Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
1.11
1.12
1.13
1.14
1.15
1.16
1.17
1.18
1.19
1.20
1.21
1.22
1.23
1.24
1.25
1.26
1.27

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

NZ_CM002273.1 (Streptomyces sp. PVA_94-07)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | azoxy-crosslink,T1PKS,butyrolactone | 31,520 | 130,306 | Low | griseoviridin/fijimycin A | NRPS:Type I+PKS:Trans-AT type I
Region 1.2 | terpene,NRPS-like,NRPS | 274,831 | 349,562 |  |
Region 1.3 | NRPS-like,T3PKS,NRPS,T1PKS | 399,182 | 502,452 | Medium | totopotensamide A/totopotensamide B | NRPS:Type I+PKS
Region 1.4 | NRPS,T1PKS | 560,646 | 610,065 | High | SGR PTMs/SGR PTM Compound b/SGR PTM Compound c/SGR PTM Compound d | NRPS:Type I+PKS
Region 1.5 | terpene | 647,179 | 673,737 | High | hopene | terpene
Region 1.6 | RiPP-like | 740,680 | 750,895 |  |
Region 1.7 | T1PKS,PKS-like | 771,534 | 819,449 | Medium | Bisenarsan | PKS:Type I
Region 1.8 | RiPP-like | 1,167,101 | 1,178,414 |  |
Region 1.9 | NI-siderophore | 1,452,319 | 1,485,318 |  |
Region 1.10 | terpene | 1,714,007 | 1,736,292 | High | geosmin | terpene:Sesquiterpene
Region 1.11 | RRE-containing | 1,862,908 | 1,884,632 |
Region 1.12 | terpene-precursor | 2,091,937 | 2,112,980 |  |
Region 1.13 | terpene | 2,122,786 | 2,143,760 | Low | julichrome Q3-3/julichrome Q3-5 | PKS
Region 1.14 | azole-containing-RiPP,RRE-containing | 2,603,848 | 2,638,520 |  |
Region 1.15 | lanthipeptide-class-iii | 2,912,898 | 2,935,471 | High | AmfS | ribosomal:RiPP:Lanthipeptide
Region 1.16 | PKS-like | 3,070,808 | 3,111,761 |
Region 1.17 | NRPS | 3,750,249 | 3,812,487 | Low | dechlorocuracomycin | NRPS:Type I
Region 1.18 | NRPS,azole-containing-RiPP | 3,970,595 | 4,079,411 | High | surugamide A/surugamide D | NRPS:Type I
Region 1.19 | NRPS | 4,546,088 | 4,590,455 | Low | dudomycin A | NRPS:Type I
Region 1.20 | NI-siderophore | 4,774,002 | 4,803,822 | High | desferrioxamin B | other:other
Region 1.21 | NRPS-like | 4,898,187 | 4,940,001 | Low | altemicidin/SB-203207/SB-203208 | other:other
Region 1.22 | ectoine | 5,646,629 | 5,657,027 | High | ectoine | other:other
Region 1.23 | T2PKS | 6,244,612 | 6,317,103 | High | enterocin | PKS:Type II
Region 1.24 | terpene | 6,432,939 | 6,461,129 | High | isorenieratene | terpene
Region 1.25 | RiPP-like | 6,542,195 | 6,553,562 | Medium | streptamidine | ribosomal:unmodified
Region 1.26 | T3PKS,T1PKS,terpene-precursor,NRPS-like,NRPS,lanthipeptide-class-ii | 6,555,445 | 6,858,963 | High | candicidin | NRPS:Type I+PKS
Region 1.27 | T1PKS,butyrolactone,azoxy-crosslink | 6,877,212 | 6,975,998 | Low | griseoviridin/fijimycin A | NRPS:Type I+PKS:Trans-AT type I

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | azoxy-crosslink,T1PKS,butyrolactone | 31,520 | 130,306 | Low | griseoviridin/fijimycin A | NRPS:Type I+PKS:Trans-AT type I
Region 1.2 | terpene,NRPS-like,NRPS | 274,831 | 349,562 |  |
Region 1.3 | NRPS-like,T3PKS,NRPS,T1PKS | 399,182 | 502,452 | Medium | totopotensamide A/totopotensamide B | NRPS:Type I+PKS
Region 1.4 | NRPS,T1PKS | 560,646 | 610,065 | High | SGR PTMs/SGR PTM Compound b/SGR PTM Compound c/SGR PTM Compound d | NRPS:Type I+PKS
Region 1.5 | terpene | 647,179 | 673,737 | High | hopene | terpene
Region 1.6 | RiPP-like | 740,680 | 750,895 |  |
Region 1.7 | T1PKS,PKS-like | 771,534 | 819,449 | Medium | Bisenarsan | PKS:Type I
Region 1.8 | RiPP-like | 1,167,101 | 1,178,414 |  |
Region 1.9 | NI-siderophore | 1,452,319 | 1,485,318 |  |
Region 1.10 | terpene | 1,714,007 | 1,736,292 | High | geosmin | terpene:Sesquiterpene
Region 1.11 | RRE-containing | 1,862,908 | 1,884,632 |
Region 1.12 | terpene-precursor | 2,091,937 | 2,112,980 |  |
Region 1.13 | terpene | 2,122,786 | 2,143,760 | Low | julichrome Q3-3/julichrome Q3-5 | PKS
Region 1.14 | azole-containing-RiPP,RRE-containing | 2,603,848 | 2,638,520 |  |
Region 1.15 | lanthipeptide-class-iii | 2,912,898 | 2,935,471 | High | AmfS | ribosomal:RiPP:Lanthipeptide
Region 1.16 | PKS-like | 3,070,808 | 3,111,761 |
Region 1.17 | NRPS | 3,750,249 | 3,812,487 | Low | dechlorocuracomycin | NRPS:Type I
Region 1.18 | NRPS,azole-containing-RiPP | 3,970,595 | 4,079,411 | High | surugamide A/surugamide D | NRPS:Type I
Region 1.19 | NRPS | 4,546,088 | 4,590,455 | Low | dudomycin A | NRPS:Type I
Region 1.20 | NI-siderophore | 4,774,002 | 4,803,822 | High | desferrioxamin B | other:other
Region 1.21 | NRPS-like | 4,898,187 | 4,940,001 | Low | altemicidin/SB-203207/SB-203208 | other:other
Region 1.22 | ectoine | 5,646,629 | 5,657,027 | High | ectoine | other:other
Region 1.23 | T2PKS | 6,244,612 | 6,317,103 | High | enterocin | PKS:Type II
Region 1.24 | terpene | 6,432,939 | 6,461,129 | High | isorenieratene | terpene
Region 1.25 | RiPP-like | 6,542,195 | 6,553,562 | Medium | streptamidine | ribosomal:unmodified
Region 1.26 | T3PKS,T1PKS,terpene-precursor,NRPS-like,NRPS,lanthipeptide-class-ii | 6,555,445 | 6,858,963 | High | candicidin | NRPS:Type I+PKS
Region 1.27 | T1PKS,butyrolactone,azoxy-crosslink | 6,877,212 | 6,975,998 | Low | griseoviridin/fijimycin A | NRPS:Type I+PKS:Trans-AT type I

No secondary metabolite regions were found in these records:
  NZ_CM002274.1 (Streptomyces sp. PVA_94-07)
  NZ_CM002275.1 (Streptomyces sp. PVA_94-07)

Compact view
NZ_CM002273.1 - Region 1 - T1PKS,azoxy-crosslink,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: 31,520 - 130,306 nt. (total: 98,787 nt) Show pHMM detection rules used
azoxy-crosslink: (azdH and LPG_synthase_C and azdO and vlmB)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
B590_RS00180: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B590_RS00185: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

B590_RS00225: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

B590_RS00230: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B590_RS00300: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

B590_RS00335: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B590_RS00375: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acylase aminotransferase transferase
B590_RS00235: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

B590_RS00290: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B590_RS00325: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

B590_RS00395: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Hydrolases: esterase hydrolase
B590_RS00305: thioesterase

smcogs
  SMCOG1004: thioesterase

B590_RS00310: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

B590_RS00340: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase
B590_RS00425: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Ligases: ligase synthase
B590_RS00255: 3-oxoacyl-(acyl carrier protein) synthase III

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

B590_RS00295: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B590_RS00355: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS00360: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS00370: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS00430: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B590_RS32940: 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 | azoxy-crosslink | T1PKS | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000849.4 |  |  |  | 1.00 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  |  |  | 0.97 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  |  |  | 0.74 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001273.3 |  |  |  | 0.43 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  |  | 0.43 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  |  |  | 0.41 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000204.5 |  |  |  | 0.39 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0000914.5 |  |  |  | 0.39 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0002578.2 |  |  |  | 0.38 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001065.5 |  |  |  | 0.36 | PKS | herboxidiene | Streptomyces chromofuscus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.78 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000850.5 |  | 0.70 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  | 0.64 | PKS | FR901512 | fungal sp. No.14919
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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: 17.58 out of 20.97
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 28.31 out of 30.12
Confidence: strong
Additional weak hits (21):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.70 out of 31.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.31 out of 26.85
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.49 out of 32.74
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.71 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.55 out of 20.01
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.60 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.93 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.48 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.48 out of 30.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.46 out of 36.53
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.96 out of 35.63
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.18 out of 29.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.09 out of 28.14
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.83 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.13 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.13 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 1, location 31519 - 130306:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - ccmal) + (ccmal) + (Me-ccmal - Me-ohmal - ohmal) + (Me-redmal) + (mal)
Non-colinear ordering:
  B590_RS00370 + B590_RS00290 + B590_RS32940 + B590_RS00360 + B590_RS00355

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 38104 - 130306:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - ccmal) + (ccmal) + (Me-ccmal - Me-ohmal - ohmal) + (Me-redmal) + (mal)
Non-colinear ordering:
  B590_RS00370 + B590_RS00290 + B590_RS32940 + B590_RS00360 + B590_RS00355

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).
B590_RS00290: mal
PKS_AT (547..842): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 174.9
  inactive: 105.9
  Methylmalonyl-CoA: 56.1
  Methoxymalonyl-CoA: 55.4
  Propionyl-CoA: 44.5
  Isobutyryl-CoA: 38.2
  2-Methylbutyryl-CoA: 26.9
  Acetyl-CoA: 18.7
  Benzoyl-CoA: 16.6
  Ethylmalonyl-CoA: 16.4
  CHC-CoA: 12.5
  fatty_acid: 10.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

B590_RS00295: X
AMP-binding (21..437): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMSFGIAGIGLFVAYGAAAQIYASTEAGSVAVC
  Nearest Stachelhaus code(s):
    Ant GIILFGVGVK (26% 8Å match)
  Stachelhaus code match:
    60% (weak)

B590_RS00355: mal
PKS_AT (570..874): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 66.7%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 160.6
  inactive: 69.6
  Methylmalonyl-CoA: 66.8
  Methoxymalonyl-CoA: 64.4
  Ethylmalonyl-CoA: 42.8
  Isobutyryl-CoA: 25.9
  Benzoyl-CoA: 25.9
  Propionyl-CoA: 25.8
  CHC-CoA: 19.4
  Acetyl-CoA: 19.0
  fatty_acid: 17.8
  trans-1,2-CPDA: 16.8
  2-Methylbutyryl-CoA: 11.1
  3-Methylbutyryl-CoA: 0.0

B590_RS00360: mmal
PKS_AT (570..868): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 206.0
  Ethylmalonyl-CoA: 191.1
  Methoxymalonyl-CoA: 164.1
  2-Methylbutyryl-CoA: 112.7
  Malonyl-CoA: 110.9
  Propionyl-CoA: 105.2
  trans-1,2-CPDA: 102.0
  CHC-CoA: 86.6
  Isobutyryl-CoA: 74.1
  Acetyl-CoA: 62.1
  Benzoyl-CoA: 60.6
  fatty_acid: 47.1
  inactive: 46.5
  3-Methylbutyryl-CoA: 27.3

B590_RS32940: mmal - mmal - mal
PKS_AT (571..870): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 210.9
  Ethylmalonyl-CoA: 203.2
  Methoxymalonyl-CoA: 167.8
  2-Methylbutyryl-CoA: 119.7
  trans-1,2-CPDA: 110.5
  Propionyl-CoA: 108.6
  Malonyl-CoA: 102.3
  CHC-CoA: 85.0
  Isobutyryl-CoA: 79.9
  Benzoyl-CoA: 55.8
  Acetyl-CoA: 46.3
  fatty_acid: 42.0
  inactive: 38.0
  3-Methylbutyryl-CoA: 17.3

PKS_AT (2366..2664): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 206.0
  Ethylmalonyl-CoA: 191.1
  Methoxymalonyl-CoA: 164.1
  2-Methylbutyryl-CoA: 112.7
  Malonyl-CoA: 110.9
  Propionyl-CoA: 105.2
  trans-1,2-CPDA: 102.0
  CHC-CoA: 86.6
  Isobutyryl-CoA: 74.1
  Acetyl-CoA: 62.1
  Benzoyl-CoA: 60.6
  fatty_acid: 47.1
  inactive: 46.5
  3-Methylbutyryl-CoA: 27.3

PKS_AT (3915..4205): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 223.1
  inactive: 103.4
  Methoxymalonyl-CoA: 70.8
  Methylmalonyl-CoA: 60.9
  Isobutyryl-CoA: 37.4
  Propionyl-CoA: 35.4
  Ethylmalonyl-CoA: 26.2
  Benzoyl-CoA: 21.2
  Acetyl-CoA: 21.0
  CHC-CoA: 18.1
  trans-1,2-CPDA: 15.8
  2-Methylbutyryl-CoA: 12.2
  fatty_acid: 11.9
  3-Methylbutyryl-CoA: 0.0

B590_RS00370: mmal - mal
PKS_AT (85..383): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 187.7
  Ethylmalonyl-CoA: 175.6
  Methoxymalonyl-CoA: 151.5
  2-Methylbutyryl-CoA: 125.1
  Malonyl-CoA: 103.9
  Propionyl-CoA: 101.5
  trans-1,2-CPDA: 88.4
  CHC-CoA: 85.5
  Isobutyryl-CoA: 67.7
  Benzoyl-CoA: 67.3
  inactive: 46.4
  Acetyl-CoA: 46.4
  3-Methylbutyryl-CoA: 34.8
  fatty_acid: 34.6

PKS_AT (1060..1354): 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: 215.6
  inactive: 112.9
  Methoxymalonyl-CoA: 69.9
  Methylmalonyl-CoA: 53.8
  Isobutyryl-CoA: 36.3
  Ethylmalonyl-CoA: 26.8
  Benzoyl-CoA: 20.4
  2-Methylbutyryl-CoA: 15.4
  CHC-CoA: 11.1
  fatty_acid: 9.4
  trans-1,2-CPDA: 8.5
  3-Methylbutyryl-CoA: 0.0
  Propionyl-CoA: -0.8
  Acetyl-CoA: -2.2

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

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
OsdR | Development and stress management regulator

NZ_CM002273.1 - Region 2 - NRPS,NRPS-like,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: 274,831 - 349,562 nt. (total: 74,732 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
B590_RS01110: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

B590_RS01115: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

B590_RS01125: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS01140: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS01230: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B590_RS01240: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

B590_RS01295: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: methyltransferase
B590_RS01330: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: deacetylase phosphatase
B590_RS01135: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

B590_RS01235: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Ligases: ligase synthase
B590_RS01220: 3-oxoacyl-(acyl carrier protein) synthase III

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

B590_RS01245: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B590_RS01250: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS01255: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | terpene | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  | 0.84 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  | 0.83 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  |  |  | 0.83 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  |  |  | 0.82 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  | 0.82 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 0.82 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  | 0.81 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  |  | 0.79 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001050.5 |  |  |  | 0.75 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0001166.5 |  |  |  | 0.75 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.73 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001050.5 |  | 0.71 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
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.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

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

Genes with terpene domains:
B590_RS01145: PT_phytoene_like
Domain 1 (279 - 513): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 27.07 out of 28.19
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.75 out of 23.05
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.62 out of 36.53
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
Additional weak hits (20):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.65 out of 27.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.24 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.41 out of 30.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.25 out of 33.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.05 out of 33.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.55 out of 36.53
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 11.72 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.24 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.67 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.78 out of 32.74
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.23 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.49 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.96 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.43 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 14.99 out of 31.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.01 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.20 out of 30.98
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.28 out of 29.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.78 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 5, location 274830 - 349562:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (mal - X) + (Thr - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 289198 - 331007:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (mal - X) + (Thr - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 291156 - 349562:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (mal - X) + (Thr - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B590_RS01245: X
AMP-binding (15..415): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MDRTWDGALLLPVSVLAGERNEYGPTETTVTVLA
  Nearest Stachelhaus code(s):
    OH-Orn DGEVVGGVTK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

B590_RS01250: X
AMP-binding (1245..1634): X
nrpys: Gly, 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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWSAFDISVLEAVALC-GEWNAYGPTECTVYATA
  Nearest Stachelhaus code(s):
    Gly DILQLGLVWK (65% 8Å match)
  Stachelhaus code match:
    60% (weak)

B590_RS01255: Thr - X
Search NORINE for peptide: strict or relaxed
AMP-binding (462..877): 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:
    LAAHFDFSVWEGNQVFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2560..2939): X
nrpys: Ile, 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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    RDASWDAVVYEAFLATGGDVHLYGPVENTTFSLG
  Nearest Stachelhaus code(s):
    Val or aIle DAYFLGVTFK (62% 8Å match)
    Val DAYFWGVTFK (56% 8Å match)
    Ile or Val DAYFWGVTFK (56% 8Å match)
    Ile DAYFWGVTFK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_CM002273.1 - Region 3 - NRPS,NRPS-like,T1PKS,T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 399,182 - 502,452 nt. (total: 103,271 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)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
B590_RS01635: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS01715: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

B590_RS01725: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B590_RS01755: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B590_RS01790: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

B590_RS33135: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Transferases: aminotransferase halogenase methyltransferase sulfotransferase
B590_RS01665: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

B590_RS01695: aminotransferase

smcogs
  SMCOG1019: aminotransferase

B590_RS01720: Sulfotransferase domain

extras
  Sulfotransfer_1: Sulfotransferase domain

B590_RS01735: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: esterase
B590_RS01760: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: hydratase lyase
B590_RS01675: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

B590_RS01700: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

B590_RS01705: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
B590_RS01650: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

B590_RS01680: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B590_RS01710: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

B590_RS01730: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B590_RS32955: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS33140: 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 | T3PKS | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002341.2 |  |  |  |  | 1.43 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002608.2 |  |  |  |  | 1.35 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0001132.4 |  |  |  |  | 1.08 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  |  |  |  | 1.08 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  |  |  |  | 1.06 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  |  | 1.02 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001807.4 |  |  |  |  | 1.01 | NRPS, PKS | totopotensamide A, totopotensamide B | Streptomyces pactum
BGC0001240.4 |  |  |  |  | 1.00 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000307.4 |  |  |  |  | 0.97 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000342.4 |  |  |  |  | 0.96 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0001132.4 |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002608.2 |  | 0.75 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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:
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 (9):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.43 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.22 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.34 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.86 out of 27.78
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.47 out of 36.54
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.09 out of 31.73
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.71 out of 39.62
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.07 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.68 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 9, location 399181 - 502452:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-ccmal - Me-ohmal - Me-redmal) + (Me-redmal - ohmal) + (Thr - Ala - Dab - X - X) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 399181 - 442403:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly) + (Thr - Ala - Dab - X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 11, location 407041 - 448184:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly) + (Thr - Ala - Dab - X - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 12, location 411462 - 470200:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-ccmal - Me-ohmal - Me-redmal) + (Me-redmal - ohmal) + (Thr - Ala - Dab - X - X) + (Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 431617 - 502452:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-ccmal - Me-ohmal - Me-redmal) + (Me-redmal - ohmal) + (Thr - Ala - Dab - X - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B590_RS33135: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (146..549): Gly
nrpys: Gly

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:
    HAKAFDISLWQSQLAVTGEVNCYGLTEVSDDSHH
  Nearest Stachelhaus code(s):
    Gly DIWQATCDDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

B590_RS01730: Thr - Ala - Dab - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (472..888): 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:
    LAAHFDFSVWEGSQVFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1576..1977): Ala
nrpys: Ala

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

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

AMP-binding (3290..3684): Dab
nrpys: Dab

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:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRAFDGSTVEVHLLTGADRSSYGPTEATVIATQ
  Nearest Stachelhaus code(s):
    Dab DGVHLGSVIK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4348..4751): X
nrpys: Dhpg, cl-me-dHpg

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:
    LPAGFDSTTFDALLLTGGEMNGYGPTESITYTHT
  Nearest Stachelhaus code(s):
    Dhpg or cl-me-dHpg DSFLLGGTYK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5416..5826): 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:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    QWMAFDASVWEWQFLCLGEHNLYGPTEASIAVTA
  Nearest Stachelhaus code(s):
    Ile DAWQLLLVAK (97% 8Å match)
  Stachelhaus code match:
    90% (moderate)

B590_RS32955: mmal - mal
PKS_AT (567..861): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 217.1
  Ethylmalonyl-CoA: 202.5
  Methoxymalonyl-CoA: 181.0
  2-Methylbutyryl-CoA: 161.8
  trans-1,2-CPDA: 132.7
  Propionyl-CoA: 122.3
  Malonyl-CoA: 114.9
  CHC-CoA: 102.9
  Isobutyryl-CoA: 77.5
  Benzoyl-CoA: 66.9
  inactive: 47.4
  3-Methylbutyryl-CoA: 47.4
  Acetyl-CoA: 44.2
  fatty_acid: 29.4

PKS_AT (2683..2981): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 186.5
  Methoxymalonyl-CoA: 72.2
  inactive: 67.3
  Methylmalonyl-CoA: 66.6
  Ethylmalonyl-CoA: 49.3
  Propionyl-CoA: 39.0
  2-Methylbutyryl-CoA: 25.9
  Isobutyryl-CoA: 22.4
  Benzoyl-CoA: 15.1
  Acetyl-CoA: 14.9
  CHC-CoA: 12.8
  trans-1,2-CPDA: 11.4
  fatty_acid: 11.1
  3-Methylbutyryl-CoA: 0.0

B590_RS33140: mal - mmal - mmal - mmal
PKS_AT (551..784): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 22.2
  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

PKS_AT (1566..1856): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 203.0
  Ethylmalonyl-CoA: 190.3
  Methoxymalonyl-CoA: 150.5
  2-Methylbutyryl-CoA: 125.3
  trans-1,2-CPDA: 117.2
  Propionyl-CoA: 108.5
  CHC-CoA: 98.1
  Malonyl-CoA: 97.8
  Isobutyryl-CoA: 65.9
  Benzoyl-CoA: 59.5
  Acetyl-CoA: 52.3
  fatty_acid: 38.3
  3-Methylbutyryl-CoA: 32.3
  inactive: 32.2

PKS_AT (3339..3634): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 193.1
  Ethylmalonyl-CoA: 177.8
  Methoxymalonyl-CoA: 138.3
  trans-1,2-CPDA: 104.1
  2-Methylbutyryl-CoA: 103.4
  Propionyl-CoA: 102.7
  Malonyl-CoA: 100.0
  CHC-CoA: 79.4
  Benzoyl-CoA: 49.7
  Isobutyryl-CoA: 46.8
  Acetyl-CoA: 44.6
  fatty_acid: 30.3
  inactive: 29.1
  3-Methylbutyryl-CoA: 25.2

PKS_AT (4887..5182): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 206.0
  Ethylmalonyl-CoA: 197.1
  Methoxymalonyl-CoA: 160.9
  2-Methylbutyryl-CoA: 134.2
  trans-1,2-CPDA: 118.2
  Propionyl-CoA: 117.4
  CHC-CoA: 95.2
  Malonyl-CoA: 94.8
  Benzoyl-CoA: 55.6
  Acetyl-CoA: 54.7
  Isobutyryl-CoA: 54.0
  3-Methylbutyryl-CoA: 37.5
  fatty_acid: 31.7
  inactive: 27.1

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

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
NtrC | Nitrogen regulatory protein C

NZ_CM002273.1 - Region 4 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 560,646 - 610,065 nt. (total: 49,420 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer oxygenase
B590_RS02130: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B590_RS02135: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

B590_RS02140: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

B590_RS02145: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

B590_RS02165: flavodoxin

smcogs
  SMCOG1134: flavodoxin

Transferases: acetyltransferase kinase
B590_RS02120: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

B590_RS02215: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Ligases: synthase
B590_RS02150: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001043.4 |  |  | 1.21 | NRPS, PKS | SGR PTMs, SGR PTM Compound b, SGR PTM Compound c, SGR PTM Compound d | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002365.2 |  |  | 1.21 | PKS, other (other) | 10-epi-HSAF, 10-epi-3-deOH-HSAF, 10-epi-maltophilin, 10-epi-xanthobaccin C, 10-epi-hydroxymaltophilin, 10-epi-FI-2 | Streptomyces sp.
BGC0000996.5 |  |  | 0.90 | NRPS, PKS | frontalamide B, frontalamide A | Streptomyces sp. SPB78
BGC0001273.3 |  |  | 0.90 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.90 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.89 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002075.3 |  |  | 0.83 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001726.4 |  |  | 0.75 | NRPS, PKS | pactamide A, pactamide B, pactamide C, pactamide D, pactamide E, pactamide F | Streptomyces pactum
BGC0001556.5 |  |  | 0.69 | NRPS, PKS | combamide | Streptomyces sp.
BGC0002509.3 |  |  | 0.69 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001043.4 |  | 0.84 | NRPS, PKS | SGR PTMs, SGR PTM Compound b, SGR PTM Compound c, SGR PTM Compound d | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002365.2 |  | 0.84 | PKS, other (other) | 10-epi-HSAF, 10-epi-3-deOH-HSAF, 10-epi-maltophilin, 10-epi-xanthobaccin C, 10-epi-hydroxymaltophilin, 10-epi-FI-2 | Streptomyces sp.
BGC0000996.5 |  | 0.75 | NRPS, PKS | frontalamide B, frontalamide A | Streptomyces sp. SPB78
BGC0001273.3 |  | 0.75 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.75 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001726.4 |  | 0.70 | NRPS, PKS | pactamide A, pactamide B, pactamide C, pactamide D, pactamide E, pactamide F | Streptomyces pactum
BGC0001556.5 |  | 0.68 | NRPS, PKS | combamide | Streptomyces sp.
BGC0002509.3 |  | 0.68 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | 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.

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: 16.38 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (16):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.18 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.69 out of 21.55
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.27 out of 19.26
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 14.97 out of 33.14
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 18.95 out of 27.04
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 35.63
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.86 out of 23.43
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.14 out of 31.73
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.79 out of 36.54
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.68 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.25 out of 28.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.24 out of 35.63
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.08 out of 27.04
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.03 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.62 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.06 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 14, location 560645 - 610065:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk - Orn)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B590_RS02150: pk - Orn
Search NORINE for peptide: strict or relaxed
PKS_AT (558..854): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 70.8%
  CE-Malonyl-CoA: 54.2%
  Acetyl-CoA: 54.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 103.7
  Methoxymalonyl-CoA: 96.6
  Malonyl-CoA: 92.4
  Ethylmalonyl-CoA: 85.6
  Propionyl-CoA: 63.6
  Isobutyryl-CoA: 60.5
  Benzoyl-CoA: 57.2
  Acetyl-CoA: 48.6
  trans-1,2-CPDA: 48.1
  2-Methylbutyryl-CoA: 46.3
  CHC-CoA: 31.9
  fatty_acid: 29.2
  inactive: 21.9
  3-Methylbutyryl-CoA: 13.6

AMP-binding (2314..2727): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    ASWAFDVFTGDRELIVGSDLNSYGVTEATIDSAC
  Nearest Stachelhaus code(s):
    Orn DVGEIGSIDK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein

NZ_CM002273.1 - Region 5 - 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: 647,179 - 673,737 nt. (total: 26,559 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
B590_RS02485: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

B590_RS02520: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase
B590_RS02460: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

B590_RS02525: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Ligases: synthetase
B590_RS02480: 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 |  | 0.69 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0001839.3 |  | 0.51 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000852.5 |  | 0.48 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000859.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium alcaliphilum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.69 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0001839.3 |  | 0.51 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000852.5 |  | 0.48 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000859.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium alcaliphilum

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:
B590_RS02475: T2TS
Domain 1 (25 - 656): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

B590_RS02480: PT_FPPS_like
Domain 1 (57 - 351): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

B590_RS02490: PT_phytoene_like
Domain 1 (17 - 299): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

B590_RS02495: PT_phytoene_like
Domain 1 (17 - 293): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.25 out of 29.72
Confidence: medium
Additional weak hits (6):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.44 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.96 out of 24.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.94 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
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.39 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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_CM002273.1 - Region 6 - 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: 740,680 - 750,895 nt. (total: 10,216 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
Ligases: ligase
B590_RS02820: 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 | 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
BGC0000554.4 |  | 0.45 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000504.5 |  | 0.43 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0000500.5 |  | 0.42 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000518.3 |  | 0.42 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736

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
BGC0000554.4 |  | 0.45 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000504.5 |  | 0.43 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0002151.2 |  | 0.43 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0002150.2 |  | 0.43 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0000500.5 |  | 0.42 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000518.3 |  | 0.42 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736

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 (4):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.07 out of 21.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.98 out of 35.63
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.97 out of 27.04
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator

NZ_CM002273.1 - Region 7 - PKS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 771,534 - 819,449 nt. (total: 47,916 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))
PKS-like: (t2pks2 or ksIII)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS 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 electron transfer oxidase
B590_RS02965: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B590_RS03020: flavodoxin

smcogs
  SMCOG1134: flavodoxin

B590_RS03030: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS03055: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

Hydrolases: hydrolase
B590_RS02985: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: synthase
B590_RS03045: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

B590_RS03050: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | T1PKS | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001276.3 |  |  | 0.60 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  |  | 0.60 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001275.3 |  |  | 0.58 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001254.3 |  |  | 0.55 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  |  | 0.55 | PKS | FR901512 | fungal sp. No.14919
BGC0001258.3 |  |  | 0.52 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0002228.3 |  |  | 0.36 | NRPS | CIML B, CIML A, CIML D, CIML C | Colletotrichum incanum
BGC0002227.3 |  |  | 0.35 | NRPS | AKML B, AKML D, AKML A, AKML C | Aspergillus luchuensis IFO 4308

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001275.3 |  | 0.63 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001258.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0002228.3 |  | 0.49 | NRPS | CIML B, CIML A, CIML D, CIML C | Colletotrichum incanum
BGC0002227.3 |  | 0.49 | NRPS | AKML B, AKML D, AKML A, AKML C | Aspergillus luchuensis IFO 4308

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
Additional weak hits (8):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.13 out of 30.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.65 out of 27.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.96 out of 27.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.33 out of 30.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.16 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.09 out of 30.98
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.27 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 17, location 771533 - 819449:
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).
B590_RS03045: mmal
PKS_AT (557..853): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 173.4
  Methoxymalonyl-CoA: 140.3
  Ethylmalonyl-CoA: 133.0
  2-Methylbutyryl-CoA: 121.2
  Malonyl-CoA: 101.9
  trans-1,2-CPDA: 101.8
  Propionyl-CoA: 97.2
  Isobutyryl-CoA: 82.9
  Benzoyl-CoA: 82.1
  CHC-CoA: 63.6
  Acetyl-CoA: 53.7
  3-Methylbutyryl-CoA: 48.6
  inactive: 36.2
  fatty_acid: 30.5

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_CM002273.1 - Region 8 - 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: 1,167,101 - 1,178,414 nt. (total: 11,314 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B590_RS04735: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: deacetylase
B590_RS04710: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001868.4 |  | 0.41 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0001221.5 |  | 0.33 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0001596.3 |  | 0.31 | PKS | fluostatin M, fluostatin N, fluostatin O, fluostatin P, fluostatin Q | Streptomyces albus
BGC0002788.2 |  | 0.30 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0001377.5 |  | 0.30 | PKS | uncialamycin | Streptomyces uncialis
BGC0001984.3 |  | 0.27 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0001060.5 |  | 0.27 | PKS | dynemicin A | Micromonospora chersina
BGC0000241.5 |  | 0.25 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440
BGC0001693.3 |  | 0.25 | PKS | nenestatin | Micromonospora echinospora
BGC0000240.5 |  | 0.24 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora pacifica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001868.4 |  | 0.41 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0001221.5 |  | 0.33 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0001596.3 |  | 0.31 | PKS | fluostatin M, fluostatin N, fluostatin O, fluostatin P, fluostatin Q | Streptomyces albus
BGC0002788.2 |  | 0.30 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0001377.5 |  | 0.30 | PKS | uncialamycin | Streptomyces uncialis
BGC0001984.3 |  | 0.27 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0001060.5 |  | 0.27 | PKS | dynemicin A | Micromonospora chersina
BGC0000241.5 |  | 0.25 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440
BGC0001693.3 |  | 0.25 | PKS | nenestatin | Micromonospora echinospora
BGC0000240.5 |  | 0.24 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora pacifica

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (1):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.23 out of 32.74
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CM002273.1 - Region 9 - 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: 1,452,319 - 1,485,318 nt. (total: 33,000 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
B590_RS05875: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
B590_RS05930: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
B590_RS05870: 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
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002633.2 |  | 0.51 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002470.2 |  | 0.50 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0001572.3 |  | 0.50 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000939.5 |  | 0.50 | other (other) | aerobactin | Grimontia hollisae

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
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002633.2 |  | 0.51 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002470.2 |  | 0.50 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0001572.3 |  | 0.50 | other (other) | desferrioxamine E | Pantoea agglomerans
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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 25.90 out of 27.18
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.14 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 (12):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.90 out of 30.22
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.37 out of 25.88
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.32 out of 27.18
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.85 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.07 out of 29.65
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.85 out of 26.06
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
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.89 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
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
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes

NZ_CM002273.1 - 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: 1,714,007 - 1,736,292 nt. (total: 22,286 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: transferase
B590_RS06985: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Lyases: cyclase
B590_RS07045: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase
B590_RS07055: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000122.5 |  | 0.36 | PKS | phenylnannolone A, phenylnannolone B, phenylnannolone C | Nannocystis pusilla
BGC0002284.3 |  | 0.34 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0001562.5 |  | 0.31 | NRPS | curacomycin | Streptomyces curacoi
BGC0002477.3 |  | 0.31 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0000727.3 |  | 0.30 | saccharide | indigoidine | Streptomyces aureofaciens
BGC0001940.3 |  | 0.30 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0002081.3 |  | 0.29 | PKS | streptoketide A, streptoketide B, streptoketide C, S2502, S2507, UWM5 | Streptomyces sp. Tue6314
BGC0000248.5 |  | 0.29 | PKS | α naphtocyclinoic acid, fogacin | Streptomyces arenae DSM 40737
BGC0000253.4 |  | 0.29 | PKS | oviedomycin | Streptomyces antibioticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000122.5 |  | 0.36 | PKS | phenylnannolone A, phenylnannolone B, phenylnannolone C | Nannocystis pusilla
BGC0002284.3 |  | 0.34 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0001562.5 |  | 0.31 | NRPS | curacomycin | Streptomyces curacoi
BGC0002477.3 |  | 0.31 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0000727.3 |  | 0.30 | saccharide | indigoidine | Streptomyces aureofaciens
BGC0001940.3 |  | 0.30 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0002081.3 |  | 0.29 | PKS | streptoketide A, streptoketide B, streptoketide C, S2502, S2507, UWM5 | Streptomyces sp. Tue6314
BGC0000248.5 |  | 0.29 | PKS | α naphtocyclinoic acid, fogacin | Streptomyces arenae DSM 40737
BGC0000253.4 |  | 0.29 | PKS | oviedomycin | Streptomyces antibioticus

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:
B590_RS07045: T1TS + T1TS
Domain 1 (2 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (351 - 717): 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 25.31
Confidence: medium
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
--- | ---
CatR | H2O2-responsive repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CM002273.1 - Region 11 - RRE-containing
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: 1,862,908 - 1,884,632 nt. (total: 21,725 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: dehydratase
B590_RS07710: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.71 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002343.3 |  | 0.34 | other (other), ribosomal | ammosester A, ammosester B, ammosester C, ammosamaic acid cogener | Streptomyces uncialis
BGC0001221.5 |  | 0.30 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0001335.5 |  | 0.27 | other (other) | borregomycin A, borregomycin B, borregomycin C, borregomycin D | uncultured bacterium
BGC0002805.2 |  | 0.25 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0000495.5 |  | 0.24 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0001484.3 |  | 0.23 | other (other) | 2'-chloropentostatin, 2'-amino-2'-deoxyadenosine | Actinomadura sp. ATCC 39365
BGC0000712.5 |  | 0.23 | saccharide | paromomycin | Streptomyces rimosus subsp. paromomycinus
BGC0001812.3 |  | 0.22 | PKS | tylactone | Micromonospora chalcea subsp. izumensis
BGC0000362.5 |  | 0.22 | NRPS | glycopeptidolipid | Mycobacterium avium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.71 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002343.3 |  | 0.34 | other (other), ribosomal | ammosester A, ammosester B, ammosester C, ammosamaic acid cogener | Streptomyces uncialis
BGC0001221.5 |  | 0.30 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0001335.5 |  | 0.27 | other (other) | borregomycin A, borregomycin B, borregomycin C, borregomycin D | uncultured bacterium
BGC0002805.2 |  | 0.25 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0000495.5 |  | 0.24 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0001484.3 |  | 0.23 | other (other) | 2'-chloropentostatin, 2'-amino-2'-deoxyadenosine | Actinomadura sp. ATCC 39365
BGC0000712.5 |  | 0.23 | saccharide | paromomycin | Streptomyces rimosus subsp. paromomycinus
BGC0001812.3 |  | 0.22 | PKS | tylactone | Micromonospora chalcea subsp. izumensis
BGC0000362.5 |  | 0.22 | NRPS | glycopeptidolipid | Mycobacterium avium

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.77 out of 27.55
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.25 out of 29.72
Confidence: medium
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (1862907...1884632)
B590_RS07710
  RRE type: Lanthipeptide_LanB_RRE
  Location: 155 - 248
  Score: 59.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
GnfM | Regulator of nitrogen-fixation genes
NtrC | Nitrogen regulatory protein C

NZ_CM002273.1 - Region 12 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,091,937 - 2,112,980 nt. (total: 21,044 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
B590_RS08680: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
B590_RS08725: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000678.5 |  | 0.41 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001605.3 |  | 0.40 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000340.5 |  | 0.38 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0000498.5 |  | 0.38 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0001910.4 |  | 0.38 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000561.5 |  | 0.38 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000678.5 |  | 0.41 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001605.3 |  | 0.40 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000340.5 |  | 0.38 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0000498.5 |  | 0.38 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0001910.4 |  | 0.38 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000561.5 |  | 0.38 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576

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

No significant matches found.

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

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

Genes with terpene domains:
B590_RS08725: PT_FPPS_like
Domain 1 (61 - 340): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (7):
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.14 out of 32.93
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.70 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.10 out of 30.98
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.69 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.89 out of 28.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CM002273.1 - Region 13 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,122,786 - 2,143,760 nt. (total: 20,975 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: oxygenase
B590_RS08855: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Hydrolases: deformylase
B590_RS08865: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Lyases: cyclase
B590_RS08860: 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
--- | --- | --- | --- | --- | ---
BGC0000660.5 |  | 0.81 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001911.3 |  | 0.41 | terpene | raimonol | Streptomyces anulatus
BGC0000678.5 |  | 0.37 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000650.3 |  | 0.36 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0002181.3 |  | 0.36 | terpene | pleuromutilin | Rhodocybe pseudopiperita
BGC0000286.3 |  | 0.36 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0002012.4 |  | 0.36 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000660.5 |  | 0.81 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001911.3 |  | 0.41 | terpene | raimonol | Streptomyces anulatus
BGC0000678.5 |  | 0.37 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000650.3 |  | 0.36 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0002181.3 |  | 0.36 | terpene | pleuromutilin | Rhodocybe pseudopiperita
BGC0000286.3 |  | 0.36 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0002012.4 |  | 0.36 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
B590_RS08860: T1TS
Domain 1 (2 - 303): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.29 out of 27.04
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.01 out of 27.18
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.21 out of 27.18
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.14 out of 24.78
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.17 out of 25.88
Confidence: medium
Additional weak hits (5):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.73 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.28 out of 27.04
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.57 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.46 out of 20.01
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes
PsrA | Oleic acid responsive regulator

NZ_CM002273.1 - Region 14 - RRE-containing,azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,603,848 - 2,638,520 nt. (total: 34,673 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase
B590_RS10955: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: amidase hydrolase
B590_RS10865: amidase

smcogs
  SMCOG1105: amidase

B590_RS10880: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

B590_RS10970: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: dehydratase
B590_RS10915: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | azole-containing-RiPP | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001145.5 |  |  | 0.42 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5 |  |  | 0.37 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001146.5 |  |  | 0.37 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000628.4 |  |  | 0.34 | ribosomal | lactocillin | Lactobacillus paragasseri JV-V03
BGC0000605.5 |  |  | 0.34 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0001640.3 |  |  | 0.33 | ribosomal | kocurin | Kocuria rosea
BGC0001472.5 |  |  | 0.33 | ribosomal | berninamycin A | Streptomyces bernensis
BGC0000569.5 |  |  | 0.32 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001860.4 |  |  | 0.32 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0002316.2 |  |  | 0.32 | ribosomal | cebulantin | Saccharopolyspora cebuensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001145.5 |  | 0.54 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5 |  | 0.51 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0000628.4 |  | 0.51 | ribosomal | lactocillin | Lactobacillus paragasseri JV-V03
BGC0001146.5 |  | 0.51 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000613.5 |  | 0.49 | ribosomal | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0001860.4 |  | 0.49 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0000605.5 |  | 0.48 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0001640.3 |  | 0.48 | ribosomal | kocurin | Kocuria rosea
BGC0001174.4 |  | 0.47 | ribosomal | corynazolicin | Corynebacterium urealyticum DSM 7111
BGC0001472.5 |  | 0.47 | ribosomal | berninamycin A | Streptomyces bernensis

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: 17.68 out of 20.47
Confidence: medium
Additional weak hits (5):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.79 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.83 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.21 out of 32.74
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.62 out of 21.55
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.71 out of 25.88
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (2603847...2636308)
B590_RS10930
  RRE type: Thiopeptide_F_RRE
  Location: 24 - 102
  Score: 59.7
  RRE type: Heterocycloanthracin_C_RRE
  Location: 23 - 107
  Score: 37.3
RRE-containing protocluster (2616297...2638520)
B590_RS10930
  RRE type: Thiopeptide_F_RRE
  Location: 24 - 102
  Score: 59.7
  RRE type: Heterocycloanthracin_C_RRE
  Location: 23 - 107
  Score: 37.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_CM002273.1 - Region 15 - lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,912,898 - 2,935,471 nt. (total: 22,574 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
B590_RS12325: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B590_RS12330: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: hydrolase
B590_RS12310: 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 | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.81 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.80 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000553.3 |  | 0.66 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000546.3 |  | 0.62 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0000513.3 |  | 0.60 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000501.3 |  | 0.56 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000518.3 |  | 0.55 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002073.3 |  | 0.50 | NRPS | dehydroxynocardamine | Corynebacterium propinquum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.81 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.80 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000553.3 |  | 0.66 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000546.3 |  | 0.62 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0000513.3 |  | 0.60 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000501.3 |  | 0.56 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000518.3 |  | 0.55 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002073.3 |  | 0.50 | NRPS | dehydroxynocardamine | Corynebacterium propinquum

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

No significant matches found.

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

#### Lanthipeptide(s) for B590_RS12285

B590_RS12280
Leader:
MALLDLQAMDTPQEEAVGDLAT
Core:
G S Q I S L L I C E Y S S L S V T L C T P
Core with dehydrations:
G Dha Q I Dha L L I Cys E Y Dha Dha L Dha V Dhb L Cys Dhb P

#### antiSMASH-DB 4.0 matches for B590_RS12280

100.0%
NC_020990.1 and 26 others:
NZ_AMPN02000002.1 Lanthipeptides: SM8_RS12785_lanthipeptide NZ_AP025692.1 Lanthipeptides: MTP06_RS18190_lanthipeptide NZ_CM002273.1 Lanthipeptides: B590_RS12280_lanthipeptide NZ_CP009802.1 Lanthipeptides: SFR_RS12925_lanthipeptide NZ_CP014485.1 Lanthipeptides: Salbus254_RS12710_lanthipeptide NZ_CP016824.1 Lanthipeptides: BEN82_RS18165_lanthipeptide NZ_CP026490.1 Lanthipeptides: C3K23_RS19520_lanthipeptide NZ_CP031742.1 Lanthipeptides: D0C37_RS13445_lanthipeptide NZ_CP047147.1 Lanthipeptides: GR131_RS18520_lanthipeptide NZ_CP053539.1 Lanthipeptides: HN026_RS11800_lanthipeptide NZ_CP056773.1 Lanthipeptides: HWN34_RS12245_lanthipeptide NZ_CP063844.1 Lanthipeptides: IPZ55_RS12410_lanthipeptide NZ_CP064783.1 Lanthipeptides: IT782_RS12060_lanthipeptide NZ_CP076385.1 Lanthipeptides: KNZ81_RS12450_lanthipeptide NZ_CP079112.1 Lanthipeptides: STALF2_RS18135_lanthipeptide NZ_CP091820.1 Lanthipeptides: L2I08_RS02835_lanthipeptide NZ_CP106650.1 Lanthipeptides: B591_RS12385_lanthipeptide NZ_CP113103.1 Lanthipeptides: OSU72_RS17905_lanthipeptide NZ_JAHUVY010000001.1 Lanthipeptides: STALF3_RS17905_lanthipeptide NZ_JALLPQ010000001.1 Lanthipeptides: MWG58_RS12385_lanthipeptide NZ_KB890715.1 Lanthipeptides: B048_RS0115750_lanthipeptide NZ_KN549183.1 Lanthipeptides: D076_RS30740_lanthipeptide NZ_KZ195583.1 Lanthipeptides: B9W68_RS12440_lanthipeptide NZ_MNPQ01000004.1 Lanthipeptides: BGV78_RS11170_lanthipeptide NZ_OX371412.1 Lanthipeptides: OZE77_RS18215_lanthipeptide NZ_VOGX01000092.1 Lanthipeptides: FRZ02_RS31600_lanthipeptide
Lanthipeptides: XNR_RS11575_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q I S L L I C E Y S S L S V T L C T P
1
G S Q I S L L I C E Y S S L S V T L C T P
21
95.2%
NZ_CM001165.1 and 4 others:
NZ_CP021118.1 Lanthipeptides: CAC01_RS28155_lanthipeptide NZ_CP049945.1 Lanthipeptides: G9U55_RS17850_lanthipeptide NZ_CP119149.1 Lanthipeptides: P0D76_RS02270_lanthipeptide NZ_RWGV01000033.1 Lanthipeptides: EJA11_RS20985_lanthipeptide
Lanthipeptides: STTU_RS29395_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L L I C E Y S S L S V T L C T P
1
G S Q V S L L I C E Y S S L S V T L C T P
21
90.5%
NZ_BDHJ01000008.1 and 4 others:
NZ_CP032543.1 Lanthipeptides: D6270_RS22715_lanthipeptide NZ_CP076457.1 Lanthipeptides: KME66_RS09945_lanthipeptide NZ_CP077652.1 Lanthipeptides: KRR37_RS22855_lanthipeptide NZ_WUEJ01000001.1 Lanthipeptides: GRQ63_RS04560_lanthipeptide
Lanthipeptides: BHQ08_RS03045_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L L+C E Y S S L S V T L C T P
1
G S Q V S L L V C E Y S S L S V T L C T P
21
with 70 more sequence matches
Only the first 10 are displayed here.
90.5%
NZ_CP045178.1:
Lanthipeptides: GBW32_RS28450_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L L I C E Y S S L S V L C T P
1
G S Q V S L L I C E Y S S L S V V L C T P
21
90.5%
NZ_ML123034.1:
Lanthipeptides: EES43_RS19795_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L L I C E+S S L S V T L C T P
1
G S Q V S L L I C E F S S L S V T L C T P
21
85.7%
NC_010572.1 and 60 others:
NC_021177.1 Lanthipeptides: SFUL_RS24355_lanthipeptide NZ_AQRK01000102.1 Lanthipeptides: YUW_RS30025_lanthipeptide NZ_ARPF01000003.1 Lanthipeptides: B083_RS0107255_lanthipeptide NZ_BMRY01000001.1 Lanthipeptides: IE140_RS02070_lanthipeptide NZ_BMSP01000003.1 Lanthipeptides: IE150_RS06495_lanthipeptide NZ_BMSZ01000003.1 Lanthipeptides: IE135_RS07550_lanthipeptide NZ_BMTW01000017.1 Lanthipeptides: IE134_RS28550_lanthipeptide NZ_BMUG01000009.1 Lanthipeptides: IE264_RS25430_lanthipeptide NZ_BMVK01000002.1 Lanthipeptides: IE272_RS07115_lanthipeptide NZ_BNBJ01000002.1 Lanthipeptides: IE304_RS05195_lanthipeptide NZ_CM003601.1 Lanthipeptides: JI76_RS25200_lanthipeptide NZ_CP010833.1 Lanthipeptides: TK78_RS10875_lanthipeptide NZ_CP011522.1 Lanthipeptides: ABE83_RS11805_lanthipeptide NZ_CP013738.1 Lanthipeptides: WQO_RS23525_lanthipeptide NZ_CP015362.1 Lanthipeptides: A6E92_RS09975_lanthipeptide NZ_CP020563.1 Lanthipeptides: B7C62_RS24450_lanthipeptide NZ_CP020570.1 Lanthipeptides: B1H20_RS34690_lanthipeptide NZ_CP024957.1 Lanthipeptides: CVT27_RS22730_lanthipeptide NZ_CP029361.1 Lanthipeptides: DIJ69_RS10225_lanthipeptide NZ_CP030930.1 Lanthipeptides: DTW94_RS22865_lanthipeptide NZ_CP061072.1 Lanthipeptides: HYC88_RS10560_lanthipeptide NZ_CP079114.1 Lanthipeptides: KV381_RS24895_lanthipeptide NZ_CP084357.1 Lanthipeptides: LEL86_RS29435_lanthipeptide NZ_CP086102.1 Lanthipeptides: LK895_RS11660_lanthipeptide NZ_CP090837.1 Lanthipeptides: LZ559_RS24025_lanthipeptide NZ_CP096281.1 Lanthipeptides: MWG59_RS25685_lanthipeptide NZ_CP101397.1 Lanthipeptides: NLU04_RS06465_lanthipeptide NZ_CP110539.1 Lanthipeptides: OH133_RS12690_lanthipeptide NZ_CP112880.1 Lanthipeptides: N7925_RS11185_lanthipeptide NZ_CP113262.1 Lanthipeptides: OUQ49_RS22935_lanthipeptide NZ_CP117709.1 Lanthipeptides: PSQ21_RS24530_lanthipeptide NZ_DS999644.1 Lanthipeptides: SSGG_RS09925_lanthipeptide NZ_GL877172.1 Lanthipeptides: SACT1_RS12960_lanthipeptide NZ_JAAWWP010000002.1 Lanthipeptides: HFV08_RS04115_lanthipeptide NZ_JAGGOV010000004.1 Lanthipeptides: J7E92_RS02930_lanthipeptide NZ_JAHHWT010000009.1 Lanthipeptides: KM153_RS24430_lanthipeptide NZ_JALDPQ010000064.1 Lanthipeptides: MQC87_RS23965_lanthipeptide NZ_JAMFLF010000002.1 Lanthipeptides: M1212_RS07295_lanthipeptide NZ_JANRMN010000004.1 Lanthipeptides: NW249_RS08610_lanthipeptide NZ_JNLT01000003.1 Lanthipeptides: CD02_RS0108685_lanthipeptide NZ_KB890925.1 Lanthipeptides: B053_RS0113845_lanthipeptide NZ_KL573549.1 Lanthipeptides: BG84_RS0119125_lanthipeptide NZ_KQ257779.1 Lanthipeptides: IQ60_RS22540_lanthipeptide NZ_KZ195572.1 Lanthipeptides: B9W61_RS11940_lanthipeptide NZ_KZ679082.1 Lanthipeptides: C6W96_RS24050_lanthipeptide NZ_KZ819154.1 Lanthipeptides: DBP12_RS10285_lanthipeptide NZ_KZ819178.1 Lanthipeptides: DBP20_RS23960_lanthipeptide NZ_KZ819182.1 Lanthipeptides: DBP21_RS24660_lanthipeptide NZ_LACR01000009.1 Lanthipeptides: YW5_RS12280_lanthipeptide NZ_LIPB01000001.1 Lanthipeptides: AMK17_RS03280_lanthipeptide NZ_LIPE01000001.1 Lanthipeptides: AMK12_RS03355_lanthipeptide NZ_LIVT01000001.1 Lanthipeptides: AMK24_RS01700_lanthipeptide NZ_LIVW01000001.1 Lanthipeptides: AMK28_RS03165_lanthipeptide NZ_LIXK01000001.1 Lanthipeptides: AMK23_RS04085_lanthipeptide NZ_LMEL01000012.1 Lanthipeptides: ASD29_RS10010_lanthipeptide NZ_LZRD01000054.1 Lanthipeptides: A3Q37_RS33745_lanthipeptide NZ_ML123117.1 Lanthipeptides: EES46_RS10300_lanthipeptide NZ_NNBN01000004.1 Lanthipeptides: CG717_RS12310_lanthipeptide NZ_VEHK01000004.1 Lanthipeptides: FS984_RS13530_lanthipeptide NZ_WWGD01000029.1 Lanthipeptides: GTY72_RS23245_lanthipeptide
Lanthipeptides: SGR_RS11800_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L L+C E Y S S L S V L C T P
1
G S Q V S L L V C E Y S S L S V V L C T P
21
85.7%
NZ_LWLE01000019.1:
Lanthipeptides: A6A29_RS44250_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L L I C E+S S L S+T L C T P
1
G S Q V S L L I C E H S S L S L T L C T P
21
81.0%
NZ_CP010519.1 and 1 other:
NZ_CP092644.1 Lanthipeptides: MID12_RS21330_lanthipeptide
Lanthipeptides: SLNWT_RS22370_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L L+C E Y S S L S V L C+P
1
G S Q V S L L V C E Y S S L S V V L C S P
21
81.0%
NZ_CP045702.1:
Lanthipeptides: F0344_RS33200_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L L+C E+S S L S+T L C T P
1
G S Q V S L L V C E H S S L S L T L C T P
21
81.0%
NZ_CP054926.1 and 11 others:
NZ_CP068598.1 Lanthipeptides: IFE09_RS23820_lanthipeptide NZ_CP071044.1 Lanthipeptides: JHY03_RS23495_lanthipeptide NZ_CP080029.1 Lanthipeptides: KZO11_RS24935_lanthipeptide NZ_JAJUKK010000008.1 Lanthipeptides: LXH09_RS27635_lanthipeptide NZ_JOJC01000009.1 Lanthipeptides: IO23_RS0108435_lanthipeptide NZ_KB891296.1 Lanthipeptides: B061_RS0103425_lanthipeptide NZ_KZ268499.1 Lanthipeptides: CE422_RS23450_lanthipeptide NZ_KZ819159.1 Lanthipeptides: DBP19_RS22830_lanthipeptide NZ_LR881952.1 Lanthipeptides: STRPST75_RS10975_lanthipeptide NZ_LZQS01000001.1 Lanthipeptides: STIB_RS05225_lanthipeptide NZ_RCOL01000001.1 Lanthipeptides: STAN_RS24840_lanthipeptide
Lanthipeptides: HUT09_RS23550_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L L+C E+S S L S V L C T P
1
G S Q V S L L V C E F S S L S V V L C T P
21
81.0%
NZ_CP058556.1 and 5 others:
NZ_CP059898.1 Lanthipeptides: H3V39_RS22935_lanthipeptide NZ_CP070242.1 Lanthipeptides: I6J39_RS23755_lanthipeptide NZ_CP070260.1 Lanthipeptides: I6J40_RS10935_lanthipeptide NZ_JAJDST010000047.1 Lanthipeptides: LJC81_RS16960_lanthipeptide NZ_WWGL01000003.1 Lanthipeptides: GTY38_RS03410_lanthipeptide
Lanthipeptides: HXS80_RS11105_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S+L+C E Y S S L S V L C T P
1
G S Q V S V L V C E Y S S L S V V L C T P
21
76.2%
NZ_AQRJ01000051.1 and 1 other:
NZ_LFBV01000002.1 Lanthipeptides: AB852_RS09920_lanthipeptide
Lanthipeptides: YW7_RS14945_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L++C E Y S S L S L C T P
1
G S Q V S L I V C E Y S S L S A L L C T P
21
66.7%
NZ_QGGR01000008.1:
Lanthipeptides: BC793_RS19230_lanthipeptide
1
G S Q I S L L I C E Y S S L S V T L C T
20
G S Q S L L+C S S L S V T C
2
G S Q A S L L L C G D S S L S V T T C N
21

#### MIBiG 4.0 matches for B590_RS12280

81.8%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
1
G S Q I S L L I C E Y S S L S V T L C T P
21
G S Q+S L L+C E Y S S L S V L C T P
2
G S Q V S L L V C E Y S S L S V V L C T P
22

#### 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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
Additional weak hits (4):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.30 out of 18.57
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.75 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.70 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.71 out of 26.06
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

B590_RS12280 - Class III
  Cleavage pHMM score: 30.10
  RODEO score: 0
  Monoisotopic mass: 2087.1 Da
  Molecular weight: 2088.4 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2106.4 Da N = 1
    2124.5 Da N = 2
    2142.5 Da N = 3
    2160.5 Da N = 4
    2178.5 Da N = 5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CM002273.1 - Region 16 - PKS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,070,808 - 3,111,761 nt. (total: 40,954 nt) Show pHMM detection rules used
PKS-like: (t2pks2 or ksIII)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
B590_RS13155: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

B590_RS13175: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: transferase
B590_RS13205: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: phosphatase
B590_RS13165: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Lyases: lyase
B590_RS13115: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

B590_RS13140: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: synthase
B590_RS13170: 3-oxoacyl-(acyl carrier protein) synthase III

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

Translocases: permease
B590_RS13090: 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 | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002313.3 |  | 0.51 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000387.5 |  | 0.48 | NRPS | mangotoxin | Pseudomonas syringae pv. syringae
BGC0002294.3 |  | 0.46 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0001985.4 |  | 0.44 | other (other) | Pyrazofurin | Streptomyces candidus
BGC0002536.3 |  | 0.44 | NRPS | alazopeptin | Kitasatospora azatica KCTC 9699
BGC0002151.2 |  | 0.42 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0002150.2 |  | 0.42 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0000131.5 |  | 0.42 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0001512.5 |  | 0.41 | PKS | BE-24566B | Streptomyces sp.
BGC0002039.3 |  | 0.41 | other (other) | coformycin, formycin A | Nocardia interforma ATCC 21072

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002313.3 |  | 0.51 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000387.5 |  | 0.48 | NRPS | mangotoxin | Pseudomonas syringae pv. syringae
BGC0002294.3 |  | 0.46 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0001985.4 |  | 0.44 | other (other) | Pyrazofurin | Streptomyces candidus
BGC0002536.3 |  | 0.44 | NRPS | alazopeptin | Kitasatospora azatica KCTC 9699
BGC0002151.2 |  | 0.42 | ribosomal | alboverticillin | Streptomyces griseocarneus
BGC0002150.2 |  | 0.42 | ribosomal | triculamin | Streptomyces triculaminicus
BGC0000131.5 |  | 0.42 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0001512.5 |  | 0.41 | PKS | BE-24566B | Streptomyces sp.
BGC0002039.3 |  | 0.41 | other (other) | coformycin, formycin A | Nocardia interforma ATCC 21072

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: 20.38 out of 23.79
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.07 out of 20.97
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.92 out of 27.04
Confidence: medium
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: 17.83 out of 20.47
Confidence: medium
Additional weak hits (9):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.60 out of 29.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.77 out of 27.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.99 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.83 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.65 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.12 out of 30.25
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.01 out of 32.93
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.07 out of 23.43
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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CcpA | Catabolite control protein A
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CM002273.1 - Region 17 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,750,249 - 3,812,487 nt. (total: 62,239 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
B590_RS16200: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acetyltransferase aminotransferase methyltransferase
B590_RS16145: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

B590_RS16250: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

B590_RS16255: aminotransferase

smcogs
  SMCOG1019: aminotransferase

B590_RS16285: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase
B590_RS16150: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

B590_RS16170: isochorismatase

smcogs
  SMCOG1027: isochorismatase

B590_RS16225: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase
B590_RS30245: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B590_RS34340: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001166.5 |  | 0.68 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.68 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001166.5 |  | 0.68 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001133.4 |  | 0.68 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.07 out of 30.12
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (15):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.82 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.05 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.68 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.28 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.67 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.34 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.38 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.60 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.84 out of 39.62
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.38 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.28 out of 23.43
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.19 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.51 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.01 out of 29.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.05 out of 27.55
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 27, location 3750248 - 3812487:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ile - D-Val - Trp) + (D-Thr - X - D-X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B590_RS34340: Thr - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (513..932): 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:
    LQTHFDFSVWEGNQVFGGEVNMYGITETTVHVTQ
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2054..2460): X
nrpys: Orn, Lys, Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    IAWTVDLFFADRELSVGSEVNAYGSTEVTIDATV
  Nearest Stachelhaus code(s):
    Arg DVADVGAIDK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (3117..3508): 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:
    TDFLFDGGVSDCMTGAAGDRNIYGPSETTLVATL
  Nearest Stachelhaus code(s):
    Phe DGWTGAILSK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

B590_RS30245: Ile - Val - Trp
Search NORINE for peptide: strict or relaxed
AMP-binding (28..428): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGQAWDGFAIEGFLMTGGELHVYGPMENGGYTTW
  Nearest Stachelhaus code(s):
    Leu DGFFLGVVYK (47% 8Å match)
    Ile DGFFLGVVYK (44% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1096..1494): 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:
    VGQAWDAFSLEGWLITGGEINGYGPVESMVFATA
  Nearest Stachelhaus code(s):
    Val DALWIGGVFK (62% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2620..3016): Trp
nrpys: Trp

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:
    YWASFDLTVTSPKAVLGGEVNEYGPTEATVGCME
  Nearest Stachelhaus code(s):
    Trp DLTKVGEVGK (85% 8Å match)
    Asn DLTKVGEVGK (74% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
OsdR | Development and stress management regulator

NZ_CM002273.1 - Region 18 - NRPS,azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,970,595 - 4,079,411 nt. (total: 108,817 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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
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Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Azole RiPPs
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
B590_RS17265: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: acyltransferase
B590_RS17215: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

B590_RS17220: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: hydrolase
B590_RS17225: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

B590_RS17260: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase
B590_RS17205: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B590_RS17210: 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001792.5 |  |  | 0.79 | NRPS | surugamide A, surugamide D | Streptomyces albidoflavus
BGC0001135.5 |  |  | 0.44 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.44 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  | 0.41 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  |  | 0.40 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.40 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  | 0.39 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.39 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  | 0.38 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  |  | 0.38 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001792.5 |  | 0.86 | NRPS | surugamide A, surugamide D | Streptomyces albidoflavus
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
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: 16.38 out of 19.26
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.16 out of 23.43
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (19):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.72 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.30 out of 27.78
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.08 out of 19.26
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.35 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.79 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.90 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.81 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 36.53
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.30 out of 36.54
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.31 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.02 out of 28.14
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.82 out of 27.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.82 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.80 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.49 out of 27.04
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.34 out of 29.65
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
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
RREFinder
TFBS Finder
Azole RiPPs
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 28, location 3970594 - 4079411:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ile - D-Ala - Ile - D-X - Lys) + (Trp - D-Leu - Val - Thr) + (Ile - D-Leu - Val - D-Ala - Val - D-Ala) + (X - D-Phe - D-Leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 29, location 3970594 - 4076299:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ile - D-Ala - Ile - D-X - Lys) + (Trp - D-Leu - Val - Thr) + (Ile - D-Leu - Val - D-Ala - Val - D-Ala) + (X - D-Phe - D-Leu)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B590_RS17205: X - Phe - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (504..890): X
nrpys: Ile, aIle

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:
    LDSSFDAATYEAFLWTGGEVHVYGPTETTTFAIS
  Nearest Stachelhaus code(s):
    Ile or aIle DAYFWGVTFK (94% 8Å match)
    Ile or Val DAYFWGVTFK (85% 8Å match)
    Leu DAYFWGVTFK (82% 8Å match)
    Val DAYFWGVTFK (82% 8Å match)
    Ile DAYFWGVTFK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1536..1941): Phe
nrpys: Phe

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

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

AMP-binding (3081..3478): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSLAFDASVLELLIFTGGEVNAYGPTETTVVATM
  Nearest Stachelhaus code(s):
    Leu DALLFGAVVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

B590_RS17210: Ile - Leu - Val - Ala - Val - Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (525..926): Ile
nrpys: Ile

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:
    RWFSFLDSVTEGTLVSSGELNLYGSSEISADSLA
  Nearest Stachelhaus code(s):
    Ile LDTTVSLADK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1587..1964): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FALAFDASVMEMLIATGGELNAYGPTEITVAASI
  Nearest Stachelhaus code(s):
    Leu DAMLAGAVAK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3090..3478): 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:
    LDHSFDAATYEVWIWTGGDVNGYGPTETTTFAVS
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4138..4508): 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:
    LWASFDVSVFEGSAVLAGEANIYGPTEATVYATG
  Nearest Stachelhaus code(s):
    Ala DVFSVAIVYK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5634..6025): 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:
    LDGSFDAATYEVWIWTGGDVNGYGPTETTTFAVT
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6686..7059): 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:
    LWASFDVSVFEGSGVLAGEANIYGPTEATVYATG
  Nearest Stachelhaus code(s):
    Ala DVFSVAIVYK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

B590_RS17215: Trp - Leu - Val - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (43..432): Trp
nrpys: Trp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAHVFDVAMADMMVVIGGEVNAYGPTEATVCTTL
  Nearest Stachelhaus code(s):
    Trp DVAMVGAVCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1104..1481): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FALAFDASVMEMLIATGGELNAYGPTEITVAASI
  Nearest Stachelhaus code(s):
    Leu DAMLAGAVAK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2622..3011): 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:
    LDHSFDAATYEVWIWTGGDVNGYGPTETTTFAVS
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3660..4072): 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:
    LATHFDFTVWEGNQVFGGEVNMYGITETTVHVTS
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

B590_RS17220: Ile - Ala - Ile - X - Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (19..406): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDTSFDAATYEVFLWTGGEVHVYGPTETTTFAVC
  Nearest Stachelhaus code(s):
    Ile DAYFWGVTFK (97% 8Å match)
    Ile or aIle DAYFWGVTFK (94% 8Å match)
    Ile or Val DAYFWGVTFK (88% 8Å match)
    Val DAYFWGVTFK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1059..1431): 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:
    LWASFDVSVFEGSAVLAGEANIYGPTEATVYATG
  Nearest Stachelhaus code(s):
    Ala DVFSVAIVYK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2567..2960): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDAATYEVFLWTGGEVHVYGPTEATTFALC
  Nearest Stachelhaus code(s):
    Ile DAYFWGVTFK (100% 8Å match)
    Ile or Val DAYFWGVTFK (88% 8Å match)
    Val DAYFWGVTFK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3624..4010): X
nrpys: Ile, aIle

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:
    LDSSFDAATYEAFLWTGGEVHVYGPTETTTFAIS
  Nearest Stachelhaus code(s):
    Ile or aIle DAYFWGVTFK (94% 8Å match)
    Ile or Val DAYFWGVTFK (85% 8Å match)
    Leu DAYFWGVTFK (82% 8Å match)
    Val DAYFWGVTFK (82% 8Å match)
    Ile DAYFWGVTFK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5135..5545): Lys
nrpys: Lys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    GSWAFDVFVSDHDTAGGADVNGYGVTEATVESCV
  Nearest Stachelhaus code(s):
    Lys DVSDAGGVEK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (4057119...4079411)
B590_RS17275
  RRE type: Goadsporin_CD_RRE
  Location: 17 - 113
  Score: 71.4
  RRE type: NHLP_CD_RRE
  Location: 18 - 110
  Score: 51.9
  RRE type: Cyanobactin_D_RRE
  Location: 17 - 94
  Score: 39.4

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
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.
No core peptides found.
NZ_CM002273.1 - Region 19 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,546,088 - 4,590,455 nt. (total: 44,368 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
B590_RS19530: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS19535: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS19560: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Hydrolases: esterase hydrolase
B590_RS19490: putative esterase

smcogs
  SMCOG1104: putative esterase

B590_RS19605: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

Lyases: lyase
B590_RS19520: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

B590_RS19525: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
B590_RS19500: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

B590_RS19540: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B590_RS19580: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000357.5 |  | 0.67 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0000342.4 |  | 0.63 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0002164.2 |  | 0.63 | NRPS | peramine | Epichloe festucae
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae
BGC0002276.2 |  | 0.63 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  | 0.63 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001833.4 |  | 0.61 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.61 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000357.5 |  | 0.67 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0000342.4 |  | 0.63 | NRPS | enniatin | Fusarium equiseti
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0002164.2 |  | 0.63 | NRPS | peramine | Epichloe festucae
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae
BGC0002276.2 |  | 0.63 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  | 0.63 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001833.4 |  | 0.61 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.61 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (13):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.32 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.74 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.18 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.00 out of 18.57
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.65 out of 19.26
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.47 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.58 out of 30.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.99 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.16 out of 21.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.72 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.27 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.44 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.31 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 31, location 4546087 - 4590455:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Asp)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B590_RS19540: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (6..422): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YSLTADLGNTCLKTLLGGEVNHYGPTETTVGVAA
  Nearest Stachelhaus code(s):
    Asp DLTKVGHVGK (71% 8Å match)
    OH-Asp DLTKVGHVGK (68% 8Å match)
    Asn DLTKLGEVGK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

NZ_CM002273.1 - Region 20 - 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: 4,774,002 - 4,803,822 nt. (total: 29,821 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 oxygenase
B590_RS20575: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

B590_RS20595: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS20620: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: carboxylase
B590_RS20630: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Lyases: decarboxylase
B590_RS20580: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: synthase
B590_RS20625: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

Translocases: transporter
B590_RS20505: 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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000941.3 |  | 0.83 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.78 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000940.5 |  | 0.71 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.71 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.63 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002690.2 |  | 0.59 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002284.3 |  | 0.57 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000941.3 |  | 0.83 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.78 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000940.5 |  | 0.71 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.71 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.63 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002690.2 |  | 0.59 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002284.3 |  | 0.57 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.84 out of 30.12
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 26.85
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 36.53 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 31.62 out of 36.53
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.65 out of 23.43
Confidence: medium
Additional weak hits (8):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.45 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.87 out of 20.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.23 out of 36.54
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.57 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.10 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.78 out of 27.18
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.67 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
BldD | Development and antibiotic global regulator
CelR | Cellobiose uptake repressor
DmdR1 | Iron(II)-dependent repressor
OsdR | Development and stress management regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CM002273.1 - Region 21 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,898,187 - 4,940,001 nt. (total: 41,815 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
B590_RS21115: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

B590_RS21145: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: aminotransferase glycosyltransferase
B590_RS21085: aminotransferase

smcogs
  SMCOG1019: aminotransferase

B590_RS21120: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Ligases: ligase
B590_RS21075: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B590_RS21110: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B590_RS21170: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.70 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002164.2 |  | 0.65 | NRPS | peramine | Epichloe festucae
BGC0001261.3 |  | 0.64 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.62 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.70 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002164.2 |  | 0.65 | NRPS | peramine | Epichloe festucae
BGC0001261.3 |  | 0.64 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.62 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.54 out of 23.79
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.88 out of 29.72
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (6):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.35 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.45 out of 30.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.71 out of 27.55
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.18 out of 27.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 33, location 4898186 - 4940001:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B590_RS21075: X
AMP-binding (5..404): X
nrpys: Ile, 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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FHLTFDATTFEALVFVGGEVNAYGPTETTTFVTR
  Nearest Stachelhaus code(s):
    Val DAFFFGGTFK (65% 8Å match)
    Ile or Val DAFWIGATFK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

B590_RS21110: X
AMP-binding (34..438): X
nrpys: Sma

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:
    NAVLNGVHLT-ASVVSAAALQGYGLTETTNFSTT
  Nearest Stachelhaus code(s):
    Sma GLTSVAGNFK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

B590_RS21170: X
AMP-binding (8..407): 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:
    YHVAFDASVFEADTMFSGEENNYGPTEAGVCVSY
  Nearest Stachelhaus code(s):
    Phe DAFVLSAVCK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_CM002273.1 - Region 22 - 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: 5,646,629 - 5,657,027 nt. (total: 10,399 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
B590_RS24280: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: aminotransferase
B590_RS24270: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

B590_RS24295: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

B590_RS24305: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

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

Reference | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.86 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.85 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.67 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.86 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.85 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.67 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000854.3 |  | 0.62 | 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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (9):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.04 out of 26.12
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.91 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.12 out of 27.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 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
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.04 out of 31.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.78 out of 28.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.95 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CM002273.1 - Region 23 - T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,244,612 - 6,317,103 nt. (total: 72,492 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 oxidase oxygenase
B590_RS27130: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B590_RS27155: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

B590_RS27180: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase acylase sulfhydrylase
B590_RS27035: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

B590_RS27160: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B590_RS27190: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

B590_RS27235: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

Hydrolases: dehalogenase
B590_RS27255: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: hydratase lyase
B590_RS27195: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

B590_RS27290: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
B590_RS27150: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B590_RS27170: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

B590_RS27175: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS27200: 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 | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000220.4 |  | 0.89 | PKS | enterocin | Streptomyces maritimus
BGC0002366.2 |  | 0.88 | PKS | enterocin, neoenterocin A, neoenterocin B | Streptomyces sp. SCSIO 11863
BGC0000231.5 |  | 0.69 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000272.3 |  | 0.61 | PKS | spore pigment | Streptomyces collinus
BGC0001723.5 |  | 0.58 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000221.5 |  | 0.58 | PKS | erdacin | uncultured soil bacterium V167
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001641.4 |  | 0.58 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000220.4 |  | 0.89 | PKS | enterocin | Streptomyces maritimus
BGC0002366.2 |  | 0.88 | PKS | enterocin, neoenterocin A, neoenterocin B | Streptomyces sp. SCSIO 11863
BGC0000231.5 |  | 0.69 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000272.3 |  | 0.61 | PKS | spore pigment | Streptomyces collinus
BGC0001723.5 |  | 0.58 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000221.5 |  | 0.58 | PKS | erdacin | uncultured soil bacterium V167
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001641.4 |  | 0.58 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
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
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.73 out of 26.85
Confidence: medium
Additional weak hits (22):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.64 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.00 out of 26.85
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.06 out of 32.74
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.37 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.82 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.97 out of 30.22
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.00 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.57 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.89 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.01 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.23 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.82 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.29 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.57 out of 35.63
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.97 out of 27.04
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.53 out of 26.06
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.53 out of 32.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.32 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).
B590_RS27150: X
AMP-binding (20..415): 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:
    AHYTHAYGLGSFFSISAAELDGVGSTEMLHIYCS
  Nearest Stachelhaus code(s):
    pNH2-Bz AYNFIAGSTK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

B590_RS27160: mal
PKS_AT (18..298): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 53.1
  Methoxymalonyl-CoA: 26.6
  Methylmalonyl-CoA: 22.9
  Propionyl-CoA: 18.1
  inactive: 17.2
  Benzoyl-CoA: 13.3
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

B590_RS27200: X
AMP-binding (36..422): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TMIQYMDPQWKMYVVLCSDREVYGSTESGLDLIM
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (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:
  6244611 to 6317103
Starter unit(s):
  benzoyl-CoA (Score: 2675.0; E-value: 0)
Malonyl elongations:
  7 (Score: 729.6; E-value: 2e-222)
Product molecular weight(s):
  benzoyl-CoA_7: 416 Da

B590_RS27150
  LIG (Score: 661.0; E-value: 2.4e-201)
  LIG AAF81733.1_Enterocin_benzoyl-CoA (Score: 1013.0; E-value: 0.0)
B590_RS27155
  OXY (Score: 35.2; E-value: 1.6e-11)
B590_RS27160
  AT (Score: 413.6; E-value: 1.4e-126)
  AT AAF81731.1_Enterocin_benzoyl-CoA (Score: 635.0; E-value: 0.0)
B590_RS27165
  ACP (Score: 89.8; E-value: 2e-28)
B590_RS27170
  CLF 7 (Score: 729.6; E-value: 2e-222)
B590_RS27175
  KS (Score: 720.3; E-value: 1.6e-219)
B590_RS27180
  KR C9 (Score: 409.1; E-value: 1.7e-125)
B590_RS27185
  MET (Score: 88.0; E-value: 1.4e-27)
B590_RS27200
  LIG (Score: 650.6; E-value: 3.3e-198)
  LIG AAF81723.1_Enterocin_benzoyl-CoA (Score: 1027.0; E-value: 0.0)
B590_RS27205
  CYC C1-C18|C2-C19 (Score: 174.2; E-value: 2.9e-54)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CM002273.1 - Region 24 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,432,939 - 6,461,129 nt. (total: 28,191 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 oxidoreductase oxygenase
B590_RS27905: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

B590_RS27940: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

B590_RS27965: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

B590_RS28025: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

B590_RS28035: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Ligases: synthase synthetase
B590_RS27935: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

B590_RS27990: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.73 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.67 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.64 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.64 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0001456.3 |  | 0.64 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000646.5 |  | 0.51 | terpene | β-carotein | uncultured bacterium
BGC0000648.3 |  | 0.51 | terpene | carotenoid | Myxococcus xanthus
BGC0000640.3 |  | 0.50 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000645.3 |  | 0.50 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000641.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC416

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.73 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.67 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.64 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.64 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0001456.3 |  | 0.64 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000646.5 |  | 0.51 | terpene | β-carotein | uncultured bacterium
BGC0000648.3 |  | 0.51 | terpene | carotenoid | Myxococcus xanthus
BGC0000640.3 |  | 0.50 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000645.3 |  | 0.50 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000641.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC416

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:
B590_RS27935: PT_FPPS_like
Domain 1 (70 - 366): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

B590_RS27945: PT_phytoene_like
Domain 1 (16 - 313): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

B590_RS27970: Lycopene_cycl
Domain 1 (5 - 382): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.48 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.85 out of 20.97
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.67 out of 28.19
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.34 out of 27.04
Confidence: strong
Additional weak hits (9):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.55 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.79 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.26 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.73 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.17 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.13 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.02 out of 26.06
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 18.77 out of 33.73
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
--- | ---
CcpA | Catabolite control protein A
DasR | N-acetylglucosamine dependent repressor
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems
ZuR variant 1 | Zinc-responsive repressor

NZ_CM002273.1 - Region 25 - 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: 6,542,195 - 6,553,562 nt. (total: 11,368 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
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.86 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0000513.3 |  | 0.43 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000519.4 |  | 0.42 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0001555.4 |  | 0.42 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000501.3 |  | 0.42 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0002005.2 |  | 0.41 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0001843.2 |  | 0.41 | NRPS | tridecaptin M | Paenibacillus sp. M-152
BGC0000554.4 |  | 0.41 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.86 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0000513.3 |  | 0.43 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000551.5 |  | 0.42 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000519.4 |  | 0.42 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0001555.4 |  | 0.42 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000501.3 |  | 0.42 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0002005.2 |  | 0.41 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0001843.2 |  | 0.41 | NRPS | tridecaptin M | Paenibacillus sp. M-152
BGC0000554.4 |  | 0.41 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (1):
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CM002273.1 - Region 26 - NRPS,NRPS-like,T1PKS,T3PKS,lanthipeptide-class-ii,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,555,445 - 6,858,963 nt. (total: 303,519 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
terpene-precursor: (PT_FPPS_like and not PT_HPP)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
B590_RS28530: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B590_RS28570: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

B590_RS28575: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B590_RS28580: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B590_RS28635: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS28730: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

B590_RS28815: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS28855: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

B590_RS28960: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS29065: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: acetyltransferase acylase acyltransferase aminotransferase formyltransferase glycosyltransferase halogenase
B590_RS28690: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B590_RS28695: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

B590_RS28735: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

B590_RS28740: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

B590_RS28860: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B590_RS28865: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

B590_RS28975: halogenase

smcogs
  SMCOG1119: halogenase

B590_RS32355: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: esterase protease
B590_RS28720: thioesterase

smcogs
  SMCOG1004: thioesterase

B590_RS28945: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

B590_RS29025: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase dehydratase
B590_RS28670: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

B590_RS28895: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Isomerases: isomerase
B590_RS28715: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase synthetase
B590_RS28525: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

B590_RS28645: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

B590_RS28675: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS28680: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS28685: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS28710: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS28850: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B590_RS28870: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B590_RS28885: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS28990: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS33825: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS34380: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS34385: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

Translocases: permease
B590_RS28470: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | T3PKS | T1PKS | terpene-precursor | NRPS-like | T1PKS | NRPS | lanthipeptide-class-ii | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000958.5 |  |  |  |  |  |  |  |  |  | 2.21 | NRPS, PKS | antimycin | Streptomyces sp. S4
BGC0001273.3 |  |  |  |  |  |  |  |  |  | 2.20 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  |  |  |  |  |  |  | 1.93 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001164.3 |  |  |  |  |  |  |  |  |  | 1.80 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  |  |  |  |  |  |  | 1.80 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001216.5 |  |  |  |  |  |  |  |  |  | 1.76 | NRPS, PKS | splenocin C | Streptomyces sp. CNQ431
BGC0002191.2 |  |  |  |  |  |  |  |  |  | 1.75 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001257.3 |  |  |  |  |  |  |  |  |  | 1.75 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  |  |  |  |  |  |  |  |  | 1.75 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001284.4 |  |  |  |  |  |  |  |  |  | 1.72 | PKS | alternariol | Parastagonospora nodorum SN15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000958.5 |  | 0.96 | NRPS, PKS | antimycin | Streptomyces sp. S4
BGC0000034.5 |  | 0.96 | NRPS, PKS | candicidin | Streptomyces sp. FR-008
BGC0001216.5 |  | 0.87 | NRPS, PKS | splenocin C | Streptomyces sp. CNQ431
BGC0001310.5 |  | 0.83 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0001455.6 |  | 0.81 | NRPS, PKS | antimycin A1B | Streptomyces argillaceus
BGC0001244.3 |  | 0.76 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  | 0.72 | 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.

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

#### Lanthipeptide(s) for B590_RS28895

allorf_6788528_6788713
Leader:
MGDGGTWGSGPHLSWRARRGPGG
Core:
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
Core with dehydrations:
R A G Dhb A R P H P R A A G Q V H R R A A Dhb Q V R G Cys R Cys A R A L Dhb R V Dha G P

#### antiSMASH-DB 4.0 matches for allorf_6788528_6788713

100.0%
NZ_CM002273.1 and 3 others:
NZ_CM002273.1 Lanthipeptides: allorf_6788528_6788713_lanthipeptide NZ_CP106650.1 Lanthipeptides: allorf_6778006_6778191_lanthipeptide NZ_CP106650.1 Lanthipeptides: allorf_6778006_6778191_lanthipeptide
Lanthipeptides: allorf_6788528_6788713_lanthipeptide
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
97.4%
NC_020990.1 and 1 other:
NC_020990.1 Lanthipeptides: allorf_6768184_6768369_lanthipeptide
Lanthipeptides: allorf_6768184_6768369_lanthipeptide
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
R A G T A R P H P R A A G V H R R A A T Q V R G C R C A R A L T R V S G P
1
R A G T A R P H P R A A G H V H R R A A T Q V R G C R C A R A L T R V S G P
38
94.7%
NZ_CP113103.1 and 1 other:
NZ_CP113103.1 Lanthipeptides: allorf_0072598_0072783_lanthipeptide
Lanthipeptides: allorf_0072598_0072783_lanthipeptide
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
R A G T A R P H R A A G V H R R A A T Q V R G C R C A R A L T R V S G P
1
R A G T A R P H L R A A G H V H R R A A T Q V R G C R C A R A L T R V S G P
38
with 8 more sequence matches
86.8%
NZ_MNPQ01000024.1 and 1 other:
NZ_MNPQ01000024.1 Lanthipeptides: allorf_033269_033448_lanthipeptide
Lanthipeptides: allorf_033269_033448_lanthipeptide
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
R A G T A P R A A G +H R R A A T Q V R G C R C A R A L T R V S G P
1
R A G T A--S P R A A G H L H R R A A T Q V R G C R C A R A L T R V S G P
36
57.9%
NZ_CP026490.1:
Lanthipeptides: allorf_0208403_0208621_lanthipeptide
5
A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
A R P+P R A A V R A T Q V +C +A L T R V S G P
5
A R P Y P R A A R H V R L R A T T Q V P V R Q C P K A L T R V S G P
38
55.3%
NZ_CP076385.1:
Lanthipeptides: allorf_6932531_6932749_lanthipeptide
5
A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
A R P+P R A A V A T Q V +C +A L T R V S G P
5
A R P Y P R A A R H V R L P A T T Q V P V R Q C P K A L T R V S G P
38
50.0%
NZ_CP009802.1 and 1 other:
NZ_CP009802.1 Lanthipeptides: allorf_7024728_7024922_lanthipeptide
Lanthipeptides: allorf_7024728_7024922_lanthipeptide
20
A T Q V R G C R C A R A L T R V S G P
38
A T Q V R G C R C A R A L T R V S G P
1
A T Q V R G C R C A R A L T R V S G P
19
26.3%
NZ_CP012109.1:
Lanthipeptides: A176_RS40855_lanthipeptide
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R
27
R A G + A G V R A+ G C
4
R A G G S D S A S V A G G S V S S R A S D S D V G C D
30
15.8%
NZ_CP061274.1:
Lanthipeptides: allorf_2084980_2085063_lanthipeptide
16
H R R A A T Q V R G C
26
H R R ++R G C
7
H R R L G G E M R G C
17
14.5%
NZ_CP067395.1 and 1 other:
NZ_CP072597.1 Lanthipeptides: J5226_RS17500_lanthipeptide
Lanthipeptides: JHW38_RS03590_lanthipeptide
19
A A T Q V R G C R C A R A L T R V S G
37
A A T Q +G C C+ +G
6
A A T Q S Q G C F C S T I Y Y N D A G
24
14.5%
NZ_FNOG01000005.1:
Lanthipeptides: BLU84_RS14530_lanthipeptide
19
A A T Q V R G C R C A R A L T R V S G P
38
A A T Q +G C C+ +G
6
A A T Q S Q G C F C S T I Y Y N D A G D
25

#### Lanthipeptide(s) for B590_RS28915

allorf_6788528_6788713
Leader:
MGDGGTWGSGPHLSWRARRGPGG
Core:
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
Core with dehydrations:
R A G Dhb A R P H P R A A G Q V H R R A A Dhb Q V R G Cys R Cys A R A L Dhb R V Dha G P

#### antiSMASH-DB 4.0 matches for allorf_6788528_6788713

100.0%
NZ_CM002273.1 and 3 others:
NZ_CM002273.1 Lanthipeptides: allorf_6788528_6788713_lanthipeptide NZ_CP106650.1 Lanthipeptides: allorf_6778006_6778191_lanthipeptide NZ_CP106650.1 Lanthipeptides: allorf_6778006_6778191_lanthipeptide
Lanthipeptides: allorf_6788528_6788713_lanthipeptide
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
97.4%
NC_020990.1 and 1 other:
NC_020990.1 Lanthipeptides: allorf_6768184_6768369_lanthipeptide
Lanthipeptides: allorf_6768184_6768369_lanthipeptide
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
R A G T A R P H P R A A G V H R R A A T Q V R G C R C A R A L T R V S G P
1
R A G T A R P H P R A A G H V H R R A A T Q V R G C R C A R A L T R V S G P
38
94.7%
NZ_CP113103.1 and 1 other:
NZ_CP113103.1 Lanthipeptides: allorf_0072598_0072783_lanthipeptide
Lanthipeptides: allorf_0072598_0072783_lanthipeptide
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
R A G T A R P H R A A G V H R R A A T Q V R G C R C A R A L T R V S G P
1
R A G T A R P H L R A A G H V H R R A A T Q V R G C R C A R A L T R V S G P
38
with 8 more sequence matches
86.8%
NZ_MNPQ01000024.1 and 1 other:
NZ_MNPQ01000024.1 Lanthipeptides: allorf_033269_033448_lanthipeptide
Lanthipeptides: allorf_033269_033448_lanthipeptide
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
R A G T A P R A A G +H R R A A T Q V R G C R C A R A L T R V S G P
1
R A G T A--S P R A A G H L H R R A A T Q V R G C R C A R A L T R V S G P
36
57.9%
NZ_CP026490.1:
Lanthipeptides: allorf_0208403_0208621_lanthipeptide
5
A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
A R P+P R A A V R A T Q V +C +A L T R V S G P
5
A R P Y P R A A R H V R L R A T T Q V P V R Q C P K A L T R V S G P
38
55.3%
NZ_CP076385.1:
Lanthipeptides: allorf_6932531_6932749_lanthipeptide
5
A R P H P R A A G Q V H R R A A T Q V R G C R C A R A L T R V S G P
38
A R P+P R A A V A T Q V +C +A L T R V S G P
5
A R P Y P R A A R H V R L P A T T Q V P V R Q C P K A L T R V S G P
38
50.0%
NZ_CP009802.1 and 1 other:
NZ_CP009802.1 Lanthipeptides: allorf_7024728_7024922_lanthipeptide
Lanthipeptides: allorf_7024728_7024922_lanthipeptide
20
A T Q V R G C R C A R A L T R V S G P
38
A T Q V R G C R C A R A L T R V S G P
1
A T Q V R G C R C A R A L T R V S G P
19
26.3%
NZ_CP012109.1:
Lanthipeptides: A176_RS40855_lanthipeptide
1
R A G T A R P H P R A A G Q V H R R A A T Q V R G C R
27
R A G + A G V R A+ G C
4
R A G G S D S A S V A G G S V S S R A S D S D V G C D
30
15.8%
NZ_CP061274.1:
Lanthipeptides: allorf_2084980_2085063_lanthipeptide
16
H R R A A T Q V R G C
26
H R R ++R G C
7
H R R L G G E M R G C
17
14.5%
NZ_CP067395.1 and 1 other:
NZ_CP072597.1 Lanthipeptides: J5226_RS17500_lanthipeptide
Lanthipeptides: JHW38_RS03590_lanthipeptide
19
A A T Q V R G C R C A R A L T R V S G
37
A A T Q +G C C+ +G
6
A A T Q S Q G C F C S T I Y Y N D A G
24
14.5%
NZ_FNOG01000005.1:
Lanthipeptides: BLU84_RS14530_lanthipeptide
19
A A T Q V R G C R C A R A L T R V S G P
38
A A T Q +G C C+ +G
6
A A T Q S Q G C F C S T I Y Y N D A G D
25

#### Legend:

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

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

Genes with terpene domains:
B590_RS28645: PT_FPPS_like
Domain 1 (80 - 368): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.29 out of 20.97
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
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 27.49 out of 30.12
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
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (34):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.64 out of 30.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.84 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.66 out of 31.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.14 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.02 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.88 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.96 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.15 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.43 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.86 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.49 out of 26.06
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.35 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.40 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.11 out of 30.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.77 out of 27.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.41 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.72 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.63 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.27 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.63 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.41 out of 27.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.72 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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.20 out of 30.11
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.65 out of 29.65
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.09 out of 30.11
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.49 out of 23.43
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.96 out of 28.14
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.77 out of 27.04
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

allorf_6788528_6788713 - Class II
  Cleavage pHMM score: -6.20
  RODEO score: 0
  Monoisotopic mass: 3975.2 Da
  Molecular weight: 3977.5 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3995.6 Da N = 1
    4013.6 Da N = 2
allorf_6788528_6788713 - Class II
  Cleavage pHMM score: -6.20
  RODEO score: 0
  Monoisotopic mass: 3975.2 Da
  Molecular weight: 3977.5 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3995.6 Da N = 1
    4013.6 Da N = 2

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 38, location 6555444 - 6858963:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - ohmal - pk - ohmal - ohmal - ohmal) + (redmal - redmal - ohmal - redmal) + (ccmal) + (Me-ohmal - Me-redmal - Me-ccmal) + (ccmal - ccmal - ccmal - ccmal - ccmal - ccmal) + (X - mal) + (mal) + (Thr - fatty_acid) + (Acetyl-CoA - mal - Pro) + (Gly - ccmal) + (mal - ohmal) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 40, location 6586774 - 6741992:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 42, location 6740583 - 6806925:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Acetyl-CoA - mal - Pro) + (Thr - fatty_acid) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 44, location 6794654 - 6858963:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - ccmal) + (mal - ohmal) + (mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
B590_RS28675: mal - mal - pk - mal - mal - mal
PKS_AT (558..859): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 216.0
  inactive: 89.9
  Methoxymalonyl-CoA: 53.9
  Methylmalonyl-CoA: 44.2
  Isobutyryl-CoA: 29.8
  Propionyl-CoA: 28.2
  Ethylmalonyl-CoA: 23.4
  2-Methylbutyryl-CoA: 23.0
  Acetyl-CoA: 18.1
  Benzoyl-CoA: 16.6
  CHC-CoA: 13.7
  trans-1,2-CPDA: 8.7
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2314..2621): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 217.0
  inactive: 103.4
  Methoxymalonyl-CoA: 60.8
  Methylmalonyl-CoA: 48.3
  Propionyl-CoA: 39.2
  Acetyl-CoA: 22.2
  Isobutyryl-CoA: 20.7
  2-Methylbutyryl-CoA: 19.3
  Benzoyl-CoA: 16.7
  Ethylmalonyl-CoA: 10.5
  trans-1,2-CPDA: 9.3
  CHC-CoA: 8.3
  fatty_acid: 8.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3873..4170): 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: 222.6
  Methylmalonyl-CoA: 220.9
  Methoxymalonyl-CoA: 179.9
  2-Methylbutyryl-CoA: 158.5
  trans-1,2-CPDA: 135.2
  Propionyl-CoA: 114.8
  CHC-CoA: 113.7
  Malonyl-CoA: 107.6
  Isobutyryl-CoA: 79.9
  Benzoyl-CoA: 63.4
  Acetyl-CoA: 52.3
  3-Methylbutyryl-CoA: 34.7
  fatty_acid: 31.5
  inactive: 29.2

PKS_AT (5407..5716): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 219.6
  inactive: 116.2
  Methoxymalonyl-CoA: 66.7
  Methylmalonyl-CoA: 59.0
  Isobutyryl-CoA: 29.0
  Propionyl-CoA: 21.9
  Benzoyl-CoA: 13.9
  CHC-CoA: 11.6
  Acetyl-CoA: 10.5
  fatty_acid: 9.5
  3-Methylbutyryl-CoA: 7.6
  trans-1,2-CPDA: 0.0
  2-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -3.1

PKS_AT (6936..7236): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 224.3
  inactive: 104.8
  Methoxymalonyl-CoA: 58.2
  Methylmalonyl-CoA: 48.7
  Propionyl-CoA: 26.4
  Acetyl-CoA: 19.1
  Benzoyl-CoA: 19.0
  CHC-CoA: 14.3
  Isobutyryl-CoA: 12.8
  Ethylmalonyl-CoA: 11.5
  2-Methylbutyryl-CoA: 10.8
  fatty_acid: 7.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (8465..8766): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 224.2
  inactive: 108.5
  Methoxymalonyl-CoA: 64.4
  Methylmalonyl-CoA: 58.4
  Isobutyryl-CoA: 34.8
  Ethylmalonyl-CoA: 32.3
  Propionyl-CoA: 22.3
  CHC-CoA: 21.0
  Benzoyl-CoA: 17.7
  Acetyl-CoA: 14.7
  2-Methylbutyryl-CoA: 12.5
  fatty_acid: 11.9
  trans-1,2-CPDA: 11.5
  3-Methylbutyryl-CoA: 0.0

B590_RS28680: mal - mal - mal - mal
PKS_AT (550..845): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 232.0
  inactive: 113.9
  Methoxymalonyl-CoA: 61.6
  Methylmalonyl-CoA: 57.1
  Benzoyl-CoA: 22.1
  Isobutyryl-CoA: 21.7
  Acetyl-CoA: 21.4
  Propionyl-CoA: 20.4
  Ethylmalonyl-CoA: 14.7
  fatty_acid: 13.0
  CHC-CoA: 11.2
  2-Methylbutyryl-CoA: 3.4
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2592..2891): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 203.4
  inactive: 95.5
  Methoxymalonyl-CoA: 55.1
  Methylmalonyl-CoA: 45.8
  Benzoyl-CoA: 19.2
  Acetyl-CoA: 17.2
  Isobutyryl-CoA: 17.1
  Ethylmalonyl-CoA: 13.8
  fatty_acid: 12.9
  Propionyl-CoA: 12.9
  CHC-CoA: 8.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (4635..4931): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 231.2
  inactive: 115.8
  Methoxymalonyl-CoA: 70.5
  Methylmalonyl-CoA: 62.9
  Propionyl-CoA: 36.0
  Isobutyryl-CoA: 28.6
  Ethylmalonyl-CoA: 23.2
  Benzoyl-CoA: 22.7
  fatty_acid: 21.1
  Acetyl-CoA: 19.7
  2-Methylbutyryl-CoA: 18.8
  CHC-CoA: 17.9
  trans-1,2-CPDA: 9.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (6160..6458): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 221.5
  inactive: 109.3
  Methoxymalonyl-CoA: 63.0
  Methylmalonyl-CoA: 55.4
  Propionyl-CoA: 25.5
  CHC-CoA: 22.1
  Acetyl-CoA: 21.0
  2-Methylbutyryl-CoA: 20.3
  Benzoyl-CoA: 20.2
  Ethylmalonyl-CoA: 19.7
  Isobutyryl-CoA: 16.8
  fatty_acid: 16.0
  trans-1,2-CPDA: 9.6
  3-Methylbutyryl-CoA: 0.0

B590_RS28685: mal
PKS_AT (547..843): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 218.3
  inactive: 112.4
  Methoxymalonyl-CoA: 59.1
  Methylmalonyl-CoA: 54.3
  Propionyl-CoA: 28.3
  Isobutyryl-CoA: 22.2
  Ethylmalonyl-CoA: 17.4
  Benzoyl-CoA: 16.1
  fatty_acid: 15.6
  Acetyl-CoA: 14.4
  CHC-CoA: 13.6
  trans-1,2-CPDA: 12.2
  2-Methylbutyryl-CoA: 1.4
  3-Methylbutyryl-CoA: 0.0

B590_RS28690: mmal - mmal - mmal
PKS_AT (573..870): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 215.1
  Ethylmalonyl-CoA: 210.1
  Methoxymalonyl-CoA: 166.3
  2-Methylbutyryl-CoA: 152.5
  trans-1,2-CPDA: 124.8
  Propionyl-CoA: 117.5
  Malonyl-CoA: 96.3
  CHC-CoA: 91.4
  Isobutyryl-CoA: 68.9
  Benzoyl-CoA: 63.6
  Acetyl-CoA: 47.6
  fatty_acid: 40.6
  inactive: 38.7
  3-Methylbutyryl-CoA: 33.0

PKS_AT (2141..2438): 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: 215.1
  Ethylmalonyl-CoA: 210.1
  Methoxymalonyl-CoA: 165.9
  2-Methylbutyryl-CoA: 152.9
  trans-1,2-CPDA: 126.0
  Propionyl-CoA: 117.8
  Malonyl-CoA: 94.5
  CHC-CoA: 92.4
  Isobutyryl-CoA: 71.1
  Benzoyl-CoA: 65.4
  Acetyl-CoA: 49.4
  fatty_acid: 42.2
  inactive: 38.3
  3-Methylbutyryl-CoA: 34.2

PKS_AT (4248..4545): 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: 206.1
  Ethylmalonyl-CoA: 202.9
  Methoxymalonyl-CoA: 169.3
  2-Methylbutyryl-CoA: 131.7
  trans-1,2-CPDA: 129.8
  Propionyl-CoA: 108.2
  Malonyl-CoA: 103.0
  CHC-CoA: 98.2
  Isobutyryl-CoA: 71.5
  Benzoyl-CoA: 57.5
  Acetyl-CoA: 41.0
  inactive: 38.2
  fatty_acid: 30.1
  3-Methylbutyryl-CoA: 28.7

B590_RS28695: mal - mal - mal - mal - mal - mal
PKS_AT (578..870): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 230.9
  inactive: 106.8
  Methoxymalonyl-CoA: 56.2
  Methylmalonyl-CoA: 49.8
  Propionyl-CoA: 29.7
  Benzoyl-CoA: 21.5
  Isobutyryl-CoA: 20.6
  Ethylmalonyl-CoA: 18.0
  Acetyl-CoA: 16.3
  trans-1,2-CPDA: 12.9
  fatty_acid: 12.5
  2-Methylbutyryl-CoA: 12.4
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2320..2612): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 227.2
  inactive: 109.3
  Methoxymalonyl-CoA: 57.7
  Methylmalonyl-CoA: 47.4
  Propionyl-CoA: 27.5
  Isobutyryl-CoA: 20.6
  Benzoyl-CoA: 20.4
  Acetyl-CoA: 19.9
  Ethylmalonyl-CoA: 14.1
  2-Methylbutyryl-CoA: 11.9
  fatty_acid: 10.9
  trans-1,2-CPDA: 9.1
  CHC-CoA: 3.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4061..4351): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 218.1
  inactive: 99.7
  Methoxymalonyl-CoA: 52.2
  Methylmalonyl-CoA: 47.4
  Acetyl-CoA: 26.2
  Propionyl-CoA: 21.9
  Benzoyl-CoA: 13.9
  Isobutyryl-CoA: 12.0
  2-Methylbutyryl-CoA: 10.0
  Ethylmalonyl-CoA: 9.9
  CHC-CoA: 9.2
  fatty_acid: 8.3
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5777..6069): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 229.5
  inactive: 111.7
  Methoxymalonyl-CoA: 54.8
  Methylmalonyl-CoA: 54.0
  Propionyl-CoA: 31.4
  Acetyl-CoA: 24.0
  Ethylmalonyl-CoA: 19.0
  Benzoyl-CoA: 18.6
  trans-1,2-CPDA: 18.0
  Isobutyryl-CoA: 17.6
  fatty_acid: 13.1
  2-Methylbutyryl-CoA: 12.3
  CHC-CoA: 3.4
  3-Methylbutyryl-CoA: 0.0

PKS_AT (7492..7783): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 221.2
  inactive: 95.5
  Methoxymalonyl-CoA: 54.3
  Methylmalonyl-CoA: 47.9
  Propionyl-CoA: 29.8
  Acetyl-CoA: 20.9
  Ethylmalonyl-CoA: 19.1
  Isobutyryl-CoA: 17.8
  Benzoyl-CoA: 13.3
  fatty_acid: 9.9
  trans-1,2-CPDA: 9.6
  2-Methylbutyryl-CoA: 7.7
  3-Methylbutyryl-CoA: 0.0
  CHC-CoA: -0.6

PKS_AT (9333..9622): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 75.0%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 210.5
  inactive: 88.7
  Methoxymalonyl-CoA: 41.1
  Methylmalonyl-CoA: 38.9
  Propionyl-CoA: 28.5
  Acetyl-CoA: 25.0
  Ethylmalonyl-CoA: 15.9
  Isobutyryl-CoA: 11.1
  Benzoyl-CoA: 9.9
  2-Methylbutyryl-CoA: 6.7
  CHC-CoA: 6.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

B590_RS28710: X - mal
AMP-binding (30..440): 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:
    NAALF--GLQSSVALTAGAVVVWGMSEAGNGTSS
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

PKS_AT (1204..1498): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 198.6
  inactive: 90.5
  Methoxymalonyl-CoA: 67.2
  Methylmalonyl-CoA: 57.1
  Isobutyryl-CoA: 48.8
  Ethylmalonyl-CoA: 32.4
  Acetyl-CoA: 31.4
  Propionyl-CoA: 31.1
  2-Methylbutyryl-CoA: 23.2
  Benzoyl-CoA: 20.3
  fatty_acid: 18.9
  CHC-CoA: 11.6
  trans-1,2-CPDA: 11.0
  3-Methylbutyryl-CoA: 7.1

B590_RS28850: X
AMP-binding (7..402): X
nrpys: Pyv, Ant

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:
    IGWCHGSMVVSTWMLYGAARQVYGMTEVGGFVTL
  Nearest Stachelhaus code(s):
    Pyv or Ant GSVWLGVGFK (100% 8Å match)
    Ant GSVWLGVGFK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

B590_RS28860: mal
PKS_AT (543..825): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 125.5
  inactive: 68.7
  Methoxymalonyl-CoA: 59.2
  Methylmalonyl-CoA: 39.2
  Ethylmalonyl-CoA: 23.7
  Propionyl-CoA: 23.3
  Isobutyryl-CoA: 15.1
  Benzoyl-CoA: 13.3
  Acetyl-CoA: 10.3
  fatty_acid: 9.4
  2-Methylbutyryl-CoA: 3.8
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

B590_RS28865: Thr - fatty_acid
Search NORINE for peptide: strict or relaxed
AMP-binding (461..875): 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:
    LASHFDFSVWEGNQVLGGEVNMYGITETTVHVTF
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

CAL_domain (1710..2121): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 16.7
  Acetyl-CoA: 13.3
  AHBA: 6.5
  NH2: 1.5
  shikimic_acid: 0.0

B590_RS28885: Acetyl-CoA - mal - Pro
Search NORINE for peptide: strict or relaxed
CAL_domain (54..488): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 22.3
  AHBA: 16.0
  fatty_acid: 14.9
  NH2: 10.7
  shikimic_acid: 0.0

PKS_AT (1197..1479): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 58.3%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 102.4
  inactive: 54.5
  Methylmalonyl-CoA: 46.9
  Methoxymalonyl-CoA: 38.8
  Propionyl-CoA: 37.1
  fatty_acid: 24.5
  CHC-CoA: 19.4
  Ethylmalonyl-CoA: 18.4
  2-Methylbutyryl-CoA: 16.8
  trans-1,2-CPDA: 15.4
  Benzoyl-CoA: 14.7
  Isobutyryl-CoA: 12.7
  3-Methylbutyryl-CoA: 8.6
  Acetyl-CoA: 7.9

AMP-binding (2584..2978): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGHTFDVSVQETFMYSAGEYNQYGPTETSVIVTS
  Nearest Stachelhaus code(s):
    Pro DVQFIAQVVK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

B590_RS32355: Gly - mal
Search NORINE for peptide: strict or relaxed
AMP-binding (567..948): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGITFDISLLELQALSGGEWNLYGPTEATVWASS
  Nearest Stachelhaus code(s):
    Gly DILQLGLVWK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

PKS_AT (2717..3006): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 119.4
  inactive: 71.1
  Methylmalonyl-CoA: 56.2
  Methoxymalonyl-CoA: 55.5
  Propionyl-CoA: 28.2
  Ethylmalonyl-CoA: 26.3
  Isobutyryl-CoA: 24.6
  Benzoyl-CoA: 17.1
  fatty_acid: 15.8
  2-Methylbutyryl-CoA: 9.0
  CHC-CoA: 8.0
  trans-1,2-CPDA: 4.8
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

B590_RS33825: mal
PKS_AT (535..831): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 75.0%
  Isobutyryl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 138.1
  Methoxymalonyl-CoA: 58.0
  inactive: 54.5
  Methylmalonyl-CoA: 53.4
  Propionyl-CoA: 42.5
  fatty_acid: 29.3
  Isobutyryl-CoA: 23.8
  Ethylmalonyl-CoA: 21.4
  2-Methylbutyryl-CoA: 9.3
  trans-1,2-CPDA: 9.2
  CHC-CoA: 9.0
  Benzoyl-CoA: 9.0
  Acetyl-CoA: 7.1
  3-Methylbutyryl-CoA: 0.0

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

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

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
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
OsdR | Development and stress management regulator

NZ_CM002273.1 - Region 27 - T1PKS,azoxy-crosslink,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: 6,877,212 - 6,975,998 nt. (total: 98,787 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
butyrolactone: AfsA
azoxy-crosslink: (azdH and LPG_synthase_C and azdO and vlmB)

#### 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
B590_RS35075: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

B590_RS35120: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B590_RS35160: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

B590_RS35230: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

B590_RS35235: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

B590_RS35280: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

B590_RS35285: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: PPTase acylase aminotransferase transferase
B590_RS35055: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

B590_RS35130: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

B590_RS35170: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

B590_RS35225: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: esterase hydrolase
B590_RS35115: thioesterase

smcogs
  SMCOG1004: thioesterase

B590_RS35150: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

B590_RS35155: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase
B590_RS35025: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Ligases: ligase synthase
B590_RS35020: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

B590_RS35080: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS35085: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS35090: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS35095: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

B590_RS35165: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

B590_RS35205: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | T1PKS | butyrolactone | azoxy-crosslink | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000849.4 |  |  |  | 1.00 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  |  |  | 0.97 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  |  |  | 0.74 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001273.3 |  |  |  | 0.43 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  |  | 0.43 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  |  |  | 0.41 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000204.5 |  |  |  | 0.39 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0000914.5 |  |  |  | 0.39 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0002578.2 |  |  |  | 0.38 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001065.5 |  |  |  | 0.36 | PKS | herboxidiene | Streptomyces chromofuscus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.78 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000850.5 |  | 0.70 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  | 0.64 | PKS | FR901512 | fungal sp. No.14919
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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: 17.58 out of 20.97
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 28.31 out of 30.12
Confidence: strong
Additional weak hits (21):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.83 out of 26.85
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.09 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.18 out of 29.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.48 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.48 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.93 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.60 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.49 out of 32.74
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.70 out of 31.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.13 out of 29.65
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.13 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.96 out of 35.63
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.46 out of 36.53
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.55 out of 20.01
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.31 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.71 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 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 45, location 6877211 - 6975998:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - ccmal) + (Me-ccmal - Me-ohmal - ohmal) + (Me-redmal) + (ccmal) + (mal)
Non-colinear ordering:
  B590_RS35080 + B590_RS35085 + B590_RS35090 + B590_RS35170 + B590_RS35095

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 46, location 6877211 - 6969413:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - ccmal) + (Me-ccmal - Me-ohmal - ohmal) + (Me-redmal) + (ccmal) + (mal)
Non-colinear ordering:
  B590_RS35080 + B590_RS35085 + B590_RS35090 + B590_RS35170 + B590_RS35095

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).
B590_RS35080: mmal - mal
PKS_AT (85..383): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 187.7
  Ethylmalonyl-CoA: 175.6
  Methoxymalonyl-CoA: 151.5
  2-Methylbutyryl-CoA: 125.1
  Malonyl-CoA: 103.9
  Propionyl-CoA: 101.5
  trans-1,2-CPDA: 88.4
  CHC-CoA: 85.5
  Isobutyryl-CoA: 67.7
  Benzoyl-CoA: 67.3
  inactive: 46.4
  Acetyl-CoA: 46.4
  3-Methylbutyryl-CoA: 34.8
  fatty_acid: 34.6

PKS_AT (1060..1354): 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: 215.6
  inactive: 112.9
  Methoxymalonyl-CoA: 69.9
  Methylmalonyl-CoA: 53.8
  Isobutyryl-CoA: 36.3
  Ethylmalonyl-CoA: 26.8
  Benzoyl-CoA: 20.4
  2-Methylbutyryl-CoA: 15.4
  CHC-CoA: 11.1
  fatty_acid: 9.4
  trans-1,2-CPDA: 8.5
  3-Methylbutyryl-CoA: 0.0
  Propionyl-CoA: -0.8
  Acetyl-CoA: -2.2

B590_RS35085: mmal - mmal - mal
PKS_AT (571..870): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 210.9
  Ethylmalonyl-CoA: 203.2
  Methoxymalonyl-CoA: 167.8
  2-Methylbutyryl-CoA: 119.7
  trans-1,2-CPDA: 110.5
  Propionyl-CoA: 108.6
  Malonyl-CoA: 102.3
  CHC-CoA: 85.0
  Isobutyryl-CoA: 79.9
  Benzoyl-CoA: 55.8
  Acetyl-CoA: 46.3
  fatty_acid: 42.0
  inactive: 38.0
  3-Methylbutyryl-CoA: 17.3

PKS_AT (2366..2664): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 206.0
  Ethylmalonyl-CoA: 191.1
  Methoxymalonyl-CoA: 164.1
  2-Methylbutyryl-CoA: 112.7
  Malonyl-CoA: 110.9
  Propionyl-CoA: 105.2
  trans-1,2-CPDA: 102.0
  CHC-CoA: 86.6
  Isobutyryl-CoA: 74.1
  Acetyl-CoA: 62.1
  Benzoyl-CoA: 60.6
  fatty_acid: 47.1
  inactive: 46.5
  3-Methylbutyryl-CoA: 27.3

PKS_AT (3915..4205): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 223.1
  inactive: 103.4
  Methoxymalonyl-CoA: 70.8
  Methylmalonyl-CoA: 60.9
  Isobutyryl-CoA: 37.4
  Propionyl-CoA: 35.4
  Ethylmalonyl-CoA: 26.2
  Benzoyl-CoA: 21.2
  Acetyl-CoA: 21.0
  CHC-CoA: 18.1
  trans-1,2-CPDA: 15.8
  2-Methylbutyryl-CoA: 12.2
  fatty_acid: 11.9
  3-Methylbutyryl-CoA: 0.0

B590_RS35090: mmal
PKS_AT (570..868): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 206.0
  Ethylmalonyl-CoA: 191.1
  Methoxymalonyl-CoA: 164.1
  2-Methylbutyryl-CoA: 112.7
  Malonyl-CoA: 110.9
  Propionyl-CoA: 105.2
  trans-1,2-CPDA: 102.0
  CHC-CoA: 86.6
  Isobutyryl-CoA: 74.1
  Acetyl-CoA: 62.1
  Benzoyl-CoA: 60.6
  fatty_acid: 47.1
  inactive: 46.5
  3-Methylbutyryl-CoA: 27.3

B590_RS35095: mal
PKS_AT (570..874): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 66.7%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 160.6
  inactive: 69.6
  Methylmalonyl-CoA: 66.8
  Methoxymalonyl-CoA: 64.4
  Ethylmalonyl-CoA: 42.8
  Isobutyryl-CoA: 25.9
  Benzoyl-CoA: 25.9
  Propionyl-CoA: 25.8
  CHC-CoA: 19.4
  Acetyl-CoA: 19.0
  fatty_acid: 17.8
  trans-1,2-CPDA: 16.8
  2-Methylbutyryl-CoA: 11.1
  3-Methylbutyryl-CoA: 0.0

B590_RS35165: X
AMP-binding (21..437): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAMSFGIAGIGLFVAYGAAAQIYASTEAGSVAVC
  Nearest Stachelhaus code(s):
    Ant GIILFGVGVK (26% 8Å match)
  Stachelhaus code match:
    60% (weak)

B590_RS35170: mal
PKS_AT (547..842): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 174.9
  inactive: 105.9
  Methylmalonyl-CoA: 56.1
  Methoxymalonyl-CoA: 55.4
  Propionyl-CoA: 44.5
  Isobutyryl-CoA: 38.2
  2-Methylbutyryl-CoA: 26.9
  Acetyl-CoA: 18.7
  Benzoyl-CoA: 16.6
  Ethylmalonyl-CoA: 16.4
  CHC-CoA: 12.5
  fatty_acid: 10.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
OsdR | Development and stress management regulator