Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
2.1
2.2
2.3
2.4
3.1
3.2
3.3
3.4
4.1
4.2
4.3
5.1
5.2
5.3
6.1
8.1
9.1
10.1
10.2

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

NZ_BNBR01000001.1 (Streptomyces griseosporeus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | NRPS | 284,342 | 331,691 | Low | clipibicyclene/azabicyclene B/azabicyclene C/azabicyclene D | NRPS:Type I+PKS
Region 1.2 | lassopeptide,terpene-precursor | 373,473 | 411,974 | High | lagmysin | ribosomal:RiPP
Region 1.3 | lanthipeptide-class-iii,RiPP-like | 633,758 | 658,652 | High | informatipeptin | ribosomal:RiPP:Lanthipeptide
Region 1.4 | terpene | 1,146,375 | 1,173,128 | High | hopene | terpene
Region 1.5 | other | 1,482,026 | 1,523,399 |  |
Region 1.6 | RiPP-like | 1,526,577 | 1,538,505 |  |
Region 1.7 | NI-siderophore,T1PKS | 1,540,548 | 1,590,062 |  |
Region 1.8 | terpene,butyrolactone | 1,739,774 | 1,761,933 | High | γ-butyrolactone | other:other
Region 1.9 | RiPP-like | 1,776,881 | 1,788,224 |  |
Region 1.10 | NI-siderophore | 2,018,079 | 2,047,926 | Low | kinamycin | PKS

NZ_BNBR01000002.1 (Streptomyces griseosporeus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | T3PKS,T1PKS,NRPS | 26,576 | 101,386 | High | antimycin A1B | NRPS:Type I+PKS
Region 2.2 | blactam | 107,818 | 129,647 |  |
Region 2.3 | terpene-precursor,melanin | 567,317 | 596,493 | Medium | melanin | other:other
Region 2.4 | terpene | 660,881 | 686,452 | Medium | carotenoid | terpene

NZ_BNBR01000003.1 (Streptomyces griseosporeus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | triceptide | 487,278 | 508,656 |  |
Region 3.2 | terpene-precursor | 513,645 | 534,706 |  |
Region 3.3 | terpene | 543,776 | 564,834 | High | albaflavenone | terpene
Region 3.4 | NRPS | 727,090 | 812,053 | High | sarpeptin A/sarpeptin B | NRPS:Type I

NZ_BNBR01000004.1 (Streptomyces griseosporeus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | NI-siderophore | 218,242 | 248,014 | High | desferrioxamin B/desferrioxamine E | other:other
Region 4.2 | melanin,T1PKS,butyrolactone,RiPP-like | 328,298 | 386,090 | Low | 4-hexadecanoyl-3-hydroxy-2-(hydroxymethyl)-2H-furan-5-one | PKS
Region 4.3 | T2PKS,butyrolactone | 821,139 | 888,469 | High | hatomarubigin A/hatomarubigin B/hatomarubigin C/hatomarubigin D | PKS

NZ_BNBR01000005.1 (Streptomyces griseosporeus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | PKS-like,butyrolactone | 238,170 | 279,207 |  |
Region 5.2 | T2PKS | 380,974 | 453,489 | High | spore pigment | PKS
Region 5.3 | arylpolyene | 497,898 | 539,058 |  |

NZ_BNBR01000006.1 (Streptomyces griseosporeus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 6.1 | furan | 447,053 | 468,120 |  |

NZ_BNBR01000008.1 (Streptomyces griseosporeus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 8.1 | azole-containing-RiPP | 182,597 | 221,958 | High | nosiheptide | ribosomal:RiPP:Thiopeptide

NZ_BNBR01000009.1 (Streptomyces griseosporeus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 9.1 | ectoine | 84,679 | 95,083 | High | ectoine | other:other

NZ_BNBR01000010.1 (Streptomyces griseosporeus)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 10.1 | indole | 1 | 15,843 | Low | Azodyrecin A/Azodyrecin B/Azodyrecin C | other:other
Region 10.2 | hydrogen-cyanide | 57,458 | 70,394 | Low | aborycin | ribosomal:RiPP

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | NRPS | 284,342 | 331,691 | Low | clipibicyclene/azabicyclene B/azabicyclene C/azabicyclene D | NRPS:Type I+PKS
Region 1.2 | lassopeptide,terpene-precursor | 373,473 | 411,974 | High | lagmysin | ribosomal:RiPP
Region 1.3 | lanthipeptide-class-iii,RiPP-like | 633,758 | 658,652 | High | informatipeptin | ribosomal:RiPP:Lanthipeptide
Region 1.4 | terpene | 1,146,375 | 1,173,128 | High | hopene | terpene
Region 1.5 | other | 1,482,026 | 1,523,399 |  |
Region 1.6 | RiPP-like | 1,526,577 | 1,538,505 |  |
Region 1.7 | NI-siderophore,T1PKS | 1,540,548 | 1,590,062 |  |
Region 1.8 | terpene,butyrolactone | 1,739,774 | 1,761,933 | High | γ-butyrolactone | other:other
Region 1.9 | RiPP-like | 1,776,881 | 1,788,224 |  |
Region 1.10 | NI-siderophore | 2,018,079 | 2,047,926 | Low | kinamycin | PKS
Region 2.1 | T3PKS,T1PKS,NRPS | 26,576 | 101,386 | High | antimycin A1B | NRPS:Type I+PKS
Region 2.2 | blactam | 107,818 | 129,647 |  |
Region 2.3 | terpene-precursor,melanin | 567,317 | 596,493 | Medium | melanin | other:other
Region 2.4 | terpene | 660,881 | 686,452 | Medium | carotenoid | terpene
Region 3.1 | triceptide | 487,278 | 508,656 |  |
Region 3.2 | terpene-precursor | 513,645 | 534,706 |  |
Region 3.3 | terpene | 543,776 | 564,834 | High | albaflavenone | terpene
Region 3.4 | NRPS | 727,090 | 812,053 | High | sarpeptin A/sarpeptin B | NRPS:Type I
Region 4.1 | NI-siderophore | 218,242 | 248,014 | High | desferrioxamin B/desferrioxamine E | other:other
Region 4.2 | melanin,T1PKS,butyrolactone,RiPP-like | 328,298 | 386,090 | Low | 4-hexadecanoyl-3-hydroxy-2-(hydroxymethyl)-2H-furan-5-one | PKS
Region 4.3 | T2PKS,butyrolactone | 821,139 | 888,469 | High | hatomarubigin A/hatomarubigin B/hatomarubigin C/hatomarubigin D | PKS
Region 5.1 | PKS-like,butyrolactone | 238,170 | 279,207 |  |
Region 5.2 | T2PKS | 380,974 | 453,489 | High | spore pigment | PKS
Region 5.3 | arylpolyene | 497,898 | 539,058 |  |
Region 6.1 | furan | 447,053 | 468,120 |  |
Region 8.1 | azole-containing-RiPP | 182,597 | 221,958 | High | nosiheptide | ribosomal:RiPP:Thiopeptide
Region 9.1 | ectoine | 84,679 | 95,083 | High | ectoine | other:other
Region 10.1 | indole | 1 | 15,843 | Low | Azodyrecin A/Azodyrecin B/Azodyrecin C | other:other
Region 10.2 | hydrogen-cyanide | 57,458 | 70,394 | Low | aborycin | ribosomal:RiPP

No secondary metabolite regions were found in these records:
  NZ_BNBR01000007.1 (Streptomyces griseosporeus)
  NZ_BNBR01000011.1 (Streptomyces griseosporeus)
  NZ_BNBR01000012.1 (Streptomyces griseosporeus)
  NZ_BNBR01000013.1 (Streptomyces griseosporeus)

Compact view
NZ_BNBR01000001.1 - Region 1 - 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: 284,342 - 331,691 nt. (total: 47,350 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
IE308_RS01215: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS01235: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

IE308_RS01280: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS01285: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS01310: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IE308_RS01320: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: acetyltransferase methyltransferase
IE308_RS01190: methyltransferase

smcogs
  SMCOG1089: methyltransferase

IE308_RS01270: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: amidase hydrolase
IE308_RS01245: amidase

smcogs
  SMCOG1105: amidase

IE308_RS01325: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase
IE308_RS01290: 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
--- | --- | --- | --- | --- | ---
BGC0001873.3 |  | 0.71 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001873.3 |  | 0.71 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.64 | 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: 18.39 out of 19.26
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.38 out of 27.04
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
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.80 out of 27.04
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (9):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.96 out of 31.73
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.41 out of 27.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.21 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.20 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.72 out of 20.97
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.51 out of 24.78
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.84 out of 32.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.81 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 284341 - 331691:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - Pro)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
IE308_RS01290: Ser - Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (485..902): 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:
    RWMTFDVSVWEWHFFSSGEVNLYGPTEATVDVSC
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1561..1964): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQSFDVHLQEAFLISAGEENQYGPTETHIVTGF
  Nearest Stachelhaus code(s):
    Pro DVQFIAQVVK (76% 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
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
DasR | N-acetylglucosamine dependent repressor

NZ_BNBR01000001.1 - Region 2 - lassopeptide,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: 373,473 - 411,974 nt. (total: 38,502 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)
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
Lasso peptides
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
IE308_RS01750: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase methyltransferase
IE308_RS01665: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

IE308_RS01830: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
IE308_RS01705: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: synthetase
IE308_RS01785: 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 | lassopeptide | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001645.3 |  |  | 0.42 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0002276.2 |  |  | 0.39 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001551.4 |  |  | 0.32 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001493.5 |  |  | 0.29 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0002289.2 |  |  | 0.27 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii
BGC0001548.4 |  |  | 0.27 | ribosomal | citrulassin A | Streptomyces albulus
BGC0002053.3 |  |  | 0.26 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001506.5 |  |  | 0.26 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0001539.4 |  |  | 0.26 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002074.2 |  |  | 0.26 | ribosomal | huascopeptin | Streptomyces huasconensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001645.3 |  | 0.74 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001551.4 |  | 0.65 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001493.5 |  | 0.63 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0002289.2 |  | 0.60 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii
BGC0001548.4 |  | 0.60 | ribosomal | citrulassin A | Streptomyces albulus
BGC0002053.3 |  | 0.60 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001506.5 |  | 0.60 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146
BGC0001539.4 |  | 0.60 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002074.2 |  | 0.60 | ribosomal | huascopeptin | Streptomyces huasconensis
BGC0001781.4 |  | 0.59 | ribosomal | sphaericin | Planomonospora sphaerica

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
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:
IE308_RS01785: PT_FPPS_like
Domain 1 (48 - 347): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.07 out of 30.12
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 25.31
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.10 out of 23.79
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (9):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.44 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.25 out of 30.25
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: 17.18 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.74 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.71 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.28 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 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.03 out of 24.78
Confidence: weak
Lasso peptides
RREFinder
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (373472...396163)
IE308_RS01700
  RRE type: Stand_Alone_Lasso_RRE
  Location: 0 - 84
  Score: 79.8

Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator

NZ_BNBR01000001.1 - Region 3 - RiPP-like,lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 633,758 - 658,652 nt. (total: 24,895 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)
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
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: dehydratase
IE308_RS02850: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

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

Reference | lanthipeptide-class-iii | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000518.3 |  |  | 0.58 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000496.5 |  |  | 0.54 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  |  | 0.47 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  |  | 0.41 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  |  | 0.40 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000553.3 |  |  | 0.38 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002698.2 |  |  | 0.33 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000546.3 |  |  | 0.28 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0001210.5 |  |  | 0.26 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000518.3 |  | 0.72 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000496.5 |  | 0.68 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.61 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000553.3 |  | 0.59 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000563.4 |  | 0.52 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0002698.2 |  | 0.52 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0002700.2 |  | 0.52 | ribosomal | bacinapeptin | Bacillus nakamurai

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

No significant matches found.

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

#### Lanthipeptide(s) for IE308_RS02890

IE308_RS02895
Leader:
MALLDLQTMESDEHTGGGGAS
Core:
T V S L L S C I S A A S V L L C L
Core with dehydrations:
Dhb V Dha L L Dha Cys I Dha A A Dha V L L Cys L

#### antiSMASH-DB 4.0 matches for IE308_RS02895

100.0%
NZ_AUKV01000001.1 and 33 others:
NZ_BMSE01000001.1 Lanthipeptides: IE153_RS00140_lanthipeptide NZ_BMTM01000009.1 Lanthipeptides: IE213_RS27820_lanthipeptide NZ_BMUK01000002.1 Lanthipeptides: IE276_RS03565_lanthipeptide NZ_BMUO01000001.1 Lanthipeptides: IE232_RS00145_lanthipeptide NZ_BMWC01000009.1 Lanthipeptides: IE255_RS28335_lanthipeptide NZ_BNBR01000001.1 Lanthipeptides: IE308_RS02895_lanthipeptide NZ_CP015098.1 Lanthipeptides: A4E84_RS37870_lanthipeptide NZ_CP023694.1 Lanthipeptides: CP976_RS39235_lanthipeptide NZ_CP026121.1 Lanthipeptides: C1703_RS37710_lanthipeptide NZ_CP029788.1 Lanthipeptides: DMT42_RS35020_lanthipeptide NZ_CP041604.2 Lanthipeptides: FNV64_RS48055_lanthipeptide NZ_CP041610.2 Lanthipeptides: FNV62_RS46395_lanthipeptide NZ_CP041611.1 Lanthipeptides: FNV63_RS47280_lanthipeptide NZ_CP041613.2 Lanthipeptides: FNV68_RS48480_lanthipeptide NZ_CP041650.2 Lanthipeptides: FNV59_RS47040_lanthipeptide NZ_CP049780.1 Lanthipeptides: G7Z13_RS32285_lanthipeptide NZ_CP049838.1 Lanthipeptides: G9272_RS40085_lanthipeptide NZ_CP075896.1 Lanthipeptides: KJK29_RS01685_lanthipeptide NZ_CP094344.1 Lanthipeptides: MQE23_RS40865_lanthipeptide NZ_GG657757.1 Lanthipeptides: SSQG_RS35880_lanthipeptide NZ_JACHCX010000007.1 Lanthipeptides: HDC93_RS16065_lanthipeptide NZ_JACHGV010000013.1 Lanthipeptides: HNR57_RS32395_lanthipeptide NZ_JACHXE010000001.1 Lanthipeptides: FHS41_RS01865_lanthipeptide NZ_JAPJYN010000013.1 Lanthipeptides: OR263_RS25210_lanthipeptide NZ_KB911710.1 Lanthipeptides: H294_RS0120310_lanthipeptide NZ_KQ948484.1 Lanthipeptides: AQJ27_RS46770_lanthipeptide NZ_KQ948484.1 Lanthipeptides: AQJ27_RS46770_lanthipeptide NZ_KZ671983.1 Lanthipeptides: BV882_RS30460_lanthipeptide NZ_LIVZ01000003.1 Lanthipeptides: AMK31_RS09050_lanthipeptide NZ_LMEQ01000023.1 Lanthipeptides: ASD48_RS25330_lanthipeptide NZ_LMIZ01000012.1 Lanthipeptides: ASE41_RS11285_lanthipeptide NZ_LT963352.1 Lanthipeptides: SCNRRL3882_RS38195_lanthipeptide NZ_QFRX01000001.1 Lanthipeptides: DI272_RS05815_lanthipeptide
Lanthipeptides: H305_RS0100085_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T V S L L S C I S A A S V L L C L
1
T V S L L S C I S A A S V L L C L
17
94.1%
NC_003155.5 and 5 others:
NZ_BBYG01000010.1 Lanthipeptides: AOQ37_RS09965_lanthipeptide NZ_KB891997.1 Lanthipeptides: B079_RS0125330_lanthipeptide NZ_KB912966.1 Lanthipeptides: B065_RS0120870_lanthipeptide NZ_MLCE01000039.1 Lanthipeptides: BKI49_RS34310_lanthipeptide NZ_MQUS01000001.1 Lanthipeptides: AV521_RS02305_lanthipeptide
Lanthipeptides: SAVERM_RS38515_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T V S L L S C+S A A S V L L C L
1
T V S L L S C V S A A S V L L C L
17
94.1%
NZ_BMSO01000020.1:
Lanthipeptides: IE184_RS33055_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T V S L+S C I S A A S V L L C L
1
T V S L I S C I S A A S V L L C L
17
with 45 more sequence matches
Only the first 10 are displayed here.
94.1%
NZ_CP013743.1 and 1 other:
NZ_JAJSBI010000005.1 Lanthipeptides: LJ657_RS12685_lanthipeptide
Lanthipeptides: AS200_RS06110_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T S L L S C I S A A S V L L C L
1
T A S L L S C I S A A S V L L C L
17
88.9%
NZ_CP021978.1:
Lanthipeptides: CEB94_RS37585_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T+S L L S C I S A A S V L L C L
2
T L S L L S C I S A A S V L L C L
18
88.9%
NZ_KL585970.1:
Lanthipeptides: IH12_RS0128915_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T V S L L S C I S A A S V+L C L
2
T V S L L S C I S A A S V M L C L
18
88.2%
NZ_CM002285.1 and 2 others:
NZ_CP047020.1 Lanthipeptides: GQF42_RS39440_lanthipeptide NZ_VISR01000012.1 Lanthipeptides: FB157_RS21700_lanthipeptide
Lanthipeptides: M878_RS54195_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T V S L L S C+S A A S+L L C L
1
T V S L L S C V S A A S I L L C L
17
88.2%
NZ_CP011497.1 and 4 others:
NZ_CP017248.1 Lanthipeptides: BFF78_RS03720_lanthipeptide NZ_CP034687.1 Lanthipeptides: ELQ87_RS02805_lanthipeptide NZ_CP106795.1 Lanthipeptides: N8I86_RS33235_lanthipeptide NZ_LIWA01000002.1 Lanthipeptides: AMK32_RS11185_lanthipeptide
Lanthipeptides: ABB07_RS02975_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T S L L S C+S A A S V L L C L
1
T A S L L S C V S A A S V L L C L
17
88.2%
NZ_CP016279.1 and 1 other:
NZ_KQ948226.1 Lanthipeptides: AQI95_RS36775_lanthipeptide
Lanthipeptides: AVL59_RS17635_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T+S L L S C+S A A S V L L C L
1
T L S L L S C V S A A S V L L C L
17
88.2%
NZ_CP047019.1 and 1 other:
NZ_KQ257821.1 Lanthipeptides: IQ63_RS17200_lanthipeptide
Lanthipeptides: A7X85_RS06550_lanthipeptide
2
V S L L S C I S A A S V L L C L
17
+S L L S C I S A A S V L L C L
1
L S L L S C I S A A S V L L C L
16
83.3%
NZ_BMSI01000009.1:
Lanthipeptides: IE189_RS23215_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T V S L L S C+S A S V L L C L
2
T V S L L S C V S A T S V L L C L
18
83.3%
NZ_BMUM01000019.1 and 1 other:
NZ_JANFDE010000009.1 Lanthipeptides: FHS35_RS28665_lanthipeptide
Lanthipeptides: IE284_RS41515_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T+S L L S C I S A A S V L C L
2
T L S L L S C I S A A S V T L C L
18
83.3%
NZ_CP092051.1:
Lanthipeptides: MCU78_RS03785_lanthipeptide
1
T V S L L S C I S A A S V L L C L
17
T V S L L S C+S A A S V L+C L
2
T V S L L S C V S A A S V L V C L
18

#### MIBiG 4.0 matches for IE308_RS02895

45.5%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
2
V S L L S C-I S A A S V L L C
16
V S L L C S+ S V+L C
5
V S L L V C E Y S S L S V V L C
20

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (4):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.21 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.78 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 26.33
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 18.93 out of 27.04
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.

IE308_RS02895 - Class III
  Cleavage pHMM score: 27.40
  RODEO score: 0
  Monoisotopic mass: 1601.9 Da
  Molecular weight: 1603.0 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1621.0 Da N = 1
    1639.0 Da N = 2
    1657.0 Da N = 3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_BNBR01000001.1 - 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: 1,146,375 - 1,173,128 nt. (total: 26,754 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
IE308_RS05110: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

IE308_RS05145: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase
IE308_RS05075: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

IE308_RS05150: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Ligases: synthase synthetase
IE308_RS05080: 1-deoxy-D-xylulose-5-phosphate synthase

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

IE308_RS05105: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.82 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.52 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000645.3 |  | 0.50 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.50 | terpene | stellatic acid | Aspergillus stellatus
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.82 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000664.5 |  | 0.52 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000645.3 |  | 0.50 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.50 | terpene | stellatic acid | Aspergillus stellatus
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis

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

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

Genes with terpene domains:
IE308_RS05100: T2TS
Domain 1 (36 - 656): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

IE308_RS05105: PT_FPPS_like
Domain 1 (83 - 377): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

IE308_RS05115: PT_phytoene_like
Domain 1 (17 - 304): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

IE308_RS05120: PT_phytoene_like
Domain 1 (36 - 308): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.75 out of 23.43
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.79 out of 21.84
Confidence: medium
Additional weak hits (8):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.29 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.62 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.27 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 30.25
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.58 out of 23.43
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.87 out of 30.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.72 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
MexT | Global virulence regulator

NZ_BNBR01000001.1 - Region 5 - other
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,482,026 - 1,523,399 nt. (total: 41,374 nt) Show pHMM detection rules used
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_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
Hydrolases: deacetylase hydrolase
IE308_RS06595: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

IE308_RS06680: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

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

Reference | other | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002573.2 |  | 0.57 | other (other) | phosphoramidon | Streptomyces mozunensis
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001184.4 |  | 0.44 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0002698.2 |  | 0.40 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000521.3 |  | 0.39 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0001684.3 |  | 0.37 | other (other) | N-acyloxyacyl glutamine | Klebsiella variicola
BGC0000542.3 |  | 0.37 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.37 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000497.3 |  | 0.37 | ribosomal | BHT-Aα, BHT-Aβ | Streptococcus ratti
BGC0002144.3 |  | 0.36 | ribosomal | phazolicin | Rhizobium sp. Pop5

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002573.2 |  | 0.57 | other (other) | phosphoramidon | Streptomyces mozunensis
BGC0000888.5 |  | 0.45 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001184.4 |  | 0.44 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0002698.2 |  | 0.40 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000521.3 |  | 0.39 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0001684.3 |  | 0.37 | other (other) | N-acyloxyacyl glutamine | Klebsiella variicola
BGC0000542.3 |  | 0.37 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000541.5 |  | 0.37 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0000497.3 |  | 0.37 | ribosomal | BHT-Aα, BHT-Aβ | Streptococcus ratti
BGC0002144.3 |  | 0.36 | ribosomal | phazolicin | Rhizobium sp. Pop5

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
Additional weak hits (18):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.23 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.75 out of 23.43
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.63 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.21 out of 20.01
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.14 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.17 out of 31.73
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.51 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.29 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.45 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.16 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.65 out of 23.43
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.15 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.66 out of 33.14
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.31 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_BNBR01000001.1 - Region 6 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,526,577 - 1,538,505 nt. (total: 11,929 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
IE308_RS06735: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

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
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001485.4 |  | 0.52 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000844.5 |  | 0.49 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002103.2 |  | 0.45 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0001224.5 |  | 0.44 | other (other) | reductasporine | uncultured bacterium
BGC0002346.3 |  | 0.42 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000503.5 |  | 0.41 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000528.5 |  | 0.41 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001374.5 |  | 0.40 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0000468.5 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001485.4 |  | 0.52 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000844.5 |  | 0.49 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002103.2 |  | 0.45 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0001224.5 |  | 0.44 | other (other) | reductasporine | uncultured bacterium
BGC0002346.3 |  | 0.42 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000503.5 |  | 0.41 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000528.5 |  | 0.41 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001374.5 |  | 0.40 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0000468.5 |  | 0.40 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
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: 18.54 out of 30.25
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_BNBR01000001.1 - Region 7 - NI-siderophore,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: 1,540,548 - 1,590,062 nt. (total: 49,515 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC
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: dehydrogenase
IE308_RS06815: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS06985: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: PPTase aminotransferase
IE308_RS06890: aminotransferase

smcogs
  SMCOG1019: aminotransferase

IE308_RS06895: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Isomerases: mutase
IE308_RS06910: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: synthase
IE308_RS06900: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: transport
IE308_RS06905: 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 | NI-siderophore | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.65 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  | 0.65 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002191.2 |  |  | 0.58 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  |  | 0.57 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  |  | 0.55 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001164.3 |  |  | 0.53 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.53 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002276.2 |  |  | 0.50 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001268.4 |  |  | 0.49 | NRPS, PKS | fusarin C | Fusarium fujikuroi

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.66 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002276.2 |  | 0.59 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001268.4 |  | 0.58 | NRPS, PKS | fusarin C | Fusarium fujikuroi

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.47 out of 20.97
Confidence: medium
Additional weak hits (14):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.17 out of 26.12
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: 17.55 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.84 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.96 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.52 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.13 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.94 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.55 out of 30.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.31 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.62 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
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.33 out of 20.01
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
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).
IE308_RS06900: mal
PKS_AT (577..857): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 66.7%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 84.8
  Methylmalonyl-CoA: 51.2
  Methoxymalonyl-CoA: 46.3
  Propionyl-CoA: 39.7
  inactive: 34.5
  Ethylmalonyl-CoA: 25.6
  Isobutyryl-CoA: 18.1
  2-Methylbutyryl-CoA: 11.9
  Benzoyl-CoA: 9.5
  Acetyl-CoA: 5.4
  3-Methylbutyryl-CoA: 5.4
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  fatty_acid: -1.5

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
VqsM | Regulator of quorum-sensing signalling systems

NZ_BNBR01000001.1 - Region 8 - butyrolactone,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,739,774 - 1,761,933 nt. (total: 22,160 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)
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
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
IE308_RS07715: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: glucanase peptidase protease
IE308_RS07670: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

IE308_RS07680: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

IE308_RS07740: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Lyases: cyclase
IE308_RS07710: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000850.5 |  |  | 1.17 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000849.4 |  |  | 1.01 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  |  | 0.98 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001181.4 |  |  | 0.63 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001201.3 |  |  | 0.43 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002127.3 |  |  | 0.33 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002578.2 |  |  | 0.33 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000844.5 |  |  | 0.30 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002031.3 |  |  | 0.28 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000595.3 |  |  | 0.25 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.85 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.83 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000849.4 |  | 0.79 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001201.3 |  | 0.57 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0002578.2 |  | 0.48 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002031.3 |  | 0.46 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000844.5 |  | 0.45 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001223.5 |  | 0.43 | other (other) | hydroxysporine | uncultured bacterium

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene |  | germacradienol | C15 | C1-C10 | OH
sesquiterpene |  | geosmin | C12 | C1-C10 | OH

Genes with terpene domains:
IE308_RS07710: T1TS + T1TS
Domain 1 (2 - 325): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (326 - 694): 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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.45 out of 20.97
Confidence: medium
Additional weak hits (4):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.47 out of 26.06
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.70 out of 27.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.19 out of 20.97
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.12 out of 27.04
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
--- | ---
CcpA | Catabolite control protein A

NZ_BNBR01000001.1 - Region 9 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,776,881 - 1,788,224 nt. (total: 11,344 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: deacetylase
IE308_RS07840: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000351.5 |  | 0.32 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155
BGC0001363.5 |  | 0.32 | NRPS, PKS | ralsolamycin | Ralstonia solanacearum GMI1000
BGC0000498.5 |  | 0.32 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0000561.5 |  | 0.32 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0002663.2 |  | 0.32 | ribosomal | amyloliquecidin GF610 | Bacillus amyloliquefaciens UMAF6639
BGC0000565.5 |  | 0.31 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000306.5 |  | 0.31 | NRPS | arylomycin | Streptomyces filamentosus NRRL 11379
BGC0002553.2 |  | 0.30 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0002387.2 |  | 0.30 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001426.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000351.5 |  | 0.32 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155
BGC0001363.5 |  | 0.32 | NRPS, PKS | ralsolamycin | Ralstonia solanacearum GMI1000
BGC0000498.5 |  | 0.32 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0000561.5 |  | 0.32 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0002663.2 |  | 0.32 | ribosomal | amyloliquecidin GF610 | Bacillus amyloliquefaciens UMAF6639
BGC0000565.5 |  | 0.31 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000306.5 |  | 0.31 | NRPS | arylomycin | Streptomyces filamentosus NRRL 11379
BGC0002553.2 |  | 0.30 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0002387.2 |  | 0.30 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001426.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (5):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.23 out of 29.38
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: 17.35 out of 24.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.35 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_BNBR01000001.1 - Region 10 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,018,079 - 2,047,926 nt. (total: 29,848 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
IE308_RS08720: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
IE308_RS08765: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
IE308_RS08715: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.53 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002692.2 |  | 0.51 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002633.2 |  | 0.50 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002683.2 |  | 0.49 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.48 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium kenyense
BGC0002470.2 |  | 0.47 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0000859.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium alcaliphilum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.53 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002692.2 |  | 0.51 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002633.2 |  | 0.50 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002683.2 |  | 0.49 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.48 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium kenyense
BGC0002470.2 |  | 0.47 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000856.3 |  | 0.47 | other (other) | ectoine | Methylophaga thalassica
BGC0000859.3 |  | 0.47 | other (other) | ectoine | Methylomicrobium alcaliphilum

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.62 out of 27.18
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 26.06 out of 27.18
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
Additional weak hits (9):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.12 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.25 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.42 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.71 out of 26.06
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.85 out of 26.12
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes

NZ_BNBR01000002.1 - Region 1 - NRPS,T1PKS,T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 26,576 - 101,386 nt. (total: 74,811 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
IE308_RS09355: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS09405: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

IE308_RS09485: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

IE308_RS37430: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

IE308_RS37435: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: PPTase aminotransferase methyltransferase
IE308_RS09290: isoprenylcysteine carboxyl methyltransferase

smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

IE308_RS09340: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

IE308_RS09395: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Hydrolases: phosphatase
IE308_RS09225: inositol monophosphatase

smcogs
  SMCOG1207: inositol monophosphatase

Ligases: ligase synthase
IE308_RS09275: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IE308_RS09280: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

IE308_RS09390: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IE308_RS09410: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IE308_RS09415: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IE308_RS09420: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: transport
IE308_RS09245: 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 | T3PKS | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001455.6 |  |  |  | 1.44 | NRPS, PKS | antimycin A1B | Streptomyces argillaceus
BGC0000958.5 |  |  |  | 1.31 | NRPS, PKS | antimycin | Streptomyces sp. S4
BGC0001216.5 |  |  |  | 1.22 | NRPS, PKS | splenocin C | Streptomyces sp. CNQ431
BGC0001276.3 |  |  |  | 0.85 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001918.3 |  |  |  | 0.84 | NRPS, PKS | JBIR-06 | Streptomyces sp.
BGC0001695.5 |  |  |  | 0.75 | NRPS | neoantimycin | Streptomyces conglobatus
BGC0000342.4 |  |  |  | 0.70 | NRPS | enniatin | Fusarium equiseti
BGC0002128.3 |  |  |  | 0.70 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001919.4 |  |  |  | 0.69 | NRPS, PKS | neoantimycin | Streptomyces orinoci
BGC0002135.2 |  |  |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001455.6 |  | 0.84 | NRPS, PKS | antimycin A1B | Streptomyces argillaceus
BGC0000958.5 |  | 0.82 | NRPS, PKS | antimycin | Streptomyces sp. S4
BGC0001216.5 |  | 0.79 | NRPS, PKS | splenocin C | Streptomyces sp. CNQ431
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000282.3 |  | 0.67 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.64 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.77 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.36 out of 20.97
Confidence: medium
Additional weak hits (20):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.75 out of 20.97
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.19 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.39 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.17 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.26 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.25 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.48 out of 30.25
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.63 out of 32.93
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.81 out of 21.84
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.68 out of 24.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.96 out of 26.85
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 23.89 out of 32.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.52 out of 26.12
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.60 out of 26.12
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.03 out of 32.93
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.20 out of 30.11
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12
Confidence: weak
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 26575 - 101386:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 48857 - 101386:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - fatty_acid) + (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).
IE308_RS09390: X
AMP-binding (7..402): X
nrpys: Ant

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    IGWCHGSMVVSTWLLYGAARQVYGMTEVGGFVTL
  Nearest Stachelhaus code(s):
    Ant GSVWLGVGFK (100% 8Å match)
    Pyv or Ant GSVWLGVGFK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

IE308_RS09410: mal
PKS_AT (562..845): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 100.0
  Methoxymalonyl-CoA: 58.3
  inactive: 48.5
  Methylmalonyl-CoA: 35.9
  Isobutyryl-CoA: 25.7
  Ethylmalonyl-CoA: 19.9
  Benzoyl-CoA: 10.9
  Propionyl-CoA: 10.6
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

IE308_RS09415: Thr - fatty_acid
Search NORINE for peptide: strict or relaxed
AMP-binding (461..874): 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:
    LATHFDFSVWEGSQVFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

CAL_domain (1703..2113): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 17.8
  AHBA: 3.3
  shikimic_acid: 0.0
  NH2: 0.0
  Acetyl-CoA: -3.1

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
CcpA | Catabolite control protein A
IolR | Regulator of the inositol catabolism

NZ_BNBR01000002.1 - Region 2 - blactam
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: 107,818 - 129,647 nt. (total: 21,830 nt) Show pHMM detection rules used
blactam: (BLS or CAS or tabtoxin)

#### 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
IE308_RS09570: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
IE308_RS09610: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: dehalogenase hydrolase
IE308_RS09615: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

IE308_RS09620: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

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 | blactam | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000846.5 |  | 0.50 | other (other) | tabtoxin | Pseudomonas syringae
BGC0000885.3 |  | 0.48 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0001374.5 |  | 0.42 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0002382.3 |  | 0.41 | ribosomal | grimoviridin | Grimontia marina
BGC0001880.3 |  | 0.41 | ribosomal | scytodecamide | Scytonema sp. UIC 10036
BGC0001151.5 |  | 0.41 | other (non-nrp beta-lactam) | valclavam, (-)-2-(2-hydroxyethyl)clavam | Streptomyces antibioticus
BGC0000938.5 |  | 0.40 | other (aminocoumarin) | fosfomycin | Streptomyces fradiae
BGC0001485.4 |  | 0.39 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000895.5 |  | 0.39 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0001545.3 |  | 0.38 | NRPS | chrysogine | Fusarium graminearum PH-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000846.5 |  | 0.50 | other (other) | tabtoxin | Pseudomonas syringae
BGC0000885.3 |  | 0.48 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0001374.5 |  | 0.42 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0002382.3 |  | 0.41 | ribosomal | grimoviridin | Grimontia marina
BGC0001880.3 |  | 0.41 | ribosomal | scytodecamide | Scytonema sp. UIC 10036
BGC0001151.5 |  | 0.41 | other (non-nrp beta-lactam) | valclavam, (-)-2-(2-hydroxyethyl)clavam | Streptomyces antibioticus
BGC0000938.5 |  | 0.40 | other (aminocoumarin) | fosfomycin | Streptomyces fradiae
BGC0001485.4 |  | 0.39 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0000895.5 |  | 0.39 | other (other) | citrulline | Lactobacillus plantarum subsp. plantarum
BGC0001545.3 |  | 0.38 | NRPS | chrysogine | Fusarium graminearum PH-1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (4):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.29 out of 28.14
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.94 out of 36.54
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.63 out of 27.18
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_BNBR01000002.1 - Region 3 - melanin,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: 567,317 - 596,493 nt. (total: 29,177 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)
melanin: melC

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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
IE308_RS11600: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS11630: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

IE308_RS11645: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: hydrolase
IE308_RS11595: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

IE308_RS11625: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: synthetase
IE308_RS11615: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000911.3 |  |  | 0.53 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  |  | 0.53 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000908.3 |  |  | 0.41 | other (other) | melanin | Streptomyces avermitilis
BGC0000909.3 |  |  | 0.30 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  |  | 0.28 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002276.2 |  |  | 0.20 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001895.4 |  |  | 0.16 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001
BGC0002397.2 |  |  | 0.15 | terpene | astallatene | Arabidopsis thaliana
BGC0000847.4 |  |  | 0.15 | other (non-nrp beta-lactam) | thienamycin | Streptomyces cattleya
BGC0000885.3 |  |  | 0.15 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000911.3 |  | 0.80 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.80 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000908.3 |  | 0.72 | other (other) | melanin | Streptomyces avermitilis
BGC0000909.3 |  | 0.64 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.61 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002397.2 |  | 0.52 | terpene | astallatene | Arabidopsis thaliana
BGC0002276.2 |  | 0.52 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000885.3 |  | 0.50 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0002400.2 |  | 0.49 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0001605.3 |  | 0.46 | terpene | gibberellin | Sinorhizobium fredii NGR234

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:
IE308_RS11615: PT_FPPS_like
Domain 1 (57 - 338): 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
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.76 out of 30.11
Confidence: medium
Additional weak hits (6):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.47 out of 23.43
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.24 out of 36.54
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.17 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.57 out of 29.65
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_BNBR01000002.1 - 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: 660,881 - 686,452 nt. (total: 25,572 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
IE308_RS11985: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS11990: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

IE308_RS12015: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

IE308_RS12035: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
IE308_RS12030: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Isomerases: mutase
IE308_RS12050: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase synthetase
IE308_RS11995: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IE308_RS12020: 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 |  | 0.81 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.75 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.75 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.73 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.73 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000648.3 |  | 0.53 | terpene | carotenoid | Myxococcus xanthus
BGC0002397.2 |  | 0.52 | terpene | astallatene | Arabidopsis thaliana
BGC0000646.5 |  | 0.51 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.50 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.81 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.75 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.75 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.73 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.73 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000648.3 |  | 0.53 | terpene | carotenoid | Myxococcus xanthus
BGC0002397.2 |  | 0.52 | terpene | astallatene | Arabidopsis thaliana
BGC0000646.5 |  | 0.51 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.50 | terpene | carotenoid | Enterobacteriaceae bacterium DC404

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
IE308_RS12010: PT_phytoene_like
Domain 1 (16 - 315): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

IE308_RS12020: PT_FPPS_like
Domain 1 (99 - 414): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

IE308_RS12025: Lycopene_cycl
Domain 1 (6 - 383): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (6):
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.02 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.08 out of 33.14
Confidence: weak
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 17.94 out of 23.05
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.01 out of 33.14
Confidence: weak
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 17.94 out of 23.05
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.53 out of 27.18
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_BNBR01000003.1 - Region 1 - triceptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 487,278 - 508,656 nt. (total: 21,379 nt) Show pHMM detection rules used
triceptide: ((cds(PF04055 and (TIGR04085 or SPASM)) and triceptide_precursor) or triceptide_rSAM)

#### Legend:

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

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

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

Reference | triceptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002316.2 |  | 0.39 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000515.4 |  | 0.33 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.32 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000556.5 |  | 0.32 | ribosomal | streptin | Streptococcus pyogenes
BGC0000536.3 |  | 0.31 | ribosomal | nisin Q | Lactococcus lactis
BGC0001789.3 |  | 0.31 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000535.4 |  | 0.31 | ribosomal | nisin A | Lactococcus lactis subsp. lactis
BGC0000559.4 |  | 0.31 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000537.3 |  | 0.31 | ribosomal | nisin U | Streptococcus uberis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002316.2 |  | 0.39 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000515.4 |  | 0.33 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000506.4 |  | 0.32 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000556.5 |  | 0.32 | ribosomal | streptin | Streptococcus pyogenes
BGC0000536.3 |  | 0.31 | ribosomal | nisin Q | Lactococcus lactis
BGC0001789.3 |  | 0.31 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000535.4 |  | 0.31 | ribosomal | nisin A | Lactococcus lactis subsp. lactis
BGC0000559.4 |  | 0.31 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000537.3 |  | 0.31 | ribosomal | nisin U | Streptococcus uberis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.88 out of 29.72
Confidence: medium
Additional weak hits (7):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.04 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.20 out of 30.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.43 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.42 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.80 out of 35.63
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 23.42 out of 32.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.21 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_BNBR01000003.1 - Region 2 - 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: 513,645 - 534,706 nt. (total: 21,062 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Ligases: synthetase
IE308_RS17080: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000948.5 |  | 0.45 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000678.5 |  | 0.41 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000677.5 |  | 0.38 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000665.5 |  | 0.36 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001928.2 |  | 0.36 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000948.5 |  | 0.45 | other (other) | α-galactosylceramide | Bacteroides fragilis NCTC 9343
BGC0000657.5 |  | 0.44 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000678.5 |  | 0.41 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000677.5 |  | 0.38 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000665.5 |  | 0.36 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0001928.2 |  | 0.36 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37

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:
IE308_RS17080: PT_FPPS_like
Domain 1 (65 - 351): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.99 out of 20.47
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (6):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.89 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.74 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.20 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_BNBR01000003.1 - Region 3 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 543,776 - 564,834 nt. (total: 21,059 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
IE308_RS17215: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Hydrolases: deformylase
IE308_RS17225: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Lyases: cyclase
IE308_RS17220: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000660.5 |  | 0.87 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.75 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.45 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001911.3 |  | 0.41 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002339.3 |  | 0.38 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0000650.3 |  | 0.37 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000678.5 |  | 0.36 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000660.5 |  | 0.87 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.75 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0002043.3 |  | 0.54 | ribosomal | cittilin A, cittilin B | Myxococcus xanthus DK 1622
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.45 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001911.3 |  | 0.41 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002339.3 |  | 0.38 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0000650.3 |  | 0.37 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000678.5 |  | 0.36 | 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:
No product predictions
Genes with terpene domains:
IE308_RS17220: T1TS
Domain 1 (4 - 330): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.29 out of 27.04
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 25.12 out of 27.18
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.63 out of 27.04
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.21 out of 27.18
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.38 out of 28.19
Confidence: medium
Additional weak hits (3):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.72 out of 29.38
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.46 out of 20.01
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
NrdR | Represses ribonucleotide reductase encoding genes
ZuR variant 1 | Zinc-responsive repressor

NZ_BNBR01000003.1 - Region 4 - 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: 727,090 - 812,053 nt. (total: 84,964 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
IE308_RS17965: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

IE308_RS17970: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

IE308_RS17995: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IE308_RS18000: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IE308_RS18035: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Hydrolases: esterase
IE308_RS18010: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: lyase
IE308_RS18135: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase
IE308_RS18005: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IE308_RS18050: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IE308_RS18055: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IE308_RS18060: 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
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.74 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001984.3 |  | 0.74 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001641.4 |  | 0.74 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001984.3 |  | 0.74 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
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.

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
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 25.83 out of 35.63
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 25.31
Confidence: medium
Additional weak hits (9):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.15 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.47 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.61 out of 29.38
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.04 out of 24.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.39 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.95 out of 24.78
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.21 out of 20.01
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.13 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 4, location 727089 - 812053:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - Asp - Tyr - Thr - D-Leu) + (Asp - Gly - Pro - Gly) + (Gly - Ala - NMe-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).
IE308_RS18005: NH2
CAL_domain (42..485): NH2
minowa: NH2

Prediction, score:
  NH2: 114.8
  fatty_acid: 33.1
  AHBA: 9.6
  shikimic_acid: -0.4
  Acetyl-CoA: -2.2

IE308_RS18050: Gly - Ala - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (477..852): 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:
    FGMTFDIAGLELQALVGGETNLYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1518..1918): Ala
nrpys: Ala

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

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

AMP-binding (2585..2988): 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:
    LAMTFDISNLETQALVGGETNVYGPTETTIWSTS
  Nearest Stachelhaus code(s):
    Gly DILQLGVIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

IE308_RS18055: Asp - Gly - Pro - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (472..851): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRASFDLTVTGTKGVLGGEINAYGPTEATVNCLE
  Nearest Stachelhaus code(s):
    Asp DLTKVGAVNK (100% 8Å match)
    Asp DLTKVGAVNK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1515..1906): 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:
    FAMTFDIAGLELQALVGGELNVYGPTETTVWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGVVWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2567..2966): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHTFDVSVQESYAVQAGEHNHYGPAETHVVTAW
  Nearest Stachelhaus code(s):
    Pro DVQYVAHVVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3634..4010): 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:
    FAMTFDIAGLELQALVGGETNLYGPTETTVWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLVWK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

IE308_RS18060: Gly - Asp - Tyr - Thr - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (476..860): 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:
    FAMTFDIAVLEQQALTGGETNMYGPTETTVWSMT
  Nearest Stachelhaus code(s):
    Gly DILQLGMVWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2165..2545): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRATFDLTVTCTKGVLGGEVNAYGPTEATVNVME
  Nearest Stachelhaus code(s):
    Asp DLTKVGAVNK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3724..4108): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDAYVSEVTLAVAGEVNAYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Tyr DASTAAAVCK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4774..5186): 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:
    LATHFDFSVWEGNQVFGGEVNMYGITETTVHVTH
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5859..6255): Leu
nrpys: Leu

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

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

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor
NrtR | NAD synthesis repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_BNBR01000004.1 - Region 1 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 218,242 - 248,014 nt. (total: 29,773 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
IE308_RS20100: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

IE308_RS20120: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IE308_RS20150: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: carboxylase methyltransferase transferase
IE308_RS20025: methyltransferase

smcogs
  SMCOG1089: methyltransferase

IE308_RS20130: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

IE308_RS20135: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Lyases: decarboxylase
IE308_RS20105: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: synthase
IE308_RS20125: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000940.5 |  | 0.85 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.84 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000941.3 |  | 0.83 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.82 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002690.2 |  | 0.63 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002464.3 |  | 0.61 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002620.2 |  | 0.60 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002284.3 |  | 0.58 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000940.5 |  | 0.85 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.84 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000941.3 |  | 0.83 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.82 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002690.2 |  | 0.63 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0002464.3 |  | 0.61 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002620.2 |  | 0.60 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0002284.3 |  | 0.58 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.26 out of 23.43
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.94 out of 36.53
Confidence: medium
Additional weak hits (14):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.87 out of 20.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.23 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.16 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.87 out of 27.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.66 out of 26.85
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.39 out of 20.97
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.24 out of 20.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.61 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.77 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.14 out of 27.04
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.99 out of 36.53
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.52 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
CRP | Cyclic AMP receptor protein
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_BNBR01000004.1 - Region 2 - RiPP-like,T1PKS,butyrolactone,melanin
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 328,298 - 386,090 nt. (total: 57,793 nt) Show pHMM detection rules used
melanin: melC
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
butyrolactone: AfsA
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
IE308_RS20575: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

IE308_RS20590: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IE308_RS20610: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

IE308_RS20630: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IE308_RS20635: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: PPTase
IE308_RS20665: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: dehalogenase esterase hydrolase phosphatase
IE308_RS20565: thioesterase

smcogs
  SMCOG1004: thioesterase

IE308_RS20595: HAD-superfamily hydrolase, subfamily IA, variant

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

IE308_RS20615: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

IE308_RS20685: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: ligase synthase
IE308_RS20570: 1-deoxy-D-xylulose-5-phosphate synthase

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

IE308_RS20625: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IE308_RS20645: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IE308_RS20650: 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 | melanin | T1PKS | butyrolactone | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000910.3 |  |  |  |  | 0.56 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  |  |  |  | 0.53 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  |  |  |  | 0.32 | other (other) | melanin | Streptomyces avermitilis
BGC0000889.5 |  |  |  |  | 0.32 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0000131.5 |  |  |  |  | 0.31 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0001160.5 |  |  |  |  | 0.31 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  |  | 0.31 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000227.5 |  |  |  |  | 0.31 | PKS | granaticin | Streptomyces violaceoruber
BGC0001276.3 |  |  |  |  | 0.30 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  |  |  | 0.30 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.82 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.80 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.67 | other (other) | melanin | Streptomyces avermitilis
BGC0002277.2 |  | 0.65 | NRPS | atromentin | Suillus grevillei
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum

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: 20.97 out of 23.79
Confidence: strong
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 25.49 out of 29.51
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.91 out of 23.79
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 25.31
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.60 out of 23.79
Confidence: medium
Additional weak hits (16):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.72 out of 26.12
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.76 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.85 out of 27.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.71 out of 25.88
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.60 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.88 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.58 out of 32.74
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.30 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.62 out of 24.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.66 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.49 out of 29.65
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.56 out of 28.14
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
RREFinder
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 328297 - 386090:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 338451 - 381505:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
IE308_RS20625: fatty_acid
CAL_domain (30..472): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 37.7
  AHBA: 18.5
  NH2: 18.0
  shikimic_acid: 13.9
  Acetyl-CoA: 0.4

IE308_RS20645: mal
PKS_AT (529..813): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 83.3%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 169.5
  inactive: 110.2
  Methylmalonyl-CoA: 64.4
  Methoxymalonyl-CoA: 63.6
  Propionyl-CoA: 37.8
  Ethylmalonyl-CoA: 29.6
  Isobutyryl-CoA: 22.2
  Acetyl-CoA: 21.0
  2-Methylbutyryl-CoA: 18.5
  CHC-CoA: 18.4
  Benzoyl-CoA: 10.9
  trans-1,2-CPDA: 9.9
  fatty_acid: 8.1
  3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

RiPP-like protocluster (373330...386090)
IE308_RS20730
  RRE type: Goadsporin_CD_RRE
  Location: 171 - 267
  Score: 59.0
  RRE type: NHLP_CD_RRE
  Location: 171 - 263
  Score: 43.8
  RRE type: Cyanobactin_D_RRE
  Location: 169 - 246
  Score: 33.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_BNBR01000004.1 - Region 3 - T2PKS,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: 821,139 - 888,469 nt. (total: 67,331 nt) Show pHMM detection rules used
Region on contig edge.
T2PKS: (t2ks and t2clf)
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
IE308_RS22840: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

IE308_RS22890: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS22905: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

IE308_RS22910: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

IE308_RS22915: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS22935: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

IE308_RS22940: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS22950: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS22960: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

IE308_RS22970: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

IE308_RS22980: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: PPTase carboxylase kinase methyltransferase transferase
IE308_RS22845: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

IE308_RS22865: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

IE308_RS22900: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

IE308_RS22925: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

IE308_RS23005: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

Lyases: cyclase dehydratase
IE308_RS22835: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

IE308_RS22870: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

IE308_RS22895: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Isomerases: mutase
IE308_RS22770: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: synthase
IE308_RS22875: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IE308_RS22880: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | T2PKS | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000848.5 |  |  | 0.95 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  |  | 0.75 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000234.5 |  |  | 0.71 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000850.5 |  |  | 0.63 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000231.5 |  |  | 0.59 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002000.4 |  |  | 0.34 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0002047.2 |  |  | 0.34 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000253.4 |  |  | 0.30 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002578.2 |  |  | 0.30 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002284.3 |  |  | 0.29 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.84 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.83 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000848.5 |  | 0.77 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.70 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.65 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002276.2 |  | 0.61 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002047.2 |  | 0.60 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0002000.4 |  | 0.58 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001513.3 |  | 0.57 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0001197.5 |  | 0.56 | PKS | frankiamicin | Frankia sp. EAN1pec

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.53 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.23 out of 23.79
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.90 out of 20.47
Confidence: medium
Additional weak hits (23):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.92 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.21 out of 26.06
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.48 out of 32.74
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.14 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.68 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.77 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.28 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.07 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.77 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.50 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.48 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.09 out of 31.73
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.00 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.51 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.48 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.12 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.77 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
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  821138 to 888469
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:
  8|9 (Score: 701.6; E-value: 5.9e-214)
Product class(es):
  angucycline
Product molecular weight(s):
  acetyl-CoA_8: 386 Da
  acetyl-CoA_9: 428 Da

IE308_RS22870
  CYC C4-C17/C2-C19 (Score: 198.3; E-value: 2.6e-61)
IE308_RS22875
  KS (Score: 784.3; E-value: 5.7e-239)
IE308_RS22880
  CLF 8|9 (Score: 701.6; E-value: 5.9e-214)
IE308_RS22885
  ACP (Score: 123.4; E-value: 6.5e-39)
IE308_RS22890
  KR C9 (Score: 489.3; E-value: 5.6e-150)
IE308_RS22895
  CYC C7-C12 (Score: 515.6; E-value: 8.1e-158)
IE308_RS22905
  OXY (Score: 574.0; E-value: 6.2e-175)
IE308_RS22910
  OXY (Score: 528.7; E-value: 3.4e-161)
IE308_RS22915
  KR (Score: 145.4; E-value: 5.7e-45)
IE308_RS22925
  MET C2O|C2N (Score: 295.7; E-value: 9.4e-91)
IE308_RS22940
  KR C15 (Score: 381.1; E-value: 5.2e-117)
IE308_RS22950
  KR (Score: 119.3; E-value: 5.1e-37)
IE308_RS22980
  DIMER (Score: 296.3; E-value: 5.2e-91)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_BNBR01000005.1 - Region 1 - PKS-like,butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 238,170 - 279,207 nt. (total: 41,038 nt) Show pHMM detection rules used
PKS-like: (t2pks2 or ksIII)
butyrolactone: AfsA

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS 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
IE308_RS24170: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

IE308_RS24230: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acylase transferase
IE308_RS24245: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

IE308_RS24250: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

IE308_RS24265: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Hydrolases: hydrolase
IE308_RS24180: isochorismatase

smcogs
  SMCOG1027: isochorismatase

IE308_RS24185: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: synthase
IE308_RS24200: 3-oxoacyl-(acyl carrier protein) synthase III

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

IE308_RS24210: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IE308_RS24310: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

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

Reference | PKS-like | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002276.2 |  |  | 0.53 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002510.2 |  |  | 0.40 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0000866.5 |  |  | 0.36 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0001197.5 |  |  | 0.36 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001987.2 |  |  | 0.35 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0001723.5 |  |  | 0.34 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000234.5 |  |  | 0.34 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000231.5 |  |  | 0.32 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000272.3 |  |  | 0.32 | PKS | spore pigment | Streptomyces collinus
BGC0002504.2 |  |  | 0.32 | PKS | nocardiopsistin A, nocardiopsistin B, nocardiopsistin C | Nocardiopsis sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002510.2 |  | 0.54 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0001197.5 |  | 0.50 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001987.2 |  | 0.50 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000866.5 |  | 0.50 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0001723.5 |  | 0.50 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002504.2 |  | 0.49 | PKS | nocardiopsistin A, nocardiopsistin B, nocardiopsistin C | Nocardiopsis sp.
BGC0000272.3 |  | 0.49 | PKS | spore pigment | Streptomyces collinus
BGC0000253.4 |  | 0.48 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000234.5 |  | 0.48 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.22 out of 18.46
Confidence: strong
Additional weak hits (9):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.10 out of 23.43
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.96 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.30 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.93 out of 20.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.88 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.13 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.77 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).
IE308_RS24245: mal
PKS_AT (9..294): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 57.1
  Methoxymalonyl-CoA: 22.0
  Methylmalonyl-CoA: 20.0
  inactive: 18.7
  fatty_acid: 17.2
  Ethylmalonyl-CoA: 8.5
  trans-1,2-CPDA: 8.3
  Propionyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

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

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

NZ_BNBR01000005.1 - Region 2 - 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: 380,974 - 453,489 nt. (total: 72,516 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase reductase
IE308_RS24880: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

IE308_RS24905: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

IE308_RS24985: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

IE308_RS24995: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

IE308_RS25015: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: methyltransferase
IE308_RS24825: methyltransferase

smcogs
  SMCOG1089: methyltransferase

IE308_RS24935: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Lyases: cyclase
IE308_RS24940: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

IE308_RS24945: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Ligases: synthase
IE308_RS24955: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

IE308_RS24960: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transport
IE308_RS25045: 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 | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000272.3 |  | 0.78 | PKS | spore pigment | Streptomyces collinus
BGC0000271.5 |  | 0.75 | PKS | spore pigment | Streptomyces avermitilis
BGC0000215.5 |  | 0.73 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.61 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.59 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001513.3 |  | 0.57 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001273.3 |  | 0.56 | PKS | asperlactone | Aspergillus ochraceus
BGC0002000.4 |  | 0.55 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001723.5 |  | 0.54 | PKS | oviedomycin | Streptomyces antibioticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000272.3 |  | 0.78 | PKS | spore pigment | Streptomyces collinus
BGC0000271.5 |  | 0.75 | PKS | spore pigment | Streptomyces avermitilis
BGC0000215.5 |  | 0.73 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.61 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.59 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001513.3 |  | 0.57 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001273.3 |  | 0.56 | PKS | asperlactone | Aspergillus ochraceus
BGC0002000.4 |  | 0.55 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001723.5 |  | 0.54 | PKS | oviedomycin | Streptomyces antibioticus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.94 out of 23.43
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.70 out of 29.72
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.94 out of 20.97
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.10 out of 23.79
Confidence: medium
Additional weak hits (17):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.45 out of 26.85
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.12 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.59 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.60 out of 32.93
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.16 out of 36.53
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
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.14 out of 20.01
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.20 out of 32.74
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.88 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.10 out of 28.19
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  380973 to 453489
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

IE308_RS24935
  MET C6|C8 (Score: 505.4; E-value: 1.3e-154)
IE308_RS24940
  CYC C4-C21/C2-C23|C2-C19 (Score: 162.4; E-value: 6.2e-51)
IE308_RS24945
  CYC C9-C14 (Score: 254.7; E-value: 5.4e-79)
IE308_RS24950
  ACP (Score: 83.7; E-value: 1.6e-26)
IE308_RS24955
  CLF (Score: 542.5; E-value: 1.3e-165)
IE308_RS24960
  KS (Score: 737.9; E-value: 6.8e-225)
IE308_RS24965
  CYC C5-C18 (Score: 206.3; E-value: 3e-64)
IE308_RS24985
  OXY (Score: 281.8; E-value: 2.7e-86)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
BldD | Development and antibiotic global regulator
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C

NZ_BNBR01000005.1 - 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: 497,898 - 539,058 nt. (total: 41,161 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
Oxidoreductases: dehydrogenase oxygenase
IE308_RS25425: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS25430: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS25510: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: aminotransferase
IE308_RS25360: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Hydrolases: hydrolase
IE308_RS25365: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: dehydratase
IE308_RS25440: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
IE308_RS25410: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IE308_RS25445: 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 | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000844.5 |  | 0.50 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001928.2 |  | 0.50 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001224.5 |  | 0.47 | other (other) | reductasporine | uncultured bacterium
BGC0001940.3 |  | 0.46 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0002031.3 |  | 0.46 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0001075.5 |  | 0.46 | PKS, terpene | aurachin RE | Rhodococcus erythropolis
BGC0000902.4 |  | 0.46 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001197.5 |  | 0.46 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002346.3 |  | 0.46 | ribosomal | kyamicin | Saccharopolyspora sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.54 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000844.5 |  | 0.50 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001928.2 |  | 0.50 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001224.5 |  | 0.47 | other (other) | reductasporine | uncultured bacterium
BGC0001940.3 |  | 0.46 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0002031.3 |  | 0.46 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0001075.5 |  | 0.46 | PKS, terpene | aurachin RE | Rhodococcus erythropolis
BGC0000902.4 |  | 0.46 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001197.5 |  | 0.46 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002346.3 |  | 0.46 | ribosomal | kyamicin | Saccharopolyspora sp.

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

No significant matches found.

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: 21.44 out of 26.85
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
Additional weak hits (11):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.61 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.54 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.11 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.00 out of 23.43
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.58 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.44 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.22 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.39 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.24 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.40 out of 33.14
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
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).
IE308_RS25410: X
AMP-binding (65..407): 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:
    LNAQFSAFVCGGALTVGGDRTTYGLTEAGRVATH
  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
--- | ---
RutR | Regulator of the pyrimidine and purine metabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_BNBR01000006.1 - Region 1 - 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: 447,053 - 468,120 nt. (total: 21,068 nt) Show pHMM detection rules used
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 oxidoreductase
IE308_RS28660: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

IE308_RS28670: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS28695: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Ligases: ligase
IE308_RS28665: 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 | furan | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002404.2 |  | 0.45 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000231.5 |  | 0.45 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001909.3 |  | 0.44 | PKS | strobilurin A | Strobilurus tenacellus
BGC0002496.3 |  | 0.44 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000234.5 |  | 0.43 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001810.3 |  | 0.43 | PKS | trehangelin | Polymorphospora rubra
BGC0000043.5 |  | 0.41 | PKS | curacin A | Moorea producens 19L
BGC0001723.5 |  | 0.41 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001633.3 |  | 0.41 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000888.5 |  | 0.41 | other (other) | bacilysin | Bacillus sp. CS93

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002404.2 |  | 0.45 | other (other) | falcarindiol | Solanum lycopersicum
BGC0000231.5 |  | 0.45 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001909.3 |  | 0.44 | PKS | strobilurin A | Strobilurus tenacellus
BGC0002496.3 |  | 0.44 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000234.5 |  | 0.43 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001810.3 |  | 0.43 | PKS | trehangelin | Polymorphospora rubra
BGC0000043.5 |  | 0.41 | PKS | curacin A | Moorea producens 19L
BGC0001723.5 |  | 0.41 | PKS | oviedomycin | Streptomyces antibioticus
BGC0001633.3 |  | 0.41 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000888.5 |  | 0.41 | other (other) | bacilysin | Bacillus sp. CS93

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 31.03 out of 36.53
Confidence: medium
Additional weak hits (2):
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.88 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
DmdR1 | Iron(II)-dependent repressor

NZ_BNBR01000008.1 - Region 1 - 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: 182,597 - 221,958 nt. (total: 39,362 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
IE308_RS32320: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IE308_RS32325: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: back translocase hydrolase
IE308_RS32295: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

IE308_RS32300: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

IE308_RS32365: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: dehydratase
IE308_RS32335: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Ligases: ligase
IE308_RS32355: 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 | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000610.5 |  | 0.92 | ribosomal | nosiheptide | Streptomyces actuosus
BGC0000608.5 |  | 0.83 | ribosomal | nocathiacin I | Actinokineospora fastidiosa
BGC0001707.5 |  | 0.69 | ribosomal | nosiheptide | Streptomyces sp.
BGC0002311.3 |  | 0.63 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001472.5 |  | 0.56 | ribosomal | berninamycin A | Streptomyces bernensis
BGC0002363.3 |  | 0.56 | ribosomal | berninamycin K, berninamycin J, berninamycin A, berninamycin B | Streptomyces sp.
BGC0001146.5 |  | 0.56 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001145.5 |  | 0.55 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000615.4 |  | 0.54 | ribosomal | TP-1161 | Nocardiopsis sp. TFS65-07
BGC0000606.5 |  | 0.54 | ribosomal | lactazole | Streptomyces lactacystinaeus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000610.5 |  | 0.92 | ribosomal | nosiheptide | Streptomyces actuosus
BGC0000608.5 |  | 0.83 | ribosomal | nocathiacin I | Actinokineospora fastidiosa
BGC0001707.5 |  | 0.69 | ribosomal | nosiheptide | Streptomyces sp.
BGC0002311.3 |  | 0.63 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0001472.5 |  | 0.56 | ribosomal | berninamycin A | Streptomyces bernensis
BGC0002363.3 |  | 0.56 | ribosomal | berninamycin K, berninamycin J, berninamycin A, berninamycin B | Streptomyces sp.
BGC0001146.5 |  | 0.56 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001145.5 |  | 0.55 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000615.4 |  | 0.54 | ribosomal | TP-1161 | Nocardiopsis sp. TFS65-07
BGC0000606.5 |  | 0.54 | ribosomal | lactazole | Streptomyces lactacystinaeus

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 (6):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.95 out of 23.43
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.53 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.25 out of 31.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 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.

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

IE308_RS32375
Leader:
MDAAHLSDLDIDALEISEFLDESRLEDSEVVAKVMSA
Core:
S C T T C E C C C S C S S
Core with dehydrations:
Dha Cys Dhb Dhb Cys E Cys Cys Cys Dha Cys Dha Dha

#### antiSMASH-DB 4.0 matches for IE308_RS32375

100.0%
NZ_BMWB01000021.1 and 4 others:
NZ_BNBR01000008.1 Thiopeptides: IE308_RS32375_thiopeptide NZ_CP029788.1 Thiopeptides: DMT42_RS37645_thiopeptide NZ_CP094344.1 Thiopeptides: MQE23_RS18145_thiopeptide NZ_QGGR01000028.1 Thiopeptides: BC793_RS39465_thiopeptide
Thiopeptides: IE198_RS26245_thiopeptide
1
S C T T C E C C C S C S S
13
S C T T C E C C C S C S S
1
S C T T C E C C C S C S S
13

#### MIBiG 4.0 matches for IE308_RS32375

42.9%
BGC0001155.5 (AGY49587.1):
Thiopeptide: GE2270
4
T C E C C C S C S
12
C C C S C S
5
V C G F C C S C S
13
18.2%
BGC0000563.4 (AEA03263.1):
Lanthipeptide: venezuelin
4
T C E C
7
T C E C
2
T C E C
5
17.9%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
4
T C E C C C S C S
12
T E C S C+
20
T V E C M P S C N
28

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

#### Types:

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

azole-containing-RiPP protocluster (182596...221958)
IE308_RS32350
  RRE type: Thiopeptide_F_RRE
  Location: 20 - 102
  Score: 94.7
  RRE type: Heterocycloanthracin_C_RRE
  Location: 23 - 104
  Score: 40.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

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.

IE308_RS32375
  Putative Type I
  Cleavage pHMM score: 10.70
  RODEO score: 34
  Monoisotopic mass: 1315.3 Da
  Molecular weight: 1316.5 Da
  Predicted peptide features:
  Central ring: pyridine tetrasubstituted (hydroxyl group present); second macrocycle
  Macrocycle: 26-member
  Tail reaction: dealkylation of C-Terminal residue; amidation
Considering maturation reactions
  Monoisotopic mass: 1221.2 Da
  Molecular weight: 1222.4 Da
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1334.5 Da N = 1
    1352.5 Da N = 2
    1370.6 Da N = 3
    1388.6 Da N = 4
    1406.6 Da N = 5
    1424.6 Da N = 6

NZ_BNBR01000009.1 - Region 1 - 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: 84,679 - 95,083 nt. (total: 10,405 nt) Show pHMM detection rules used
ectoine: ectoine_synt

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
IE308_RS33785: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

IE308_RS33795: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

IE308_RS33810: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

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

Reference | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.86 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.85 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.67 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.59 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.86 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.85 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.67 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.59 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
Additional weak hits (3):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.18 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_BNBR01000010.1 - 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: 1 - 15,843 nt. (total: 15,843 nt) Show pHMM detection rules used
Region on contig edge.
indole: (indsynth or dmat or indole_PTase)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
IE308_RS35180: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

IE308_RS35210: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IE308_RS35215: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Hydrolases: hydrolase
IE308_RS35225: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

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
--- | --- | --- | --- | --- | ---
BGC0002128.3 |  | 0.58 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001483.4 |  | 0.55 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001294.5 |  | 0.52 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0000278.3 |  | 0.46 | PKS | urdamycin | Streptomyces fradiae
BGC0001868.4 |  | 0.44 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0001840.2 |  | 0.44 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325
BGC0002805.2 |  | 0.43 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001910.4 |  | 0.43 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000231.5 |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002128.3 |  | 0.58 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001483.4 |  | 0.55 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001294.5 |  | 0.52 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0000278.3 |  | 0.46 | PKS | urdamycin | Streptomyces fradiae
BGC0001868.4 |  | 0.44 | other (phenazine) | iodinin | Xenorhabdus szentirmaii DSM 16338
BGC0001840.2 |  | 0.44 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325
BGC0002805.2 |  | 0.43 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001910.4 |  | 0.43 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000231.5 |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26
Confidence: medium
Additional weak hits (3):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.44 out of 21.55
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.04 out of 18.57
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.72 out of 20.97
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_BNBR01000010.1 - Region 2 - 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: 57,458 - 70,394 nt. (total: 12,937 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: oxidoreductase reductase
IE308_RS35465: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

IE308_RS35475: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Hydrolases: peptidase
IE308_RS35455: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: decarboxylase
IE308_RS35450: putative carboxymuconolactone decarboxylase

smcogs
  SMCOG1298: putative carboxymuconolactone decarboxylase

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

Reference | hydrogen-cyanide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002436.2 |  | 0.38 | other (other) | coformycin | Streptomyces citricolor
BGC0002285.2 |  | 0.37 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001647.3 |  | 0.32 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0001007.5 |  | 0.31 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin b | Salinispora arenicola CNS-205
BGC0001006.5 |  | 0.30 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin B | Salinispora tropica CNB-440
BGC0000240.5 |  | 0.23 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora pacifica
BGC0000135.5 |  | 0.22 | PKS | reveromycin A | Streptomyces sp. SN-593

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0002436.2 |  | 0.38 | other (other) | coformycin | Streptomyces citricolor
BGC0002285.2 |  | 0.37 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001647.3 |  | 0.32 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0001007.5 |  | 0.31 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin b | Salinispora arenicola CNS-205
BGC0001006.5 |  | 0.30 | NRPS, PKS | lymphostin, neolymphostinol B, lymphostinol, neolymphostin B | Salinispora tropica CNB-440
BGC0000240.5 |  | 0.23 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora pacifica
BGC0000135.5 |  | 0.22 | PKS | reveromycin A | Streptomyces sp. SN-593

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
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.39 out of 25.31
Confidence: medium
Additional weak hits (4):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.09 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.88 out of 31.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.29 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor