Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
1.11
2.1
2.2
2.3
2.4
2.5
2.6
3.1
3.2
3.3
3.4
3.5
3.6
5.1
5.2
5.3
6.1
6.2
7.1
7.2
7.3
7.4
9.1
9.2
10.1
11.1

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

NZ_RCDD01000001.1 (Actinokineospora cianjurensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | NAPAA | 215,669 | 249,541 | High | ε-Poly-L-lysine | NRPS:Type I
Region 1.2 | ectoine | 267,217 | 277,615 | High | ectoine | other:other
Region 1.3 | hydrogen-cyanide | 506,262 | 518,902 |  |
Region 1.4 | terpene-precursor,T1PKS | 1,836,145 | 2,029,578 | Medium | stambomycin A/stambomycin B/stambomycin C/stambomycin D | PKS:Type I+saccharide:hybrid/tailoring
Region 1.5 | T1PKS,NRPS-like | 2,060,440 | 2,123,171 | Medium | guadinomine/guadinomine B/guadinomic acid | NRPS:Type I+PKS
Region 1.6 | terpene | 2,255,190 | 2,280,180 | Low | isorenieratene | terpene
Region 1.7 | RiPP-like | 2,418,015 | 2,428,818 |
Region 1.8 | NI-siderophore,terpene-precursor | 2,448,452 | 2,482,865 | Low | nonactin/monactin/dinactin/trinactin/tetranactin | PKS
Region 1.9 | NRPS | 2,509,828 | 2,576,375 |  |
Region 1.10 | lanthipeptide-class-i | 2,745,170 | 2,769,275 |
Region 1.11 | lanthipeptide-class-iv | 2,891,804 | 2,914,830 |  |

NZ_RCDD01000002.1 (Actinokineospora cianjurensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | T1PKS,hglE-KS | 180,894 | 249,825 |  |
Region 2.2 | butyrolactone | 267,866 | 278,660 |  |
Region 2.3 | NRPS,T3PKS | 352,278 | 441,171 | Low | friulimicin A/friulimicin B/friulimicin C/friulimicin D | NRPS:Type I
Region 2.4 | terpene | 876,592 | 897,725 |
Region 2.5 | RiPP-like | 990,495 | 1,002,600 |
Region 2.6 | azole-containing-RiPP | 1,141,318 | 1,176,115 | Low | GE2270 | ribosomal:RiPP:Thiopeptide

NZ_RCDD01000003.1 (Actinokineospora cianjurensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | T1PKS,NRPS-like,ectoine | 3,882 | 67,048 |  |
Region 3.2 | NRPS,T1PKS,lanthipeptide-class-ii | 72,860 | 158,166 | Low | mannopeptimycin | NRPS:Type I
Region 3.3 | T1PKS | 187,096 | 232,456 | Low | calicheamicin | PKS
Region 3.4 | redox-cofactor | 249,649 | 271,674 | Low | lankacidin C | NRPS:Type I+PKS
Region 3.5 | NRPS,NRPS-like | 289,941 | 336,088 | Medium | anthramycin | NRPS:Type I
Region 3.6 | 2dos | 339,195 | 368,217 | Low | istamycin | saccharide

NZ_RCDD01000005.1 (Actinokineospora cianjurensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | NRP-metallophore,NRPS | 89,606 | 179,208 | Low | amychelin | NRPS:Type I
Region 5.2 | NRPS | 354,229 | 397,471 | Low | thiolutin | NRPS:Type I
Region 5.3 | furan | 401,422 | 422,414 |  |

NZ_RCDD01000006.1 (Actinokineospora cianjurensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 6.1 | thioamitides | 7,303 | 29,128 |  |
Region 6.2 | terpene | 34,382 | 56,866 | Low | ochronotic pigment | other:other

NZ_RCDD01000007.1 (Actinokineospora cianjurensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 7.1 | indole | 20,277 | 41,353 |  |
Region 7.2 | terpene | 58,725 | 80,848 | High | geosmin | terpene:Sesquiterpene
Region 7.3 | arylpolyene | 162,236 | 203,282 |  |
Region 7.4 | lanthipeptide-class-i | 252,145 | 270,086 |

NZ_RCDD01000009.1 (Actinokineospora cianjurensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 9.1 | NRP-metallophore,NRPS | 4,156 | 96,007 | Low | frankobactin A1/frankobactin A2/frankobactin A3/frankobactin B1/frankobactin B2/frankobactin B3/frankobactin C1 | NRPS:Type I
Region 9.2 | T2PKS,NRPS-like | 97,059 | 188,667 | High | kinanthraquinone B/kinanthraquinone | PKS

NZ_RCDD01000010.1 (Actinokineospora cianjurensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 10.1 | T3PKS | 55,248 | 96,294 |  |

NZ_RCDD01000011.1 (Actinokineospora cianjurensis)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 11.1 | NAPAA | 93,171 | 127,301 | Low | γ-poly-L-2,4-diaminobutyric acid | NRPS:Type I

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | NAPAA | 215,669 | 249,541 | High | ε-Poly-L-lysine | NRPS:Type I
Region 1.2 | ectoine | 267,217 | 277,615 | High | ectoine | other:other
Region 1.3 | hydrogen-cyanide | 506,262 | 518,902 |  |
Region 1.4 | terpene-precursor,T1PKS | 1,836,145 | 2,029,578 | Medium | stambomycin A/stambomycin B/stambomycin C/stambomycin D | PKS:Type I+saccharide:hybrid/tailoring
Region 1.5 | T1PKS,NRPS-like | 2,060,440 | 2,123,171 | Medium | guadinomine/guadinomine B/guadinomic acid | NRPS:Type I+PKS
Region 1.6 | terpene | 2,255,190 | 2,280,180 | Low | isorenieratene | terpene
Region 1.7 | RiPP-like | 2,418,015 | 2,428,818 |
Region 1.8 | NI-siderophore,terpene-precursor | 2,448,452 | 2,482,865 | Low | nonactin/monactin/dinactin/trinactin/tetranactin | PKS
Region 1.9 | NRPS | 2,509,828 | 2,576,375 |  |
Region 1.10 | lanthipeptide-class-i | 2,745,170 | 2,769,275 |
Region 1.11 | lanthipeptide-class-iv | 2,891,804 | 2,914,830 |  |
Region 2.1 | T1PKS,hglE-KS | 180,894 | 249,825 |  |
Region 2.2 | butyrolactone | 267,866 | 278,660 |  |
Region 2.3 | NRPS,T3PKS | 352,278 | 441,171 | Low | friulimicin A/friulimicin B/friulimicin C/friulimicin D | NRPS:Type I
Region 2.4 | terpene | 876,592 | 897,725 |
Region 2.5 | RiPP-like | 990,495 | 1,002,600 |
Region 2.6 | azole-containing-RiPP | 1,141,318 | 1,176,115 | Low | GE2270 | ribosomal:RiPP:Thiopeptide
Region 3.1 | T1PKS,NRPS-like,ectoine | 3,882 | 67,048 |  |
Region 3.2 | NRPS,T1PKS,lanthipeptide-class-ii | 72,860 | 158,166 | Low | mannopeptimycin | NRPS:Type I
Region 3.3 | T1PKS | 187,096 | 232,456 | Low | calicheamicin | PKS
Region 3.4 | redox-cofactor | 249,649 | 271,674 | Low | lankacidin C | NRPS:Type I+PKS
Region 3.5 | NRPS,NRPS-like | 289,941 | 336,088 | Medium | anthramycin | NRPS:Type I
Region 3.6 | 2dos | 339,195 | 368,217 | Low | istamycin | saccharide
Region 5.1 | NRP-metallophore,NRPS | 89,606 | 179,208 | Low | amychelin | NRPS:Type I
Region 5.2 | NRPS | 354,229 | 397,471 | Low | thiolutin | NRPS:Type I
Region 5.3 | furan | 401,422 | 422,414 |  |
Region 6.1 | thioamitides | 7,303 | 29,128 |  |
Region 6.2 | terpene | 34,382 | 56,866 | Low | ochronotic pigment | other:other
Region 7.1 | indole | 20,277 | 41,353 |  |
Region 7.2 | terpene | 58,725 | 80,848 | High | geosmin | terpene:Sesquiterpene
Region 7.3 | arylpolyene | 162,236 | 203,282 |  |
Region 7.4 | lanthipeptide-class-i | 252,145 | 270,086 |
Region 9.1 | NRP-metallophore,NRPS | 4,156 | 96,007 | Low | frankobactin A1/frankobactin A2/frankobactin A3/frankobactin B1/frankobactin B2/frankobactin B3/frankobactin C1 | NRPS:Type I
Region 9.2 | T2PKS,NRPS-like | 97,059 | 188,667 | High | kinanthraquinone B/kinanthraquinone | PKS
Region 10.1 | T3PKS | 55,248 | 96,294 |  |
Region 11.1 | NAPAA | 93,171 | 127,301 | Low | γ-poly-L-2,4-diaminobutyric acid | NRPS:Type I

No secondary metabolite regions were found in these records:
  NZ_RCDD01000004.1 (Actinokineospora cianjurensis)
  NZ_RCDD01000008.1 (Actinokineospora cianjurensis)
  NZ_RCDD01000012.1 (Actinokineospora cianjurensis)
  NZ_RCDD01000013.1 (Actinokineospora cianjurensis)
  NZ_RCDD01000014.1 (Actinokineospora cianjurensis)
  NZ_RCDD01000015.1 (Actinokineospora cianjurensis)
  NZ_RCDD01000016.1 (Actinokineospora cianjurensis)
  NZ_RCDD01000017.1 (Actinokineospora cianjurensis)
  NZ_RCDD01000018.1 (Actinokineospora cianjurensis)

Compact view
NZ_RCDD01000001.1 - Region 1 - NAPAA
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 215,669 - 249,541 nt. (total: 33,873 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CLV68_RS01040: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

Hydrolases: hydrolase
CLV68_RS01005: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Isomerases: racemase
CLV68_RS01010: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase
CLV68_RS01065: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.66 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.59 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.66 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.59 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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: 18.39 out of 19.26
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 22.28 out of 25.88
Confidence: medium
Additional weak hits (5):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.50 out of 30.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.85 out of 25.88
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.22 out of 29.38
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.59 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 1, location 215668 - 249541:
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).
CLV68_RS01065: X
AMP-binding (44..415): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAELFDASCEELSTIFGGEWNTYGPTEATVVACG
  Nearest Stachelhaus code(s):
    Lys DAEDIGTVVK (71% 8Å match)
    Gln or Tyr DAESVGTVVK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
PsrA | Oleic acid responsive regulator

NZ_RCDD01000001.1 - Region 2 - 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: 267,217 - 277,615 nt. (total: 10,399 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
CLV68_RS01260: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: aminotransferase
CLV68_RS01250: 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
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.81 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.81 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
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
BGC0000855.3 |  | 0.55 | other (other) | ectoine | Methylomicrobium kenyense
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
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.81 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.81 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
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
BGC0000855.3 |  | 0.55 | other (other) | ectoine | Methylomicrobium kenyense
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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (2):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.29 out of 23.43
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RCDD01000001.1 - Region 3 - 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: 506,262 - 518,902 nt. (total: 12,641 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 synthase
CLV68_RS02330: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CLV68_RS02345: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

CLV68_RS02355: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CLV68_RS02375: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

Hydrolases: hydrolase peptidase synthase
CLV68_RS02325: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

CLV68_RS02375: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

CLV68_RS02385: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

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

Reference | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.53 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002436.2 |  | 0.36 | other (other) | coformycin | Streptomyces citricolor
BGC0001739.3 |  | 0.35 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0002669.2 |  | 0.35 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87
BGC0001386.5 |  | 0.33 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77
BGC0001007.5 |  | 0.33 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin b | Salinispora arenicola CNS-205
BGC0001860.4 |  | 0.33 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0000613.5 |  | 0.33 | ribosomal | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0001575.4 |  | 0.32 | NRPS | PZN5, PZN6, PZN7, PZN9, PZN10, PZN11 | Ruminococcus sp. 5_1_39BFAA
BGC0001006.5 |  | 0.32 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin B | Salinispora tropica CNB-440

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.53 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002436.2 |  | 0.36 | other (other) | coformycin | Streptomyces citricolor
BGC0001739.3 |  | 0.35 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0002669.2 |  | 0.35 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87
BGC0001386.5 |  | 0.33 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77
BGC0001007.5 |  | 0.33 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin b | Salinispora arenicola CNS-205
BGC0001860.4 |  | 0.33 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0000613.5 |  | 0.33 | ribosomal | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0001575.4 |  | 0.32 | NRPS | PZN5, PZN6, PZN7, PZN9, PZN10, PZN11 | Ruminococcus sp. 5_1_39BFAA
BGC0001006.5 |  | 0.32 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin B | Salinispora tropica CNB-440

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.71 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
Additional weak hits (2):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.81 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.29 out of 25.88
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism

NZ_RCDD01000001.1 - Region 4 - T1PKS,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,836,145 - 2,029,578 nt. (total: 193,434 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)
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
Terpene
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CLV68_RS08785: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CLV68_RS08820: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CLV68_RS09290: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CLV68_RS35000: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase aminotransferase glycosyltransferase methyltransferase transferase
CLV68_RS08730: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CLV68_RS08735: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CLV68_RS08750: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CLV68_RS08910: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

CLV68_RS09190: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CLV68_RS09265: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CLV68_RS09270: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CLV68_RS09275: methyltransferase

smcogs
  SMCOG1248: methyltransferase

CLV68_RS09285: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: esterase
CLV68_RS08805: thioesterase

smcogs
  SMCOG1004: thioesterase

CLV68_RS08815: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
CLV68_RS09260: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase synthetase
CLV68_RS08755: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS08770: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

CLV68_RS08895: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS09195: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS34495: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CLV68_RS34975: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS34980: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS34985: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS34990: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS34995: 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-precursor | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000016.4 |  |  | 0.47 | other (other) | amphotericin B | Streptomyces nodosus
BGC0001817.5 |  |  | 0.46 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0001273.3 |  |  | 0.43 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.43 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  |  | 0.42 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  |  | 0.42 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002610.3 |  |  | 0.39 | terpene | stellatic acid | Aspergillus stellatus
BGC0002162.3 |  |  | 0.39 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002397.2 |  |  | 0.36 | terpene | astallatene | Arabidopsis thaliana
BGC0002047.2 |  |  | 0.34 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis

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
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.66 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002191.2 |  | 0.65 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001817.5 |  | 0.64 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
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:
CLV68_RS08770: PT_FPPS_like
Domain 1 (74 - 358): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.78 out of 29.72
Confidence: medium
Additional weak hits (9):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.23 out of 20.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.66 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.78 out of 23.43
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.82 out of 32.74
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.18 out of 36.54
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.42 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.71 out of 30.22
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 4, location 1836144 - 2029578:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - ccmal - ohmal - ohmal) + (redmal - ohemal - Me-ccmal) + (ohmal) + (ohmal - redmal) + (redmal - ohmal - ohmal - redmal - ohmal) + (ohmal - redmal - ohmal - ohmal - ohmal) + (Me-ohmal - ohmal - Me-redmal) + (ohmal - Me-ohmal) + (ccmal - Me-ccmal) + (Me-ohmal - ohmal - mal)
Non-colinear ordering:
  CLV68_RS34980 + CLV68_RS34495 + CLV68_RS08895 + CLV68_RS34975 + CLV68_RS34985 + CLV68_RS34990 + CLV68_RS34995 + CLV68_RS09190 + CLV68_RS09195 + CLV68_RS35000

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 1841693 - 2029578:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - ccmal - ohmal - ohmal) + (redmal - ohemal - Me-ccmal) + (ohmal) + (ohmal - redmal) + (redmal - ohmal - ohmal - redmal - ohmal) + (ohmal - redmal - ohmal - ohmal - ohmal) + (Me-ohmal - ohmal - Me-redmal) + (ohmal - Me-ohmal) + (ccmal - Me-ccmal) + (Me-ohmal - ohmal - mal)
Non-colinear ordering:
  CLV68_RS34980 + CLV68_RS34495 + CLV68_RS08895 + CLV68_RS34975 + CLV68_RS34985 + CLV68_RS34990 + CLV68_RS34995 + CLV68_RS09190 + CLV68_RS09195 + CLV68_RS35000

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).
CLV68_RS08755: X
AMP-binding (42..429): 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:
    GGAIHGRAVPWSEAISTFDVQVWGQTETGPLTFR
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CLV68_RS34495: mal - emal - mmal
PKS_AT (555..821): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 163.9
  inactive: 65.3
  Methoxymalonyl-CoA: 58.3
  Methylmalonyl-CoA: 51.3
  Acetyl-CoA: 23.1
  Ethylmalonyl-CoA: 15.9
  Isobutyryl-CoA: 14.8
  fatty_acid: 13.9
  Propionyl-CoA: 13.7
  Benzoyl-CoA: 11.6
  trans-1,2-CPDA: 9.4
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (2399..2697): emal
ATSignature: Ethylmalonyl-CoA, Methylmalonyl-CoA, Methoxymalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 183.9
  Methylmalonyl-CoA: 182.6
  Methoxymalonyl-CoA: 155.4
  2-Methylbutyryl-CoA: 128.5
  trans-1,2-CPDA: 121.5
  Propionyl-CoA: 101.9
  Malonyl-CoA: 95.6
  CHC-CoA: 95.6
  Isobutyryl-CoA: 77.2
  Acetyl-CoA: 42.9
  Benzoyl-CoA: 39.7
  fatty_acid: 35.1
  3-Methylbutyryl-CoA: 32.3
  inactive: 12.0

PKS_AT (3845..4132): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 200.9
  Ethylmalonyl-CoA: 191.0
  Methoxymalonyl-CoA: 177.2
  2-Methylbutyryl-CoA: 140.0
  Propionyl-CoA: 116.2
  trans-1,2-CPDA: 108.6
  Malonyl-CoA: 99.8
  CHC-CoA: 86.6
  Isobutyryl-CoA: 77.1
  Acetyl-CoA: 53.6
  Benzoyl-CoA: 43.6
  3-Methylbutyryl-CoA: 35.7
  inactive: 29.4
  fatty_acid: 17.0

CLV68_RS08895: mal
PKS_AT (540..812): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 166.9
  inactive: 61.7
  Methoxymalonyl-CoA: 55.5
  Methylmalonyl-CoA: 45.1
  Propionyl-CoA: 26.2
  Isobutyryl-CoA: 16.6
  Acetyl-CoA: 16.3
  Benzoyl-CoA: 15.8
  fatty_acid: 12.4
  2-Methylbutyryl-CoA: 11.6
  Ethylmalonyl-CoA: 9.6
  CHC-CoA: 8.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

CLV68_RS34975: mal - mal
PKS_AT (547..813): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 174.3
  inactive: 72.3
  Methoxymalonyl-CoA: 64.0
  Methylmalonyl-CoA: 61.0
  Isobutyryl-CoA: 33.0
  Propionyl-CoA: 28.6
  Acetyl-CoA: 22.9
  Ethylmalonyl-CoA: 20.0
  CHC-CoA: 18.0
  fatty_acid: 17.0
  Benzoyl-CoA: 15.8
  trans-1,2-CPDA: 13.5
  2-Methylbutyryl-CoA: 11.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (1909..2194): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 198.9
  inactive: 90.5
  Methoxymalonyl-CoA: 64.7
  Methylmalonyl-CoA: 54.7
  Isobutyryl-CoA: 27.0
  Ethylmalonyl-CoA: 25.4
  Acetyl-CoA: 23.1
  Propionyl-CoA: 22.8
  fatty_acid: 20.4
  Benzoyl-CoA: 11.7
  2-Methylbutyryl-CoA: 9.8
  CHC-CoA: 8.6
  trans-1,2-CPDA: 8.4
  3-Methylbutyryl-CoA: 0.0

CLV68_RS34980: mmal - mal - mal - mal
PKS_AT (505..790): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 200.6
  Ethylmalonyl-CoA: 188.0
  Methoxymalonyl-CoA: 165.6
  2-Methylbutyryl-CoA: 138.5
  trans-1,2-CPDA: 120.7
  Propionyl-CoA: 100.1
  Malonyl-CoA: 99.4
  Isobutyryl-CoA: 84.6
  CHC-CoA: 81.1
  Benzoyl-CoA: 69.5
  inactive: 42.9
  3-Methylbutyryl-CoA: 37.4
  Acetyl-CoA: 26.5
  fatty_acid: 16.7

PKS_AT (1444..1705): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 70.8%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 163.3
  Methoxymalonyl-CoA: 70.9
  Methylmalonyl-CoA: 64.8
  inactive: 57.2
  Isobutyryl-CoA: 34.4
  Ethylmalonyl-CoA: 30.3
  Acetyl-CoA: 26.6
  Propionyl-CoA: 22.1
  2-Methylbutyryl-CoA: 17.9
  CHC-CoA: 16.9
  Benzoyl-CoA: 16.7
  fatty_acid: 16.0
  trans-1,2-CPDA: 13.9
  3-Methylbutyryl-CoA: 8.9

PKS_AT (2978..3241): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 62.5%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 167.4
  inactive: 60.4
  Methoxymalonyl-CoA: 57.8
  Methylmalonyl-CoA: 49.7
  Propionyl-CoA: 25.5
  Acetyl-CoA: 24.4
  Isobutyryl-CoA: 23.3
  Ethylmalonyl-CoA: 17.7
  fatty_acid: 16.9
  Benzoyl-CoA: 13.0
  2-Methylbutyryl-CoA: 9.4
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4349..4616): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 62.5%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 180.3
  Methoxymalonyl-CoA: 73.3
  inactive: 66.4
  Methylmalonyl-CoA: 59.9
  Isobutyryl-CoA: 33.5
  Acetyl-CoA: 28.8
  Ethylmalonyl-CoA: 26.7
  Propionyl-CoA: 25.2
  fatty_acid: 22.7
  Benzoyl-CoA: 18.3
  trans-1,2-CPDA: 13.9
  CHC-CoA: 11.5
  2-Methylbutyryl-CoA: 8.9
  3-Methylbutyryl-CoA: 0.0

CLV68_RS34985: mal - mal - mal - mal - mal
PKS_AT (555..815): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 62.5%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 173.8
  Methoxymalonyl-CoA: 61.3
  inactive: 54.4
  Methylmalonyl-CoA: 51.4
  Propionyl-CoA: 25.2
  Acetyl-CoA: 22.8
  Isobutyryl-CoA: 20.5
  Ethylmalonyl-CoA: 14.9
  fatty_acid: 13.7
  2-Methylbutyryl-CoA: 12.4
  Benzoyl-CoA: 10.3
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2498..2763): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 62.5%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 182.8
  inactive: 73.6
  Methoxymalonyl-CoA: 67.0
  Methylmalonyl-CoA: 57.2
  Propionyl-CoA: 29.8
  Isobutyryl-CoA: 29.1
  Acetyl-CoA: 26.6
  Ethylmalonyl-CoA: 22.6
  fatty_acid: 19.7
  Benzoyl-CoA: 15.0
  CHC-CoA: 11.3
  2-Methylbutyryl-CoA: 9.6
  trans-1,2-CPDA: 8.6
  3-Methylbutyryl-CoA: 4.6

PKS_AT (3820..4081): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 175.8
  inactive: 75.1
  Methoxymalonyl-CoA: 62.3
  Methylmalonyl-CoA: 55.3
  Acetyl-CoA: 23.9
  Isobutyryl-CoA: 21.4
  Propionyl-CoA: 20.9
  Ethylmalonyl-CoA: 18.0
  Benzoyl-CoA: 14.2
  fatty_acid: 12.1
  CHC-CoA: 10.5
  2-Methylbutyryl-CoA: 8.9
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5138..5397): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 62.5%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 165.9
  Methoxymalonyl-CoA: 67.3
  inactive: 64.4
  Methylmalonyl-CoA: 55.6
  Isobutyryl-CoA: 38.2
  Acetyl-CoA: 29.1
  fatty_acid: 23.0
  Propionyl-CoA: 19.1
  Ethylmalonyl-CoA: 17.6
  Benzoyl-CoA: 13.6
  CHC-CoA: 11.0
  2-Methylbutyryl-CoA: 9.1
  trans-1,2-CPDA: 9.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (6987..7244): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 62.5%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 170.4
  Methoxymalonyl-CoA: 66.4
  inactive: 63.2
  Methylmalonyl-CoA: 54.2
  Isobutyryl-CoA: 29.1
  Acetyl-CoA: 26.3
  Propionyl-CoA: 25.9
  Ethylmalonyl-CoA: 22.5
  fatty_acid: 20.7
  Benzoyl-CoA: 13.5
  2-Methylbutyryl-CoA: 10.1
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CLV68_RS34990: mal - mal - mal - mal - mal
PKS_AT (541..800): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 66.7%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 170.5
  inactive: 75.3
  Methoxymalonyl-CoA: 65.5
  Methylmalonyl-CoA: 57.0
  Isobutyryl-CoA: 28.9
  Acetyl-CoA: 27.6
  Propionyl-CoA: 23.3
  Ethylmalonyl-CoA: 20.6
  fatty_acid: 14.9
  Benzoyl-CoA: 13.4
  CHC-CoA: 12.3
  2-Methylbutyryl-CoA: 11.3
  trans-1,2-CPDA: 9.6
  3-Methylbutyryl-CoA: 0.0

PKS_AT (1908..2171): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 66.7%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 173.9
  Methoxymalonyl-CoA: 73.2
  inactive: 69.8
  Methylmalonyl-CoA: 58.4
  Isobutyryl-CoA: 41.2
  Acetyl-CoA: 28.7
  Propionyl-CoA: 26.5
  Ethylmalonyl-CoA: 23.1
  fatty_acid: 20.1
  Benzoyl-CoA: 16.0
  trans-1,2-CPDA: 11.5
  CHC-CoA: 11.3
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (3916..4181): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 66.7%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 173.1
  Methoxymalonyl-CoA: 70.5
  inactive: 68.7
  Methylmalonyl-CoA: 62.1
  Propionyl-CoA: 32.5
  Ethylmalonyl-CoA: 31.0
  Acetyl-CoA: 29.0
  Isobutyryl-CoA: 25.7
  Benzoyl-CoA: 17.1
  CHC-CoA: 14.0
  fatty_acid: 13.7
  2-Methylbutyryl-CoA: 13.1
  trans-1,2-CPDA: 12.3
  3-Methylbutyryl-CoA: 5.6

PKS_AT (5246..5525): 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: 182.3
  inactive: 82.7
  Methoxymalonyl-CoA: 61.3
  Methylmalonyl-CoA: 52.3
  Propionyl-CoA: 31.0
  Isobutyryl-CoA: 24.3
  Ethylmalonyl-CoA: 23.7
  Acetyl-CoA: 17.8
  fatty_acid: 17.7
  Benzoyl-CoA: 13.4
  2-Methylbutyryl-CoA: 10.4
  CHC-CoA: 8.3
  trans-1,2-CPDA: 7.9
  3-Methylbutyryl-CoA: 0.0

PKS_AT (6736..6992): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 66.7%
  Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 183.9
  inactive: 90.4
  Methoxymalonyl-CoA: 73.4
  Methylmalonyl-CoA: 60.4
  Isobutyryl-CoA: 32.5
  Ethylmalonyl-CoA: 30.3
  Acetyl-CoA: 27.2
  Propionyl-CoA: 26.2
  Benzoyl-CoA: 23.3
  fatty_acid: 15.8
  trans-1,2-CPDA: 8.9
  CHC-CoA: 7.3
  2-Methylbutyryl-CoA: 3.2
  3-Methylbutyryl-CoA: 0.0

CLV68_RS34995: mmal - mal - mmal
PKS_AT (556..840): 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: 210.3
  Ethylmalonyl-CoA: 206.5
  Methoxymalonyl-CoA: 169.6
  trans-1,2-CPDA: 136.7
  2-Methylbutyryl-CoA: 132.3
  CHC-CoA: 108.1
  Propionyl-CoA: 97.8
  Malonyl-CoA: 91.6
  Isobutyryl-CoA: 73.5
  Benzoyl-CoA: 61.1
  Acetyl-CoA: 40.7
  3-Methylbutyryl-CoA: 32.2
  inactive: 18.7
  fatty_acid: 17.9

PKS_AT (1938..2198): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 66.7%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 174.4
  inactive: 76.2
  Methoxymalonyl-CoA: 63.9
  Methylmalonyl-CoA: 55.4
  Propionyl-CoA: 32.6
  Acetyl-CoA: 23.1
  Isobutyryl-CoA: 21.3
  Ethylmalonyl-CoA: 18.2
  fatty_acid: 11.0
  Benzoyl-CoA: 10.4
  2-Methylbutyryl-CoA: 7.2
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3361..3674): 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: 204.4
  Ethylmalonyl-CoA: 192.8
  Methoxymalonyl-CoA: 162.4
  2-Methylbutyryl-CoA: 131.6
  trans-1,2-CPDA: 122.2
  Propionyl-CoA: 87.8
  Malonyl-CoA: 79.4
  CHC-CoA: 78.5
  Benzoyl-CoA: 57.2
  Isobutyryl-CoA: 55.0
  Acetyl-CoA: 21.7
  inactive: 19.6
  fatty_acid: 16.8
  3-Methylbutyryl-CoA: 3.7

CLV68_RS09190: mal - mmal
PKS_AT (539..812): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 66.7%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 162.6
  Methoxymalonyl-CoA: 64.2
  Methylmalonyl-CoA: 54.2
  inactive: 47.4
  Ethylmalonyl-CoA: 25.0
  Acetyl-CoA: 24.3
  Isobutyryl-CoA: 20.7
  Propionyl-CoA: 19.8
  fatty_acid: 18.5
  CHC-CoA: 17.9
  Benzoyl-CoA: 17.3
  2-Methylbutyryl-CoA: 10.2
  trans-1,2-CPDA: 8.0
  3-Methylbutyryl-CoA: 4.0

PKS_AT (1999..2277): 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: 201.1
  Ethylmalonyl-CoA: 196.7
  Methoxymalonyl-CoA: 165.4
  2-Methylbutyryl-CoA: 132.4
  trans-1,2-CPDA: 112.8
  Propionyl-CoA: 106.7
  CHC-CoA: 93.0
  Malonyl-CoA: 87.3
  Isobutyryl-CoA: 78.5
  Benzoyl-CoA: 60.1
  3-Methylbutyryl-CoA: 48.4
  Acetyl-CoA: 38.6
  inactive: 29.8
  fatty_acid: 20.0

CLV68_RS09195: mal - mmal
PKS_AT (564..837): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 182.0
  inactive: 71.0
  Methoxymalonyl-CoA: 69.5
  Methylmalonyl-CoA: 63.7
  fatty_acid: 31.0
  Ethylmalonyl-CoA: 28.0
  Propionyl-CoA: 25.7
  Isobutyryl-CoA: 25.7
  Acetyl-CoA: 20.5
  Benzoyl-CoA: 16.6
  CHC-CoA: 13.1
  2-Methylbutyryl-CoA: 11.4
  trans-1,2-CPDA: 9.3
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2181..2468): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 206.4
  Ethylmalonyl-CoA: 200.2
  Methoxymalonyl-CoA: 165.6
  2-Methylbutyryl-CoA: 148.1
  trans-1,2-CPDA: 124.9
  Propionyl-CoA: 118.2
  CHC-CoA: 100.2
  Malonyl-CoA: 99.9
  Isobutyryl-CoA: 76.2
  Benzoyl-CoA: 66.3
  Acetyl-CoA: 54.7
  fatty_acid: 30.2
  3-Methylbutyryl-CoA: 23.7
  inactive: 18.8

CLV68_RS35000: mmal - mal - mal
PKS_AT (556..848): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 203.1
  Ethylmalonyl-CoA: 193.4
  Methoxymalonyl-CoA: 159.7
  2-Methylbutyryl-CoA: 149.2
  trans-1,2-CPDA: 133.1
  Propionyl-CoA: 105.1
  CHC-CoA: 102.0
  Malonyl-CoA: 86.4
  Isobutyryl-CoA: 84.3
  Benzoyl-CoA: 59.0
  Acetyl-CoA: 54.7
  3-Methylbutyryl-CoA: 47.1
  inactive: 32.4
  fatty_acid: 22.9

PKS_AT (1968..2241): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 75.0%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.9
  inactive: 103.5
  Methoxymalonyl-CoA: 70.9
  Methylmalonyl-CoA: 60.5
  Isobutyryl-CoA: 33.2
  Propionyl-CoA: 32.8
  Ethylmalonyl-CoA: 26.5
  Acetyl-CoA: 22.0
  fatty_acid: 17.9
  Benzoyl-CoA: 14.3
  2-Methylbutyryl-CoA: 12.3
  CHC-CoA: 7.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4440..4723): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 168.2
  Methoxymalonyl-CoA: 72.0
  inactive: 69.2
  Methylmalonyl-CoA: 55.7
  Propionyl-CoA: 28.4
  Acetyl-CoA: 16.4
  Isobutyryl-CoA: 15.0
  CHC-CoA: 14.9
  trans-1,2-CPDA: 12.7
  fatty_acid: 12.7
  Ethylmalonyl-CoA: 11.8
  2-Methylbutyryl-CoA: 9.8
  Benzoyl-CoA: 8.1
  3-Methylbutyryl-CoA: 0.0

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

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
NtrC | Nitrogen regulatory protein C

NZ_RCDD01000001.1 - Region 5 - 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: 2,060,440 - 2,123,171 nt. (total: 62,732 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### 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
CLV68_RS09545: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CLV68_RS09580: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CLV68_RS09585: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CLV68_RS09600: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Lyases: dehydratase
CLV68_RS09605: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
CLV68_RS09565: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS09570: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CLV68_RS09575: 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 | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001217.5 |  |  | 1.18 | other (other) | PreQ0 Base | Streptomyces qinglanensis
BGC0001273.3 |  |  | 0.87 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.86 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.85 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000979.3 |  |  | 0.69 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E9
BGC0000980.3 |  |  | 0.69 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 22D11
BGC0001160.5 |  |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001257.3 |  |  | 0.62 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002154.2 |  |  | 0.62 | 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
--- | --- | --- | --- | --- | ---
BGC0001217.5 |  | 0.84 | other (other) | PreQ0 Base | Streptomyces qinglanensis
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000979.3 |  | 0.67 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E9
BGC0000980.3 |  | 0.67 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 22D11
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000041.3 |  | 0.65 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001257.3 |  | 0.65 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.09 out of 20.47
Confidence: medium
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: 17.88 out of 20.47
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.14 out of 25.31
Confidence: medium
Additional weak hits (8):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.35 out of 25.88
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.86 out of 27.18
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.96 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.40 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.38 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 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 7, location 2060439 - 2123171:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CLV68_RS09565: mal
PKS_AT (532..812): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 167.5
  inactive: 134.1
  Methoxymalonyl-CoA: 83.8
  Methylmalonyl-CoA: 78.0
  Isobutyryl-CoA: 53.8
  Propionyl-CoA: 40.9
  Ethylmalonyl-CoA: 33.5
  Benzoyl-CoA: 32.1
  2-Methylbutyryl-CoA: 29.3
  CHC-CoA: 21.0
  trans-1,2-CPDA: 14.0
  Acetyl-CoA: 12.3
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

CLV68_RS09570: mal
PKS_AT (544..821): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 173.1
  inactive: 119.7
  Methoxymalonyl-CoA: 67.4
  Methylmalonyl-CoA: 61.5
  Propionyl-CoA: 47.5
  Ethylmalonyl-CoA: 25.3
  Isobutyryl-CoA: 24.9
  2-Methylbutyryl-CoA: 24.3
  Benzoyl-CoA: 24.2
  trans-1,2-CPDA: 18.8
  Acetyl-CoA: 14.3
  CHC-CoA: 13.5
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

CLV68_RS09575: mal
PKS_AT (551..844): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 79.2%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 170.8
  inactive: 103.0
  Methoxymalonyl-CoA: 85.4
  Methylmalonyl-CoA: 80.2
  Propionyl-CoA: 56.4
  Isobutyryl-CoA: 38.6
  2-Methylbutyryl-CoA: 36.8
  Ethylmalonyl-CoA: 32.4
  CHC-CoA: 28.1
  Benzoyl-CoA: 26.4
  Acetyl-CoA: 20.5
  fatty_acid: 18.4
  trans-1,2-CPDA: 17.9
  3-Methylbutyryl-CoA: 15.5

CLV68_RS09580: X - mal
AMP-binding (23..411): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHCFDFSFHEAFAVTTGEHNHYGATEFQDATTH
  Nearest Stachelhaus code(s):
    Gua DFHFITHDAK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

PKS_AT (1122..1387): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 83.3%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 176.9
  inactive: 140.0
  Methoxymalonyl-CoA: 56.6
  Methylmalonyl-CoA: 54.9
  Propionyl-CoA: 38.6
  Acetyl-CoA: 26.0
  Ethylmalonyl-CoA: 14.5
  Isobutyryl-CoA: 12.6
  Benzoyl-CoA: 11.9
  fatty_acid: 9.3
  trans-1,2-CPDA: 6.2
  CHC-CoA: 5.2
  2-Methylbutyryl-CoA: 5.1
  3-Methylbutyryl-CoA: -0.4

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CatR | H2O2-responsive repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_RCDD01000001.1 - 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: 2,255,190 - 2,280,180 nt. (total: 24,991 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
CLV68_RS10375: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: acyltransferase
CLV68_RS10330: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Ligases: synthetase
CLV68_RS10380: 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
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.58 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.57 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.55 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.55 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000649.3 |  | 0.53 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.48 | terpene | carotenoid | Myxococcus xanthus
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000640.3 |  | 0.45 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000641.3 |  | 0.45 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.44 | terpene | carotenoid | Enterobacteriaceae bacterium DC260

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.58 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.57 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.55 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.55 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000649.3 |  | 0.53 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.48 | terpene | carotenoid | Myxococcus xanthus
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000640.3 |  | 0.45 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000641.3 |  | 0.45 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.44 | 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 | C30 carotenoid | diapophytoene | C30 | acyclic | none
triterpene |  | squalene | C30 | acyclic | none
triterpene |  | PSPP | C30 | acyclic | PP
tetraterpene | C40 carotenoid | phytoene | C40 | acyclic | none
triterpene |  | hydroxysqualene | C30 | acyclic | OH

Genes with terpene domains:
CLV68_RS10365: PT_phytoene_like
Domain 1 (10 - 284): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

CLV68_RS10380: PT_FPPS_like
Domain 1 (41 - 337): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 25.93 out of 29.65
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 22.33 out of 24.78
Confidence: medium
Additional weak hits (6):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.37 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.17 out of 32.93
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.90 out of 35.63
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.62 out of 27.04
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 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
--- | ---
CRP | Cyclic AMP receptor protein
LexA variant 1 | Repressor of DNA damage response
LexA variant 2 | Repressor of DNA damage response

NZ_RCDD01000001.1 - Region 7 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,418,015 - 2,428,818 nt. (total: 10,804 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: protease
CLV68_RS11030: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000595.3 |  | 0.32 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000597.4 |  | 0.29 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0001760.5 |  | 0.27 | NRPS | rimosamide | Streptomyces rimosus subsp. rimosus ATCC 10970
BGC0000842.5 |  | 0.26 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0002026.3 |  | 0.21 | NRPS, PKS | thaxteramide A1, thaxteramide A2, thaxteramide B1, thaxteramide B2 | Jahnella sp. MSr9139
BGC0001435.4 |  | 0.19 | NRPS, PKS | ikarugamycin | Streptomyces sp. ZJ306

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000595.3 |  | 0.32 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000597.4 |  | 0.29 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0001760.5 |  | 0.27 | NRPS | rimosamide | Streptomyces rimosus subsp. rimosus ATCC 10970
BGC0000842.5 |  | 0.26 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0002026.3 |  | 0.21 | NRPS, PKS | thaxteramide A1, thaxteramide A2, thaxteramide B1, thaxteramide B2 | Jahnella sp. MSr9139
BGC0001435.4 |  | 0.19 | NRPS, PKS | ikarugamycin | Streptomyces sp. ZJ306

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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.67 out of 19.26
Confidence: medium
Additional weak hits (1):
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RCDD01000001.1 - Region 8 - NI-siderophore,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,448,452 - 2,482,865 nt. (total: 34,414 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC
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 oxygenase
CLV68_RS11205: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CLV68_RS11215: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

CLV68_RS11255: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CLV68_RS11275: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: carboxylase transferase
CLV68_RS11265: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

CLV68_RS11270: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Hydrolases: dehalogenase
CLV68_RS11240: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: decarboxylase
CLV68_RS11210: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: synthetase
CLV68_RS11260: 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 | NI-siderophore | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001572.3 |  |  | 0.51 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002305.2 |  |  | 0.42 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0002284.3 |  |  | 0.39 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002692.2 |  |  | 0.35 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002690.2 |  |  | 0.32 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0001478.5 |  |  | 0.31 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000677.5 |  |  | 0.29 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000941.3 |  |  | 0.28 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002007.2 |  |  | 0.28 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0002683.2 |  |  | 0.26 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001572.3 |  | 0.67 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0001478.5 |  | 0.64 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0000941.3 |  | 0.62 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000940.5 |  | 0.59 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.58 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0002305.2 |  | 0.58 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000244.4 |  | 0.58 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0001531.5 |  | 0.54 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002073.3 |  | 0.53 | NRPS | dehydroxynocardamine | Corynebacterium propinquum
BGC0002692.2 |  | 0.52 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae

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:
CLV68_RS11260: PT_FPPS_like
Domain 1 (25 - 215): 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.02 out of 23.79
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (11):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.97 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.37 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.54 out of 28.14
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.44 out of 30.22
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.65 out of 29.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.85 out of 24.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.57 out of 36.53
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.92 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_RCDD01000001.1 - Region 9 - 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: 2,509,828 - 2,576,375 nt. (total: 66,548 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
Hydrolases: hydrolase
CLV68_RS11480: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase
CLV68_RS11485: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CLV68_RS11490: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS11530: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

Translocases: transporter
CLV68_RS11520: 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 | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001133.4 |  | 0.69 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.68 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001133.4 |  | 0.69 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.68 | NRPS | AbT1 | Aureobasidium pullulans

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.58 out of 27.04
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
Additional weak hits (13):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.28 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.47 out of 20.97
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.00 out of 30.11
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.56 out of 29.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.18 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.84 out of 32.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.76 out of 27.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.21 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 13, location 2509827 - 2576375:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Ser) + (D-Orn - Orn - D-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).
CLV68_RS11485: X - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (13..382): X
nrpys: Leu, 3OH-Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAESFDASVLEMLIIVGGDINAYGPTESTVVTSW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (82% 8Å match)
    Leu DALLIGAVVK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1961..2336): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWTTFDVSVWEWHFLCSGEHNLYGPTEAAVDVTH
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

CLV68_RS11490: Orn - Orn - X - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (474..848): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSHAFDTSLEGLDLMLGGEHNFYGPTETTVDALS
  Nearest Stachelhaus code(s):
    Orn DTEDMGFVDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1933..2305): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDHAFDTSLEGFDLMLGGEVNYYGPTETTVDATV
  Nearest Stachelhaus code(s):
    Orn DTEDMGYVDK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2932..3304): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHQSFDTAVEGFDVTLGGEVNLYGPTEVTVDATW
  Nearest Stachelhaus code(s):
    Orn DTEDMGLVDK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4320..4684): X
nrpys: Leu, 3OH-Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAESFDASVLEMLIIVGGDINAYGPTEVTVVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (85% 8Å match)
    Leu DALLIGAVVK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5323..5687): X
nrpys: Leu, 3OH-Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAESFDASVLEMLIIVGGDINAYGPTESTVVATW
  Nearest Stachelhaus code(s):
    Leu or 3OH-Leu DALLIGAVVK (88% 8Å match)
    Leu DALLIGAVVK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor

NZ_RCDD01000001.1 - Region 10 - 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: 2,745,170 - 2,769,275 nt. (total: 24,106 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
CLV68_RS12325: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

CLV68_RS12330: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000542.3 |  | 0.48 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.48 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000544.4 |  | 0.46 | ribosomal | planosporicin | Planomonospora alba
BGC0001289.5 |  | 0.44 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000556.5 |  | 0.41 | ribosomal | streptin | Streptococcus pyogenes
BGC0000508.3 |  | 0.41 | ribosomal | epidermin | Staphylococcus epidermidis
BGC0001618.3 |  | 0.41 | ribosomal | hyicin 3682 | Staphylococcus hyicus
BGC0000506.4 |  | 0.40 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000559.4 |  | 0.39 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000542.3 |  | 0.48 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.48 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000544.4 |  | 0.46 | ribosomal | planosporicin | Planomonospora alba
BGC0001289.5 |  | 0.44 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000556.5 |  | 0.41 | ribosomal | streptin | Streptococcus pyogenes
BGC0000508.3 |  | 0.41 | ribosomal | epidermin | Staphylococcus epidermidis
BGC0001618.3 |  | 0.41 | ribosomal | hyicin 3682 | Staphylococcus hyicus
BGC0000506.4 |  | 0.40 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000559.4 |  | 0.39 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633

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.
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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.65 out of 18.46
Confidence: strong
Additional weak hits (2):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.20 out of 21.55
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.36 out of 39.62
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 (2745169...2769275)
CLV68_RS12325
  RRE type: Lanthipeptide_LanB_RRE
  Location: 152 - 235
  Score: 62.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_RCDD01000001.1 - Region 11 - lanthipeptide-class-iv
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: 2,891,804 - 2,914,830 nt. (total: 23,027 nt) Show pHMM detection rules used
lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
CLV68_RS12960: dihydropteridine reductase

smcogs
  SMCOG1159: dihydropteridine reductase

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-iv | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001226.4 |  | 0.50 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000528.5 |  | 0.45 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000527.5 |  | 0.41 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001789.3 |  | 0.36 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000537.3 |  | 0.35 | ribosomal | nisin U | Streptococcus uberis
BGC0000846.5 |  | 0.35 | other (other) | tabtoxin | Pseudomonas syringae
BGC0001782.3 |  | 0.34 | 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
BGC0000842.5 |  | 0.34 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0002064.2 |  | 0.33 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0000188.5 |  | 0.33 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001226.4 |  | 0.50 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000528.5 |  | 0.45 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000527.5 |  | 0.41 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001789.3 |  | 0.36 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000537.3 |  | 0.35 | ribosomal | nisin U | Streptococcus uberis
BGC0000846.5 |  | 0.35 | other (other) | tabtoxin | Pseudomonas syringae
BGC0001782.3 |  | 0.34 | 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
BGC0000842.5 |  | 0.34 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0002064.2 |  | 0.33 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0000188.5 |  | 0.33 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.96 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.12 out of 23.79
Confidence: medium
Additional weak hits (4):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 24.87 out of 33.73
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.86 out of 25.88
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.34 out of 26.85
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RCDD01000002.1 - Region 1 - T1PKS,hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 180,894 - 249,825 nt. (total: 68,932 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
hglE-KS: (hglE or hglD)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
CLV68_RS15565: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CLV68_RS15570: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

CLV68_RS15715: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CLV68_RS15720: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

CLV68_RS35155: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acetyltransferase glycosyltransferase sulfotransferase
CLV68_RS15635: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

CLV68_RS15655: Sulfotransferase domain

extras
  Sulfotransfer_4: Sulfotransferase domain

CLV68_RS15690: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: deacetylase hydrolase phosphatase protease
CLV68_RS15645: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

CLV68_RS15695: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CLV68_RS15730: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

CLV68_RS35880: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

Isomerases: mutase
CLV68_RS15555: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: synthase
CLV68_RS15650: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS15705: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS15710: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.65 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001160.5 |  |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  |  | 0.58 | PKS | FR901512 | fungal sp. No.14919
BGC0001164.3 |  |  | 0.57 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001254.3 |  |  | 0.56 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001284.4 |  |  | 0.56 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002276.2 |  |  | 0.48 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000041.3 |  |  | 0.47 | PKS | oronofacic acid | Pseudomonas syringae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  | 0.63 | PKS | FR901512 | fungal sp. No.14919
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001254.3 |  | 0.62 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001268.4 |  | 0.58 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0000041.3 |  | 0.58 | PKS | oronofacic acid | Pseudomonas syringae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.58 out of 30.11
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
Additional weak hits (14):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.03 out of 21.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.11 out of 26.85
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.60 out of 20.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.56 out of 30.22
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.94 out of 33.73
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.02 out of 30.22
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.92 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.94 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.75 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.54 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.45 out of 35.63
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.71 out of 29.25
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.05 out of 27.04
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.64 out of 32.93
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 180893 - 249825:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal) + (Me-mal)
Non-colinear ordering:
  CLV68_RS15650 + CLV68_RS15705 + CLV68_RS15700

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 180893 - 243346:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal) + (Me-mal)
Non-colinear ordering:
  CLV68_RS15650 + CLV68_RS15705 + CLV68_RS15700

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 203351 - 249825:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal) + (Me-mal)
Non-colinear ordering:
  CLV68_RS15650 + CLV68_RS15705 + CLV68_RS15700

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).
CLV68_RS15650: mmal
PKS_AT (511..809): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 87.5%
  Malonyl-CoA: 83.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 176.0
  Ethylmalonyl-CoA: 153.6
  Methoxymalonyl-CoA: 149.0
  2-Methylbutyryl-CoA: 111.8
  trans-1,2-CPDA: 111.7
  Propionyl-CoA: 103.2
  CHC-CoA: 101.5
  Malonyl-CoA: 91.2
  Isobutyryl-CoA: 79.8
  Acetyl-CoA: 67.5
  Benzoyl-CoA: 58.5
  3-Methylbutyryl-CoA: 33.4
  fatty_acid: 22.5
  inactive: 18.9

CLV68_RS15705: mmal
PKS_AT (592..825): mmal
ATSignature: (unknown)
No matches above 50%
minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 8.5
  Malonyl-CoA: 4.7
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

CLV68_RS15710: mal
PKS_AT (1155..1435): 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: 80.5
  Methylmalonyl-CoA: 42.8
  Methoxymalonyl-CoA: 42.7
  Propionyl-CoA: 31.1
  trans-1,2-CPDA: 21.6
  CHC-CoA: 21.6
  fatty_acid: 17.6
  inactive: 16.4
  2-Methylbutyryl-CoA: 2.1
  Ethylmalonyl-CoA: 0.2
  Isobutyryl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
MexT | Global virulence regulator
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_RCDD01000002.1 - Region 2 - 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: 267,866 - 278,660 nt. (total: 10,795 nt) Show pHMM detection rules used
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
CLV68_RS15920: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Ligases: synthase
CLV68_RS15895: 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 | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002578.2 |  | 0.41 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001364.3 |  | 0.39 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000528.5 |  | 0.37 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001810.3 |  | 0.36 | PKS | trehangelin | Polymorphospora rubra
BGC0000903.3 |  | 0.36 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0002554.2 |  | 0.35 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
BGC0002621.2 |  | 0.35 | other (other) | angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine | Streptomyces angustmyceticus
BGC0000286.3 |  | 0.35 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0001080.5 |  | 0.34 | other (phenazine) | endophenazine A, endophenazine B | Streptomyces anulatus
BGC0000914.5 |  | 0.34 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002578.2 |  | 0.41 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001364.3 |  | 0.39 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0000528.5 |  | 0.37 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001810.3 |  | 0.36 | PKS | trehangelin | Polymorphospora rubra
BGC0000903.3 |  | 0.36 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0002554.2 |  | 0.35 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
BGC0002621.2 |  | 0.35 | other (other) | angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine | Streptomyces angustmyceticus
BGC0000286.3 |  | 0.35 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0001080.5 |  | 0.34 | other (phenazine) | endophenazine A, endophenazine B | Streptomyces anulatus
BGC0000914.5 |  | 0.34 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.87 out of 32.38
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.36 out of 32.93
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.33 out of 27.18
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_RCDD01000002.1 - Region 3 - NRPS,T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 352,278 - 441,171 nt. (total: 88,894 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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 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 oxygenase
CLV68_RS16540: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

CLV68_RS16545: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CLV68_RS16565: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CLV68_RS16575: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: carbamoyltransferase methyltransferase
CLV68_RS16385: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

CLV68_RS16500: Methylation

MITE
  MITE0000085Methylation (identity: 68.90%)
smcogs
  SMCOG1042: O-methyltransferase

CLV68_RS16505: Methylation

MITE
  MITE0000085Methylation (identity: 65.50%)
smcogs
  SMCOG1042: O-methyltransferase

CLV68_RS16520: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: amidase
CLV68_RS16490: amidase

smcogs
  SMCOG1105: amidase

Lyases: lyase
CLV68_RS16435: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

CLV68_RS16440: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
CLV68_RS16395: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CLV68_RS16400: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CLV68_RS16410: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

CLV68_RS16525: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

CLV68_RS16550: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001758.4 |  |  | 0.45 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  | 0.45 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  |  | 0.43 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  |  | 0.42 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  |  | 0.42 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  |  | 0.41 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001132.4 |  |  | 0.41 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  |  | 0.41 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  |  | 0.41 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.40 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  | 0.73 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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 (15):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.14 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 27.04
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.98 out of 32.74
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.43 out of 31.73
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.69 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.63 out of 32.74
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.03 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.89 out of 28.19
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
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 5, location 352277 - 441171:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 352277 - 414728:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val - X - Val) + (Ile - Val - Trp - 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).
CLV68_RS16395: Ile - Val - Trp - X
Search NORINE for peptide: strict or relaxed
AMP-binding (473..849): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YSSSFDGTVFEAFMSTGGDMHAYGPTETTVFSIH
  Nearest Stachelhaus code(s):
    Ile DGFFLGVVFK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1498..1884): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDSSFDASVYEVYMWTGGDVHVYGPTETTVFCSY
  Nearest Stachelhaus code(s):
    Ile DAYFWGVTFK (79% 8Å match)
    Val DAYWWGGVFK (74% 8Å match)
    Ile or Val DAYFWGVTFK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2534..2917): Trp
nrpys: Trp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWSSFDLSVTGGKAVLGGEINEYGPTEATVGCAE
  Nearest Stachelhaus code(s):
    Trp DLTKVGEVGK (79% 8Å match)
    Asn DLTKVGEVGK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3570..3940): X
nrpys: Arg, Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTQAFDSWLEGRDVVLGGEYNLYGPTECTVDAFA
  Nearest Stachelhaus code(s):
    Arg DTEDVGCVDK (74% 8Å match)
    Orn DTEDMGLVDK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

CLV68_RS16400: Val - X - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (464..838): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDHSFDASVYEVYMWTGGDVHVYGPTETTVFCSH
  Nearest Stachelhaus code(s):
    Ile DAYFWGVTFK (76% 8Å match)
    Val DAYFWGVTFK (74% 8Å match)
    Ile or Val DAYFWGVTFK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1479..1865): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FDSSFDAAVFEVYMWTGGDVHVYGPTETTVFCSH
  Nearest Stachelhaus code(s):
    Dab DAFFWGEVFK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2511..2905): 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:
    TNQSWDAFALEGYLMTGGEVNGYSPLENTIFTVC
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---

NZ_RCDD01000002.1 - 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: 876,592 - 897,725 nt. (total: 21,134 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
CLV68_RS18485: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: cyclase
CLV68_RS18510: 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.53 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000866.5 |  | 0.41 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000507.5 |  | 0.41 | ribosomal | epicidin | Staphylococcus epidermidis
BGC0001184.4 |  | 0.40 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0001197.5 |  | 0.40 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000534.3 |  | 0.39 | ribosomal | mutacin K8 | Streptococcus mutans
BGC0000671.3 |  | 0.39 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0001605.3 |  | 0.38 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001768.4 |  | 0.38 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.53 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000866.5 |  | 0.41 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000507.5 |  | 0.41 | ribosomal | epicidin | Staphylococcus epidermidis
BGC0001184.4 |  | 0.40 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0001197.5 |  | 0.40 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000534.3 |  | 0.39 | ribosomal | mutacin K8 | Streptococcus mutans
BGC0000671.3 |  | 0.39 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0001605.3 |  | 0.38 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001768.4 |  | 0.38 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4

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

Genes with terpene domains:
CLV68_RS18505: Lycopene_cycl
Domain 1 (5 - 347): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
Additional weak hits (4):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.01 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
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
--- | ---
RpoN | Regulator of nitrogen assimilation and virulence

NZ_RCDD01000002.1 - Region 5 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 990,495 - 1,002,600 nt. (total: 12,106 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001146.5 |  | 0.27 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001637.3 |  | 0.24 | NRPS | kleboxymycin | Klebsiella oxytoca
BGC0001127.5 |  | 0.23 | NRPS | jagaricin | Janthinobacterium agaricidamnosum
BGC0000615.4 |  | 0.23 | ribosomal | TP-1161 | Nocardiopsis sp. TFS65-07
BGC0000415.5 |  | 0.23 | NRPS | quinomycin | Streptomyces griseovariabilis subsp. bandungensis
BGC0001228.5 |  | 0.23 | NRPS | retimycin A | Salinispora arenicola CNT005
BGC0002284.3 |  | 0.22 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000450.5 |  | 0.22 | NRPS | triostin A | Streptomyces triostinicus
BGC0002315.2 |  | 0.22 | PKS | accramycin A | Streptomyces sp.
BGC0000446.5 |  | 0.21 | NRPS | tilivalline, 9-deoxy tilivalline, dihydroxy tilivalline, dehydro tilivalline, dihydroxy-dehydro tilivalline | Klebsiella oxytoca

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001146.5 |  | 0.27 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001637.3 |  | 0.24 | NRPS | kleboxymycin | Klebsiella oxytoca
BGC0001127.5 |  | 0.23 | NRPS | jagaricin | Janthinobacterium agaricidamnosum
BGC0000615.4 |  | 0.23 | ribosomal | TP-1161 | Nocardiopsis sp. TFS65-07
BGC0000415.5 |  | 0.23 | NRPS | quinomycin | Streptomyces griseovariabilis subsp. bandungensis
BGC0001228.5 |  | 0.23 | NRPS | retimycin A | Salinispora arenicola CNT005
BGC0002284.3 |  | 0.22 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000450.5 |  | 0.22 | NRPS | triostin A | Streptomyces triostinicus
BGC0002315.2 |  | 0.22 | PKS | accramycin A | Streptomyces sp.
BGC0000446.5 |  | 0.21 | NRPS | tilivalline, 9-deoxy tilivalline, dihydroxy tilivalline, dehydro tilivalline, dihydroxy-dehydro tilivalline | Klebsiella oxytoca

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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RCDD01000002.1 - Region 6 - azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,141,318 - 1,176,115 nt. (total: 34,798 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CLV68_RS19635: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: protease
CLV68_RS19690: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

CLV68_RS19705: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Lyases: dehydratase
CLV68_RS19655: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001146.5 |  | 0.59 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001145.5 |  | 0.58 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001640.3 |  | 0.55 | ribosomal | kocurin | Kocuria rosea
BGC0000613.5 |  | 0.54 | ribosomal | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001860.4 |  | 0.54 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0000605.5 |  | 0.53 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0001472.5 |  | 0.53 | ribosomal | berninamycin A | Streptomyces bernensis
BGC0000603.5 |  | 0.53 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0002311.3 |  | 0.53 | ribosomal | cutimycin | Cutibacterium acnes KPA171202

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001146.5 |  | 0.59 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001145.5 |  | 0.58 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001640.3 |  | 0.55 | ribosomal | kocurin | Kocuria rosea
BGC0000613.5 |  | 0.54 | ribosomal | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001860.4 |  | 0.54 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0000605.5 |  | 0.53 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365
BGC0001472.5 |  | 0.53 | ribosomal | berninamycin A | Streptomyces bernensis
BGC0000603.5 |  | 0.53 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0002311.3 |  | 0.53 | ribosomal | cutimycin | Cutibacterium acnes KPA171202

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: 18.00 out of 20.47
Confidence: medium
Additional weak hits (3):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.60 out of 29.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.10 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.57 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
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (1141317...1176115)
CLV68_RS33440
  RRE type: Thiopeptide_F_RRE
  Location: 0 - 75
  Score: 47.8
CLV68_RS19630
  RRE type: Thiopeptide_F_RRE
  Location: 11 - 91
  Score: 64.0
  RRE type: Heterocycloanthracin_C_RRE
  Location: 12 - 97
  Score: 27.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_RCDD01000003.1 - Region 1 - NRPS-like,T1PKS,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: 3,882 - 67,048 nt. (total: 63,167 nt) Show pHMM detection rules used
Region on contig edge.
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
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
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
CLV68_RS19925: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CLV68_RS19965: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: formyltransferase halogenase methyltransferase
CLV68_RS19990: halogenase

smcogs
  SMCOG1119: halogenase

CLV68_RS20000: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

CLV68_RS20060: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase
CLV68_RS20035: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
CLV68_RS19920: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

CLV68_RS19950: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS20005: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS20010: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS20020: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

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

Reference | T1PKS | NRPS-like | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001249.5 |  |  |  | 1.01 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001244.3 |  |  |  | 0.90 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002164.2 |  |  |  | 0.85 | NRPS | peramine | Epichloe festucae
BGC0001261.3 |  |  |  | 0.84 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  |  |  | 0.81 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002135.2 |  |  |  | 0.79 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  |  |  | 0.78 | NRPS | enniatin | Fusarium equiseti
BGC0001778.5 |  |  |  | 0.67 | other (other) | showdomycin | Streptomyces showdoensis
BGC0002191.2 |  |  |  | 0.59 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001050.5 |  |  |  | 0.58 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001244.3 |  | 0.75 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001249.5 |  | 0.70 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002164.2 |  | 0.64 | NRPS | peramine | Epichloe festucae
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
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
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
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919

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):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.96 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.94 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.77 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.16 out of 28.14
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.88 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 3881 - 67048:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CLV68_RS19950: X
AMP-binding (13..361): 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:
    FWAAFDLCLLDTQAVHTGDRNVYGCTETNDSLIH
  Nearest Stachelhaus code(s):
    Gly DILQVGVIWK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

CLV68_RS20000: Gly - mal
Search NORINE for peptide: strict or relaxed
AMP-binding (559..934): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FGMTFDISLLELQACSGGEWNLYGPTEATIWVTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

PKS_AT (2663..2953): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 70.8%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 123.3
  inactive: 62.3
  Methoxymalonyl-CoA: 61.3
  Methylmalonyl-CoA: 46.2
  Propionyl-CoA: 27.6
  2-Methylbutyryl-CoA: 20.0
  Isobutyryl-CoA: 17.8
  CHC-CoA: 16.9
  fatty_acid: 13.5
  trans-1,2-CPDA: 0.0
  Ethylmalonyl-CoA: -0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

CLV68_RS20010: mal
PKS_AT (1588..1878): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 75.0%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 131.4
  inactive: 70.9
  Methoxymalonyl-CoA: 46.4
  Methylmalonyl-CoA: 44.1
  fatty_acid: 34.0
  Propionyl-CoA: 21.7
  Ethylmalonyl-CoA: 13.2
  Isobutyryl-CoA: 4.0
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---

NZ_RCDD01000003.1 - Region 2 - NRPS,T1PKS,lanthipeptide-class-ii
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: 72,860 - 158,166 nt. (total: 85,307 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
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
CLV68_RS20275: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase methyltransferase
CLV68_RS20225: aminotransferase

smcogs
  SMCOG1019: aminotransferase

CLV68_RS20230: aminotransferase

smcogs
  SMCOG1019: aminotransferase

CLV68_RS20250: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: hydrolase
CLV68_RS20190: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: cyclase
CLV68_RS20320: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: ligase synthase
CLV68_RS20185: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS20200: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS20205: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CLV68_RS20285: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

CLV68_RS20300: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | NRPS | NRPS | T1PKS | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000342.4 |  |  |  |  | 1.07 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  |  |  |  | 1.04 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  |  | 1.02 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  |  |  | 1.02 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  |  |  |  | 0.96 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  |  |  | 0.96 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  |  |  |  | 0.95 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  |  |  |  | 0.94 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000307.4 |  |  |  |  | 0.94 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  |  |  |  | 0.91 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0002135.2 |  | 0.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  | 0.69 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

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
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 CLV68_RS20320

CLV68_RS20325
Leader:
MRDDDFLDQGRAGAWRVMPAVTFGVRAAALAGLVITAGAASAVAFG
Core:
A L D D P A A A V A F D W P G S T T C C P E L P N
Core with dehydrations:
A L D D P A A A V A F D W P G Dha Dhb Dhb Cys Cys P E L P N

#### antiSMASH-DB 4.0 matches for CLV68_RS20325

100.0%
NZ_FOGI01000013.1 and 1 other:
NZ_RCDD01000003.1 Lanthipeptides: CLV68_RS20325_lanthipeptide
Lanthipeptides: BMY07_RS27390_lanthipeptide
1
A L D D P A A A V A F D W P G S T T C C P E L P N
25
A L D D P A A A V A F D W P G S T T C C P E L P N
1
A L D D P A A A V A F D W P G S T T C C P E L P N
25
56.0%
NZ_LN850107.1:
Lanthipeptides: BN1701_RS15195_lanthipeptide
2
L D D P A A A V A F D W P G S T T C C P E L P N
25
D D P A W P S T T C C P E P
1
F D D P A T L S G I-W P T S T T C C P E D P K
23
50.0%
NZ_JAMTCO010000021.1:
Lanthipeptides: LV75_RS33045_lanthipeptide
1
A L D D P A A A V A F D W P G S T T C C P E L P N
25
A D D P A + +W P G S T T C C P+
1
A F D D P T A-I T T N W P G S T T C C G N R P D
24
with 9 more sequence matches
45.2%
NZ_FNDV01000004.1:
Lanthipeptides: BLR56_RS33870_lanthipeptide
2
L D D P A A A V A F D W P G S T T C C P E L P N
25
D D P A + W P S T T C C P E P
10
F D D P A N L A S--W P T S T T C C P E K P K
31
36.8%
NZ_JAMTCR010000003.1:
Lanthipeptides: LV79_RS16640_lanthipeptide
1
A L D D P A A A V A F D W P G S T T C C P E L P N
25
A D D P A A V A +W P G S T T C C P E L P N
34
A F D D P A A-V A A N W P G S T T C C P E L P N
57
28.0%
NZ_CP022961.1:
Lanthipeptides: CIK06_RS16610_lanthipeptide
15
G S T T C C P
21
G S T T C C P
10
G S T T C C P
16
24.0%
NZ_AP018365.1:
Lanthipeptides: RVR_RS00125_lanthipeptide
8
A V A F D W P G S T T C C
20
+V W G S +C C
1
S V V A S W Q G S F S C C
13
24.0%
NZ_JALMDK010000027.1:
Lanthipeptides: MZC64_RS46660_lanthipeptide
15
G S T T C C P
21
G T T C C P
9
G I T T C C P
15
24.0%
NZ_LT607733.1:
Lanthipeptides: GA0070610_RS10040_lanthipeptide
17
T T C C P E
22
T T C C P E
16
T T C C P E
21
17.6%
NZ_CP041604.2 and 3 others:
NZ_CP041610.2 Lanthipeptides: allorf_00763119_00763355_lanthipeptide NZ_CP041611.1 Lanthipeptides: allorf_00813099_00813335_lanthipeptide NZ_CP041650.2 Lanthipeptides: allorf_01115923_01116159_lanthipeptide
Lanthipeptides: allorf_01200858_01201094_lanthipeptide
4
D P A A A V A F D W P G S T T C C P E
22
D + W P G + C P
6
D T G S G R R R P W P G H R S P C P R
24
15.4%
NC_017803.1:
Lanthipeptides: ACPL_RS19820_lanthipeptide
16
S T T C C P
21
S T T C C P
29
S T T C C P
34
11.9%
NZ_JALBFU010000003.1:
Lanthipeptides: allorf_276835_277062_lanthipeptide
15
G S T T C C P E L P N
25
G S C P L P N
3
G S C E C A P S L P N
13
allorf_139535_139630
Leader:
MQAHTGPGG
Core:
H R G P T Q L A R D F L D H I G P A G V A C
Core with dehydrations:
H R G P Dhb Q L A R D F L D H I G P A G V A Cys

#### antiSMASH-DB 4.0 matches for allorf_139535_139630

100.0%
NZ_RCDD01000003.1:
Lanthipeptides: allorf_139535_139630_lanthipeptide
1
H R G P T Q L A R D F L D H I G P A G V A C
22
H R G P T Q L A R D F L D H I G P A G V A C
1
H R G P T Q L A R D F L D H I G P A G V A C
22
72.7%
NZ_FOGI01000013.1:
Lanthipeptides: allorf_141216_141311_lanthipeptide
2
R G P T Q L A R D F L D H I G P A G V A C
22
R P T Q L A D F L D H G G V A C
2
R D P T Q L A G D F L D H R G L V G V A C
22

#### MIBiG 4.0 matches for allorf_139535_139630

7.8%
BGC0002120.3 (NQE92413.1):
Lanthipeptide: nocathioamide A
17
P A G V A C
22
P A A C
35
P A A P A C
40
allorf_150273_150407
Leader:
MGSSRILPMSHGG
Core:
P R D L G A I P Q T C R L W P E Y F Y S T G H V Y T S W Y L R
Core with dehydrations:
P R D L G A I P Q Dhb Cys R L W P E Y F Y Dha Dhb G H V Y Dhb Dha W Y L R

#### antiSMASH-DB 4.0 matches for allorf_150273_150407

100.0%
NZ_RCDD01000003.1:
Lanthipeptides: allorf_150273_150407_lanthipeptide
1
P R D L G A I P Q T C R L W P E Y F Y S T G H V Y T S W Y L R
31
P R D L G A I P Q T C R L W P E Y F Y S T G H V Y T S W Y L R
1
P R D L G A I P Q T C R L W P E Y F Y S T G H V Y T S W Y L R
31
16.1%
NZ_CAOJCM010000001.1:
Lanthipeptides: allorf_0381374_0381505_lanthipeptide
9
Q T C R L W P E Y F Y S T
21
+C R+ P++F T
9
H S C R I A P D H F E R T
21

#### MIBiG 4.0 matches for allorf_150273_150407

16.1%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
10
T C R L W P E Y F Y S T
21
+C R L + Y T
7
S C R L G N K G A Y C T
18
allorf_150382_150618
Leader:
MGRMRDDPMFVRSCCSGRQSHEAVWKRPAKPWDREWAGQTMRVVAGG
Core:
A S S R G I A V R S G Q S E V R A E S G E I A V L C A G A M R
Core with dehydrations:
A Dha Dha R G I A V R Dha G Q Dha E V R A E Dha G E I A V L Cys A G A M R

#### antiSMASH-DB 4.0 matches for allorf_150382_150618

100.0%
NZ_RCDD01000003.1:
Lanthipeptides: allorf_150382_150618_lanthipeptide
1
A S S R G I A V R S G Q S E V R A E S G E I A V L C A G A M R
31
A S S R G I A V R S G Q S E V R A E S G E I A V L C A G A M R
1
A S S R G I A V R S G Q S E V R A E S G E I A V L C A G A M R
31

#### 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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.35 out of 27.04
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.52 out of 23.79
Confidence: medium
Additional weak hits (7):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.96 out of 30.22
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.47 out of 32.74
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.60 out of 35.63
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.87 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
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
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.

CLV68_RS20325 - Class II
  Cleavage pHMM score: -3.80
  RODEO score: 0
  Monoisotopic mass: 2506.1 Da
  Molecular weight: 2507.7 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2525.8 Da N = 1
allorf_139535_139630 - Class II
  Cleavage pHMM score: -4.90
  RODEO score: 0
  Monoisotopic mass: 2312.2 Da
  Molecular weight: 2313.6 Da
  Number of bridges: 1
allorf_150273_150407 - Class II
  Cleavage pHMM score: -2.20
  RODEO score: 0
  Monoisotopic mass: 3684.8 Da
  Molecular weight: 3687.1 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3705.1 Da N = 1
    3723.2 Da N = 2
    3741.2 Da N = 3
    3759.2 Da N = 4
allorf_150382_150618 - Class II
  Cleavage pHMM score: -1.30
  RODEO score: 0
  Monoisotopic mass: 3027.6 Da
  Molecular weight: 3029.4 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3047.4 Da N = 1
    3065.4 Da N = 2
    3083.5 Da N = 3
    3101.5 Da N = 4

Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 3, location 72859 - 158166:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - X) + (Val - X) + (D-X - D-Arg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 72859 - 127118:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 109493 - 158166:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal - 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).
CLV68_RS20185: X
AMP-binding (9..421): 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:
    YHNFFDPSVFDAFSVFIGEDNVYGPTELTVACTR
  Nearest Stachelhaus code(s):
    Ala DVFFVGLVAK (56% 8Å match)
  Stachelhaus code match:
    70% (weak)

CLV68_RS20200: X - Arg
Search NORINE for peptide: strict or relaxed
AMP-binding (501..904): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    IVWSVDLFFGDLITAIGSETNNYGATETTVDSTV
  Nearest Stachelhaus code(s):
    ohEnd DLSVMGAVDK (74% 8Å match)
    Hty DLGFTGAVCK (47% 8Å match)
    Lys DADDAGTVDK (41% 8Å match)
  Stachelhaus code match:
    60% (weak)

AMP-binding (2014..2408): Arg
nrpys: Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAEHFDAAQNENSFVCGGEVNAYGPTECSVTATC
  Nearest Stachelhaus code(s):
    Arg DAESVGAVDK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

CLV68_RS20205: Val - X
Search NORINE for peptide: strict or relaxed
AMP-binding (227..619): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDENFDALTYEVWIWTGGEVNGYGPTECTTYSTS
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1274..1527): X
No predictions made
CLV68_RS20300: mal - X
PKS_AT (520..790): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 82.0
  Methylmalonyl-CoA: 43.3
  Methoxymalonyl-CoA: 40.0
  inactive: 34.6
  fatty_acid: 26.9
  Isobutyryl-CoA: 24.6
  Benzoyl-CoA: 23.7
  Ethylmalonyl-CoA: 20.1
  CHC-CoA: 16.2
  Propionyl-CoA: 14.7
  trans-1,2-CPDA: 9.2
  2-Methylbutyryl-CoA: 8.6
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

AMP-binding (1927..2293): X
nrpys: Val, Leu, Ile, Abu, Ival

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

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

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism

NZ_RCDD01000003.1 - Region 3 - 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: 187,096 - 232,456 nt. (total: 45,361 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 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
CLV68_RS20650: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: aminotransferase methyltransferase sulfhydrylase
CLV68_RS20600: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

CLV68_RS20605: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

CLV68_RS20655: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CLV68_RS20665: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

CLV68_RS20680: methyltransferase

smcogs
  SMCOG1089: methyltransferase

CLV68_RS20700: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: lyase
CLV68_RS20710: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000056.3 |  | 0.70 | PKS | esperamicin | Actinomadura verrucosospora
BGC0001244.3 |  | 0.56 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001164.3 |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002387.2 |  | 0.51 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001994.4 |  | 0.50 | other (other) | β-ethynylserine | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002313.3 |  | 0.48 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000902.4 |  | 0.46 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000675.5 |  | 0.45 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000815.4 |  | 0.44 | other (other) | loline, N-acetylnorloline, N-formylloline | Epichloe uncinata
BGC0000285.5 |  | 0.44 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000056.3 |  | 0.70 | PKS | esperamicin | Actinomadura verrucosospora
BGC0001244.3 |  | 0.56 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001164.3 |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002387.2 |  | 0.51 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001994.4 |  | 0.50 | other (other) | β-ethynylserine | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002313.3 |  | 0.48 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000902.4 |  | 0.46 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000675.5 |  | 0.45 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000815.4 |  | 0.44 | other (other) | loline, N-acetylnorloline, N-formylloline | Epichloe uncinata
BGC0000285.5 |  | 0.44 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (7):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.05 out of 21.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.35 out of 25.75
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.75 out of 31.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.62 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.83 out of 24.78
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).
CLV68_RS20625: mal
PKS_AT (602..828): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 62.5%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 89.1
  Methoxymalonyl-CoA: 59.1
  Methylmalonyl-CoA: 49.5
  inactive: 39.2
  Isobutyryl-CoA: 35.2
  Ethylmalonyl-CoA: 32.8
  Propionyl-CoA: 21.0
  fatty_acid: 18.9
  Benzoyl-CoA: 16.9
  Acetyl-CoA: 12.9
  trans-1,2-CPDA: 11.8
  2-Methylbutyryl-CoA: 8.9
  CHC-CoA: 7.9
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---

NZ_RCDD01000003.1 - Region 4 - redox-cofactor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 249,649 - 271,674 nt. (total: 22,026 nt) Show pHMM detection rules used
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: back translocase
CLV68_RS20825: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

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

Reference | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001294.5 |  | 0.41 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0001100.5 |  | 0.34 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0001387.5 |  | 0.30 | other (other) | nucleocidin | Streptomyces calvus
BGC0000204.5 |  | 0.30 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0001148.5 |  | 0.30 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus
BGC0000905.5 |  | 0.29 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000610.5 |  | 0.29 | ribosomal | nosiheptide | Streptomyces actuosus
BGC0000632.5 |  | 0.29 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0000192.3 |  | 0.28 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0001078.5 |  | 0.28 | PKS, terpene | furaquinocin B | Streptomyces sp. KO-3988

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001294.5 |  | 0.41 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0001100.5 |  | 0.34 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0001387.5 |  | 0.30 | other (other) | nucleocidin | Streptomyces calvus
BGC0000204.5 |  | 0.30 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0001148.5 |  | 0.30 | NRPS, ribosomal | pheganomycin | Streptomyces cirratus
BGC0000905.5 |  | 0.29 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000610.5 |  | 0.29 | ribosomal | nosiheptide | Streptomyces actuosus
BGC0000632.5 |  | 0.29 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0000192.3 |  | 0.28 | PKS | aclacinomycin | Streptomyces galilaeus
BGC0001078.5 |  | 0.28 | PKS, terpene | furaquinocin B | Streptomyces sp. KO-3988

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.15 out of 27.04
Confidence: medium
Additional weak hits (5):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.83 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.52 out of 39.62
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.20 out of 30.11
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (249648...271674)
CLV68_RS20860
  RRE type: PqqD_RRE
  Location: 5 - 84
  Score: 62.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor

NZ_RCDD01000003.1 - Region 5 - NRPS,NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 289,941 - 336,088 nt. (total: 46,148 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidase oxidoreductase oxygenase
CLV68_RS21080: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CLV68_RS21100: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CLV68_RS21155: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

CLV68_RS21170: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Transferases: aminotransferase glycosyltransferase methyltransferase
CLV68_RS21105: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CLV68_RS21115: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CLV68_RS21125: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CLV68_RS21140: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Hydrolases: hydrolase peptidase
CLV68_RS21110: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

CLV68_RS21145: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

Ligases: ligase
CLV68_RS21085: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CLV68_RS21090: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease
CLV68_RS20985: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001135.5 |  |  | 0.59 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  |  | 0.59 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002164.2 |  |  | 0.59 | 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
BGC0001261.3 |  |  | 0.58 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  |  | 0.57 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001166.5 |  |  | 0.57 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001250.4 |  |  | 0.57 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  | 0.57 | NRPS | epichloenin A | Epichloe festucae
BGC0001240.4 |  |  | 0.57 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.63 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002164.2 |  | 0.63 | NRPS | peramine | Epichloe festucae
BGC0000357.5 |  | 0.63 | 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
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.62 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001166.5 |  | 0.62 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001250.4 |  | 0.62 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.62 | NRPS | epichloenin A | Epichloe festucae
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
Additional weak hits (3):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.05 out of 30.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.54 out of 30.25
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 9, location 289940 - 336088:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 289940 - 334299:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 11, location 294300 - 336088:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CLV68_RS21085: X
AMP-binding (492..882): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNQMFDVIAEEGFFYVTGESNIYGPSEAHLCTGE
  Nearest Stachelhaus code(s):
    proPro DVLYYTALCK (74% 8Å match)
    Trp or Tyr DVMFYTALVK (62% 8Å match)
  Stachelhaus code match:
    70% (weak)

CLV68_RS21090: X
AMP-binding (24..413): 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:
    VHLAFAASTTDTNLIVSGDFNAFGCTENSALTAV
  Nearest Stachelhaus code(s):
    mxAnt AATHLSATLK (82% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

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

NZ_RCDD01000003.1 - Region 6 - 2dos
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: 339,195 - 368,217 nt. (total: 29,023 nt) Show pHMM detection rules used
2dos: ((DOIS or DHQ_synthase or ValA or salQ) and DegT_DnrJ_EryC1 and (LipV or ADSI-DH or cds(ADH_N and ADH_zinc_N)))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CLV68_RS21240: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: aminotransferase glycosyltransferase
CLV68_RS21220: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CLV68_RS21235: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

CLV68_RS21270: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

CLV68_RS21295: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: decarboxylase
CLV68_RS21200: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

CLV68_RS21230: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: synthase
CLV68_RS21255: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate 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 | 2dos | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000700.5 |  | 0.50 | saccharide | istamycin | Streptomyces tenjimariensis
BGC0000772.5 |  | 0.47 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0001817.5 |  | 0.46 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0000905.5 |  | 0.44 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000906.3 |  | 0.44 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000882.5 |  | 0.44 | other (other) | mildiomycin | Streptomyces rimofaciens
BGC0000708.5 |  | 0.44 | saccharide | lividomycin | Streptomyces lividus
BGC0000706.3 |  | 0.43 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000602.5 |  | 0.43 | ribosomal | subtilosin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000716.5 |  | 0.43 | saccharide | spectinomycin | Streptomyces netropsis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000700.5 |  | 0.50 | saccharide | istamycin | Streptomyces tenjimariensis
BGC0000772.5 |  | 0.47 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0001817.5 |  | 0.46 | other (other) | vancosamine | Streptomyces sp. WAC2288
BGC0000905.5 |  | 0.44 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000906.3 |  | 0.44 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000882.5 |  | 0.44 | other (other) | mildiomycin | Streptomyces rimofaciens
BGC0000708.5 |  | 0.44 | saccharide | lividomycin | Streptomyces lividus
BGC0000706.3 |  | 0.43 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000602.5 |  | 0.43 | ribosomal | subtilosin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000716.5 |  | 0.43 | saccharide | spectinomycin | Streptomyces netropsis

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: 18.00 out of 20.47
Confidence: medium
Additional weak hits (4):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.25 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.90 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.83 out of 35.63
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.85 out of 20.01
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RCDD01000005.1 - Region 1 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 89,606 - 179,208 nt. (total: 89,603 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
CLV68_RS26060: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CLV68_RS26095: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

Hydrolases: hydrolase
CLV68_RS25970: HAD-superfamily hydrolase, subfamily IA, variant

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

CLV68_RS26000: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CLV68_RS26075: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
CLV68_RS26065: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
CLV68_RS26015: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS26020: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS26025: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CLV68_RS26070: 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 | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001185.5 |  |  | 0.90 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0001133.4 |  |  | 0.87 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.87 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  | 0.86 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  |  | 0.86 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  |  | 0.84 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002286.3 |  |  | 0.84 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.83 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.83 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  |  | 0.82 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001185.5 |  | 0.75 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0001133.4 |  | 0.74 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.74 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 24.72 out of 29.72
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.02 out of 36.53
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.62 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.86 out of 36.53
Confidence: medium
Additional weak hits (8):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.40 out of 30.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.17 out of 25.88
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.43 out of 27.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.55 out of 26.85
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.92 out of 26.06
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: 20.83 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.98 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 89605 - 179208:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - Ser - D-X - D-Fo-OH-Orn - D-Ser) + (D-Thr - D-Lys) + (D-Lys - Lys - Fo-OH-Orn - Gly)

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).
CLV68_RS26015: Gly - Ser - X - Fo-OH-Orn - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (445..815): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FDMTFDISGLEVQALVGGETNLYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1431..1820): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFLCSGEHNLYGPTEASVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2449..2841): X
nrpys: (unknown)

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

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

AMP-binding (3844..4235): Fo-OH-Orn
nrpys: Fo-OH-Orn

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

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

AMP-binding (5284..5668): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFLCSGEHNLYGPTEASVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

CLV68_RS26020: Thr - Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (452..843): Thr
nrpys: Thr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LATHFDFSVWEGNQIFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1905..2267): Lys
nrpys: Lys

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:
    LSHAFDASLDPWDAGTGGEFNFYGPTECTVDTVV
  Nearest Stachelhaus code(s):
    Lys DADDGGFVDK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

CLV68_RS26025: Lys - Lys - Fo-OH-Orn - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (459..820): Lys
nrpys: Lys

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:
    LAHAFDASLDPWDAGTGGEFNFYGPTESTVDAVV
  Nearest Stachelhaus code(s):
    Lys DADDGGFVDK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1872..2232): Lys
nrpys: Lys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSHAFDASVDGWDAGTGGEFNFYGPTETTVDATF
  Nearest Stachelhaus code(s):
    Lys DADDGGFVDK (62% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2882..3270): Fo-OH-Orn
nrpys: Fo-OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWQAFDISVNELYLWCGGEYHGYGPAETTIGVSH
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DINYWGGIGK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3911..4288): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAMTFDIAVLEVQALVGGEVNLYGPTETTVWSTS
  Nearest Stachelhaus code(s):
    Gly DILQLGLVWK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

CLV68_RS26070: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (31..429): diOH-Bz
nrpys: diOH-Bz

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    SESLFPMSSPGGGVQVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PMPAQGVVNK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_RCDD01000005.1 - Region 2 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 354,229 - 397,471 nt. (total: 43,243 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase reductase
CLV68_RS26880: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CLV68_RS26885: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

CLV68_RS26890: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

CLV68_RS26960: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

CLV68_RS26990: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

CLV68_RS27000: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

CLV68_RS27010: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Hydrolases: esterase hydrolase
CLV68_RS26895: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

CLV68_RS26900: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

CLV68_RS26985: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase
CLV68_RS26975: 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 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000373.5 |  | 0.62 | NRPS | holomycin | Streptomyces clavuligerus ATCC 27064
BGC0000357.5 |  | 0.62 | 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

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.63 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000373.5 |  | 0.62 | NRPS | holomycin | Streptomyces clavuligerus ATCC 27064
BGC0000357.5 |  | 0.62 | 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

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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.76 out of 26.85
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.27 out of 23.79
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.45 out of 26.33
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.52 out of 24.78
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (10):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.26 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.64 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.90 out of 30.22
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.46 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.77 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.71 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.82 out of 24.78
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.74 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 2, location 354228 - 397471:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Cys)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CLV68_RS26975: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (493..891): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDIAFDLSVYDGNSLLSGDVSLGGATEGSIWSVF
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
RutR | Regulator of the pyrimidine and purine metabolism

NZ_RCDD01000005.1 - Region 3 - furan
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 401,422 - 422,414 nt. (total: 20,993 nt) Show pHMM detection rules used
Region on contig edge.
furan: (mmyO or AvrD)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
CLV68_RS27075: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CLV68_RS27135: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CLV68_RS27145: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Hydrolases: esterase
CLV68_RS35460: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

Ligases: synthase
CLV68_RS27120: 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 | furan | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002554.2 |  | 0.45 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
BGC0001903.3 |  | 0.44 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0000914.5 |  | 0.44 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0002711.2 |  | 0.44 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0001364.3 |  | 0.44 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001850.4 |  | 0.43 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0000922.5 |  | 0.43 | PKS | 2-heptyl-3-hydroxy-4-quinolone, 2,4-Quinolinediol, 2-heptylquinolin-4(1H)-one | Pseudomonas aeruginosa PAO1
BGC0001965.4 |  | 0.42 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus
BGC0002066.3 |  | 0.41 | NRPS, PKS | harzianopyridone | Trichoderma harzianum
BGC0000769.3 |  | 0.41 | saccharide | glycopeptidolipid | Mycobacterium avium subsp. hominissuis A5

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002554.2 |  | 0.45 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
BGC0001903.3 |  | 0.44 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0000914.5 |  | 0.44 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0002711.2 |  | 0.44 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0001364.3 |  | 0.44 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001850.4 |  | 0.43 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0000922.5 |  | 0.43 | PKS | 2-heptyl-3-hydroxy-4-quinolone, 2,4-Quinolinediol, 2-heptylquinolin-4(1H)-one | Pseudomonas aeruginosa PAO1
BGC0001965.4 |  | 0.42 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus
BGC0002066.3 |  | 0.41 | NRPS, PKS | harzianopyridone | Trichoderma harzianum
BGC0000769.3 |  | 0.41 | saccharide | glycopeptidolipid | Mycobacterium avium subsp. hominissuis A5

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47
Confidence: medium
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.78 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.71 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.06 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.92 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.15 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RCDD01000006.1 - Region 1 - thioamitides
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,303 - 29,128 nt. (total: 21,826 nt) Show pHMM detection rules used
Region on contig edge.
thioamitides: ((YcaO or TIGR03604) and TfuA)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: protease
CLV68_RS27255: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

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

Reference | thioamitides | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.48 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0001849.4 |  | 0.47 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0002560.3 |  | 0.45 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0002488.3 |  | 0.44 | other (other) | bacillopaline | Paenibacillus mucilaginosus KNP414
BGC0000504.5 |  | 0.44 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000500.5 |  | 0.42 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0000502.5 |  | 0.41 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0002674.2 |  | 0.40 | ribosomal | enterocin F4-9 | Enterococcus faecalis
BGC0002699.2 |  | 0.40 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001696.5 |  | 0.40 | ribosomal | neothioviridamide | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.48 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0001849.4 |  | 0.47 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0002560.3 |  | 0.45 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0002488.3 |  | 0.44 | other (other) | bacillopaline | Paenibacillus mucilaginosus KNP414
BGC0000504.5 |  | 0.44 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000500.5 |  | 0.42 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0000502.5 |  | 0.41 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0002674.2 |  | 0.40 | ribosomal | enterocin F4-9 | Enterococcus faecalis
BGC0002699.2 |  | 0.40 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001696.5 |  | 0.40 | ribosomal | neothioviridamide | Streptomyces sp.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 22.40
Confidence: strong
Additional weak hits (1):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.92 out of 21.55
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
HypR | L-hydroxyproline utilization repressor

NZ_RCDD01000006.1 - Region 2 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 34,382 - 56,866 nt. (total: 22,485 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acetyltransferase sulfhydrylase
CLV68_RS27430: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

CLV68_RS27455: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: dehalogenase
CLV68_RS27365: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: cyclase
CLV68_RS27410: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase synthetase
CLV68_RS27445: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

CLV68_RS35805: 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
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.58 | terpene | astallatene | Arabidopsis thaliana
BGC0000918.3 |  | 0.56 | other (other) | ochronotic pigment | Streptomyces avermitilis
BGC0002400.2 |  | 0.54 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000866.5 |  | 0.50 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.48 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0000677.5 |  | 0.47 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002398.2 |  | 0.47 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000894.4 |  | 0.46 | other (other) | citrinin | Monascus aurantiacus
BGC0002309.2 |  | 0.45 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000678.5 |  | 0.44 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.58 | terpene | astallatene | Arabidopsis thaliana
BGC0000918.3 |  | 0.56 | other (other) | ochronotic pigment | Streptomyces avermitilis
BGC0002400.2 |  | 0.54 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000866.5 |  | 0.50 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000867.3 |  | 0.48 | other (other) | polyhydroxyalkanoic acids | Ectothiorhodospira shaposhnikovii
BGC0000677.5 |  | 0.47 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002398.2 |  | 0.47 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000894.4 |  | 0.46 | other (other) | citrinin | Monascus aurantiacus
BGC0002309.2 |  | 0.45 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000678.5 |  | 0.44 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

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:
CLV68_RS35805: PT_FPPS_like
Domain 1 (53 - 335): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

CLV68_RS27410: T1TS
Domain 1 (16 - 323): 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.
No hits above weak threshold.
Weak hits (15):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.78 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.57 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.53 out of 29.38
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.04 out of 30.11
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.07 out of 30.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.84 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.12 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.89 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.63 out of 30.98
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.21 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 21.93 out of 30.11
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.56 out of 29.25
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_RCDD01000007.1 - Region 1 - 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: 20,277 - 41,353 nt. (total: 21,077 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
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 | indole | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001294.5 |  | 0.49 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002128.3 |  | 0.35 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001483.4 |  | 0.30 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001197.5 |  | 0.26 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001910.4 |  | 0.24 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.24 | terpene | raimonol | Streptomyces anulatus
BGC0002805.2 |  | 0.22 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001840.2 |  | 0.20 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001294.5 |  | 0.49 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002128.3 |  | 0.35 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001483.4 |  | 0.30 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001197.5 |  | 0.26 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001910.4 |  | 0.24 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.24 | terpene | raimonol | Streptomyces anulatus
BGC0002805.2 |  | 0.22 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001840.2 |  | 0.20 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
Additional weak hits (3):
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.41 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 30.11
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.04 out of 23.43
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RCDD01000007.1 - Region 2 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 58,725 - 80,848 nt. (total: 22,124 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
CLV68_RS28890: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CLV68_RS28925: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Lyases: cyclase dehydratase
CLV68_RS28935: Terpene synthase/cyclase metal-binding domain protein

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

CLV68_RS28980: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
CLV68_RS28985: 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
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002127.3 |  | 0.48 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002031.3 |  | 0.46 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000902.4 |  | 0.46 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000844.5 |  | 0.46 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001223.5 |  | 0.43 | other (other) | hydroxysporine | uncultured bacterium
BGC0001336.5 |  | 0.42 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001485.4 |  | 0.40 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002482.2 |  | 0.40 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0000285.5 |  | 0.39 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002127.3 |  | 0.48 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002031.3 |  | 0.46 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000902.4 |  | 0.46 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000844.5 |  | 0.46 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001223.5 |  | 0.43 | other (other) | hydroxysporine | uncultured bacterium
BGC0001336.5 |  | 0.42 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001485.4 |  | 0.40 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002482.2 |  | 0.40 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0000285.5 |  | 0.39 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea

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

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:
CLV68_RS28935: T1TS + T1TS
Domain 1 (1 - 328): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (333 - 700): 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:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.01 out of 23.43
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.43 out of 23.79
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.13 out of 23.43
Confidence: medium
Additional weak hits (4):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.28 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.98 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.03 out of 23.43
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.06 out of 35.63
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
--- | ---
BldD | Development and antibiotic global regulator
IolR | Regulator of the inositol catabolism

NZ_RCDD01000007.1 - Region 3 - arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 162,236 - 203,282 nt. (total: 41,047 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: PPTase glycosyltransferase
CLV68_RS29360: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CLV68_RS29390: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: hydrolase
CLV68_RS29295: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Ligases: ligase synthase
CLV68_RS29305: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS29320: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS29330: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS29335: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS29370: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

CLV68_RS29375: 3-oxoacyl-(acyl carrier protein) synthase III

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

CLV68_RS29405: 1-deoxy-D-xylulose-5-phosphate synthase

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

CLV68_RS29410: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.56 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.56 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.56 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.56 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  | 0.55 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001535.3 |  | 0.54 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0002458.3 |  | 0.51 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0002711.2 |  | 0.47 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0002547.2 |  | 0.45 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces youssoufiensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.56 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.56 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.56 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.56 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  | 0.55 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001535.3 |  | 0.54 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0002458.3 |  | 0.51 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0002711.2 |  | 0.47 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0002547.2 |  | 0.45 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces youssoufiensis

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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.03 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.72 out of 27.04
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.15 out of 29.72
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
Additional weak hits (7):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.05 out of 20.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.16 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
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.71 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.07 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.85 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CLV68_RS29305: X
AMP-binding (34..368): 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:
    ERYS-IVHVLGGIGIVAGEGTMYGMTEIGVIATD
  Nearest Stachelhaus code(s):
    Ser DVWSIAMVHK (41% 8Å match)
    Ala DVWIYAAVIK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

CLV68_RS29330: X
AMP-binding (38..430): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    AHRLHAATLIAL-GWNTGD-----------VSTR
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_RCDD01000007.1 - Region 4 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 252,145 - 270,086 nt. (total: 17,942 nt) Show pHMM detection rules used
Region on contig edge.
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
CLV68_RS29675: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

CLV68_RS29680: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001289.5 |  | 0.44 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000544.4 |  | 0.40 | ribosomal | planosporicin | Planomonospora alba
BGC0000529.5 |  | 0.35 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000796.3 |  | 0.26 | saccharide | S-layer glycan | Paenibacillus alvei

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0001289.5 |  | 0.44 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000544.4 |  | 0.40 | ribosomal | planosporicin | Planomonospora alba
BGC0000529.5 |  | 0.35 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000796.3 |  | 0.26 | saccharide | S-layer glycan | Paenibacillus alvei

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 CLV68_RS29675

CLV68_RS29670
Leader:
MTAQLTPTNGSALDLDLTIVESAPVIPA
Core:
L M G N T D D N C G S S C Q S A C S N S D C E
Core with dehydrations:
L M G N Dhb D D N Cys G Dha Dha Cys Q Dha A Cys Dha N Dha D Cys E

#### antiSMASH-DB 4.0 matches for CLV68_RS29670

100.0%
NZ_RCDD01000007.1 and 1 other:
NZ_RCDD01000007.1 Lanthipeptides: CLV68_RS29670_lanthipeptide
Lanthipeptides: CLV68_RS29670_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C E
23
L M G N T D D N C G S S C Q S A C S N S D C E
1
L M G N T D D N C G S S C Q S A C S N S D C E
23
91.3%
NZ_CP012752.1 and 1 other:
NZ_CP012752.1 Lanthipeptides: AOZ06_RS53485_lanthipeptide
Lanthipeptides: AOZ06_RS53485_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C E
23
L M G N T D D N C G S C Q S A C S N S+C E
1
L M G N T D D N C G V S C Q S A C S N S N C E
23
87.0%
NZ_CP012752.1 and 1 other:
NZ_CP012752.1 Lanthipeptides: AOZ06_RS55260_lanthipeptide
Lanthipeptides: AOZ06_RS55260_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L M N T D D N C G S S C Q S A C S N S C
2
L M R N T D D N C G S S C Q S A C S N S T C
23
with 176 more sequence matches
Only the first 10 are displayed here.
82.6%
NZ_LN850107.1 and 1 other:
NZ_LN850107.1 Lanthipeptides: BN1701_RS34435_lanthipeptide
Lanthipeptides: BN1701_RS34435_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L M N T D D N C G S+C Q S A C S N S C
1
L M T N T D D N C G S T C Q S A C S N S S C
22
79.2%
NZ_CP012752.1:
Lanthipeptides: AOZ06_RS53490_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L M N T D D N C G+S C Q S A C S N S C
2
L M R N T D D N C G T S C Q S A C S N S T C
23
78.3%
NZ_SLWS01000019.1 and 1 other:
NZ_SLWS01000019.1 Lanthipeptides: EV192_RS50115_lanthipeptide
Lanthipeptides: EV192_RS50115_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L M N T D D N C G +C Q S A C S N S C
1
L M R N T D D N C G Q T C Q S A C S N S T C
22
73.9%
NZ_JAMTCR010000003.1 and 1 other:
NZ_JAMTCR010000003.1 Lanthipeptides: LV79_RS15365_lanthipeptide
Lanthipeptides: LV79_RS15365_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L M +T D D N C G++C Q S A C S N S C
1
L M R S T D D N C G A T C Q S A C S N S T C
22
64.0%
NZ_FOLM01000004.1 and 1 other:
NZ_FOLM01000004.1 Lanthipeptides: BM242_RS10130_lanthipeptide
Lanthipeptides: BM242_RS10130_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L+ +T D D N C S+C Q S A C S N S C
1
L L N D T D D N C T S T C Q S A C S N S T C
22
62.5%
NZ_CP045031.1 and 2 others:
NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide
Lanthipeptides: F9V55_RS07565_lanthipeptide
2
M G N T D D N C G S S C Q S A C S N S D C
22
+ +T D N C G S+C Q S A C S N S C
1
L N D T S D N C G S T C Q S A C S N S T C
21
62.5%
NZ_LJFZ01000009.1 and 2 others:
NZ_LJFZ01000009.1 Lanthipeptides: UK94_RS32440_lanthipeptide NZ_LJFZ01000009.1 Lanthipeptides: UK94_RS32440_lanthipeptide
Lanthipeptides: UK94_RS32440_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L+ +T D N C S+C Q S A C S N S C
1
L L N S T S D N C T S T C Q S A C S N S T C
22
60.9%
NZ_CP029042.1 and 2 others:
NZ_CP045178.1 Lanthipeptides: GBW32_RS14380_lanthipeptide NZ_JAHLXF010000013.1 Lanthipeptides: KQY13_RS21225_lanthipeptide
Lanthipeptides: DDE74_RS17120_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S
20
L M +T D N C G S S C S A C+ S
3
L M C S T G D N C G S S C P S A C T T S
22
60.9%
NZ_KQ257877.1 and 1 other:
NZ_KQ257877.1 Lanthipeptides: IQ64_RS44800_lanthipeptide
Lanthipeptides: IQ64_RS44800_lanthipeptide
2
M G N T D D N C G S S C Q S A C S N S D C E
23
+ +T D C G +C Q S A C S N S C E
1
L N D T G D G C G Q T C Q S A C S N S T C E
22
60.9%
NZ_ML123117.1:
Lanthipeptides: EES46_RS09865_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S
20
L M T D N C G S S C S A C+ S
3
L M C G T G D N C G S S C P S A C T T S
22

#### MIBiG 4.0 matches for CLV68_RS29670

7.8%
BGC0002120.3 (NQE92413.1):
Lanthipeptide: nocathioamide A
6
D D N C G S S C Q S A C
17
D D A C
29
D D E S S R P A A P A C
40

#### Lanthipeptide(s) for CLV68_RS29685

CLV68_RS29670
Leader:
MTAQLTPTNGSALDLDLTIVESAPVIPA
Core:
L M G N T D D N C G S S C Q S A C S N S D C E
Core with dehydrations:
L M G N Dhb D D N Cys G Dha Dha Cys Q Dha A Cys Dha N Dha D Cys E

#### antiSMASH-DB 4.0 matches for CLV68_RS29670

100.0%
NZ_RCDD01000007.1 and 1 other:
NZ_RCDD01000007.1 Lanthipeptides: CLV68_RS29670_lanthipeptide
Lanthipeptides: CLV68_RS29670_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C E
23
L M G N T D D N C G S S C Q S A C S N S D C E
1
L M G N T D D N C G S S C Q S A C S N S D C E
23
91.3%
NZ_CP012752.1 and 1 other:
NZ_CP012752.1 Lanthipeptides: AOZ06_RS53485_lanthipeptide
Lanthipeptides: AOZ06_RS53485_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C E
23
L M G N T D D N C G S C Q S A C S N S+C E
1
L M G N T D D N C G V S C Q S A C S N S N C E
23
87.0%
NZ_CP012752.1 and 1 other:
NZ_CP012752.1 Lanthipeptides: AOZ06_RS55260_lanthipeptide
Lanthipeptides: AOZ06_RS55260_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L M N T D D N C G S S C Q S A C S N S C
2
L M R N T D D N C G S S C Q S A C S N S T C
23
with 176 more sequence matches
Only the first 10 are displayed here.
82.6%
NZ_LN850107.1 and 1 other:
NZ_LN850107.1 Lanthipeptides: BN1701_RS34435_lanthipeptide
Lanthipeptides: BN1701_RS34435_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L M N T D D N C G S+C Q S A C S N S C
1
L M T N T D D N C G S T C Q S A C S N S S C
22
79.2%
NZ_CP012752.1:
Lanthipeptides: AOZ06_RS53490_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L M N T D D N C G+S C Q S A C S N S C
2
L M R N T D D N C G T S C Q S A C S N S T C
23
78.3%
NZ_SLWS01000019.1 and 1 other:
NZ_SLWS01000019.1 Lanthipeptides: EV192_RS50115_lanthipeptide
Lanthipeptides: EV192_RS50115_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L M N T D D N C G +C Q S A C S N S C
1
L M R N T D D N C G Q T C Q S A C S N S T C
22
73.9%
NZ_JAMTCR010000003.1 and 1 other:
NZ_JAMTCR010000003.1 Lanthipeptides: LV79_RS15365_lanthipeptide
Lanthipeptides: LV79_RS15365_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L M +T D D N C G++C Q S A C S N S C
1
L M R S T D D N C G A T C Q S A C S N S T C
22
64.0%
NZ_FOLM01000004.1 and 1 other:
NZ_FOLM01000004.1 Lanthipeptides: BM242_RS10130_lanthipeptide
Lanthipeptides: BM242_RS10130_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L+ +T D D N C S+C Q S A C S N S C
1
L L N D T D D N C T S T C Q S A C S N S T C
22
62.5%
NZ_CP045031.1 and 2 others:
NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide NZ_JAGPXX010000003.1 Lanthipeptides: KBZ10_RS05935_lanthipeptide
Lanthipeptides: F9V55_RS07565_lanthipeptide
2
M G N T D D N C G S S C Q S A C S N S D C
22
+ +T D N C G S+C Q S A C S N S C
1
L N D T S D N C G S T C Q S A C S N S T C
21
62.5%
NZ_LJFZ01000009.1 and 2 others:
NZ_LJFZ01000009.1 Lanthipeptides: UK94_RS32440_lanthipeptide NZ_LJFZ01000009.1 Lanthipeptides: UK94_RS32440_lanthipeptide
Lanthipeptides: UK94_RS32440_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S D C
22
L+ +T D N C S+C Q S A C S N S C
1
L L N S T S D N C T S T C Q S A C S N S T C
22
60.9%
NZ_CP029042.1 and 2 others:
NZ_CP045178.1 Lanthipeptides: GBW32_RS14380_lanthipeptide NZ_JAHLXF010000013.1 Lanthipeptides: KQY13_RS21225_lanthipeptide
Lanthipeptides: DDE74_RS17120_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S
20
L M +T D N C G S S C S A C+ S
3
L M C S T G D N C G S S C P S A C T T S
22
60.9%
NZ_KQ257877.1 and 1 other:
NZ_KQ257877.1 Lanthipeptides: IQ64_RS44800_lanthipeptide
Lanthipeptides: IQ64_RS44800_lanthipeptide
2
M G N T D D N C G S S C Q S A C S N S D C E
23
+ +T D C G +C Q S A C S N S C E
1
L N D T G D G C G Q T C Q S A C S N S T C E
22
60.9%
NZ_ML123117.1:
Lanthipeptides: EES46_RS09865_lanthipeptide
1
L M G N T D D N C G S S C Q S A C S N S
20
L M T D N C G S S C S A C+ S
3
L M C G T G D N C G S S C P S A C T T S
22

#### MIBiG 4.0 matches for CLV68_RS29670

7.8%
BGC0002120.3 (NQE92413.1):
Lanthipeptide: nocathioamide A
6
D D N C G S S C Q S A C
17
D D A C
29
D D E S S R P A A P A C
40

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (4):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.55 out of 30.22
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.24 out of 27.04
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.14 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

CLV68_RS29670 - Class I
  Cleavage pHMM score: -2.60
  RODEO score: 21
  Monoisotopic mass: 2231.8 Da
  Molecular weight: 2233.3 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2251.3 Da N = 1
    2269.3 Da N = 2
CLV68_RS29670 - Class I
  Cleavage pHMM score: -2.60
  RODEO score: 21
  Monoisotopic mass: 2231.8 Da
  Molecular weight: 2233.3 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2251.3 Da N = 1
    2269.3 Da N = 2

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (252144...270086)
CLV68_RS29675
  RRE type: Lanthipeptide_LanB_RRE
  Location: 161 - 246
  Score: 58.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_RCDD01000009.1 - Region 1 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,156 - 96,007 nt. (total: 91,852 nt) Show pHMM detection rules used
Region on contig edge.
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase
CLV68_RS30975: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

CLV68_RS30985: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

CLV68_RS30995: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

CLV68_RS31010: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

CLV68_RS31015: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

CLV68_RS31135: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

CLV68_RS31150: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CLV68_RS31215: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Transferases: acyltransferase
CLV68_RS31190: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Lyases: lyase
CLV68_RS31000: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Isomerases: isomerase
CLV68_RS31100: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
CLV68_RS31105: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS31110: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS31115: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS31120: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

CLV68_RS31125: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport
CLV68_RS30895: 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 | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  | 0.82 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  |  | 0.82 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.82 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.80 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  | 0.78 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  | 0.77 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  |  | 0.77 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.71 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.70 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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: 20.07 out of 23.43
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.36 out of 25.31
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.13 out of 36.53
Confidence: medium
Additional weak hits (11):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.06 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.55 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.35 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.39 out of 20.97
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.12 out of 36.53
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 32.93
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.85 out of 27.18
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.20 out of 29.65
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.91 out of 32.93
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.38 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 1, location 4155 - 96007:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser) + (D-Asn) + (D-Thr - Orn - X - D-Fo-OH-Orn) + (Orn)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
CLV68_RS31105: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (544..913): Ser
nrpys: Ser

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDLSFDLSVFDANCLLGGDVALGGTTETAIHSTV
  Nearest Stachelhaus code(s):
    Ser DLFNLGLIHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

CLV68_RS31110: X
AMP-binding (34..433): X
nrpys: Sal

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    NASLFPLACPGGALQVGGAQQVFGMAEGLLNYTR
  Nearest Stachelhaus code(s):
    Sal PLPAQGVLNK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

CLV68_RS31115: Asn
Search NORINE for peptide: strict or relaxed
AMP-binding (477..864): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWSSFDFTVTPGKIVIAGEINEYGPTETTVGCLL
  Nearest Stachelhaus code(s):
    Asn DFTKVGEVGK (62% 8Å match)
  Stachelhaus code match:
    90% (moderate)

CLV68_RS31120: Thr - Orn - X - Fo-OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (445..822): Thr
nrpys: Thr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAAHFDFSVWEGNQIFGGEVNMYGITETTVHVTF
  Nearest Stachelhaus code(s):
    Thr DFWNIGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1906..2289): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAHLFDGSVDPWDAATGAELNLYGPTECTVDALW
  Nearest Stachelhaus code(s):
    Orn DGEDAGLVDK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2927..3307): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSHVFDAAVDPWDAATGAEVNFYGPTEATVDASW
  Nearest Stachelhaus code(s):
    Lys DADDGGFVDK (59% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3948..4340): Fo-OH-Orn
nrpys: Fo-OH-Orn

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

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

CLV68_RS31125: Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (433..797): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAHLFDGSVDPWDAATGAELNLYGPTECTVDATW
  Nearest Stachelhaus code(s):
    Orn DGEDAGLVDK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
CatR | H2O2-responsive repressor
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_RCDD01000009.1 - Region 2 - NRPS-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: 97,059 - 188,667 nt. (total: 91,609 nt) Show pHMM detection rules used
Region on contig edge.
T2PKS: (t2ks and t2clf)
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 oxidoreductase oxygenase
CLV68_RS31275: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CLV68_RS31380: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CLV68_RS31390: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CLV68_RS31395: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CLV68_RS31410: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

CLV68_RS31425: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

CLV68_RS31445: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

CLV68_RS31460: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Transferases: aminotransferase glycosyltransferase methyltransferase
CLV68_RS31345: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CLV68_RS31405: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

CLV68_RS31450: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

CLV68_RS31455: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: deacetylase hydrolase protease
CLV68_RS31240: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

CLV68_RS31290: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

CLV68_RS31330: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

CLV68_RS31480: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

CLV68_RS31540: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: cyclase dehydratase
CLV68_RS31360: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

CLV68_RS31385: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

CLV68_RS31470: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: isomerase
CLV68_RS31545: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
CLV68_RS31365: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

CLV68_RS31370: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

CLV68_RS31580: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease
CLV68_RS31245: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | T2PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000231.5 |  |  | 0.59 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  |  | 0.48 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  |  | 0.33 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001366.5 |  |  | 0.33 | PKS | BE-24566B, zunyimycin A | Streptomyces sp. FJS31-2
BGC0002047.2 |  |  | 0.31 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000236.5 |  |  | 0.30 | PKS | kinamycin | Streptomyces murayamaensis
BGC0001940.3 |  |  | 0.30 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0000275.4 |  |  | 0.29 | PKS | tetracenomycin C | Streptomyces glaucescens
BGC0002477.3 |  |  | 0.28 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0002012.4 |  |  | 0.28 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.84 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.77 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002276.2 |  | 0.75 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001723.5 |  | 0.66 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002047.2 |  | 0.65 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0001895.4 |  | 0.61 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0000272.3 |  | 0.60 | PKS | spore pigment | Streptomyces collinus
BGC0002672.2 |  | 0.59 | PKS | saccharothrixin D, saccharothrixin E, saccharothrixin F, saccharothrixin G, saccharothrixin H, saccharothrixin I, saccharothrixin J, saccharothrixin K, saccharothrixin L, saccharothrixin M | Saccharothrix sp.
BGC0000235.5 |  | 0.59 | PKS | kiamycin | Streptomyces sp. W007
BGC0001513.3 |  | 0.58 | PKS | anthrabenzoxocinone | Actinobacteria 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.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.31 out of 18.57
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 24.75 out of 29.65
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.94 out of 27.04
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 25.31
Confidence: medium
Additional weak hits (18):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.89 out of 39.62
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.58 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.50 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.72 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.60 out of 36.54
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.42 out of 29.65
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.29 out of 26.85
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.35 out of 25.88
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.78 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.49 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: 20.42 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.93 out of 35.63
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.77 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.96 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Type II PKS
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 97058 - 188667:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 164348 - 188667:
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).
CLV68_RS31580: X
AMP-binding (44..481): 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:
    LEIA---SVKN-SLVGGGDA----------WASC
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Cluster section:
  97058 to 169559
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:
  8|9 (Score: 694.3; E-value: 1e-211)
Product class(es):
  angucycline
Product molecular weight(s):
  acetyl-CoA_8: 609 Da
  acetyl-CoA_9: 651 Da

CLV68_RS31250
  OXY (Score: 48.7; E-value: 1.4e-15)
CLV68_RS31275
  KR (Score: 79.4; E-value: 8e-25)
CLV68_RS31360
  CYC C4-C17/C2-C19 (Score: 192.5; E-value: 1.6e-59)
CLV68_RS31365
  KS (Score: 789.6; E-value: 1.4e-240)
CLV68_RS31370
  CLF 8|9 (Score: 694.3; E-value: 1e-211)
CLV68_RS31375
  ACP (Score: 138.9; E-value: 9.8e-44)
CLV68_RS31380
  KR C9 (Score: 480.4; E-value: 2.9e-147)
CLV68_RS31385
  CYC C7-C12 (Score: 475.9; E-value: 9.9e-146)
CLV68_RS31390
  OXY (Score: 579.5; E-value: 1.3e-176)
CLV68_RS31395
  OXY (Score: 571.5; E-value: 3.5e-174)
CLV68_RS31405
  GT (Score: 402.3; E-value: 6.5e-123)
CLV68_RS31445
  OXY (Score: 496.8; E-value: 1.5e-151)
CLV68_RS31450
  MET (Score: 265.8; E-value: 1.2e-81)
CLV68_RS31455
  MET (Score: 264.5; E-value: 3e-81)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CatR | H2O2-responsive repressor
DasR | N-acetylglucosamine dependent repressor
LexA variant 1 | Repressor of DNA damage response
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_RCDD01000010.1 - Region 1 - 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: 55,248 - 96,294 nt. (total: 41,047 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
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
CLV68_RS31975: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

CLV68_RS32000: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

Transferases: methyltransferase
CLV68_RS31930: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: glucosidase
CLV68_RS31850: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Ligases: synthase
CLV68_RS31925: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001077.4 |  | 0.58 | 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
BGC0002362.3 |  | 0.50 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0000902.4 |  | 0.50 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0002285.2 |  | 0.48 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000285.5 |  | 0.47 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001336.5 |  | 0.42 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000665.5 |  | 0.41 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002482.2 |  | 0.40 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0001605.3 |  | 0.40 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000678.5 |  | 0.40 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001077.4 |  | 0.58 | 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
BGC0002362.3 |  | 0.50 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0000902.4 |  | 0.50 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0002285.2 |  | 0.48 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0000285.5 |  | 0.47 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001336.5 |  | 0.42 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0000665.5 |  | 0.41 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002482.2 |  | 0.40 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0001605.3 |  | 0.40 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000678.5 |  | 0.40 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

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: 24.38 out of 30.11
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.70 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.74 out of 27.04
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.98 out of 24.78
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.01 out of 27.04
Confidence: medium
Additional weak hits (17):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.75 out of 26.12
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.73 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.80 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.80 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.81 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.32 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.06 out of 26.85
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.75 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.58 out of 28.14
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.08 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.02 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.65 out of 32.74
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.96 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.22 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.69 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_RCDD01000011.1 - Region 1 - NAPAA
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 93,171 - 127,301 nt. (total: 34,131 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
CLV68_RS32725: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CLV68_RS32730: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CLV68_RS32770: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

CLV68_RS32775: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

CLV68_RS32780: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
CLV68_RS32795: 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 | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002535.2 |  | 0.62 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000357.5 |  | 0.60 | 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
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002535.2 |  | 0.62 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000357.5 |  | 0.60 | 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
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001249.5 |  | 0.60 | NRPS | dimethylcoprogen | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.74 out of 29.72
Confidence: medium
Additional weak hits (18):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.19 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.61 out of 30.97
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.77 out of 23.43
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.34 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.62 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.95 out of 30.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.75 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.27 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.93 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.32 out of 29.38
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.22 out of 31.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.90 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.80 out of 24.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.94 out of 29.25
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.97 out of 39.62
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.28 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 1, location 93170 - 127301:
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).
CLV68_RS32790: X
AMP-binding (37..428): 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:
    FVAMFDFSVEEVCCLVSGELNVYGPTEATVTATW
  Nearest Stachelhaus code(s):
    Ile or Val DFLCLGVVIK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

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