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Overview
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1.32

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

NZ_CP021121.1 (Streptomyces marincola)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | T1PKS,phenazine | 96,263 | 235,930 | High | ionostatin | PKS
Region 2 | butyrolactone,RiPP-like | 270,726 | 292,443 |
Region 3 | T3PKS | 357,719 | 398,828 | High | naringenin | PKS:Type III
Region 4 | terpene | 415,718 | 440,052 | Low | hopene | terpene
Region 5 | NI-siderophore | 962,598 | 995,279 |  |
Region 6 | terpene | 1,509,943 | 1,540,360 | Low | fluostatin M/fluostatin N/fluostatin O/fluostatin P/fluostatin Q | PKS:Type II aromatic
Region 7 | RRE-containing | 1,687,698 | 1,708,891 |
Region 8 | PKS-like | 1,887,072 | 1,928,097 |  |
Region 9 | lassopeptide | 2,359,588 | 2,382,124 |
Region 10 | hydrogen-cyanide | 2,418,916 | 2,432,082 | Low | aborycin | ribosomal:RiPP
Region 11 | T1PKS | 2,437,847 | 2,488,556 | Low | lobosamide A/lobosamide B/lobosamide C | PKS
Region 12 | terpene | 2,729,886 | 2,750,932 | Low | isorenieratene | terpene
Region 13 | T2PKS,PKS-like | 2,753,106 | 2,825,591 | Low | nenestatin | PKS
Region 14 | terpene | 2,928,509 | 2,950,794 | High | geosmin | terpene:Sesquiterpene
Region 15 | lanthipeptide-class-i | 3,202,477 | 3,226,525 |  |
Region 16 | NRPS-like | 3,237,545 | 3,281,741 |  |
Region 17 | terpene | 3,415,023 | 3,436,270 | Low | isorenieratene | terpene
Region 18 | hglE-KS,T1PKS,terpene | 4,118,982 | 4,170,716 |  |
Region 19 | lanthipeptide-class-i | 4,271,925 | 4,296,932 |
Region 20 | T1PKS | 4,423,714 | 4,539,830 | High | heronamide A/heronamide B/heronamide C/heronamide D/heronamide E/heronamide F | NRPS:Type I+PKS
Region 21 | NRPS | 4,572,995 | 4,619,150 |  |
Region 22 | melanin | 4,759,340 | 4,769,756 | Low | grixazone A | terpene
Region 23 | lanthipeptide-class-iii | 4,839,975 | 4,862,626 | High | AmfS | ribosomal:RiPP:Lanthipeptide
Region 24 | T1PKS | 4,900,156 | 4,971,664 | Low | camporidine A/camporidine B | other:other+PKS
Region 25 | terpene,azole-containing-RiPP | 5,038,287 | 5,075,657 | Low | lactazole | ribosomal:RiPP:Thiopeptide
Region 26 | ectoine | 5,392,316 | 5,402,711 | High | ectoine | other:ectoine
Region 27 | NI-siderophore | 5,428,792 | 5,458,594 | Low | legonoxamine A/desferrioxamine B/legonoxamine B | other:other
Region 28 | T1PKS | 5,585,517 | 5,633,154 |  |
Region 29 | terpene-precursor | 5,711,906 | 5,732,988 | Low | stenothricin | NRPS:Type I
Region 30 | T1PKS,NRPS,NRPS-like | 5,940,396 | 6,065,600 | High | piericidin A1 | PKS
Region 31 | terpene | 6,151,707 | 6,173,614 |
Region 32 | indole | 6,216,758 | 6,240,060 | Low | spiroindimicin A/spiroindimicin B/spiroindimicin C/spiroindimicin D/indimicin A/indimicin B/indimicin C/indimicin D/indimicin E/lynamicin A/lynamicin D/lynamicin F/lynamicin G | other:other

NZ_CP021121.1 - Region 1 - T1PKS,phenazine
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: 96,263 - 235,930 nt. (total: 139,668 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))
phenazine: phzB

#### 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 oxygenase
CAG99_RS00445: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS00520: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS00525: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CAG99_RS00530: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CAG99_RS00645: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

CAG99_RS00670: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS00685: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CAG99_RS00705: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CAG99_RS28620: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: methyltransferase
CAG99_RS00500: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: hydrolase
CAG99_RS00495: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
CAG99_RS00490: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: synthase
CAG99_RS28625: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transport
CAG99_RS00695: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | T1PKS | phenazine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.44 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.43 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001868.4 |  |  | 0.40 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0002439.3 |  |  | 0.36 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0000936.5 |  |  | 0.34 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1
BGC0002561.3 |  |  | 0.34 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0001850.4 |  |  | 0.33 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0000067.5 |  |  | 0.33 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001444.5 |  |  | 0.32 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0000041.3 |  |  | 0.32 | PKS | oronofacic acid | Pseudomonas syringae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000067.5 |  | 0.66 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000041.3 |  | 0.65 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001065.5 |  | 0.64 | PKS | herboxidiene | Streptomyces chromofuscus
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-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:
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.21 out of 23.79
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 30.12 out of 30.12
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 28.31 out of 30.12
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 28.31 out of 30.12
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.64 out of 27.04
Confidence: medium
Additional weak hits (18):
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.72 out of 29.51
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.34 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.90 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.46 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.81 out of 27.78
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.06 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.03 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.42 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.84 out of 39.62
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.13 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.52 out of 29.65
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.82 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.98 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.00 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.58 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 96262 - 235930:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - redmal - Me-ccmal - redmal - Me-ccmal - redmal - ohmal - Me-ohmal - ccmal) + (ccmal - ccmal - redmal - redmal - ccmal) + (ohmal - Me-mal) + (Me-redmal) + (Me-redmal)
Non-colinear ordering:
  CAG99_RS28625 + CAG99_RS28620 + CAG99_RS28615 + CAG99_RS00530 + CAG99_RS00525

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).
CAG99_RS00525: mmal
PKS_AT (569..867): 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: 201.0
  Ethylmalonyl-CoA: 187.9
  Methoxymalonyl-CoA: 158.2
  2-Methylbutyryl-CoA: 124.8
  trans-1,2-CPDA: 115.7
  Propionyl-CoA: 97.9
  Malonyl-CoA: 83.2
  CHC-CoA: 79.8
  Isobutyryl-CoA: 68.2
  Benzoyl-CoA: 63.0
  3-Methylbutyryl-CoA: 45.3
  Acetyl-CoA: 39.9
  fatty_acid: 33.1
  inactive: 30.2

CAG99_RS00530: mmal
PKS_AT (572..870): 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: 197.9
  Ethylmalonyl-CoA: 183.6
  Methoxymalonyl-CoA: 156.1
  2-Methylbutyryl-CoA: 124.1
  trans-1,2-CPDA: 114.3
  Propionyl-CoA: 97.3
  Malonyl-CoA: 79.5
  CHC-CoA: 78.0
  Isobutyryl-CoA: 66.5
  Benzoyl-CoA: 61.6
  3-Methylbutyryl-CoA: 43.5
  Acetyl-CoA: 41.1
  inactive: 30.1
  fatty_acid: 27.7

CAG99_RS28615: mal - mmal
PKS_AT (558..852): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 206.9
  inactive: 93.5
  Methoxymalonyl-CoA: 63.6
  Methylmalonyl-CoA: 55.8
  Propionyl-CoA: 23.4
  Benzoyl-CoA: 21.1
  Ethylmalonyl-CoA: 20.1
  Isobutyryl-CoA: 19.0
  Acetyl-CoA: 17.9
  CHC-CoA: 12.2
  2-Methylbutyryl-CoA: 11.2
  fatty_acid: 10.6
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2141..2437): mmal
ATSignature: Methylmalonyl-CoA, Ethylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 164.6
  Methoxymalonyl-CoA: 150.2
  Ethylmalonyl-CoA: 149.9
  Malonyl-CoA: 102.4
  2-Methylbutyryl-CoA: 100.3
  trans-1,2-CPDA: 85.2
  Propionyl-CoA: 83.5
  CHC-CoA: 78.6
  Isobutyryl-CoA: 61.7
  3-Methylbutyryl-CoA: 49.5
  Benzoyl-CoA: 49.4
  Acetyl-CoA: 35.4
  inactive: 33.4
  fatty_acid: 22.7

CAG99_RS28620: mal - mal - mal - mal - mal
PKS_AT (556..850): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 213.4
  inactive: 97.9
  Methoxymalonyl-CoA: 64.0
  Methylmalonyl-CoA: 54.2
  Propionyl-CoA: 23.1
  Ethylmalonyl-CoA: 22.9
  Benzoyl-CoA: 21.0
  Isobutyryl-CoA: 20.8
  Acetyl-CoA: 19.1
  CHC-CoA: 16.5
  fatty_acid: 12.5
  2-Methylbutyryl-CoA: 10.6
  trans-1,2-CPDA: 9.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2298..2592): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.5
  inactive: 96.7
  Methoxymalonyl-CoA: 61.7
  Methylmalonyl-CoA: 51.4
  Propionyl-CoA: 21.1
  Benzoyl-CoA: 20.7
  Acetyl-CoA: 19.5
  Isobutyryl-CoA: 18.2
  Ethylmalonyl-CoA: 17.1
  CHC-CoA: 15.4
  fatty_acid: 9.5
  trans-1,2-CPDA: 9.4
  2-Methylbutyryl-CoA: 9.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4068..4362): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.9
  inactive: 105.7
  Methoxymalonyl-CoA: 59.7
  Methylmalonyl-CoA: 52.1
  Propionyl-CoA: 24.7
  Isobutyryl-CoA: 23.5
  Ethylmalonyl-CoA: 20.7
  Acetyl-CoA: 19.9
  Benzoyl-CoA: 19.5
  CHC-CoA: 16.1
  2-Methylbutyryl-CoA: 14.3
  fatty_acid: 8.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (6157..6451): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 212.1
  inactive: 102.6
  Methoxymalonyl-CoA: 59.7
  Methylmalonyl-CoA: 51.8
  Propionyl-CoA: 23.6
  Isobutyryl-CoA: 22.4
  Benzoyl-CoA: 21.8
  CHC-CoA: 21.1
  Acetyl-CoA: 20.5
  Ethylmalonyl-CoA: 17.4
  fatty_acid: 12.9
  2-Methylbutyryl-CoA: 12.2
  trans-1,2-CPDA: 8.5
  3-Methylbutyryl-CoA: 0.0

PKS_AT (8244..8538): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.2
  inactive: 98.4
  Methoxymalonyl-CoA: 65.4
  Methylmalonyl-CoA: 55.0
  Isobutyryl-CoA: 26.5
  Propionyl-CoA: 23.6
  Benzoyl-CoA: 22.2
  Ethylmalonyl-CoA: 18.4
  Acetyl-CoA: 17.9
  CHC-CoA: 14.0
  2-Methylbutyryl-CoA: 13.7
  fatty_acid: 9.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

CAG99_RS28625: mmal - mal - mmal - mal - mmal - mal - mal - mmal - mal
PKS_AT (558..856): 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: 197.9
  Ethylmalonyl-CoA: 183.6
  Methoxymalonyl-CoA: 156.1
  2-Methylbutyryl-CoA: 124.1
  trans-1,2-CPDA: 114.3
  Propionyl-CoA: 97.3
  Malonyl-CoA: 79.5
  CHC-CoA: 78.0
  Isobutyryl-CoA: 66.5
  Benzoyl-CoA: 61.6
  3-Methylbutyryl-CoA: 43.5
  Acetyl-CoA: 41.1
  inactive: 30.1
  fatty_acid: 27.7

PKS_AT (1572..1866): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 210.1
  inactive: 96.0
  Methoxymalonyl-CoA: 62.5
  Methylmalonyl-CoA: 51.5
  Propionyl-CoA: 22.5
  Ethylmalonyl-CoA: 22.1
  Isobutyryl-CoA: 21.6
  Benzoyl-CoA: 21.2
  Acetyl-CoA: 18.0
  CHC-CoA: 17.5
  fatty_acid: 12.0
  2-Methylbutyryl-CoA: 9.7
  trans-1,2-CPDA: 8.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3662..3960): 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: 201.0
  Ethylmalonyl-CoA: 186.8
  Methoxymalonyl-CoA: 158.2
  2-Methylbutyryl-CoA: 125.1
  trans-1,2-CPDA: 116.9
  Propionyl-CoA: 98.9
  Malonyl-CoA: 83.6
  CHC-CoA: 78.6
  Isobutyryl-CoA: 67.9
  Benzoyl-CoA: 62.6
  3-Methylbutyryl-CoA: 45.0
  Acetyl-CoA: 39.7
  fatty_acid: 34.1
  inactive: 31.6

PKS_AT (5415..5709): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.0
  inactive: 104.9
  Methoxymalonyl-CoA: 60.7
  Methylmalonyl-CoA: 52.3
  Propionyl-CoA: 25.4
  Isobutyryl-CoA: 22.9
  Benzoyl-CoA: 21.9
  Acetyl-CoA: 21.5
  Ethylmalonyl-CoA: 19.4
  CHC-CoA: 18.4
  fatty_acid: 12.5
  2-Methylbutyryl-CoA: 11.3
  trans-1,2-CPDA: 8.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (7509..7807): 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: 203.1
  Ethylmalonyl-CoA: 188.7
  Methoxymalonyl-CoA: 159.9
  2-Methylbutyryl-CoA: 128.3
  trans-1,2-CPDA: 119.3
  Propionyl-CoA: 101.4
  Malonyl-CoA: 85.3
  CHC-CoA: 78.8
  Isobutyryl-CoA: 71.6
  Benzoyl-CoA: 63.2
  3-Methylbutyryl-CoA: 47.2
  Acetyl-CoA: 35.7
  fatty_acid: 33.8
  inactive: 30.7

PKS_AT (9271..9565): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 203.9
  inactive: 92.8
  Methoxymalonyl-CoA: 54.9
  Methylmalonyl-CoA: 46.7
  Acetyl-CoA: 22.6
  Propionyl-CoA: 22.4
  Benzoyl-CoA: 18.0
  CHC-CoA: 16.4
  Isobutyryl-CoA: 14.9
  Ethylmalonyl-CoA: 13.9
  2-Methylbutyryl-CoA: 12.4
  trans-1,2-CPDA: 9.9
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (11355..11646): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 91.7%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 231.2
  inactive: 125.6
  Methoxymalonyl-CoA: 59.7
  Methylmalonyl-CoA: 52.0
  Isobutyryl-CoA: 34.4
  Propionyl-CoA: 30.7
  Benzoyl-CoA: 30.0
  Ethylmalonyl-CoA: 25.8
  Acetyl-CoA: 21.8
  2-Methylbutyryl-CoA: 12.0
  fatty_acid: 10.0
  CHC-CoA: 5.4
  trans-1,2-CPDA: 5.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (12954..13252): 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: 203.1
  Ethylmalonyl-CoA: 188.7
  Methoxymalonyl-CoA: 159.9
  2-Methylbutyryl-CoA: 128.3
  trans-1,2-CPDA: 119.3
  Propionyl-CoA: 101.4
  Malonyl-CoA: 85.3
  CHC-CoA: 78.8
  Isobutyryl-CoA: 71.6
  Benzoyl-CoA: 63.2
  3-Methylbutyryl-CoA: 47.2
  Acetyl-CoA: 35.7
  fatty_acid: 33.8
  inactive: 30.7

PKS_AT (14498..14792): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 210.0
  inactive: 97.8
  Methoxymalonyl-CoA: 64.9
  Methylmalonyl-CoA: 52.7
  Propionyl-CoA: 22.2
  Benzoyl-CoA: 21.8
  Isobutyryl-CoA: 20.3
  Acetyl-CoA: 17.9
  CHC-CoA: 15.9
  Ethylmalonyl-CoA: 15.1
  2-Methylbutyryl-CoA: 8.9
  fatty_acid: 8.6
  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
--- | ---
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator
OsdR | Development and stress management regulator

NZ_CP021121.1 - Region 2 - RiPP-like,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: 270,726 - 292,443 nt. (total: 21,718 nt) Show pHMM detection rules used
butyrolactone: AfsA
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
CAG99_RS00920: methyltransferase

smcogs
  SMCOG1089: methyltransferase

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

Reference | butyrolactone | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000849.4 |  |  | 0.48 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  |  | 0.46 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  |  | 0.35 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  |  | 0.15 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001485.4 |  |  | 0.13 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000468.5 |  |  | 0.11 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  |  | 0.11 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000470.6 |  |  | 0.11 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000469.6 |  |  | 0.10 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001070.5 |  |  | 0.09 | NRPS, PKS | kirromycin | Streptomyces collinus Tu 365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.77 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.68 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.47 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001485.4 |  | 0.44 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000470.6 |  | 0.41 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0000468.5 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000469.6 |  | 0.38 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0001753.3 |  | 0.37 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.03 out of 27.18
Confidence: medium
Additional weak hits (5):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.03 out of 25.88
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.39 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.40 out of 26.33
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.32 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.16 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NrdR | Represses ribonucleotide reductase encoding genes

NZ_CP021121.1 - Region 3 - 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: 357,719 - 398,828 nt. (total: 41,110 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CAG99_RS01335: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: aminotransferase
CAG99_RS01395: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Ligases: synthase
CAG99_RS01340: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

CAG99_RS01385: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

Translocases: transporter
CAG99_RS01410: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.83 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.72 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001948.3 |  | 0.57 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0001238.3 |  | 0.54 | other (other) | biotin | Aspergillus nidulans
BGC0001239.3 |  | 0.54 | other (other) | biotin | Aspergillus nidulans
BGC0000948.5 |  | 0.52 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000844.5 |  | 0.50 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002332.2 |  | 0.48 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001310.5 |  | 0.83 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.72 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0000902.4 |  | 0.67 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.61 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001948.3 |  | 0.57 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0001238.3 |  | 0.54 | other (other) | biotin | Aspergillus nidulans
BGC0001239.3 |  | 0.54 | other (other) | biotin | Aspergillus nidulans
BGC0000948.5 |  | 0.52 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000844.5 |  | 0.50 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002332.2 |  | 0.48 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella 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:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.06 out of 23.43
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.55 out of 23.43
Confidence: medium
Additional weak hits (3):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.22 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.21 out of 20.01
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.78 out of 20.01
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
--- | ---
BldD | Development and antibiotic global regulator

NZ_CP021121.1 - Region 4 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 415,718 - 440,052 nt. (total: 24,335 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
CAG99_RS01595: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: transferase
CAG99_RS01600: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Lyases: cyclase dehydratase
CAG99_RS01530: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

CAG99_RS01610: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthetase
CAG99_RS01555: 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
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000663.5 |  | 0.54 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000630.3 |  | 0.47 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000639.3 |  | 0.47 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000641.3 |  | 0.47 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000642.3 |  | 0.47 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000645.3 |  | 0.47 | terpene | carotenoid | Halobacillus halophilus DSM 2266

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000663.5 |  | 0.54 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000630.3 |  | 0.47 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000639.3 |  | 0.47 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000641.3 |  | 0.47 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000642.3 |  | 0.47 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000645.3 |  | 0.47 | terpene | carotenoid | Halobacillus halophilus DSM 2266

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 |  | 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:
CAG99_RS01555: PT_FPPS_like
Domain 1 (53 - 351): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

CAG99_RS01565: PT_phytoene_like
Domain 1 (13 - 307): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

CAG99_RS01570: PT_phytoene_like
Domain 1 (20 - 286): 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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.92 out of 26.85
Confidence: medium
Additional weak hits (8):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.77 out of 21.55
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 32.93
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.58 out of 25.31
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.58 out of 25.31
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.00 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.07 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.32 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.72 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
PP | Diphosphate
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
OsdR | Development and stress management regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_CP021121.1 - Region 5 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 962,598 - 995,279 nt. (total: 32,682 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
CAG99_RS04055: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Isomerases: mutase
CAG99_RS04050: 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 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.53 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0001531.5 |  | 0.51 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002464.3 |  | 0.47 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002683.2 |  | 0.47 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002633.2 |  | 0.47 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002470.2 |  | 0.47 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000946.5 |  | 0.46 | other (other) | vibrioferrin | Vibrio parahaemolyticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001713.5 |  | 0.53 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0001531.5 |  | 0.51 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002464.3 |  | 0.47 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002683.2 |  | 0.47 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002633.2 |  | 0.47 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002470.2 |  | 0.47 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000946.5 |  | 0.46 | other (other) | vibrioferrin | Vibrio parahaemolyticus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.54 out of 18.46
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.03 out of 20.97
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.17 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
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (7):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.97 out of 32.74
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88
Confidence: weak
LexA variant 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
--- | ---
CcpA | Catabolite control protein A
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP021121.1 - Region 6 - 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: 1,509,943 - 1,540,360 nt. (total: 30,418 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
CAG99_RS06405: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Hydrolases: dehalogenase
CAG99_RS06425: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: synthase synthetase
CAG99_RS06415: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

CAG99_RS06450: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002318.2 |  | 0.46 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000272.3 |  | 0.44 | PKS | spore pigment | Streptomyces collinus
BGC0001596.3 |  | 0.44 | PKS | fluostatin M, fluostatin N, fluostatin O, fluostatin P, fluostatin Q | Streptomyces albus
BGC0001911.3 |  | 0.44 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.44 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000041.3 |  | 0.43 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002309.2 |  | 0.43 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002318.2 |  | 0.46 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000272.3 |  | 0.44 | PKS | spore pigment | Streptomyces collinus
BGC0001596.3 |  | 0.44 | PKS | fluostatin M, fluostatin N, fluostatin O, fluostatin P, fluostatin Q | Streptomyces albus
BGC0001911.3 |  | 0.44 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.44 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000041.3 |  | 0.43 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002309.2 |  | 0.43 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488

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:
CAG99_RS06415: PT_FPPS_like
Domain 1 (48 - 341): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

CAG99_RS06460: T2TS
Domain 1 (235 - 523): Type 2 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.
No hits above weak threshold.
Weak hits (11):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.15 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.72 out of 28.14
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.03 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.40 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.71 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.24 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.65 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.42 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.70 out of 24.78
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_CP021121.1 - Region 7 - 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: 1,687,698 - 1,708,891 nt. (total: 21,194 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
Oxidoreductases: dehydrogenase oxidoreductase
CAG99_RS07145: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

CAG99_RS07180: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: acetyltransferase
CAG99_RS07200: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

Hydrolases: amidase
CAG99_RS07150: amidase

smcogs
  SMCOG1105: amidase

Lyases: cyclase
CAG99_RS07125: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

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
--- | --- | --- | --- | --- | ---
BGC0000585.5 |  | 0.47 | ribosomal | microcin C7 | Escherichia coli
BGC0002690.2 |  | 0.39 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0001510.5 |  | 0.38 | other (other) | anisomycin | Streptomyces hygrospinosus
BGC0002656.2 |  | 0.37 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49
BGC0002594.2 |  | 0.35 | PKS | orcinol, orsellinic acid | Fusarium graminearum PH-1
BGC0001636.4 |  | 0.34 | NRPS | KK-1 | Curvularia clavata
BGC0001810.3 |  | 0.33 | PKS | trehangelin | Polymorphospora rubra
BGC0000937.5 |  | 0.32 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372
BGC0000703.4 |  | 0.32 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001065.5 |  | 0.31 | PKS | herboxidiene | Streptomyces chromofuscus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000585.5 |  | 0.47 | ribosomal | microcin C7 | Escherichia coli
BGC0002690.2 |  | 0.39 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0001510.5 |  | 0.38 | other (other) | anisomycin | Streptomyces hygrospinosus
BGC0002656.2 |  | 0.37 | PKS | oryzanaphthopyran A, oryzanaphthopyran B, oryzanaphthopyran C, oryzanthrone A, oryzanthrone B, chlororyzanthrone A, chlororyzanthrone B | Streptacidiphilus oryzae TH49
BGC0002594.2 |  | 0.35 | PKS | orcinol, orsellinic acid | Fusarium graminearum PH-1
BGC0001636.4 |  | 0.34 | NRPS | KK-1 | Curvularia clavata
BGC0001810.3 |  | 0.33 | PKS | trehangelin | Polymorphospora rubra
BGC0000937.5 |  | 0.32 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372
BGC0000703.4 |  | 0.32 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001065.5 |  | 0.31 | PKS | herboxidiene | Streptomyces chromofuscus

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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.34 out of 20.97
Confidence: medium
Additional weak hits (5):
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
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.35 out of 29.65
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.91 out of 23.43
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.26 out of 30.22
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
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (1687697...1708891)
CAG99_RS07165
  RRE type: Pantocin_Microcin_RRE
  Location: 7 - 102
  Score: 63.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A

NZ_CP021121.1 - Region 8 - 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: 1,887,072 - 1,928,097 nt. (total: 41,026 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: dehydrogenase oxygenase
CAG99_RS08030: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CAG99_RS08035: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CAG99_RS08055: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

CAG99_RS08085: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CAG99_RS08095: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: aminotransferase
CAG99_RS08015: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Ligases: ligase synthase
CAG99_RS08075: 3-oxoacyl-(acyl carrier protein) synthase III

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

CAG99_RS08100: 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 | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002277.2 |  | 0.62 | NRPS | atromentin | Suillus grevillei
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002405.2 |  | 0.48 | saccharide | mid-chain acyl sugars | Solanum lycopersicum
BGC0000131.5 |  | 0.47 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0001831.3 |  | 0.47 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000858.3 |  | 0.47 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002277.2 |  | 0.62 | NRPS | atromentin | Suillus grevillei
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002405.2 |  | 0.48 | saccharide | mid-chain acyl sugars | Solanum lycopersicum
BGC0000131.5 |  | 0.47 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0001831.3 |  | 0.47 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000858.3 |  | 0.47 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica

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
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (12):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.52 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.00 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.07 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.20 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.74 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.68 out of 30.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.57 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.85 out of 35.63
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.58 out of 20.01
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.06 out of 29.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.46 out of 29.65
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CAG99_RS08100: NH2
CAL_domain (39..477): NH2
minowa: NH2

Prediction, score:
  NH2: 109.1
  fatty_acid: 23.2
  Acetyl-CoA: 4.3
  shikimic_acid: 0.0
  AHBA: 0.0

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

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

NZ_CP021121.1 - Region 9 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,359,588 - 2,382,124 nt. (total: 22,537 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
CAG99_RS10265: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000571.3 |  | 0.49 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001639.3 |  | 0.46 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0001634.3 |  | 0.44 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001551.4 |  | 0.43 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0001356.4 |  | 0.42 | ribosomal | paeninodin | Paenibacillus dendritiformis C454
BGC0002289.2 |  | 0.42 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii
BGC0000617.5 |  | 0.41 | ribosomal | coagulin | Bacillus coagulans
BGC0001638.4 |  | 0.40 | ribosomal | klebsazolicin | Klebsiella pneumoniae subsp. ozaenae
BGC0002579.2 |  | 0.39 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000571.3 |  | 0.49 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001639.3 |  | 0.46 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0001634.3 |  | 0.44 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001551.4 |  | 0.43 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0001356.4 |  | 0.42 | ribosomal | paeninodin | Paenibacillus dendritiformis C454
BGC0002289.2 |  | 0.42 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii
BGC0000617.5 |  | 0.41 | ribosomal | coagulin | Bacillus coagulans
BGC0001638.4 |  | 0.40 | ribosomal | klebsazolicin | Klebsiella pneumoniae subsp. ozaenae
BGC0002579.2 |  | 0.39 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum

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

No significant matches found.

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.04 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
Lasso peptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP021121.1 - Region 10 - hydrogen-cyanide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,418,916 - 2,432,082 nt. (total: 13,167 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase reductase
CAG99_RS10425: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CAG99_RS10435: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

CAG99_RS10440: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

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

Reference | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002116.3 |  | 0.41 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0002285.2 |  | 0.40 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001391.3 |  | 0.39 | ribosomal | thusin | Bacillus thuringiensis serovar rongseni
BGC0000488.4 |  | 0.37 | ribosomal | circularin A | Clostridium beijerinckii
BGC0000435.5 |  | 0.36 | NRPS | syringafactin A, syringafactin B, syringafactin C, syringafactin D, syringafactin E, syringafactin F | Pseudomonas syringae pv. tomato str. DC3000
BGC0000323.5 |  | 0.36 | NRPS | cichofactin A, cichofactin B | Pseudomonas cichorii
BGC0002092.3 |  | 0.36 | NRPS | stechlisin B2, stechlisin C3, stechlisin D3, tensin, stechlisin E2, stechlisin F | Pseudomonas sp.
BGC0001838.4 |  | 0.36 | NRPS | WLIP | Pseudomonas putida
BGC0001842.4 |  | 0.36 | NRPS | gacamide A | Pseudomonas fluorescens Pf0-1
BGC0001429.4 |  | 0.35 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca DW4/3-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002116.3 |  | 0.41 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0002285.2 |  | 0.40 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001391.3 |  | 0.39 | ribosomal | thusin | Bacillus thuringiensis serovar rongseni
BGC0000488.4 |  | 0.37 | ribosomal | circularin A | Clostridium beijerinckii
BGC0000435.5 |  | 0.36 | NRPS | syringafactin A, syringafactin B, syringafactin C, syringafactin D, syringafactin E, syringafactin F | Pseudomonas syringae pv. tomato str. DC3000
BGC0000323.5 |  | 0.36 | NRPS | cichofactin A, cichofactin B | Pseudomonas cichorii
BGC0002092.3 |  | 0.36 | NRPS | stechlisin B2, stechlisin C3, stechlisin D3, tensin, stechlisin E2, stechlisin F | Pseudomonas sp.
BGC0001838.4 |  | 0.36 | NRPS | WLIP | Pseudomonas putida
BGC0001842.4 |  | 0.36 | NRPS | gacamide A | Pseudomonas fluorescens Pf0-1
BGC0001429.4 |  | 0.35 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca DW4/3-1

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.
No hits above weak threshold.
Weak hits (8):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.96 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.28 out of 27.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.28 out of 36.53
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 20.42 out of 22.40
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.23 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.81 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.43 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP021121.1 - Region 11 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,437,847 - 2,488,556 nt. (total: 50,710 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CAG99_RS10560: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

CAG99_RS10570: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CAG99_RS10575: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

Hydrolases: hydrolase
CAG99_RS10600: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: synthase synthetase
CAG99_RS10585: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CAG99_RS10590: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CAG99_RS10635: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000041.3 |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001273.3 |  | 0.63 | PKS | asperlactone | Aspergillus ochraceus
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000041.3 |  | 0.64 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001273.3 |  | 0.63 | PKS | asperlactone | Aspergillus ochraceus
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15

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
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.85 out of 30.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.11 out of 36.54
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.52 out of 21.55
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.65 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.45 out of 28.14
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.61 out of 26.85
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 14, location 2437846 - 2488556:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (ccmal)
Non-colinear ordering:
  CAG99_RS10585 + CAG99_RS10590

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).
CAG99_RS10585: mal
PKS_AT (579..873): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 183.9
  inactive: 81.6
  Methoxymalonyl-CoA: 61.3
  Methylmalonyl-CoA: 58.3
  Isobutyryl-CoA: 27.5
  Propionyl-CoA: 27.0
  Ethylmalonyl-CoA: 22.5
  2-Methylbutyryl-CoA: 19.4
  Benzoyl-CoA: 18.6
  Acetyl-CoA: 16.5
  fatty_acid: 9.8
  CHC-CoA: 9.0
  3-Methylbutyryl-CoA: 7.4
  trans-1,2-CPDA: 5.7

CAG99_RS10590: mal
PKS_AT (570..847): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 170.3
  inactive: 67.8
  Methoxymalonyl-CoA: 54.2
  Methylmalonyl-CoA: 49.0
  Propionyl-CoA: 26.2
  Acetyl-CoA: 16.7
  Benzoyl-CoA: 12.4
  trans-1,2-CPDA: 10.0
  Ethylmalonyl-CoA: 9.2
  fatty_acid: 7.4
  2-Methylbutyryl-CoA: 7.3
  CHC-CoA: 6.2
  Isobutyryl-CoA: 2.9
  3-Methylbutyryl-CoA: -1.7

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP021121.1 - Region 12 - 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: 2,729,886 - 2,750,932 nt. (total: 21,047 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 electron transfer
CAG99_RS11910: flavodoxin

smcogs
  SMCOG1134: flavodoxin

CAG99_RS11925: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001456.3 |  | 0.54 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000664.5 |  | 0.53 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.50 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.50 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000649.3 |  | 0.48 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000650.3 |  | 0.45 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000924.5 |  | 0.45 | other (other) | pyrrolnitrin | Pseudomonas chlororaphis
BGC0000648.3 |  | 0.45 | terpene | carotenoid | Myxococcus xanthus
BGC0000645.3 |  | 0.40 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000639.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC260

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001456.3 |  | 0.54 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000664.5 |  | 0.53 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.50 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.50 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000649.3 |  | 0.48 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000650.3 |  | 0.45 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000924.5 |  | 0.45 | other (other) | pyrrolnitrin | Pseudomonas chlororaphis
BGC0000648.3 |  | 0.45 | terpene | carotenoid | Myxococcus xanthus
BGC0000645.3 |  | 0.40 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000639.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC260

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 |  | 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:
CAG99_RS11930: PT_phytoene_like
Domain 1 (16 - 331): 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40
Confidence: strong
Additional weak hits (1):
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.43 out of 29.51
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
HypR | L-hydroxyproline utilization repressor
OsdR | Development and stress management regulator

NZ_CP021121.1 - Region 13 - PKS-like,T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,753,106 - 2,825,591 nt. (total: 72,486 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)
PKS-like: (t2pks2 or ksIII)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CAG99_RS12130: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CAG99_RS12150: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS12160: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CAG99_RS12280: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

CAG99_RS12285: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: acylase aminotransferase glycosyltransferase methyltransferase transferase
CAG99_RS12115: methyltransferase

smcogs
  SMCOG1248: methyltransferase

CAG99_RS12120: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CAG99_RS12165: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

CAG99_RS12175: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CAG99_RS12180: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CAG99_RS12195: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase protease
CAG99_RS12050: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

CAG99_RS12255: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase dehydratase
CAG99_RS12110: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

CAG99_RS12135: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

CAG99_RS12155: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

CAG99_RS12170: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

CAG99_RS12275: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
CAG99_RS12140: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CAG99_RS12145: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CAG99_RS12190: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | T2PKS | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000231.5 |  |  | 0.83 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001817.5 |  |  | 0.81 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0001723.5 |  |  | 0.80 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000234.5 |  |  | 0.71 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001661.5 |  |  | 0.59 | PKS | mayamycin | Streptomyces sp.
BGC0002276.2 |  |  | 0.59 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001273.3 |  |  | 0.58 | PKS | asperlactone | Aspergillus ochraceus
BGC0002477.3 |  |  | 0.58 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0001160.5 |  |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002000.4 |  |  | 0.55 | PKS | setomimycin | Streptomyces aurantiacus JA 4570

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.73 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001817.5 |  | 0.72 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0001723.5 |  | 0.72 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000234.5 |  | 0.68 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001661.5 |  | 0.63 | PKS | mayamycin | Streptomyces sp.
BGC0002276.2 |  | 0.63 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002477.3 |  | 0.63 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0001273.3 |  | 0.63 | PKS | asperlactone | Aspergillus ochraceus
BGC0001160.5 |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0000235.5 |  | 0.61 | PKS | kiamycin | Streptomyces sp. W007

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.15 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: 17.68 out of 20.47
Confidence: medium
Additional weak hits (18):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.49 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.37 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.48 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.19 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 14.98 out of 20.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.25 out of 30.22
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.19 out of 27.04
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.73 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.76 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.98 out of 36.53
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.57 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.90 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.57 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 32.93
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.78 out of 35.63
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
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).
CAG99_RS12195: mal
PKS_AT (19..308): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 62.5%
  inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 67.8
  Methylmalonyl-CoA: 46.1
  Methoxymalonyl-CoA: 38.9
  inactive: 26.6
  Propionyl-CoA: 19.3
  trans-1,2-CPDA: 11.8
  CHC-CoA: 11.4
  Acetyl-CoA: 10.3
  2-Methylbutyryl-CoA: 10.2
  Ethylmalonyl-CoA: 10.0
  Benzoyl-CoA: 8.3
  fatty_acid: 6.8
  Isobutyryl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Cluster section:
  2753105 to 2825591
Starter unit(s):
  propionyl-CoA (Score: 778.0; E-value: 6.93e-155)
Malonyl elongations:
  8|9 (Score: 648.1; E-value: 1e-197)
Product class(es):
  angucycline
Product molecular weight(s):
  propionyl-CoA_8: 770 Da
  propionyl-CoA_9: 812 Da

CAG99_RS12115
  MET (Score: 30.4; E-value: 4.8e-10)
CAG99_RS12130
  OXY (Score: 569.5; E-value: 1.4e-173)
CAG99_RS12135
  CYC C4-C17/C2-C19 (Score: 177.5; E-value: 6.2e-55)
CAG99_RS12140
  KS (Score: 751.7; E-value: 4.5e-229)
CAG99_RS12145
  CLF 8|9 (Score: 648.1; E-value: 1e-197)
CAG99_RS12150
  KR C9 (Score: 468.9; E-value: 9.3e-144)
CAG99_RS12155
  CYC C7-C12 (Score: 483.7; E-value: 4.4e-148)
CAG99_RS12160
  OXY (Score: 518.9; E-value: 3.2e-158)
CAG99_RS12175
  GT (Score: 313.1; E-value: 8.3e-96)
CAG99_RS12180
  GT (Score: 302.3; E-value: 1.5e-92)
CAG99_RS12185
  ACP (Score: 89.3; E-value: 2.9e-28)
CAG99_RS12190
  KSIII (Score: 461.9; E-value: 2.9e-141)
  KSIII ABC00733.1_Cosmomycin_propionyl-CoA (Score: 430.0; E-value: 6.93e-155)
CAG99_RS12195
  AT (Score: 433.7; E-value: 1.1e-132)
  AT BAB72049.1_Aklavinone_propionyl-CoA (Score: 348.0; E-value: 9.53e-123)
CAG99_RS12280
  OXY (Score: 23.9; E-value: 4.5e-08)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
MexT | Global virulence regulator
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP021121.1 - Region 14 - 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: 2,928,509 - 2,950,794 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
Oxidoreductases: dehydrogenase
CAG99_RS12860: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase
CAG99_RS12805: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

Hydrolases: protease
CAG99_RS12815: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Lyases: cyclase
CAG99_RS12830: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.76 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0001928.2 |  | 0.49 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000888.5 |  | 0.48 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001184.4 |  | 0.43 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000231.5 |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002493.3 |  | 0.40 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001197.5 |  | 0.40 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000671.3 |  | 0.40 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0000509.4 |  | 0.39 | ribosomal | epilancin 15x | Staphylococcus epidermidis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.76 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0001928.2 |  | 0.49 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000888.5 |  | 0.48 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001184.4 |  | 0.43 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000231.5 |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002493.3 |  | 0.40 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001197.5 |  | 0.40 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000671.3 |  | 0.40 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0000509.4 |  | 0.39 | ribosomal | epilancin 15x | Staphylococcus epidermidis

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:
CAG99_RS12830: T1TS + T1TS
Domain 1 (2 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (379 - 719): 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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.37 out of 23.79
Confidence: medium
Additional weak hits (11):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
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
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.42 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.40 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.40 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.68 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.42 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.50 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.93 out of 24.78
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism

NZ_CP021121.1 - Region 15 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,202,477 - 3,226,525 nt. (total: 24,049 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CAG99_RS14140: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
CAG99_RS14120: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase dehydratase
CAG99_RS14145: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

CAG99_RS14150: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.54 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000563.4 |  | 0.49 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.49 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000542.3 |  | 0.48 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000556.5 |  | 0.47 | ribosomal | streptin | Streptococcus pyogenes
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000544.4 |  | 0.46 | ribosomal | planosporicin | Planomonospora alba
BGC0000503.5 |  | 0.45 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001660.3 |  | 0.45 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0002346.3 |  | 0.44 | ribosomal | kyamicin | Saccharopolyspora sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.54 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000563.4 |  | 0.49 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.49 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000542.3 |  | 0.48 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000556.5 |  | 0.47 | ribosomal | streptin | Streptococcus pyogenes
BGC0001579.4 |  | 0.46 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000544.4 |  | 0.46 | ribosomal | planosporicin | Planomonospora alba
BGC0000503.5 |  | 0.45 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0001660.3 |  | 0.45 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0002346.3 |  | 0.44 | ribosomal | kyamicin | Saccharopolyspora 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.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 25.70 out of 32.38
Confidence: medium
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 27.32 out of 32.93
Confidence: medium
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 25.70 out of 32.38
Confidence: medium
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 25.46 out of 32.38
Confidence: medium
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 26.96 out of 32.93
Confidence: medium
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 27.98 out of 32.38
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
Additional weak hits (7):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.23 out of 30.25
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.50 out of 32.93
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.30 out of 32.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.86 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.97 out of 25.88
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.75 out of 29.65
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (3202476...3226525)
CAG99_RS14150
  RRE type: Lanthipeptide_LanB_RRE
  Location: 126 - 211
  Score: 32.8

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CsoR | Copper-responsive repressor
RicR | Copper-responsive regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP021121.1 - Region 16 - 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: 3,237,545 - 3,281,741 nt. (total: 44,197 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 oxidase
CAG99_RS14260: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

CAG99_RS14280: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CAG99_RS14335: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Hydrolases: hydrolase
CAG99_RS14330: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

CAG99_RS14400: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase synthase
CAG99_RS14325: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

CAG99_RS14350: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CAG99_RS14365: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.71 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000307.4 |  | 0.61 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000342.4 |  | 0.60 | NRPS | enniatin | Fusarium equiseti
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001268.4 |  | 0.55 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0000375.5 |  | 0.52 | NRPS | indigoidine | Streptomyces chromofuscus
BGC0000308.5 |  | 0.48 | NRPS | aureusimine A, aureusimine B, aureusimine C | Staphylococcus aureus subsp. aureus str. JKD6008

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.71 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000307.4 |  | 0.61 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000342.4 |  | 0.60 | NRPS | enniatin | Fusarium equiseti
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001268.4 |  | 0.55 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0000375.5 |  | 0.52 | NRPS | indigoidine | Streptomyces chromofuscus
BGC0000308.5 |  | 0.48 | NRPS | aureusimine A, aureusimine B, aureusimine C | Staphylococcus aureus subsp. aureus str. JKD6008

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: 19.52 out of 19.52
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (12):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.21 out of 32.74
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.68 out of 26.85
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.62 out of 20.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.42 out of 26.33
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.84 out of 28.14
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.47 out of 36.54
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.19 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.24 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.19 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.58 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 20, location 3237544 - 3281741:
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).
CAG99_RS14350: X
AMP-binding (30..429): X
nrpys: (unknown)

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:
    QWLTFDAAQWEAQCFSGGEINLYGPTETTVNASA
  Nearest Stachelhaus code(s):
    Gln DAWQFGLINK (91% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production

NZ_CP021121.1 - Region 17 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,415,023 - 3,436,270 nt. (total: 21,248 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
CAG99_RS15115: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CAG99_RS15120: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CAG99_RS15140: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
CAG99_RS15135: methyltransferase

smcogs
  SMCOG1089: methyltransferase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001456.3 |  | 0.55 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000664.5 |  | 0.55 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.53 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.52 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.52 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0002258.3 |  | 0.43 | PKS | shimalactone A, shimalactone B | Aspergillus stellatus
BGC0001647.3 |  | 0.37 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0000636.3 |  | 0.35 | terpene | carotenoid | Brevibacterium linens
BGC0000843.5 |  | 0.34 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0001386.5 |  | 0.34 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001456.3 |  | 0.55 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000664.5 |  | 0.55 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.53 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.52 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.52 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0002258.3 |  | 0.43 | PKS | shimalactone A, shimalactone B | Aspergillus stellatus
BGC0001647.3 |  | 0.37 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0000636.3 |  | 0.35 | terpene | carotenoid | Brevibacterium linens
BGC0000843.5 |  | 0.34 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0001386.5 |  | 0.34 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77

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:
CAG99_RS15130: Lycopene_cycl
Domain 1 (3 - 378): 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.
No hits above weak threshold.
Weak hits (10):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.70 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.83 out of 30.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.68 out of 39.62
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.10 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.21 out of 30.97
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.07 out of 32.38
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
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
--- | ---

NZ_CP021121.1 - Region 18 - T1PKS,hglE-KS,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,118,982 - 4,170,716 nt. (total: 51,735 nt) Show pHMM detection rules used
hglE-KS: (hglE or hglD)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
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
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
CAG99_RS18340: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CAG99_RS18440: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS18465: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CAG99_RS28945: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: acetyltransferase acylase aminotransferase glycosyltransferase
CAG99_RS18300: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

CAG99_RS18355: glycosyltransferase

smcogs
  SMCOG1102: glycosyltransferase

CAG99_RS18375: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CAG99_RS18395: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CAG99_RS18445: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: hydrolase
CAG99_RS18390: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CAG99_RS18475: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: cyclase
CAG99_RS18360: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase
CAG99_RS18380: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | hglE-KS | T1PKS | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  |  | 0.85 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  |  | 0.85 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  |  |  | 0.78 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  | 0.77 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000863.3 |  |  |  | 0.77 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0002192.3 |  |  |  | 0.76 | PKS | FR901512 | fungal sp. No.14919
BGC0001268.4 |  |  |  | 0.67 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002648.2 |  |  |  | 0.63 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0002631.2 |  |  |  | 0.61 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001910.4 |  |  |  | 0.61 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.63 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.63 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000863.3 |  | 0.62 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001258.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0002192.3 |  | 0.59 | PKS | FR901512 | fungal sp. No.14919
BGC0001257.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001268.4 |  | 0.55 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002648.2 |  | 0.55 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL

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:
CAG99_RS18360: T1TS
Domain 1 (10 - 312): 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:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.71 out of 26.33
Confidence: medium
Additional weak hits (10):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.58 out of 36.54
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 15.94 out of 26.12
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.47 out of 39.62
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.67 out of 29.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.28 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.91 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.23 out of 32.74
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.22 out of 24.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.69 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.55 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
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 22, location 4118981 - 4170716:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mxmal) + (mal)
Non-colinear ordering:
  CAG99_RS18380 + CAG99_RS18385 + CAG99_RS18375

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).
CAG99_RS18375: mal
PKS_AT (1222..1516): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 58.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 82.5
  Methylmalonyl-CoA: 35.6
  Methoxymalonyl-CoA: 33.8
  inactive: 33.3
  Propionyl-CoA: 13.4
  Ethylmalonyl-CoA: 12.8
  CHC-CoA: 8.4
  Isobutyryl-CoA: 4.7
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -0.4

CAG99_RS18380: mxmal
PKS_AT (648..857): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 14.3
  inactive: 12.9
  CHC-CoA: 11.0
  Malonyl-CoA: 1.2
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methylmalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator

NZ_CP021121.1 - Region 19 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,271,925 - 4,296,932 nt. (total: 25,008 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: electron transfer
CAG99_RS18975: flavodoxin

smcogs
  SMCOG1134: flavodoxin

Lyases: cyclase dehydratase
CAG99_RS19000: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

CAG99_RS19005: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.44 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000506.4 |  | 0.40 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000511.5 |  | 0.38 | ribosomal | ericin S | Bacillus subtilis
BGC0000529.5 |  | 0.36 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0001221.5 |  | 0.34 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0002343.3 |  | 0.34 | other (other), ribosomal | ammosester A, ammosester B, ammosester C, ammosamaic acid cogener | Streptomyces uncialis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.44 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000542.3 |  | 0.44 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000506.4 |  | 0.40 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000511.5 |  | 0.38 | ribosomal | ericin S | Bacillus subtilis
BGC0000529.5 |  | 0.36 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0001221.5 |  | 0.34 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0002343.3 |  | 0.34 | other (other), ribosomal | ammosester A, ammosester B, ammosester C, ammosamaic acid cogener | Streptomyces uncialis

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

No significant matches found.

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

No significant matches found.

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

#### Lanthipeptide(s) for CAG99_RS18995

CAG99_RS19010
Leader:
MEVPMESLATSAHSAGVLMSSGEPADWELDVSIVEGGPAAD
Core:
Q L I R L T G D G C N S T C A T A C V S C P
Core with dehydrations:
Q L I R L Dhb G D G Cys N Dha Dhb Cys A Dhb A Cys V Dha Cys P

#### antiSMASH-DB 4.0 matches for CAG99_RS19010

100.0%
NZ_CP021121.1 and 1 other:
NZ_CP021121.1 Lanthipeptides: CAG99_RS19010_lanthipeptide
Lanthipeptides: CAG99_RS19010_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T G D G C N S T C A T A C V S C P
1
Q L I R L T G D G C N S T C A T A C V S C P
22
95.5%
NC_016109.1 and 4 others:
NC_016109.1 Lanthipeptides: KSE_RS29105_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide
Lanthipeptides: KSE_RS29105_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A T A C V S C P
1
Q L I R L T N D G C N S T C A T A C V S C P
22
95.5%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS22650_lanthipeptide
Lanthipeptides: C7M71_RS22650_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A T A C V S C P
1
Q L I R L T D D G C N S T C A T A C V S C P
22
with 169 more sequence matches
Only the first 10 are displayed here.
95.5%
NZ_NDXL01000003.1 and 1 other:
NZ_NDXL01000003.1 Lanthipeptides: B7024_RS36425_lanthipeptide
Lanthipeptides: B7024_RS36425_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A T A C V S C P
1
Q L I R L T S D G C N S T C A T A C V S C P
22
90.9%
NZ_JACERG010000017.1 and 1 other:
NZ_JACERG010000017.1 Lanthipeptides: H1X69_RS24645_lanthipeptide
Lanthipeptides: H1X69_RS24645_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A+A C V S C P
1
Q L I R L T N D G C N S T C A S A C V S C P
22
86.4%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS16225_lanthipeptide
Lanthipeptides: GBF35_RS16225_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R+T D G C N S T C A T A C S C P
1
Q L I R M T D D G C N S T C A T A C N S C P
22
82.6%
NZ_BCBX01000061.1 and 1 other:
NZ_BCBX01000061.1 Lanthipeptides: AP234_RS35640_lanthipeptide
Lanthipeptides: AP234_RS35640_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C
21
Q L I R+T D G C N S T C A T A C V S C
1
Q L I R M T D D G C N S T C A T A C V S C
21
82.6%
NZ_CP119143.1 and 1 other:
NZ_CP119143.1 Lanthipeptides: PYR72_RS32440_lanthipeptide
Lanthipeptides: PYR72_RS32440_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R+T D G C N S T C A T A C S C P
1
Q L I R M T D D G C N S T C A T A C T S C P
22
78.3%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS37485_lanthipeptide
Lanthipeptides: GBF35_RS37485_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C
21
Q L I R+T D G C N S T C T A C V S C
1
Q L I R M T D D G C N S T C G T A C V S C
21
77.3%
NZ_CP026652.1 and 1 other:
NZ_CP026652.1 Lanthipeptides: C4B68_RS00400_lanthipeptide
Lanthipeptides: C4B68_RS00400_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T D G C S T C +A C S C P
1
Q L I R L T N D G C G S T C Q S A C T S C P
22
60.9%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C-V S C P
22
+L I R+T D G C +T C T A C +C P
1
R L I R M T D D G C G T T C E T A C S T T C P
23
59.1%
NZ_KL997433.1 and 1 other:
NZ_KL997433.1 Lanthipeptides: IQ62_RS26155_lanthipeptide
Lanthipeptides: IQ62_RS26155_lanthipeptide
5
L T G D G C N S T C A T A C V S C
21
L T D G C S T C A+A C S C
1
L T D D G C G S T C A S A C T S C
17
59.1%
NZ_LN850107.1 and 1 other:
NZ_LN850107.1 Lanthipeptides: BN1701_RS34270_lanthipeptide
Lanthipeptides: BN1701_RS34270_lanthipeptide
3
I R L T G D G C N S T C A T A C V S C P
22
+R L T D G C +T C +A C S C P
1
L R L T D D G C G A T C E S A C N S C P
20

#### Lanthipeptide(s) for CAG99_RS19005

CAG99_RS19010
Leader:
MEVPMESLATSAHSAGVLMSSGEPADWELDVSIVEGGPAAD
Core:
Q L I R L T G D G C N S T C A T A C V S C P
Core with dehydrations:
Q L I R L Dhb G D G Cys N Dha Dhb Cys A Dhb A Cys V Dha Cys P

#### antiSMASH-DB 4.0 matches for CAG99_RS19010

100.0%
NZ_CP021121.1 and 1 other:
NZ_CP021121.1 Lanthipeptides: CAG99_RS19010_lanthipeptide
Lanthipeptides: CAG99_RS19010_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T G D G C N S T C A T A C V S C P
1
Q L I R L T G D G C N S T C A T A C V S C P
22
95.5%
NC_016109.1 and 4 others:
NC_016109.1 Lanthipeptides: KSE_RS29105_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide NZ_AP023440.1 Lanthipeptides: IGS71_RS16730_lanthipeptide
Lanthipeptides: KSE_RS29105_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A T A C V S C P
1
Q L I R L T N D G C N S T C A T A C V S C P
22
95.5%
NZ_CP031264.1 and 1 other:
NZ_CP031264.1 Lanthipeptides: C7M71_RS22650_lanthipeptide
Lanthipeptides: C7M71_RS22650_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A T A C V S C P
1
Q L I R L T D D G C N S T C A T A C V S C P
22
with 169 more sequence matches
Only the first 10 are displayed here.
95.5%
NZ_NDXL01000003.1 and 1 other:
NZ_NDXL01000003.1 Lanthipeptides: B7024_RS36425_lanthipeptide
Lanthipeptides: B7024_RS36425_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A T A C V S C P
1
Q L I R L T S D G C N S T C A T A C V S C P
22
90.9%
NZ_JACERG010000017.1 and 1 other:
NZ_JACERG010000017.1 Lanthipeptides: H1X69_RS24645_lanthipeptide
Lanthipeptides: H1X69_RS24645_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T D G C N S T C A+A C V S C P
1
Q L I R L T N D G C N S T C A S A C V S C P
22
86.4%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS16225_lanthipeptide
Lanthipeptides: GBF35_RS16225_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R+T D G C N S T C A T A C S C P
1
Q L I R M T D D G C N S T C A T A C N S C P
22
82.6%
NZ_BCBX01000061.1 and 1 other:
NZ_BCBX01000061.1 Lanthipeptides: AP234_RS35640_lanthipeptide
Lanthipeptides: AP234_RS35640_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C
21
Q L I R+T D G C N S T C A T A C V S C
1
Q L I R M T D D G C N S T C A T A C V S C
21
82.6%
NZ_CP119143.1 and 1 other:
NZ_CP119143.1 Lanthipeptides: PYR72_RS32440_lanthipeptide
Lanthipeptides: PYR72_RS32440_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R+T D G C N S T C A T A C S C P
1
Q L I R M T D D G C N S T C A T A C T S C P
22
78.3%
NZ_CP045572.1 and 1 other:
NZ_CP045572.1 Lanthipeptides: GBF35_RS37485_lanthipeptide
Lanthipeptides: GBF35_RS37485_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C
21
Q L I R+T D G C N S T C T A C V S C
1
Q L I R M T D D G C N S T C G T A C V S C
21
77.3%
NZ_CP026652.1 and 1 other:
NZ_CP026652.1 Lanthipeptides: C4B68_RS00400_lanthipeptide
Lanthipeptides: C4B68_RS00400_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C V S C P
22
Q L I R L T D G C S T C +A C S C P
1
Q L I R L T N D G C G S T C Q S A C T S C P
22
60.9%
NC_007777.1 and 1 other:
NC_007777.1 Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
Lanthipeptides: FRANCCI3_RS10225_lanthipeptide
1
Q L I R L T G D G C N S T C A T A C-V S C P
22
+L I R+T D G C +T C T A C +C P
1
R L I R M T D D G C G T T C E T A C S T T C P
23
59.1%
NZ_KL997433.1 and 1 other:
NZ_KL997433.1 Lanthipeptides: IQ62_RS26155_lanthipeptide
Lanthipeptides: IQ62_RS26155_lanthipeptide
5
L T G D G C N S T C A T A C V S C
21
L T D G C S T C A+A C S C
1
L T D D G C G S T C A S A C T S C
17
59.1%
NZ_LN850107.1 and 1 other:
NZ_LN850107.1 Lanthipeptides: BN1701_RS34270_lanthipeptide
Lanthipeptides: BN1701_RS34270_lanthipeptide
3
I R L T G D G C N S T C A T A C V S C P
22
+R L T D G C +T C +A C S C P
1
L R L T D D G C G A T C E S A C N S C P
20

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 26.51 out of 33.73
Confidence: medium
Additional weak hits (3):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.31 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.15 out of 30.25
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

CAG99_RS19010 - Class I
  Cleavage pHMM score: -13.00
  RODEO score: 19
  Monoisotopic mass: 2122.0 Da
  Molecular weight: 2123.4 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2141.5 Da N = 1
CAG99_RS19010 - Class I
  Cleavage pHMM score: -13.00
  RODEO score: 19
  Monoisotopic mass: 2122.0 Da
  Molecular weight: 2123.4 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2141.5 Da N = 1

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (4271924...4296932)
CAG99_RS19005
  RRE type: Lanthipeptide_LanB_RRE
  Location: 153 - 242
  Score: 69.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
HipB | Bacterial antitoxin HipB

NZ_CP021121.1 - Region 20 - 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: 4,423,714 - 4,539,830 nt. (total: 116,117 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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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
CAG99_RS19615: nucleotide sugar dehydrogenase

smcogs
  SMCOG1152: nucleotide sugar dehydrogenase

CAG99_RS19740: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CAG99_RS19785: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS19790: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CAG99_RS19820: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS19835: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase aminotransferase halogenase methyltransferase
CAG99_RS19625: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CAG99_RS19635: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CAG99_RS19695: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CAG99_RS19715: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CAG99_RS19765: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CAG99_RS19800: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CAG99_RS19810: halogenase

smcogs
  SMCOG1119: halogenase

CAG99_RS19815: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase
CAG99_RS19730: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: dehydratase
CAG99_RS19630: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
CAG99_RS19665: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

CAG99_RS19700: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CAG99_RS19720: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CAG99_RS19725: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CAG99_RS19735: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CAG99_RS19755: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CAG99_RS19770: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CAG99_RS19775: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001349.5 |  | 0.99 | NRPS, PKS | heronamide A, heronamide B, heronamide C, heronamide D, heronamide E, heronamide F | Streptomyces sp. SCSIO 03032
BGC0002101.3 |  | 0.79 | PKS | heronamide C, heronamide A, heronamide B | Streptomyces sp. CMB-0406 CBM-0406
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.75 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000097.5 |  | 0.75 | PKS | ML-449 | Streptomyces sp. MP39-85
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000029.5 |  | 0.71 | PKS | BE-14106 | Streptomyces sp. DSM 21069
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001349.5 |  | 0.99 | NRPS, PKS | heronamide A, heronamide B, heronamide C, heronamide D, heronamide E, heronamide F | Streptomyces sp. SCSIO 03032
BGC0002101.3 |  | 0.79 | PKS | heronamide C, heronamide A, heronamide B | Streptomyces sp. CMB-0406 CBM-0406
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.75 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000097.5 |  | 0.75 | PKS | ML-449 | Streptomyces sp. MP39-85
BGC0001275.3 |  | 0.75 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000029.5 |  | 0.71 | PKS | BE-14106 | Streptomyces sp. DSM 21069
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.50 out of 26.85
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.71 out of 23.79
Confidence: medium
Additional weak hits (12):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.40 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.70 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.72 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.61 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 11.99 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.79 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.47 out of 27.78
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.69 out of 30.98
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.18 out of 27.04
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.51 out of 24.78
Confidence: weak
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 25, location 4423713 - 4539830:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (ccmal - pk) + (ccmal - ccmal) + (Me-mal - ccmal - ccmal) + (ccmal) + (pk - ccmal) + (ccmal)
Non-colinear ordering:
  CAG99_RS19815 + CAG99_RS19775 + CAG99_RS19735 + CAG99_RS19700 + CAG99_RS19715 + CAG99_RS19720 + CAG99_RS19725

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).
CAG99_RS19695: mal
PKS_AT (567..859): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 192.5
  inactive: 85.7
  Methoxymalonyl-CoA: 57.7
  Methylmalonyl-CoA: 45.8
  Isobutyryl-CoA: 33.6
  Propionyl-CoA: 28.5
  Acetyl-CoA: 20.7
  Ethylmalonyl-CoA: 18.3
  Benzoyl-CoA: 13.3
  fatty_acid: 12.3
  CHC-CoA: 9.7
  2-Methylbutyryl-CoA: 9.3
  trans-1,2-CPDA: 7.7
  3-Methylbutyryl-CoA: 0.0

CAG99_RS19700: mmal - mal - mal
PKS_AT (534..827): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 95.8%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 200.6
  Ethylmalonyl-CoA: 195.9
  Methoxymalonyl-CoA: 168.3
  2-Methylbutyryl-CoA: 143.0
  trans-1,2-CPDA: 125.2
  Propionyl-CoA: 111.4
  Malonyl-CoA: 93.9
  CHC-CoA: 91.3
  Isobutyryl-CoA: 69.4
  Benzoyl-CoA: 60.0
  Acetyl-CoA: 57.6
  inactive: 42.8
  fatty_acid: 32.9
  3-Methylbutyryl-CoA: 32.7

PKS_AT (1551..1848): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 199.0
  inactive: 102.4
  Methoxymalonyl-CoA: 53.0
  Methylmalonyl-CoA: 38.2
  Isobutyryl-CoA: 29.0
  Propionyl-CoA: 28.4
  Acetyl-CoA: 20.3
  Ethylmalonyl-CoA: 19.7
  Benzoyl-CoA: 19.5
  2-Methylbutyryl-CoA: 10.0
  CHC-CoA: 9.8
  trans-1,2-CPDA: 6.5
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3342..3636): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 197.2
  inactive: 107.5
  Methoxymalonyl-CoA: 50.2
  Methylmalonyl-CoA: 34.9
  Propionyl-CoA: 24.0
  Isobutyryl-CoA: 22.6
  Acetyl-CoA: 18.3
  Benzoyl-CoA: 11.4
  CHC-CoA: 10.1
  Ethylmalonyl-CoA: 8.5
  2-Methylbutyryl-CoA: 8.5
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

CAG99_RS19715: mal
PKS_AT (528..804): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 190.6
  inactive: 103.5
  Methoxymalonyl-CoA: 60.6
  Methylmalonyl-CoA: 54.2
  Isobutyryl-CoA: 32.3
  Ethylmalonyl-CoA: 31.6
  Propionyl-CoA: 27.2
  Benzoyl-CoA: 25.1
  Acetyl-CoA: 24.6
  fatty_acid: 19.2
  trans-1,2-CPDA: 18.6
  2-Methylbutyryl-CoA: 15.8
  CHC-CoA: 14.1
  3-Methylbutyryl-CoA: 0.0

CAG99_RS19720: pk - mal
PKS_AT (560..834): 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: 197.5
  Methylmalonyl-CoA: 197.1
  Methoxymalonyl-CoA: 155.7
  2-Methylbutyryl-CoA: 135.0
  CHC-CoA: 102.8
  Propionyl-CoA: 102.2
  trans-1,2-CPDA: 102.1
  Malonyl-CoA: 74.0
  Isobutyryl-CoA: 68.3
  Benzoyl-CoA: 47.4
  3-Methylbutyryl-CoA: 36.7
  Acetyl-CoA: 32.9
  fatty_acid: 30.1
  inactive: 19.2

PKS_AT (2203..2478): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 209.2
  inactive: 100.1
  Methoxymalonyl-CoA: 59.8
  Methylmalonyl-CoA: 53.1
  Isobutyryl-CoA: 35.4
  Propionyl-CoA: 29.5
  Acetyl-CoA: 26.8
  Ethylmalonyl-CoA: 24.7
  Benzoyl-CoA: 23.3
  2-Methylbutyryl-CoA: 20.4
  CHC-CoA: 15.7
  fatty_acid: 14.4
  trans-1,2-CPDA: 14.0
  3-Methylbutyryl-CoA: 0.0

CAG99_RS19725: mal
PKS_AT (552..828): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 190.6
  inactive: 103.5
  Methoxymalonyl-CoA: 60.6
  Methylmalonyl-CoA: 54.2
  Isobutyryl-CoA: 32.3
  Ethylmalonyl-CoA: 31.6
  Propionyl-CoA: 27.2
  Benzoyl-CoA: 25.1
  Acetyl-CoA: 24.6
  fatty_acid: 19.2
  trans-1,2-CPDA: 18.6
  2-Methylbutyryl-CoA: 15.8
  CHC-CoA: 14.1
  3-Methylbutyryl-CoA: 0.0

CAG99_RS19735: mal - mal
PKS_AT (552..831): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.6
  inactive: 99.1
  Methylmalonyl-CoA: 62.9
  Methoxymalonyl-CoA: 62.6
  Propionyl-CoA: 46.5
  Isobutyryl-CoA: 34.4
  CHC-CoA: 27.8
  Ethylmalonyl-CoA: 26.9
  Benzoyl-CoA: 22.9
  fatty_acid: 21.9
  2-Methylbutyryl-CoA: 21.5
  Acetyl-CoA: 20.9
  trans-1,2-CPDA: 9.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2171..2446): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 195.2
  inactive: 107.8
  Methoxymalonyl-CoA: 61.5
  Methylmalonyl-CoA: 56.6
  Isobutyryl-CoA: 33.9
  Ethylmalonyl-CoA: 31.6
  Propionyl-CoA: 30.6
  Benzoyl-CoA: 25.1
  Acetyl-CoA: 24.6
  fatty_acid: 19.2
  trans-1,2-CPDA: 18.6
  2-Methylbutyryl-CoA: 15.5
  CHC-CoA: 14.1
  3-Methylbutyryl-CoA: 0.0

CAG99_RS19755: X
AMP-binding (18..405): X
nrpys: bMe-Asp

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:
    YLLVFDCAMFECFSFFAGEENLYGPTELTITVTG
  Nearest Stachelhaus code(s):
    bMe-Asp DCFFFALITK (85% 8Å match)
    Ala DCFFFALITK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

CAG99_RS19765: pk
PKS_AT (4..267): pk
ATSignature: (unknown)
No matches above 50%
minowa: Propionyl-CoA

Prediction, score:
  Propionyl-CoA: 15.7
  CHC-CoA: 14.5
  Methylmalonyl-CoA: 11.5
  Methoxymalonyl-CoA: 9.6
  2-Methylbutyryl-CoA: 9.1
  Ethylmalonyl-CoA: 8.2
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Malonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CAG99_RS19770: X
AMP-binding (24..436): 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:
    FGASFDFSLFDFDCVFTGETNGYGATETMAASIT
  Nearest Stachelhaus code(s):
    dn-dohHep DVFDFGGVAK (47% 8Å match)
    4Me-Pro DVFYVMAAAK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

CAG99_RS19775: mal - pk
PKS_AT (646..939): 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: 203.8
  inactive: 113.4
  Methoxymalonyl-CoA: 62.4
  Methylmalonyl-CoA: 53.9
  Propionyl-CoA: 38.4
  Isobutyryl-CoA: 34.0
  2-Methylbutyryl-CoA: 22.8
  Acetyl-CoA: 15.8
  Benzoyl-CoA: 14.8
  Ethylmalonyl-CoA: 14.6
  trans-1,2-CPDA: 10.2
  CHC-CoA: 8.8
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2340..2638): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 221.5
  Methylmalonyl-CoA: 217.3
  Methoxymalonyl-CoA: 178.5
  trans-1,2-CPDA: 153.0
  2-Methylbutyryl-CoA: 140.6
  Propionyl-CoA: 113.4
  Malonyl-CoA: 110.9
  CHC-CoA: 93.1
  Benzoyl-CoA: 86.9
  Isobutyryl-CoA: 77.3
  Acetyl-CoA: 52.9
  3-Methylbutyryl-CoA: 46.6
  fatty_acid: 43.7
  inactive: 30.4

CAG99_RS19815: mal
PKS_AT (13..305): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 70.8%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 76.1
  Methylmalonyl-CoA: 39.3
  Methoxymalonyl-CoA: 38.4
  Propionyl-CoA: 24.9
  inactive: 21.6
  trans-1,2-CPDA: 20.1
  2-Methylbutyryl-CoA: 15.9
  CHC-CoA: 13.3
  fatty_acid: 9.2
  Isobutyryl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -4.8

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
IolR | Regulator of the inositol catabolism
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP021121.1 - Region 21 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,572,995 - 4,619,150 nt. (total: 46,156 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 oxygenase
CAG99_RS20075: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS20090: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CAG99_RS20095: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CAG99_RS20125: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

Transferases: acetyltransferase halogenase methyltransferase
CAG99_RS19990: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

CAG99_RS20040: methyltransferase

smcogs
  SMCOG1248: methyltransferase

CAG99_RS20070: halogenase

smcogs
  SMCOG1119: halogenase

Hydrolases: esterase
CAG99_RS28105: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase
CAG99_RS20050: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CAG99_RS20055: 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
--- | --- | --- | --- | --- | ---
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.62 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.62 | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
Additional weak hits (21):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.19 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.65 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 12.73 out of 18.57
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.30 out of 39.62
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
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.45 out of 27.04
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.25 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.62 out of 36.54
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.46 out of 28.19
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.85 out of 32.74
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.81 out of 30.98
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.95 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.31 out of 35.63
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.66 out of 23.43
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.61 out of 30.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 35.63
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.15 out of 28.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.66 out of 23.43
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 26, location 4572994 - 4619150:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CAG99_RS20050: X - X
AMP-binding (12..376): 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:
    ENIVHALGQFCAIALSGSNRQTYGSTEAGSVCWD
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

AMP-binding (1060..1450): 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:
    TDD------FDTAVVVSGEVHVYGGAEWGPAVSR
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CAG99_RS20055: X
AMP-binding (7..391): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YAYGFDVTIDEPYVRTGGELNEYGPTETVAGAVF
  Nearest Stachelhaus code(s):
    4Me-Pro DVQYVGHAIK (44% 8Å match)
    Thr DGDYVRLAGK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

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

NZ_CP021121.1 - Region 22 - melanin
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,759,340 - 4,769,756 nt. (total: 10,417 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
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 | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.78 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000911.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.52 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.43 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000662.5 |  | 0.42 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000889.5 |  | 0.38 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.37 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0000679.5 |  | 0.24 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0000700.5 |  | 0.24 | saccharide | istamycin | Streptomyces tenjimariensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.78 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000911.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.52 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.43 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000662.5 |  | 0.42 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000889.5 |  | 0.38 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.37 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0000679.5 |  | 0.24 | terpene | diazepinomicin | Micromonospora sp. M42
BGC0000700.5 |  | 0.24 | saccharide | istamycin | Streptomyces tenjimariensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (5):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.59 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.21 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.00 out of 29.65
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.30 out of 23.43
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP021121.1 - Region 23 - 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: 4,839,975 - 4,862,626 nt. (total: 22,652 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
CAG99_RS21225: 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 |  | 0.68 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.60 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000518.3 |  | 0.56 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000553.3 |  | 0.54 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000563.4 |  | 0.52 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002698.2 |  | 0.51 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.68 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.60 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000518.3 |  | 0.56 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000553.3 |  | 0.54 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000563.4 |  | 0.52 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002698.2 |  | 0.51 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566

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

No significant matches found.

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

#### Lanthipeptide(s) for CAG99_RS21190

CAG99_RS21195
Leader:
MSLLDLQSMEPEVASGGGGE
Core:
G D L S S L S L L I C D T H S S N S V I L C L
Core with dehydrations:
G D L Dha Dha L Dha L L I Cys D Dhb H Dha Dha N Dha V I L Cys L

#### antiSMASH-DB 4.0 matches for CAG99_RS21195

100.0%
NZ_CP021121.1 and 1 other:
NZ_CP084541.1 Lanthipeptides: LC193_RS06630_lanthipeptide
Lanthipeptides: CAG99_RS21195_lanthipeptide
1
G D L S S L S L L I C D T H S S N S V I L C L
23
G D L S S L S L L I C D T H S S N S V I L C L
1
G D L S S L S L L I C D T H S S N S V I L C L
23
69.6%
NZ_AUBE01000003.1:
Lanthipeptides: G412_RS38950_lanthipeptide
4
S S L S L L I C D T H S S N S V I L C L
23
S S L S L L C D H S S N S +L C L
1
S S L S L L A C D K H S S N S F L L C L
20
65.2%
NC_016582.1:
Lanthipeptides: SBI_RS53340_lanthipeptide
1
G D L S S L S L L I C D T H S S N S V I L C L
23
G S S+S L L+C D H S S+S +L C L
1
G G E S S V S L L L C D K H S S H S N L L C L
23
with 50 more sequence matches
Only the first 10 are displayed here.
60.9%
NZ_BBQG01000022.1 and 5 others:
NZ_CP048875.1 Lanthipeptides: G3260_RS30690_lanthipeptide NZ_CP050693.1 Lanthipeptides: HC362_RS03880_lanthipeptide NZ_CP103060.1 Lanthipeptides: NR995_RS03375_lanthipeptide NZ_KE150472.1 Lanthipeptides: HMPREF1486_RS35560_lanthipeptide NZ_VJOK01000001.1 Lanthipeptides: FM076_RS28910_lanthipeptide
Lanthipeptides: TU22_RS34220_lanthipeptide
4
S S L S L L I C D T H S S N S V I L C L
23
S S S L L+C D H S S+S +L C L
1
S S A S L L L C D K H S S H S T L L C L
20
60.9%
NZ_FNVO01000002.1 and 2 others:
NZ_FNVO01000002.1 Lanthipeptides: C4U03_RS04695_lanthipeptide NZ_FNVO01000002.1 Lanthipeptides: C4U03_RS04695_lanthipeptide
Lanthipeptides: C4U03_RS04695_lanthipeptide
5
S L S L L I C D T H S S N S V I L C L
23
S+S L L+C D H S S+S I L C L
1
S V S L L L C D K H S S H S T I L C L
19
60.9%
NZ_FOLM01000007.1:
Lanthipeptides: BM242_RS14445_lanthipeptide
4
S S L S L L I C D T H S S N S V I L C L
23
S S+S L L+C D H S S+S +L C L
2
S S V S L L L C D K H S S H S N L L C L
21
56.5%
NZ_BNBU01000005.1:
Lanthipeptides: IE303_RS19905_lanthipeptide
4
S S L S L L I C D T H S S N S V I L C L
23
S L S L L+C D S S V L C L
3
S Q L S L L L C D--S V A S V A L C L
20
56.5%
NZ_CP032402.1 and 1 other:
NZ_CP032402.1 Lanthipeptides: D3U04_RS17070_lanthipeptide
Lanthipeptides: D3U04_RS17070_lanthipeptide
5
S L S L L I C D T H S S N S V I L C L
23
S S L L+C D H S S S +L C L
1
S A S L L L C D K H S S Q S T V L C L
19
56.5%
NZ_FMHI01000010.1:
Lanthipeptides: H180DRAFT_RS29175_lanthipeptide
4
S S L S L L I C D T H S S N S V I L C L
23
S S S L L+C D S S+S +L C L
2
S S A S L L L C D K F S S H S T L L C L
21
56.5%
NZ_FOGO01000006.1 and 1 other:
NZ_LJGV01000022.1 Lanthipeptides: AN217_RS28695_lanthipeptide
Lanthipeptides: BMX65_RS32100_lanthipeptide
4
S S L S L L I C D T H S S N S V I L C L
23
S S S L L+C D S S+S +L C L
1
S S A S L L L C D K L S S H S A L L C L
20
56.5%
NZ_JAEVFI010000019.1:
Lanthipeptides: JJV70_RS15420_lanthipeptide
5
S L S L L I C D T H S S N S V I L C L
23
++S L L I C D H S S I L C L
1
N V S L L I C D K H S G A S T I L C L
19
52.2%
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
4
S S L S L L I C D T H S S N S V I L C
22
S +S L L I C+ +S S S V L C
2
S Q I S L L I C E-Y S S L S V T L C
19
52.2%
NZ_CM000913.1 and 1 other:
NZ_CP016559.1 Lanthipeptides: BB341_RS04185_lanthipeptide
Lanthipeptides: SCLAV_RS23790_lanthipeptide
4
S S L S L L I C D T H S S N S V I L C
22
S S S L L+C H S S S++L C
3
S S Q S L L V C G P H S S Q S L L L C
21

#### MIBiG 4.0 matches for CAG99_RS21195

47.8%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
4
S S L S L L I C D T H S S N S V I L C
22
S +S L L+C+ +S S S V+L C
3
S Q V S L L V C E-Y S S L S V V L C
20
21.7%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
2
D L S S L S L L I C
11
+ S S L S+++C
11
E Y S S L S V V L C
20

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.86 out of 21.84
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
Additional weak hits (12):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.87 out of 20.01
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.18 out of 26.85
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.04 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.50 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.83 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.14 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.81 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.65 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.40 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.86 out of 29.65
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.75 out of 32.93
Confidence: weak
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.

CAG99_RS21195 - Class III
  Cleavage pHMM score: 15.70
  RODEO score: 0
  Monoisotopic mass: 2263.2 Da
  Molecular weight: 2264.6 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2282.6 Da N = 1
    2300.6 Da N = 2
    2318.6 Da N = 3
    2336.7 Da N = 4
    2354.7 Da N = 5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MexT | Global virulence regulator
OsdR | Development and stress management regulator

NZ_CP021121.1 - Region 24 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,900,156 - 4,971,664 nt. (total: 71,509 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
CAG99_RS21475: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

CAG99_RS21520: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

CAG99_RS21530: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS21540: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS21555: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

Transferases: aminotransferase
CAG99_RS21480: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Ligases: ligase synthase
CAG99_RS21420: cobaltochelatase subunit CobN

smcogs
  SMCOG1263: cobaltochelatase subunit CobN

CAG99_RS21495: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CAG99_RS21500: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CAG99_RS21505: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001164.3 |  | 0.64 | 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
BGC0001276.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001164.3 |  | 0.64 | 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
BGC0001276.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.62 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 24.69 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 24.78 out of 30.11
Confidence: medium
Additional weak hits (18):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 25.75
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.02 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.16 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.69 out of 32.74
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.32 out of 29.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.39 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.62 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
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.99 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.36 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.88 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.08 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.72 out of 27.04
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.69 out of 33.14
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.21 out of 20.01
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.58 out of 26.12
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 29, location 4900155 - 4971664:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - ccmal - ccmal) + (ccmal - ccmal) + (ccmal)
Non-colinear ordering:
  CAG99_RS21505 + CAG99_RS21500 + CAG99_RS21495

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).
CAG99_RS21495: mal
PKS_AT (568..855): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 138.4
  inactive: 79.9
  Methoxymalonyl-CoA: 47.2
  Methylmalonyl-CoA: 28.4
  Propionyl-CoA: 26.0
  trans-1,2-CPDA: 17.7
  Ethylmalonyl-CoA: 14.1
  fatty_acid: 13.4
  Isobutyryl-CoA: 11.7
  2-Methylbutyryl-CoA: 9.0
  Acetyl-CoA: 7.9
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CAG99_RS21500: mal - mal
PKS_AT (593..880): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 137.4
  inactive: 80.2
  Methoxymalonyl-CoA: 49.4
  Methylmalonyl-CoA: 29.1
  Propionyl-CoA: 23.9
  trans-1,2-CPDA: 16.4
  Ethylmalonyl-CoA: 16.0
  Isobutyryl-CoA: 13.3
  2-Methylbutyryl-CoA: 12.6
  fatty_acid: 11.3
  Acetyl-CoA: 8.9
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2349..2636): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 137.7
  inactive: 81.0
  Methoxymalonyl-CoA: 49.2
  Methylmalonyl-CoA: 29.0
  Propionyl-CoA: 25.7
  trans-1,2-CPDA: 18.3
  Ethylmalonyl-CoA: 15.0
  Isobutyryl-CoA: 12.0
  fatty_acid: 11.4
  2-Methylbutyryl-CoA: 11.0
  Acetyl-CoA: 8.9
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CAG99_RS21505: mal - mal - mal
PKS_AT (550..837): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 138.1
  inactive: 81.0
  Methoxymalonyl-CoA: 47.7
  Methylmalonyl-CoA: 28.6
  Propionyl-CoA: 25.3
  trans-1,2-CPDA: 21.8
  Ethylmalonyl-CoA: 12.7
  Isobutyryl-CoA: 12.5
  Acetyl-CoA: 9.3
  2-Methylbutyryl-CoA: 9.2
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (1571..1861): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 174.5
  inactive: 71.9
  Methylmalonyl-CoA: 56.9
  Methoxymalonyl-CoA: 56.5
  Isobutyryl-CoA: 38.0
  Acetyl-CoA: 25.9
  Ethylmalonyl-CoA: 19.2
  Propionyl-CoA: 18.3
  Benzoyl-CoA: 16.8
  fatty_acid: 12.1
  CHC-CoA: 11.1
  trans-1,2-CPDA: 10.3
  2-Methylbutyryl-CoA: 5.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3373..3673): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 197.5
  inactive: 111.0
  Methoxymalonyl-CoA: 69.5
  Methylmalonyl-CoA: 50.1
  Propionyl-CoA: 39.2
  Ethylmalonyl-CoA: 24.3
  Isobutyryl-CoA: 22.3
  trans-1,2-CPDA: 20.6
  2-Methylbutyryl-CoA: 19.6
  Acetyl-CoA: 18.4
  fatty_acid: 12.8
  Benzoyl-CoA: 11.0
  CHC-CoA: 9.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor

NZ_CP021121.1 - Region 25 - azole-containing-RiPP,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,038,287 - 5,075,657 nt. (total: 37,371 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CAG99_RS21970: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: glucosidase
CAG99_RS22040: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Lyases: cyclase dehydratase hydratase
CAG99_RS21960: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

CAG99_RS21965: Terpene synthase/cyclase metal-binding domain protein

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

CAG99_RS21995: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Translocases: transporter
CAG99_RS22025: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | terpene | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000683.3 |  |  | 0.98 | terpene | avermitilol | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000606.5 |  |  | 0.24 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0000678.5 |  |  | 0.22 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001483.4 |  |  | 0.21 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001146.5 |  |  | 0.20 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0002285.2 |  |  | 0.20 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001145.5 |  |  | 0.18 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5 |  |  | 0.17 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0002805.2 |  |  | 0.16 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001012.3 |  |  | 0.16 | NRPS, PKS | meridamycin | Streptomyces violaceusniger

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000683.3 |  | 0.78 | terpene | avermitilol | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000606.5 |  | 0.58 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0001146.5 |  | 0.52 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0002285.2 |  | 0.52 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001145.5 |  | 0.49 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5 |  | 0.48 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0001174.4 |  | 0.47 | ribosomal | corynazolicin | Corynebacterium urealyticum DSM 7111
BGC0001640.3 |  | 0.45 | ribosomal | kocurin | Kocuria rosea
BGC0001173.5 |  | 0.45 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0001860.4 |  | 0.44 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833

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:
CAG99_RS21965: T1TS
Domain 1 (2 - 316): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.91 out of 19.26
Confidence: medium
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 27.06 out of 35.63
Confidence: medium
Additional weak hits (9):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.03 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.37 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.78 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.43 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.00 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.04 out of 29.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.58 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.37 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.38 out of 28.19
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
Terpene
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (5047239...5075657)
CAG99_RS22000
  RRE type: Thiopeptide_F_RRE
  Location: 46 - 126
  Score: 39.3

Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
NrtR | NAD synthesis repressor

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_CP021121.1 - Region 26 - ectoine
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,392,316 - 5,402,711 nt. (total: 10,396 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
CAG99_RS23515: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

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

Reference | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.85 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.85 | other (other) | ectoine | Streptomyces anulatus
BGC0000852.5 |  | 0.71 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.56 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000859.3 |  | 0.55 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.55 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.54 | other (other) | ectoine | Methylophaga alcalica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.85 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.85 | other (other) | ectoine | Streptomyces anulatus
BGC0000852.5 |  | 0.71 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.56 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000859.3 |  | 0.55 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.55 | other (other) | ectoine | Methylophaga thalassica
BGC0000857.3 |  | 0.54 | other (other) | ectoine | Methylophaga alcalica

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05
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 (7):
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.54 out of 29.51
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.31 out of 21.55
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.86 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.71 out of 25.88
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.25 out of 36.53
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.73 out of 26.06
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production

NZ_CP021121.1 - Region 27 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,428,792 - 5,458,594 nt. (total: 29,803 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: glycosyltransferase
CAG99_RS23805: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.65 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.63 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.59 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002464.3 |  | 0.58 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0001572.3 |  | 0.55 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000940.5 |  | 0.53 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.53 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002690.2 |  | 0.48 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0001531.5 |  | 0.47 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002620.2 |  | 0.46 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.65 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.63 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2 |  | 0.59 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002464.3 |  | 0.58 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0001572.3 |  | 0.55 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000940.5 |  | 0.53 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.53 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002690.2 |  | 0.48 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0001531.5 |  | 0.47 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002620.2 |  | 0.46 | 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.62 out of 36.53
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 25.31
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.19 out of 36.53
Confidence: medium
Additional weak hits (23):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.12 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.61 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.56 out of 36.54
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.42 out of 20.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.97 out of 31.73
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.62 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.68 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.92 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.67 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.10 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.03 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.05 out of 30.97
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.07 out of 30.98
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.96 out of 28.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.29 out of 32.93
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.88 out of 39.62
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.57 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.07 out of 30.11
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
DmdR1 | Iron(II)-dependent repressor
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP021121.1 - Region 28 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,585,517 - 5,633,154 nt. (total: 47,638 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
CAG99_RS24535: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: aminotransferase
CAG99_RS24555: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

CAG99_RS24560: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Hydrolases: hydrolase
CAG99_RS24570: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CAG99_RS24615: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: hydratase
CAG99_RS24630: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: synthase
CAG99_RS24575: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002191.2 |  | 0.73 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002191.2 |  | 0.73 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.75 out of 23.05
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.66 out of 23.43
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
Additional weak hits (13):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.89 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.37 out of 26.33
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.93 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.75 out of 26.06
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.75 out of 23.43
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.01 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.52 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 15.87 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.83 out of 29.65
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.26 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.71 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 35, location 5585516 - 5633154:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-pk)

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).
CAG99_RS24575: pk
PKS_AT (536..834): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 62.5%
  Methylmalonyl-CoA: 58.3%
  Propionyl-CoA: 54.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 99.3
  Methoxymalonyl-CoA: 94.8
  Malonyl-CoA: 83.5
  Ethylmalonyl-CoA: 64.4
  Propionyl-CoA: 56.1
  Isobutyryl-CoA: 51.5
  2-Methylbutyryl-CoA: 48.7
  Acetyl-CoA: 33.4
  CHC-CoA: 33.3
  trans-1,2-CPDA: 31.9
  fatty_acid: 27.7
  Benzoyl-CoA: 26.4
  3-Methylbutyryl-CoA: 14.6
  inactive: 9.6

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
BldD | Development and antibiotic global regulator
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP021121.1 - Region 29 - 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: 5,711,906 - 5,732,988 nt. (total: 21,083 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase phosphate reductase
CAG99_RS25070: N-acetyl-gamma-glutamyl-phosphate reductase

smcogs
  SMCOG1219: N-acetyl-gamma-glutamyl-phosphate reductase

CAG99_RS25120: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

CAG99_RS25130: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CAG99_RS25140: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: acetyltransferase acyltransferase aminotransferase kinase
CAG99_RS25080: acetylglutamate kinase

smcogs
  SMCOG1174: acetylglutamate kinase

CAG99_RS25085: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

CAG99_RS25105: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

CAG99_RS25145: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Hydrolases: dehalogenase
CAG99_RS25125: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: lyase
CAG99_RS25115: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: synthase synthetase
CAG99_RS25095: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

CAG99_RS25110: argininosuccinate synthase

smcogs
  SMCOG1291: argininosuccinate 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-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0000895.5 |  | 0.47 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0000859.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000858.3 |  | 0.47 | other (other) | ectoine | Methylobacter marinus
BGC0000278.3 |  | 0.46 | PKS | urdamycin | Streptomyces fradiae
BGC0000678.5 |  | 0.45 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000919.5 |  | 0.45 | other (other) | phaseolotoxin | Pseudomonas syringae
BGC0000431.5 |  | 0.44 | NRPS | stenothricin | Streptomyces filamentosus NRRL 15998
BGC0000854.3 |  | 0.44 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000265.5 |  | 0.44 | PKS | rhodomycin | Streptomyces purpurascens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0000895.5 |  | 0.47 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0000859.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000858.3 |  | 0.47 | other (other) | ectoine | Methylobacter marinus
BGC0000278.3 |  | 0.46 | PKS | urdamycin | Streptomyces fradiae
BGC0000678.5 |  | 0.45 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000919.5 |  | 0.45 | other (other) | phaseolotoxin | Pseudomonas syringae
BGC0000431.5 |  | 0.44 | NRPS | stenothricin | Streptomyces filamentosus NRRL 15998
BGC0000854.3 |  | 0.44 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000265.5 |  | 0.44 | PKS | rhodomycin | Streptomyces purpurascens

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:
CAG99_RS25095: PT_FPPS_like
Domain 1 (61 - 351): 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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (4):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.39 out of 20.01
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.22 out of 28.14
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.21 out of 36.54
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production

NZ_CP021121.1 - Region 30 - NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,940,396 - 6,065,600 nt. (total: 125,205 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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 oxygenase
CAG99_RS26110: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS26115: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS26130: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

CAG99_RS26225: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS26260: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CAG99_RS26290: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS26315: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS26385: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CAG99_RS26450: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

CAG99_RS29200: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase kinase methyltransferase
CAG99_RS26255: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CAG99_RS26265: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CAG99_RS26510: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

CAG99_RS29125: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase protease
CAG99_RS26170: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

CAG99_RS26200: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CAG99_RS26250: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

CAG99_RS26275: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

CAG99_RS26280: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: lyase
CAG99_RS26400: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
CAG99_RS26210: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CAG99_RS26215: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CAG99_RS26230: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CAG99_RS26405: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CAG99_RS26410: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | T1PKS | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001169.5 |  |  |  | 0.96 | PKS | piericidin A1 | Streptomyces sp. SCSIO 03032
BGC0002276.2 |  |  |  | 0.82 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001268.4 |  |  |  | 0.81 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002135.2 |  |  |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  |  |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0002164.2 |  |  |  | 0.60 | NRPS | peramine | Epichloe festucae
BGC0000357.5 |  |  |  | 0.58 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001250.4 |  |  |  | 0.58 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  |  | 0.58 | NRPS | epichloenin A | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001169.5 |  | 0.99 | PKS | piericidin A1 | Streptomyces sp. SCSIO 03032
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000124.5 |  | 0.72 | PKS | piericidin A1 | Streptomyces piomogenus
BGC0000041.3 |  | 0.69 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001742.5 |  | 0.66 | PKS | piericidin A1 | Candidatus Streptomyces philanthi bv. triangulum
BGC0001268.4 |  | 0.65 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.88 out of 20.97
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.94 out of 26.85
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 27.11 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
Additional weak hits (33):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.14 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.33 out of 30.25
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.10 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.62 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.85 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.05 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.14 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.31 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.51 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.69 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.08 out of 36.53
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.28 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.85 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.26 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.87 out of 32.74
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.53 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.44 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.97 out of 29.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.14 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.19 out of 24.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.12 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.43 out of 28.14
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.64 out of 23.43
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.52 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.53 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.09 out of 24.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.97 out of 27.04
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.57 out of 36.53
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 37, location 5940395 - 6065600:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 38, location 5940395 - 6021945:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-ccmal) + (Me-ohmal - Me-ccmal) + (pk) + (pk) + (ccmal) + (Me-mal - mal)
Non-colinear ordering:
  CAG99_RS26210 + CAG99_RS26215 + CAG99_RS29200 + CAG99_RS26225 + CAG99_RS26230 + CAG99_RS29125

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 39, location 6019392 - 6063751:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 40, location 6023767 - 6065600:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Pro)

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).
CAG99_RS26210: mmal - mmal
PKS_AT (1..283): mmal
ATSignature: Isobutyryl-CoA

Top 3 matches:
  Isobutyryl-CoA: 66.7%
  2-Methylbutyryl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 133.4
  Ethylmalonyl-CoA: 126.3
  Propionyl-CoA: 109.4
  Methoxymalonyl-CoA: 106.4
  2-Methylbutyryl-CoA: 104.1
  CHC-CoA: 91.5
  trans-1,2-CPDA: 81.9
  Isobutyryl-CoA: 60.6
  Malonyl-CoA: 60.4
  Benzoyl-CoA: 32.1
  Acetyl-CoA: 31.8
  fatty_acid: 28.8
  inactive: 13.8
  3-Methylbutyryl-CoA: 8.4

PKS_AT (970..1246): 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: 174.7
  Ethylmalonyl-CoA: 161.2
  Methoxymalonyl-CoA: 133.8
  2-Methylbutyryl-CoA: 107.5
  trans-1,2-CPDA: 92.3
  Propionyl-CoA: 86.8
  CHC-CoA: 72.5
  Malonyl-CoA: 64.4
  Isobutyryl-CoA: 56.7
  Benzoyl-CoA: 37.4
  inactive: 32.7
  Acetyl-CoA: 27.6
  fatty_acid: 27.0
  3-Methylbutyryl-CoA: 11.6

CAG99_RS26215: mmal - mmal
PKS_AT (594..870): 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: 174.7
  Ethylmalonyl-CoA: 161.2
  Methoxymalonyl-CoA: 133.8
  2-Methylbutyryl-CoA: 107.5
  trans-1,2-CPDA: 92.3
  Propionyl-CoA: 86.8
  CHC-CoA: 72.5
  Malonyl-CoA: 64.4
  Isobutyryl-CoA: 56.7
  Benzoyl-CoA: 37.4
  inactive: 32.7
  Acetyl-CoA: 27.6
  fatty_acid: 27.0
  3-Methylbutyryl-CoA: 11.6

PKS_AT (2129..2405): 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: 174.7
  Ethylmalonyl-CoA: 161.2
  Methoxymalonyl-CoA: 133.8
  2-Methylbutyryl-CoA: 107.5
  trans-1,2-CPDA: 92.3
  Propionyl-CoA: 86.8
  CHC-CoA: 72.5
  Malonyl-CoA: 64.4
  Isobutyryl-CoA: 56.7
  Benzoyl-CoA: 37.4
  inactive: 32.7
  Acetyl-CoA: 27.6
  fatty_acid: 27.0
  3-Methylbutyryl-CoA: 11.6

CAG99_RS29200: pk
PKS_AT (572..724): pk
ATSignature: (unknown)
No matches above 50%
minowa: CHC-CoA

Prediction, score:
  CHC-CoA: 22.2
  Methylmalonyl-CoA: 17.0
  trans-1,2-CPDA: 16.2
  Propionyl-CoA: 13.1
  Methoxymalonyl-CoA: 12.6
  2-Methylbutyryl-CoA: 12.4
  inactive: 0.0
  fatty_acid: 0.0
  Malonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  Ethylmalonyl-CoA: -1.9

CAG99_RS26225: pk
PKS_AT (554..824): 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: 213.6
  Methylmalonyl-CoA: 212.7
  Methoxymalonyl-CoA: 165.7
  2-Methylbutyryl-CoA: 161.0
  trans-1,2-CPDA: 135.6
  Propionyl-CoA: 113.9
  CHC-CoA: 99.9
  Malonyl-CoA: 85.6
  Isobutyryl-CoA: 85.5
  Benzoyl-CoA: 70.4
  Acetyl-CoA: 49.4
  3-Methylbutyryl-CoA: 34.6
  fatty_acid: 28.7
  inactive: 26.3

CAG99_RS26230: mal
PKS_AT (570..883): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 190.7
  inactive: 87.8
  Methoxymalonyl-CoA: 47.9
  Methylmalonyl-CoA: 38.6
  Propionyl-CoA: 25.4
  Benzoyl-CoA: 11.3
  fatty_acid: 11.0
  Acetyl-CoA: 10.4
  Isobutyryl-CoA: 9.6
  3-Methylbutyryl-CoA: 6.7
  CHC-CoA: 4.1
  Ethylmalonyl-CoA: 4.0
  2-Methylbutyryl-CoA: 2.6
  trans-1,2-CPDA: 0.0

CAG99_RS29125: mmal - mal
PKS_AT (595..871): 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: 174.7
  Ethylmalonyl-CoA: 161.2
  Methoxymalonyl-CoA: 133.8
  2-Methylbutyryl-CoA: 107.5
  trans-1,2-CPDA: 92.3
  Propionyl-CoA: 86.8
  CHC-CoA: 72.5
  Malonyl-CoA: 64.4
  Isobutyryl-CoA: 56.7
  Benzoyl-CoA: 37.4
  inactive: 32.7
  Acetyl-CoA: 27.6
  fatty_acid: 27.0
  3-Methylbutyryl-CoA: 11.6

PKS_AT (1608..1910): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 66.7%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 165.7
  inactive: 75.3
  Methoxymalonyl-CoA: 47.7
  Methylmalonyl-CoA: 37.4
  Propionyl-CoA: 22.0
  fatty_acid: 11.2
  Isobutyryl-CoA: 10.2
  Acetyl-CoA: 10.2
  Ethylmalonyl-CoA: 10.0
  Benzoyl-CoA: 8.1
  2-Methylbutyryl-CoA: 6.5
  CHC-CoA: 5.1
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

CAG99_RS26405: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (474..868): 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:
    LWQTFDVSFQESFLATAGEDNHYGPSETHVVVAE
  Nearest Stachelhaus code(s):
    Pro DVQFAAHVVK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

CAG99_RS26410: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (113..507): 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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LPDAWDAFSLEGWLLTGGEVNGYGPVESCVFATT
  Nearest Stachelhaus code(s):
    Val DALWLGGVFK (56% 8Å match)
  Stachelhaus code match:
    100% (strong)

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
AfsR | Pleiotropic regulatory for antibiotic production
CcpA | Catabolite control protein A
RutR | Regulator of the pyrimidine and purine metabolism
ZuR variant 1 | Zinc-responsive repressor

NZ_CP021121.1 - Region 31 - 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: 6,151,707 - 6,173,614 nt. (total: 21,908 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
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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
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
CAG99_RS26805: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

CAG99_RS26825: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CAG99_RS26850: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CAG99_RS26875: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CAG99_RS26885: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: kinase methyltransferase
CAG99_RS26845: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CAG99_RS26865: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Hydrolases: deacetylase
CAG99_RS26815: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

Ligases: synthase
CAG99_RS26795: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

CAG99_RS26810: 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000737.3 |  | 0.48 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000739.3 |  | 0.46 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000740.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000746.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000747.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000748.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000752.3 |  | 0.43 | saccharide | capsular polysaccharide | Actinobacillus pleuropneumoniae serovar 6 str. Femo
BGC0000734.3 |  | 0.42 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000762.3 |  | 0.42 | saccharide | exopolysaccharide | Rhizobium leguminosarum bv. viciae
BGC0001077.4 |  | 0.41 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000737.3 |  | 0.48 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000739.3 |  | 0.46 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000740.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000746.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000747.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000748.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000752.3 |  | 0.43 | saccharide | capsular polysaccharide | Actinobacillus pleuropneumoniae serovar 6 str. Femo
BGC0000734.3 |  | 0.42 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000762.3 |  | 0.42 | saccharide | exopolysaccharide | Rhizobium leguminosarum bv. viciae
BGC0001077.4 |  | 0.41 | PKS | 6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone | Actinoplanes missouriensis 431

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
CAG99_RS26840: T2TS
Domain 1 (5 - 619): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.07 out of 25.31
Confidence: medium
Additional weak hits (5):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.60 out of 21.55
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.61 out of 25.31
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.12 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.38 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.34 out of 35.63
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP021121.1 - Region 32 - indole
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,216,758 - 6,240,060 nt. (total: 23,303 nt) Show pHMM detection rules used
indole: (indsynth or dmat or indole_PTase)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
CAG99_RS27095: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CAG99_RS27100: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

CAG99_RS27110: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: halogenase
CAG99_RS27105: flavin-dependent trp 5 halogenase

halogenases
  flavin-dependent trp 5 halogenase
smcogs
  SMCOG1119: halogenase

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 | indole | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001782.3 |  | 0.85 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0001224.5 |  | 0.63 | other (other) | reductasporine | uncultured bacterium
BGC0001336.5 |  | 0.60 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001223.5 |  | 0.57 | other (other) | hydroxysporine | uncultured bacterium
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000817.4 |  | 0.54 | other (other) | methylarcyriarubin | uncultured bacterium
BGC0000830.5 |  | 0.52 | other (aminocoumarin) | violacein | uncultured bacterium
BGC0001310.5 |  | 0.50 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0000831.3 |  | 0.50 | other (other) | violacein | Duganella sp. B2
BGC0001335.5 |  | 0.50 | other (other) | borregomycin A, borregomycin B, borregomycin C, borregomycin D | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001782.3 |  | 0.85 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0001224.5 |  | 0.63 | other (other) | reductasporine | uncultured bacterium
BGC0001336.5 |  | 0.60 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001223.5 |  | 0.57 | other (other) | hydroxysporine | uncultured bacterium
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000817.4 |  | 0.54 | other (other) | methylarcyriarubin | uncultured bacterium
BGC0000830.5 |  | 0.52 | other (aminocoumarin) | violacein | uncultured bacterium
BGC0001310.5 |  | 0.50 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0000831.3 |  | 0.50 | other (other) | violacein | Duganella sp. B2
BGC0001335.5 |  | 0.50 | other (other) | borregomycin A, borregomycin B, borregomycin C, borregomycin D | uncultured bacterium

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
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 (9):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.89 out of 32.74
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.16 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.31 out of 27.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.66 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.58 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.73 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.51 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.04 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.32 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---