acid: 13.3
  Ethylmalonyl-CoA: 11.5
  trans-1,2-CPDA: 8.7
  CHC-CoA: 2.1
  3-Methylbutyryl-CoA: 0.0

CPH93_RS34975: emal
PKS_AT (529..827): emal
ATSignature: Ethylmalonyl-CoA

Top 3 matches:
  Ethylmalonyl-CoA: 100.0%
  Methylmalonyl-CoA: 79.2%
  Malonyl-CoA: 75.0%

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 233.8
  Methylmalonyl-CoA: 191.6
  Methoxymalonyl-CoA: 153.4
  trans-1,2-CPDA: 119.5
  2-Methylbutyryl-CoA: 114.0
  Propionyl-CoA: 94.5
  CHC-CoA: 90.2
  Malonyl-CoA: 88.7
  Isobutyryl-CoA: 76.1
  Benzoyl-CoA: 61.6
  Acetyl-CoA: 44.8
  inactive: 31.3
  3-Methylbutyryl-CoA: 26.7
  fatty_acid: 22.1

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems