Select genomic region:
Overview
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### Identified secondary metabolite regions using strictness 'relaxed'

NZ_CP104794.1 (Streptomyces sp. FZ201)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | terpene-precursor,melanin | 466,282 | 491,007 | Medium | melanin | other:other
Region 2 | NRP-metallophore,NRPS | 903,807 | 968,216 | High | scabichelin | NRPS:Type I
Region 3 | T1PKS | 1,012,881 | 1,125,225 | High | ionostatin | PKS
Region 4 | T3PKS | 1,139,353 | 1,180,417 | High | flaviolin/1,3,6,8-tetrahydroxynaphthalene | PKS
Region 5 | NRPS-like | 1,757,079 | 1,800,795 |  |
Region 6 | ectoine | 1,903,356 | 1,913,760 | High | ectoine | other:other
Region 7 | NRPS,T1PKS | 2,628,982 | 2,679,478 | Medium | SCO-2138 | ribosomal:unmodified
Region 8 | melanin | 2,988,494 | 2,998,964 |  |
Region 9 | NI-siderophore | 3,077,662 | 3,107,434 | High | desferrioxamin B/desferrioxamine E | other:other
Region 10 | thioamide-NRP,t3nrps-iterative,NRPS,T3PKS | 3,373,789 | 3,457,608 | Low | feglymycin | NRPS:Type I
Region 11 | lassopeptide,lanthipeptide-class-i | 3,620,065 | 3,649,731 | High | citrulassin F | ribosomal:RiPP
Region 12 | lanthipeptide-class-i | 4,094,911 | 4,121,239 |
Region 13 | furan | 4,194,341 | 4,215,369 |  |
Region 14 | butyrolactone | 4,348,687 | 4,359,628 |
Region 15 | azole-containing-RiPP | 4,566,424 | 4,590,221 |  |
Region 16 | phosphonate | 4,737,674 | 4,755,857 | Low | rhizocticin A | other:other
Region 17 | terpene | 5,712,716 | 5,733,801 | High | albaflavenone | terpene
Region 18 | terpene-precursor | 5,739,787 | 5,760,863 |  |
Region 19 | NI-siderophore | 6,295,729 | 6,325,459 | Low | kinamycin | PKS
Region 20 | T1PKS,T2PKS | 6,458,639 | 6,548,836 | Low | pyrrolomycin A/pyrrolomycin B/pyrrolomycin C/pyrrolomycin D | PKS
Region 21 | RiPP-like | 6,643,095 | 6,654,378 |  |
Region 22 | butyrolactone,terpene | 6,700,788 | 6,723,096 | High | γ-butyrolactone | other:other
Region 23 | NI-siderophore | 6,868,904 | 6,899,999 |  |
Region 24 | T3PKS | 6,931,044 | 6,972,105 |  |
Region 25 | hydrogen-cyanide | 7,212,465 | 7,225,320 | Low | aborycin | ribosomal:RiPP
Region 26 | terpene | 7,307,366 | 7,333,980 | High | hopene | terpene
Region 27 | T1PKS,butyrolactone,PKS-like | 7,464,895 | 7,683,158 | Low | cyphomycin | PKS
Region 28 | RiPP-like | 7,791,116 | 7,802,531 |
Region 29 | betalactone | 7,811,537 | 7,845,820 |  |
Region 30 | RiPP-like | 7,989,827 | 8,000,042 | Low | informatipeptin | ribosomal:RiPP:Lanthipeptide
Region 31 | RiPP-like | 8,041,048 | 8,052,910 |
Region 32 | T1PKS,NRPS-like,NRPS | 8,237,717 | 8,308,417 | Low | BE-43547A1/BE-43547A2/BE-43547B1/BE-43547B2/BE-43547B3/BE-43547C1/BE-43547C2 | NRPS:Type I+PKS:Type I
Region 33 | terpene | 8,320,062 | 8,340,988 |
Region 34 | redox-cofactor | 8,471,485 | 8,494,191 |
Region 35 | NRPS | 8,501,235 | 8,583,210 | Low | endopyrrole B/endopyrrole A | NRPS:Type I

NZ_CP104794.1 - Region 1 - 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: 466,282 - 491,007 nt. (total: 24,726 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
N6J21_RS02165: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

N6J21_RS02180: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

N6J21_RS02210: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Hydrolases: hydrolase
N6J21_RS02130: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

N6J21_RS02160: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: synthetase
N6J21_RS02150: 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
--- | --- | --- | --- | --- | --- | ---
BGC0000910.3 |  |  | 1.04 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  |  | 1.01 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  |  | 0.60 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  |  | 0.55 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  |  | 0.54 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  |  | 0.30 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  |  | 0.24 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0000662.5 |  |  | 0.24 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001592.5 |  |  | 0.23 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0000633.3 |  |  | 0.22 | terpene | carotenoid | Streptomyces avermitilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.80 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.79 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.63 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.62 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.61 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002397.2 |  | 0.53 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.50 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000885.3 |  | 0.48 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000677.5 |  | 0.45 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002398.2 |  | 0.44 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana

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:
N6J21_RS02150: 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.
No hits above weak threshold.
Weak hits (3):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.72 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.66 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
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP104794.1 - Region 2 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 903,807 - 968,216 nt. (total: 64,410 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
N6J21_RS04245: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: formyltransferase methyltransferase
N6J21_RS04220: methyltransferase

smcogs
  SMCOG1089: methyltransferase

N6J21_RS04240: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

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

Reference | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000423.5 |  |  | 1.19 | NRPS | scabichelin | Streptomyces scabiei 87.22
BGC0002135.2 |  |  | 0.76 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  | 0.74 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  |  | 0.69 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001825.4 |  |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  |  | 0.67 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000423.5 |  | 0.84 | NRPS | scabichelin | Streptomyces scabiei 87.22
BGC0002135.2 |  | 0.70 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.68 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001825.4 |  | 0.68 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  | 0.67 | NRPS | AbT1 | Aureobasidium pullulans
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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.58 out of 20.97
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.86 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.03 out of 36.53
Confidence: medium
Additional weak hits (10):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.77 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.23 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.61 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.76 out of 33.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.38 out of 36.53
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.57 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.40 out of 36.53
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.65 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.21 out of 20.01
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 903806 - 968216:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-Fo-OH-Orn - Ser - NMe-OH-Orn - X - D-OH-Orn)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
N6J21_RS04220: Fo-OH-Orn - Ser - OH-Orn - X - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (228..626): Fo-OH-Orn
nrpys: Fo-OH-Orn

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

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

AMP-binding (1655..2053): 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:
    RWMTFDVSVWEWHFFSSGEHNLYGPTEAAVDVTH
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2710..3111): OH-Orn
nrpys: OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    MNHVFDMSWEEWNVLLGGEYNLYGPTEYTINTLG
  Nearest Stachelhaus code(s):
    OH-Orn DMENLGLINK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (4144..4540): X
nrpys: Orn, Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAHAFDGSWDPWDLSVGGEHDLYGPTECAVDAYG
  Nearest Stachelhaus code(s):
    Orn DGEDAGLVDK (88% 8Å match)
    Arg DADDVGLVDK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (5194..5600): OH-Orn
nrpys: OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSHWFDASWQPWEVGVGGEFNLYGPTESTVDALV
  Nearest Stachelhaus code(s):
    OH-Orn DAQEGGLVDK (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
--- | ---
CcpA | Catabolite control protein A
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP104794.1 - Region 3 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,012,881 - 1,125,225 nt. (total: 112,345 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase reductase
N6J21_RS04575: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

N6J21_RS04605: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

N6J21_RS04625: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

N6J21_RS04695: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

N6J21_RS04755: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: acylase glycosyltransferase kinase
N6J21_RS04555: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

N6J21_RS04640: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

N6J21_RS04660: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

N6J21_RS04680: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

N6J21_RS04720: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: esterase
N6J21_RS04705: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: synthase
N6J21_RS04630: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

N6J21_RS04635: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

N6J21_RS04645: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

N6J21_RS04650: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS04655: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
N6J21_RS04590: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002446.3 |  | 0.73 | PKS | ionostatin | Streptomyces sp.
BGC0000067.5 |  | 0.68 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000018.5 |  | 0.65 | PKS | angolamycin | Streptomyces eurythermus
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  | 0.73 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002446.3 |  | 0.73 | PKS | ionostatin | Streptomyces sp.
BGC0000067.5 |  | 0.68 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000018.5 |  | 0.65 | PKS | angolamycin | Streptomyces eurythermus
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.58 out of 27.55
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 28.31 out of 30.12
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
Additional weak hits (7):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.63 out of 25.75
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.99 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.07 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.03 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.32 out of 39.62
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.67 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 5, location 1012880 - 1125225:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (redmal) + (ohmal - Me-ohmal) + (ccmal) + (Me-redmal - Me-redmal) + (ohmal - Me-mal) + (Me-redmal - Me-redmal) + (Me-redmal)
Non-colinear ordering:
  N6J21_RS04680 + N6J21_RS04660 + N6J21_RS04655 + N6J21_RS04650 + N6J21_RS04645 + N6J21_RS04640 + N6J21_RS04635 + N6J21_RS04630

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).
N6J21_RS04630: mmal
PKS_AT (569..864): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 198.0
  Ethylmalonyl-CoA: 188.6
  Methoxymalonyl-CoA: 163.5
  2-Methylbutyryl-CoA: 125.2
  trans-1,2-CPDA: 106.6
  Propionyl-CoA: 93.9
  Malonyl-CoA: 87.8
  CHC-CoA: 75.6
  Isobutyryl-CoA: 58.3
  Benzoyl-CoA: 50.5
  Acetyl-CoA: 34.9
  fatty_acid: 34.6
  3-Methylbutyryl-CoA: 29.0
  inactive: 24.3

N6J21_RS04635: mmal - mmal
PKS_AT (565..860): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 193.9
  Ethylmalonyl-CoA: 183.0
  Methoxymalonyl-CoA: 157.1
  2-Methylbutyryl-CoA: 121.9
  trans-1,2-CPDA: 101.1
  Propionyl-CoA: 91.7
  Malonyl-CoA: 85.4
  CHC-CoA: 74.0
  Isobutyryl-CoA: 56.4
  Benzoyl-CoA: 47.0
  Acetyl-CoA: 35.6
  fatty_acid: 32.6
  3-Methylbutyryl-CoA: 29.1
  inactive: 19.1

PKS_AT (2642..2937): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 197.2
  Ethylmalonyl-CoA: 188.6
  Methoxymalonyl-CoA: 163.6
  2-Methylbutyryl-CoA: 125.4
  trans-1,2-CPDA: 101.6
  Propionyl-CoA: 99.4
  Malonyl-CoA: 89.8
  CHC-CoA: 82.0
  Isobutyryl-CoA: 58.7
  Benzoyl-CoA: 52.3
  Acetyl-CoA: 41.2
  fatty_acid: 30.6
  3-Methylbutyryl-CoA: 28.9
  inactive: 25.9

N6J21_RS04640: mal - mmal
PKS_AT (559..833): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.5
  inactive: 110.0
  Methoxymalonyl-CoA: 56.0
  Methylmalonyl-CoA: 46.0
  Propionyl-CoA: 30.5
  Acetyl-CoA: 15.1
  Isobutyryl-CoA: 15.0
  CHC-CoA: 13.5
  Benzoyl-CoA: 13.0
  Ethylmalonyl-CoA: 12.1
  fatty_acid: 10.8
  2-Methylbutyryl-CoA: 10.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2073..2371): mmal
ATSignature: Ethylmalonyl-CoA, Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 173.7
  Ethylmalonyl-CoA: 164.3
  Methoxymalonyl-CoA: 147.5
  2-Methylbutyryl-CoA: 114.7
  Propionyl-CoA: 97.0
  CHC-CoA: 88.6
  trans-1,2-CPDA: 87.1
  Malonyl-CoA: 80.2
  Isobutyryl-CoA: 55.3
  Benzoyl-CoA: 40.0
  Acetyl-CoA: 30.6
  3-Methylbutyryl-CoA: 29.0
  fatty_acid: 28.3
  inactive: 12.2

N6J21_RS04645: mmal - mmal
PKS_AT (563..858): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 199.2
  Ethylmalonyl-CoA: 191.0
  Methoxymalonyl-CoA: 164.0
  2-Methylbutyryl-CoA: 126.0
  trans-1,2-CPDA: 110.4
  Propionyl-CoA: 94.5
  Malonyl-CoA: 92.3
  CHC-CoA: 77.2
  Isobutyryl-CoA: 57.9
  Benzoyl-CoA: 51.1
  fatty_acid: 35.9
  Acetyl-CoA: 35.7
  3-Methylbutyryl-CoA: 30.9
  inactive: 24.6

PKS_AT (2627..2922): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 186.5
  Ethylmalonyl-CoA: 174.4
  Methoxymalonyl-CoA: 159.0
  2-Methylbutyryl-CoA: 114.1
  trans-1,2-CPDA: 99.3
  Propionyl-CoA: 93.5
  Malonyl-CoA: 86.1
  CHC-CoA: 70.9
  Isobutyryl-CoA: 54.4
  Benzoyl-CoA: 47.6
  Acetyl-CoA: 34.3
  fatty_acid: 32.9
  3-Methylbutyryl-CoA: 31.0
  inactive: 29.5

N6J21_RS04650: mal
PKS_AT (554..836): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 196.3
  inactive: 96.3
  Methoxymalonyl-CoA: 46.1
  Methylmalonyl-CoA: 33.7
  Propionyl-CoA: 19.2
  Benzoyl-CoA: 12.5
  Acetyl-CoA: 11.9
  Isobutyryl-CoA: 8.5
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

N6J21_RS04655: mal - mmal
PKS_AT (1854..2145): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 83.3%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 215.8
  inactive: 106.6
  Methoxymalonyl-CoA: 60.8
  Methylmalonyl-CoA: 51.4
  Acetyl-CoA: 20.8
  Propionyl-CoA: 20.7
  Benzoyl-CoA: 14.5
  Ethylmalonyl-CoA: 13.9
  2-Methylbutyryl-CoA: 8.7
  Isobutyryl-CoA: 7.8
  CHC-CoA: 7.3
  fatty_acid: 7.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3394..3689): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 198.4
  Ethylmalonyl-CoA: 191.9
  Methoxymalonyl-CoA: 167.8
  2-Methylbutyryl-CoA: 124.9
  trans-1,2-CPDA: 102.6
  Propionyl-CoA: 99.5
  Malonyl-CoA: 92.8
  CHC-CoA: 75.3
  Isobutyryl-CoA: 61.5
  Benzoyl-CoA: 51.6
  Acetyl-CoA: 36.5
  fatty_acid: 35.5
  3-Methylbutyryl-CoA: 30.9
  inactive: 25.5

N6J21_RS04660: mal
PKS_AT (544..753): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 147.0
  inactive: 75.4
  Methoxymalonyl-CoA: 42.4
  Methylmalonyl-CoA: 32.8
  Acetyl-CoA: 15.4
  Benzoyl-CoA: 13.3
  Isobutyryl-CoA: 12.6
  CHC-CoA: 11.5
  Ethylmalonyl-CoA: 10.7
  Propionyl-CoA: 9.9
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

N6J21_RS04680: mal
PKS_AT (563..865): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 87.5%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 210.5
  inactive: 100.1
  Methoxymalonyl-CoA: 61.5
  Methylmalonyl-CoA: 46.1
  Isobutyryl-CoA: 22.5
  Ethylmalonyl-CoA: 22.4
  Propionyl-CoA: 19.7
  Benzoyl-CoA: 18.2
  Acetyl-CoA: 13.9
  fatty_acid: 10.3
  2-Methylbutyryl-CoA: 9.6
  CHC-CoA: 7.6
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
GnfM | Regulator of nitrogen-fixation genes
OsdR | Development and stress management regulator

NZ_CP104794.1 - Region 4 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,139,353 - 1,180,417 nt. (total: 41,065 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer oxidoreductase oxygenase reductase
N6J21_RS04820: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

N6J21_RS04835: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

N6J21_RS04840: flavodoxin

smcogs
  SMCOG1134: flavodoxin

N6J21_RS04870: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

N6J21_RS04875: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

N6J21_RS04880: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

N6J21_RS04890: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

N6J21_RS04905: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

N6J21_RS04920: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

N6J21_RS04930: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: aminotransferase
N6J21_RS05010: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: deformylase hydrolase
N6J21_RS04830: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

N6J21_RS04940: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Ligases: synthase
N6J21_RS04915: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002127.3 |  | 0.87 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001310.5 |  | 0.81 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0000902.4 |  | 0.75 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.62 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000706.3 |  | 0.48 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001078.5 |  | 0.47 | PKS, terpene | furaquinocin B | Streptomyces sp. KO-3988
BGC0000860.3 |  | 0.46 | other (other) | ectoine | Methylarcula marina
BGC0000853.3 |  | 0.46 | other (other) | ectoine | Streptomyces anulatus
BGC0000280.5 |  | 0.45 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.45 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002127.3 |  | 0.87 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001310.5 |  | 0.81 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0000902.4 |  | 0.75 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000285.5 |  | 0.62 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0000706.3 |  | 0.48 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0001078.5 |  | 0.47 | PKS, terpene | furaquinocin B | Streptomyces sp. KO-3988
BGC0000860.3 |  | 0.46 | other (other) | ectoine | Methylarcula marina
BGC0000853.3 |  | 0.46 | other (other) | ectoine | Streptomyces anulatus
BGC0000280.5 |  | 0.45 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens
BGC0000281.3 |  | 0.45 | PKS | 2,4-diacetylphloroglucinol | Pseudomonas fluorescens

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:
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.24 out of 29.51
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.96 out of 20.97
Confidence: medium
Additional weak hits (5):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.91 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.10 out of 27.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.03 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.63 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.66 out of 29.38
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
DosR | Hypoxia stress response regulator

NZ_CP104794.1 - Region 5 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,757,079 - 1,800,795 nt. (total: 43,717 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidase oxygenase
N6J21_RS07850: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

N6J21_RS07855: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Transferases: glycosyltransferase
N6J21_RS07865: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: hydrolase
N6J21_RS07830: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: lyase
N6J21_RS07820: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
N6J21_RS07760: Pseudouridine synthase

smcogs
  SMCOG1154: Pseudouridine synthase

N6J21_RS07815: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000307.4 |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.61 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000307.4 |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.61 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.10 out of 23.79
Confidence: medium
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 31.21 out of 35.63
Confidence: strong
Additional weak hits (11):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.68 out of 29.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.15 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.86 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.15 out of 30.25
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.78 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.60 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.44 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.57 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 7, location 1757078 - 1800795:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ala)

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).
N6J21_RS07815: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (219..613): 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:
    LWSTFDLSVYEANTNVAGEYNLYGPSEDTTYSTW
  Nearest Stachelhaus code(s):
    Ala DLYNNALTYK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
NrtR | NAD synthesis repressor

NZ_CP104794.1 - Region 6 - 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: 1,903,356 - 1,913,760 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
N6J21_RS08400: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

N6J21_RS08435: 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 |  | 0.85 | 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 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.85 | 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 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (5):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.33 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.86 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.78 out of 21.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.04 out of 26.12
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP104794.1 - Region 7 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,628,982 - 2,679,478 nt. (total: 50,497 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: kinase transferase
N6J21_RS11735: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

N6J21_RS11860: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Ligases: ligase synthase
N6J21_RS11730: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

N6J21_RS11765: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

N6J21_RS11775: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

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

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.70 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001164.3 |  |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001135.5 |  |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001160.5 |  |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001261.3 |  |  | 0.65 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  |  | 0.64 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.62 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.61 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  |  | 0.61 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  | 0.58 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.65 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.64 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

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

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 (9):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.14 out of 26.85
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.54 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.08 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.08 out of 21.55
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.35 out of 30.98
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.70 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.20 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 9, location 2628981 - 2679478:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Acetyl-CoA - mal - 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).
N6J21_RS11730: X
AMP-binding (11..387): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TALH---LVLGGFGVSGSAIERYGMTETLMNTSI
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

N6J21_RS11765: Acetyl-CoA - mal - Pro
Search NORINE for peptide: strict or relaxed
CAL_domain (154..483): Acetyl-CoA
minowa: Acetyl-CoA

Prediction, score:
  Acetyl-CoA: 12.9
  shikimic_acid: 0.0
  fatty_acid: 0.0
  NH2: 0.0
  AHBA: 0.0

PKS_AT (1247..1519): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 115.4
  Methylmalonyl-CoA: 65.6
  Methoxymalonyl-CoA: 61.8
  inactive: 57.1
  Ethylmalonyl-CoA: 39.1
  Propionyl-CoA: 37.8
  Benzoyl-CoA: 30.6
  Acetyl-CoA: 29.1
  2-Methylbutyryl-CoA: 26.7
  Isobutyryl-CoA: 24.8
  trans-1,2-CPDA: 24.3
  fatty_acid: 18.3
  CHC-CoA: 15.6
  3-Methylbutyryl-CoA: 10.9

AMP-binding (2541..2919): 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:
    LAHTFDVSVQETFMFSAGEHNQYGPTETSVIVTS
  Nearest Stachelhaus code(s):
    Pro DVQFAAQVVK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---

NZ_CP104794.1 - Region 8 - 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: 2,988,494 - 2,998,964 nt. (total: 10,471 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
N6J21_RS13250: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

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

Reference | melanin | 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 |  | 0.66 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.47 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.38 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.37 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.36 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0002316.2 |  | 0.36 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000528.5 |  | 0.36 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

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 |  | 0.66 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.47 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.38 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.37 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.36 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0002316.2 |  | 0.36 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000528.5 |  | 0.36 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (4):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.25 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.83 out of 27.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.73 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.44 out of 26.06
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP104794.1 - Region 9 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,077,662 - 3,107,434 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
N6J21_RS13630: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

N6J21_RS13655: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

N6J21_RS13675: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: carboxylase transferase
N6J21_RS13640: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

N6J21_RS13645: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Lyases: decarboxylase
N6J21_RS13670: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: synthase
N6J21_RS13650: 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 |  | 0.86 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.85 | 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
BGC0002284.3 |  | 0.60 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002073.3 |  | 0.57 | NRPS | dehydroxynocardamine | Corynebacterium propinquum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000940.5 |  | 0.86 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.85 | 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
BGC0002284.3 |  | 0.60 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002073.3 |  | 0.57 | NRPS | dehydroxynocardamine | Corynebacterium propinquum

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.94 out of 36.53
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.63 out of 27.04
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.71 out of 20.47
Confidence: medium
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: 17.92 out of 20.47
Confidence: medium
Additional weak hits (2):
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
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
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
DasR | N-acetylglucosamine dependent repressor
DmdR1 | Iron(II)-dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP104794.1 - Region 10 - NRPS,T3PKS,t3nrps-iterative,thioamide-NRP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,373,789 - 3,457,608 nt. (total: 83,820 nt) Show pHMM detection rules used
thioamide-NRP: (ATP-grasp and AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC))
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
N6J21_RS14950: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

N6J21_RS14955: nucleotide sugar dehydrogenase

smcogs
  SMCOG1152: nucleotide sugar dehydrogenase

N6J21_RS14985: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

N6J21_RS15220: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

N6J21_RS15245: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acetyltransferase aminotransferase methyltransferase
N6J21_RS15155: aminotransferase

smcogs
  SMCOG1019: aminotransferase

N6J21_RS15195: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

N6J21_RS15240: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: decarboxylase hydratase
N6J21_RS15085: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

N6J21_RS15170: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

N6J21_RS15175: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
N6J21_RS15130: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

N6J21_RS15160: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

N6J21_RS15165: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

N6J21_RS15185: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

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

Reference | thioamide-NRP | t3nrps-iterative | NRPS | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002075.3 |  |  |  |  | 1.70 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  |  |  |  | 1.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  |  |  | 1.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  |  |  | 1.63 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  |  |  |  | 1.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  |  |  |  | 1.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  |  |  | 1.55 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  |  |  | 1.53 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  |  |  | 1.50 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  |  |  | 1.48 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002135.2 |  | 0.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.71 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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: 18.20 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.52 out of 23.79
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
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
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.24 out of 19.26
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.65 out of 24.78
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.76 out of 27.04
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
Additional weak hits (25):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.09 out of 30.22
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.23 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.37 out of 21.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.19 out of 25.75
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.81 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.41 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.78 out of 20.97
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.18 out of 26.85
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.51 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.09 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.04 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.47 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.59 out of 21.55
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.87 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.73 out of 32.93
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.84 out of 32.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.63 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.58 out of 20.01
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.93 out of 35.63
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.56 out of 27.18
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.22 out of 35.63
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.04 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 12, location 3373788 - 3457608:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe - Dhpg) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 3373788 - 3456417:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe - Dhpg) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 14, location 3416549 - 3457608:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Phe - Dhpg) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
N6J21_RS15130: Phe - Dhpg
Search NORINE for peptide: strict or relaxed
AMP-binding (453..832): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LRFAFDGSVWEMTVITASEENSYGPTETTVCASG
  Nearest Stachelhaus code(s):
    His DTWTIASVDK (71% 8Å match)
    Phe DAWTIAGVCK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1492..1892): Dhpg
nrpys: Dhpg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPSFDASTYEASLTTGGDRTTYGPTEMTLCVTG
  Nearest Stachelhaus code(s):
    Dhpg DAYHGGTLCK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

N6J21_RS15160: X
AMP-binding (462..862): 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:
    LALTFDASVAELQALNAGEVNQYGPTETTVYSTL
  Nearest Stachelhaus code(s):
    Tyr DAATLAAVAK (59% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
LexA variant 2 | Repressor of DNA damage response
OsdR | Development and stress management regulator
RpoN | Regulator of nitrogen assimilation and virulence

NZ_CP104794.1 - Region 11 - lanthipeptide-class-i,lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,620,065 - 3,649,731 nt. (total: 29,667 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
N6J21_RS16020: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

N6J21_RS16090: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Hydrolases: hydrolase
N6J21_RS16045: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: cyclase dehydratase
N6J21_RS16075: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

N6J21_RS16080: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lassopeptide | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001552.3 |  |  | 1.03 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002576.2 |  |  | 0.89 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001550.3 |  |  | 0.86 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001549.3 |  |  | 0.84 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001539.4 |  |  | 0.79 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002053.3 |  |  | 0.79 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001551.4 |  |  | 0.78 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001889.2 |  |  | 0.77 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0001507.3 |  |  | 0.69 | ribosomal | anantin C | Streptomyces olindensis
BGC0002289.2 |  |  | 0.63 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001552.3 |  | 0.79 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001550.3 |  | 0.74 | ribosomal | citrulassin D | Streptomyces katrae
BGC0001549.3 |  | 0.73 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001539.4 |  | 0.72 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002053.3 |  | 0.71 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001551.4 |  | 0.71 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001889.2 |  | 0.71 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0001507.3 |  | 0.67 | ribosomal | anantin C | Streptomyces olindensis
BGC0002289.2 |  | 0.65 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii

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 N6J21_RS16080

N6J21_RS16070
Leader:
MAGNEFDLDVRVTSPSAGAVDQ
Core:
P M S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C V Q Q P
Core with dehydrations:
P M Dha I Dha Dha L L Dhb R Dha L Cys Dhb R V Dhb Cys R G Dhb Cys Dhb Cys V Cys Dhb Dhb N Cys Dhb A G Cys V Q Q P

#### antiSMASH-DB 4.0 matches for N6J21_RS16070

100.0%
NZ_CP104794.1:
Lanthipeptides: N6J21_RS16070_lanthipeptide
1
P M S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C V Q Q P
38
P M S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C V Q Q P
1
P M S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C V Q Q P
38
58.5%
NZ_CP017248.1 and 1 other:
NZ_CP071839.1 Lanthipeptides: S1361_RS32765_lanthipeptide
Lanthipeptides: BFF78_RS08045_lanthipeptide
1
P M S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G
33
P S I S S L L T R++C T R V T C+ C T V C T T C T+G
1
P A S I S S L L T R A V C T R V T C K A N C T Y V C T T V C T S G
33
50.0%
NZ_BNCE01000001.1:
Lanthipeptides: IE320_RS02935_lanthipeptide
3
S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C
34
S I S + T R++C T R V T C+ T T C C T C T C
1
S I S G I A T R T I C T R V T C Q V T K T C A C T Q M C T I L C
32
with 22 more sequence matches
Only the first 10 are displayed here.
50.0%
NZ_CP007574.1:
Lanthipeptides: DC74_RS44240_lanthipeptide
3
S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C
34
S I S S+ T R++C T+V C T T C V C T+ C T C
1
S I S S V A T R T V C T K V G C S V T K T C V C T S M C T I F C
32
50.0%
NZ_JACHJE010000002.1:
Lanthipeptides: FHS32_RS05815_lanthipeptide
3
S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C
34
S I S++ T R++C T R V T C+ T T C C T+ C T C
1
S I S T I A T R T I C T R V T C Q V T K T C A C T S M C T I L C
32
48.8%
NZ_JALGBX010000020.1 and 1 other:
NZ_JANAVF010000016.1 Lanthipeptides: NLX94_RS30150_lanthipeptide
Lanthipeptides: MTF69_RS28785_lanthipeptide
1
P M S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C V
35
P S I S + T R++C T R V T C+ + T C V C T C T C V
6
P P S I S G I A T R T V C T R V T C Q A S K T C V C T A M C T V F C V
40
46.5%
NZ_JAJJMU010000017.1:
Lanthipeptides: LOC25_RS25050_lanthipeptide
1
P M S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C V
35
P S I S++ T R++C T R V C T T C C T+ C T C V
6
P P S I S T I A T R T V C T R V G C S V T K T C A C T S M C T I L C V
40
46.3%
NZ_CP045803.1:
Lanthipeptides: V519_RS20085_lanthipeptide
3
S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C V
35
S I S S+ T R++C T+V C+ T T C C T+ C T C V
6
S I S S I A T R T V C T K V G C K V T K T C A C T S M C T I F C V
38
44.7%
NZ_JALMDK010000007.1:
Lanthipeptides: MZC64_RS28180_lanthipeptide
3
S I S S L L T R S L C T R V T C R G T C T C V C T T N-C T A G C V Q Q
37
S I+S++T R C T R T C C T C T A G C ++
1
S I T S V I T R L A C T R T P L C S R F T C Q C T Q G A C T A G C P K R
36
44.2%
NZ_VIUV01000009.1:
Lanthipeptides: FB570_RS21545_lanthipeptide
1
P M S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C V
35
P S I S++ T R++C T+V C+ T T C C T+ C T C V
6
P P S I S T I A T R T V C T K V G C Q V T K T C A C T S M C T I F C V
40
42.1%
NZ_LDCN01000003.1:
Lanthipeptides: allorf_808935_809114_lanthipeptide
14
T R V T C R G T C T C V C T T N C T A G C
34
T R V T C+ T C T C V C T C T G C
10
T R V T C K S T C T C V C T A M C T P G C
30
39.5%
NZ_CP047318.1:
Lanthipeptides: GSY65_RS20765_lanthipeptide
1
P M S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C
34
P S I S + T R++C T+ C+ T T C C T+ C T C
6
P P S I S Q I A T R T V C T K S V C Q V T S T C A C T S V C T V F C
39
37.2%
NZ_JAAVVL010000001.1:
Lanthipeptides: GWK25_RS02255_lanthipeptide
1
P M S I S S L L T R S L C T R V T C R G T C T C V C T T N C T A G C
34
P S I S + T+++C T+ C+ T T C C T+ C T C
6
P P S I S Q I A T K T V C T K S V C Q V T S T C A C T S V C T V F C
39

#### MIBiG 4.0 matches for N6J21_RS16070

15.8%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
22
C T C V C T T N C T A G C
34
C T C T G C
7
C T P G C K T G A L M G C
19
13.2%
BGC0001155.5 (AGY49587.1):
Thiopeptide: GE2270
21
T C T C V C T T N C T
31
+C C V C C+
1
S C N C V C G F C C S
11
13.2%
BGC0002110.3 (QKV49894.1):
Lanthipeptide: birimositide
27
T T N C T A G C
34
T T C T+ C
19
T T K C T S K C
26
with 2 more sequence matches
10.5%
BGC0000563.4 (AEA03263.1):
Lanthipeptide: venezuelin
21
T C T C V
25
T C C V
2
T C E C V
6
7.9%
BGC0000563.4 (AEA03263.1):
Lanthipeptide: venezuelin
8
L T R S L C T R V T C
18
L ++C ++C
11
L L N T V C I G I S C
21

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
Additional weak hits (6):
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: 15.57 out of 20.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.95 out of 21.55
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.70 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.34 out of 28.19
Confidence: weak
Lanthipeptides
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

N6J21_RS16070 - Class I
  Cleavage pHMM score: -0.80
  RODEO score: 24
  Monoisotopic mass: 3777.8 Da
  Molecular weight: 3780.5 Da
  Number of bridges: 7
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3798.5 Da N = 1
    3816.5 Da N = 2
    3834.5 Da N = 3
    3852.5 Da N = 4
    3870.6 Da N = 5

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 (3620064...3642554)
N6J21_RS16050
  RRE type: Stand_Alone_Lasso_RRE
  Location: 0 - 83
  Score: 82.9
N6J21_RS16080
  RRE type: Lanthipeptide_LanB_RRE
  Location: 147 - 236
  Score: 40.7
lanthipeptide-class-i protocluster (3625181...3649731)
N6J21_RS16050
  RRE type: Stand_Alone_Lasso_RRE
  Location: 0 - 83
  Score: 82.9
N6J21_RS16080
  RRE type: Lanthipeptide_LanB_RRE
  Location: 147 - 236
  Score: 40.7

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP104794.1 - Region 12 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,094,911 - 4,121,239 nt. (total: 26,329 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
N6J21_RS18290: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

N6J21_RS18295: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.49 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000544.4 |  | 0.46 | ribosomal | planosporicin | Planomonospora alba
BGC0002316.2 |  | 0.45 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002635.2 |  | 0.42 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0002120.3 |  | 0.40 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000529.5 |  | 0.38 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000796.3 |  | 0.25 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0000703.4 |  | 0.25 | saccharide | kanamycin | Streptomyces kanamyceticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.76 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.49 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000544.4 |  | 0.46 | ribosomal | planosporicin | Planomonospora alba
BGC0002316.2 |  | 0.45 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000541.5 |  | 0.44 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002635.2 |  | 0.42 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0002120.3 |  | 0.40 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000529.5 |  | 0.38 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000796.3 |  | 0.25 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0000703.4 |  | 0.25 | saccharide | kanamycin | Streptomyces kanamyceticus

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

No significant matches found.

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.93 out of 26.33
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.28 out of 27.04
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.28 out of 27.55
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.87 out of 24.78
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47
Confidence: medium
Additional weak hits (14):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.71 out of 32.74
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.46 out of 27.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.76 out of 26.85
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.29 out of 18.57
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.83 out of 26.85
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.90 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.79 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.80 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.19 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.77 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.19 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.60 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.03 out of 29.65
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (4094910...4121239)
N6J21_RS18295
  RRE type: Lanthipeptide_LanB_RRE
  Location: 115 - 207
  Score: 65.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
DasR | N-acetylglucosamine dependent repressor
GnfM | Regulator of nitrogen-fixation genes
LexA variant 2 | Repressor of DNA damage response
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP104794.1 - Region 13 - 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: 4,194,341 - 4,215,369 nt. (total: 21,029 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 oxygenase
N6J21_RS18810: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

N6J21_RS18825: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: aminotransferase
N6J21_RS18755: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase peptidase
N6J21_RS18745: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

N6J21_RS18785: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

Ligases: synthase
N6J21_RS18800: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | furan | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002458.3 |  | 0.51 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0002554.2 |  | 0.47 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
BGC0001903.3 |  | 0.46 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0001633.3 |  | 0.44 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0002711.2 |  | 0.44 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0001850.4 |  | 0.42 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0002712.2 |  | 0.41 | PKS | WS-5995 D, WS-5995 B, WS-5995 C, SEK 43 | Streptomyces yanglinensis
BGC0000261.5 |  | 0.41 | PKS | R1128 | Streptomyces sp. R1128
BGC0001965.4 |  | 0.41 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus
BGC0002476.2 |  | 0.41 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002458.3 |  | 0.51 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0002554.2 |  | 0.47 | other (other) | carquinostatin A, carquinostatin B | Streptomyces exfoliatus
BGC0001903.3 |  | 0.46 | other (other) | neocarazostatin A | Streptomyces sp. MA37
BGC0001633.3 |  | 0.44 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0002711.2 |  | 0.44 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0001850.4 |  | 0.42 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0002712.2 |  | 0.41 | PKS | WS-5995 D, WS-5995 B, WS-5995 C, SEK 43 | Streptomyces yanglinensis
BGC0000261.5 |  | 0.41 | PKS | R1128 | Streptomyces sp. R1128
BGC0001965.4 |  | 0.41 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus
BGC0002476.2 |  | 0.41 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655

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: 16.68 out of 19.26
Confidence: medium
Additional weak hits (6):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.53 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.91 out of 23.43
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.07 out of 30.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.37 out of 20.97
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.61 out of 35.63
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.83 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP104794.1 - Region 14 - butyrolactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,348,687 - 4,359,628 nt. (total: 10,942 nt) Show pHMM detection rules used
butyrolactone: AfsA

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
N6J21_RS19460: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: dehydratase
N6J21_RS19455: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
N6J21_RS19450: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.77 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.77 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002276.2 |  | 0.59 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002578.2 |  | 0.43 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000231.5 |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.38 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000936.5 |  | 0.37 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1
BGC0002561.3 |  | 0.37 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0000871.4 |  | 0.37 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.77 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.77 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002276.2 |  | 0.59 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002578.2 |  | 0.43 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000231.5 |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.38 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000936.5 |  | 0.37 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1
BGC0002561.3 |  | 0.37 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0000871.4 |  | 0.37 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.24 out of 19.26
Confidence: medium
Additional weak hits (4):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.75 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.13 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.40 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP104794.1 - Region 15 - 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: 4,566,424 - 4,590,221 nt. (total: 23,798 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase halogenase
N6J21_RS20480: flavin-dependent cycline orsellinic halogenase

halogenases
  flavin-dependent cycline orsellinic halogenase
smcogs
  SMCOG1119: halogenase

N6J21_RS20520: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: hydrolase
N6J21_RS20465: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

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

Reference | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.76 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002698.2 |  | 0.52 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001555.4 |  | 0.51 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000565.5 |  | 0.51 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0001638.4 |  | 0.50 | ribosomal | klebsazolicin | Klebsiella pneumoniae subsp. ozaenae
BGC0002699.2 |  | 0.49 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0002584.2 |  | 0.49 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0002551.2 |  | 0.48 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002341.2 |  | 0.76 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002698.2 |  | 0.52 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001555.4 |  | 0.51 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000565.5 |  | 0.51 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0001638.4 |  | 0.50 | ribosomal | klebsazolicin | Klebsiella pneumoniae subsp. ozaenae
BGC0002699.2 |  | 0.49 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0002584.2 |  | 0.49 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000588.5 |  | 0.49 | ribosomal | microcin L | Escherichia coli
BGC0002551.2 |  | 0.48 | other (other), ribosomal, terpene | muscoride A, muscoride B | Nostoc sp. UHCC-0398

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
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.90 out of 23.43
Confidence: medium
Additional weak hits (5):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.54 out of 20.97
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.94 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.65 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.28 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.61 out of 28.19
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (4566423...4590221)
N6J21_RS20490
  RRE type: NHLP_CD_RRE
  Location: 2 - 94
  Score: 63.5
  RRE type: Cyanobactin_D_RRE
  Location: 4 - 78
  Score: 53.1
  RRE type: Goadsporin_CD_RRE
  Location: 4 - 97
  Score: 50.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
VqsM | Regulator of quorum-sensing signalling systems

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_CP104794.1 - Region 16 - phosphonate
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,737,674 - 4,755,857 nt. (total: 18,184 nt) Show pHMM detection rules used
phosphonate: (phosphonates and minimum(1, [2-Hacid_dh_C, Aldedh, Aminotran_1_2, Aminotran_5, AurF, CTP_transf_like, DUF4992, Fe-ADH, HMGL-like, Metallophos_2, NTP_transf_3, NTP_transf_5, PALP, PEP_mutase, TPP_enzyme_C, TPP_enzyme_N, phosphonates]) and not (phosphonatesHydrolase or phosphonatesMeIsocitrateLyase))

#### 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
N6J21_RS21230: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Lyases: lyase
N6J21_RS21220: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: synthase
N6J21_RS21250: 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 | phosphonate | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000926.5 |  | 0.66 | other (other) | rhizocticin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000897.5 |  | 0.50 | other (other) | dehydrophos | Streptomyces luridus
BGC0001859.4 |  | 0.49 | other (phosphonate) | fosfomycin | Pseudomonas syringae
BGC0002036.4 |  | 0.48 | other (other) | dehydrofosmidomycin | Streptomyces lavendulae
BGC0000904.5 |  | 0.48 | other (other) | FR-900098 | Streptomyces rubellomurinus
BGC0001739.3 |  | 0.46 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0000937.5 |  | 0.46 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372
BGC0002670.2 |  | 0.45 | other (other) | fosfonochlorin | Fusarium oxysporum f. sp. lycopersici 4287
BGC0002313.3 |  | 0.45 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000883.5 |  | 0.43 | other (other) | arginomycin | Streptomyces arginensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000926.5 |  | 0.66 | other (other) | rhizocticin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000897.5 |  | 0.50 | other (other) | dehydrophos | Streptomyces luridus
BGC0001859.4 |  | 0.49 | other (phosphonate) | fosfomycin | Pseudomonas syringae
BGC0002036.4 |  | 0.48 | other (other) | dehydrofosmidomycin | Streptomyces lavendulae
BGC0000904.5 |  | 0.48 | other (other) | FR-900098 | Streptomyces rubellomurinus
BGC0001739.3 |  | 0.46 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0000937.5 |  | 0.46 | other (other) | fosfazinomycin A, fosfazinomycin B | Streptomyces sp. WM6372
BGC0002670.2 |  | 0.45 | other (other) | fosfonochlorin | Fusarium oxysporum f. sp. lycopersici 4287
BGC0002313.3 |  | 0.45 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000883.5 |  | 0.43 | other (other) | arginomycin | Streptomyces arginensis

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 (9):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 26.85
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.55 out of 31.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.68 out of 24.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.32 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.21 out of 26.06
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.29 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.92 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.20 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP104794.1 - Region 17 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,712,716 - 5,733,801 nt. (total: 21,086 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
N6J21_RS25890: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Hydrolases: deformylase
N6J21_RS25880: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Lyases: cyclase
N6J21_RS25885: Terpene synthase/cyclase metal-binding domain protein

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

Translocases: transporter
N6J21_RS25925: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000660.5 |  | 0.87 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.76 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002012.4 |  | 0.42 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772
BGC0001910.4 |  | 0.41 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.41 | terpene | raimonol | Streptomyces anulatus
BGC0001294.5 |  | 0.41 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002339.3 |  | 0.38 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0000678.5 |  | 0.38 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000650.3 |  | 0.37 | terpene | carotenoid | Algoriphagus sp. KK10202C

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000660.5 |  | 0.87 | terpene | albaflavenone | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.76 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002012.4 |  | 0.42 | PKS | julichrome Q3-3, julichrome Q3-5 | Streptomyces afghaniensis 772
BGC0001910.4 |  | 0.41 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001911.3 |  | 0.41 | terpene | raimonol | Streptomyces anulatus
BGC0001294.5 |  | 0.41 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002339.3 |  | 0.38 | terpene | 2-hydroxysorangiadenosine | Vitiosangium cumulatum
BGC0000678.5 |  | 0.38 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000650.3 |  | 0.37 | terpene | carotenoid | Algoriphagus sp. KK10202C

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:
N6J21_RS25885: T1TS
Domain 1 (4 - 339): 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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 25.12 out of 27.18
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.21 out of 27.18
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.29 out of 27.04
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.52 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
Additional weak hits (3):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.94 out of 27.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.46 out of 20.01
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.31 out of 35.63
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
DasR | N-acetylglucosamine dependent repressor
NrdR | Represses ribonucleotide reductase encoding genes
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP104794.1 - Region 18 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,739,787 - 5,760,863 nt. (total: 21,077 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
N6J21_RS26010: 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
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000677.5 |  | 0.38 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000678.5 |  | 0.36 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002309.2 |  | 0.36 | 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
BGC0001911.3 |  | 0.34 | terpene | raimonol | Streptomyces anulatus

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
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000677.5 |  | 0.38 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000678.5 |  | 0.36 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0002309.2 |  | 0.36 | 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
BGC0001911.3 |  | 0.34 | terpene | raimonol | Streptomyces anulatus

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:
N6J21_RS26010: PT_FPPS_like
Domain 1 (63 - 356): 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: 17.92 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
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.96 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.19 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 24.69 out of 30.11
Confidence: medium
Additional weak hits (9):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.58 out of 26.12
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.83 out of 29.25
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.89 out of 23.43
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.20 out of 23.43
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 23.42 out of 32.38
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.30 out of 20.01
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
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
--- | ---
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism
ToxT | Regulator of MSHA biosynthesis
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP104794.1 - Region 19 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,295,729 - 6,325,459 nt. (total: 29,731 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
N6J21_RS28580: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
N6J21_RS28540: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
N6J21_RS28585: 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 |  | 0.54 | 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 |  | 0.50 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000859.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000858.3 |  | 0.48 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.48 | other (other) | ectoine | Methylophaga thalassica
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

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002469.2 |  | 0.54 | 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 |  | 0.50 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000852.5 |  | 0.49 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000859.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.48 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000858.3 |  | 0.48 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.48 | other (other) | ectoine | Methylophaga thalassica
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

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.79 out of 20.97
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
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 26.06 out of 27.18
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 24.62 out of 27.18
Confidence: strong
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 (6):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.42 out of 26.12
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
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
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.92 out of 26.06
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP104794.1 - Region 20 - T1PKS,T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,458,639 - 6,548,836 nt. (total: 90,198 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
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 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
N6J21_RS29215: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

N6J21_RS29225: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

N6J21_RS29235: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

N6J21_RS29260: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

N6J21_RS29325: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

N6J21_RS29345: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

N6J21_RS29355: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

N6J21_RS29390: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

N6J21_RS29435: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

N6J21_RS29480: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

N6J21_RS29510: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: PPTase acylase carbamoyltransferase halogenase transferase
N6J21_RS29255: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

N6J21_RS29270: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

N6J21_RS29280: flavin-dependent pyrrole halogenase

halogenases
  flavin-dependent pyrrole halogenase
smcogs
  SMCOG1119: halogenase

N6J21_RS29305: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

N6J21_RS29315: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

N6J21_RS29320: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

N6J21_RS29330: conventional flavin-dependent halogenase

halogenases
  conventional flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

N6J21_RS29335: flavin-dependent pyrrole halogenase

halogenases
  flavin-dependent pyrrole halogenase
smcogs
  SMCOG1119: halogenase

N6J21_RS29340: ambiguous flavin-dependent halogenase

halogenases
  ambiguous flavin-dependent halogenase
smcogs
  SMCOG1119: halogenase

N6J21_RS29395: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

N6J21_RS29465: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

Hydrolases: back translocase esterase
N6J21_RS29290: thioesterase

smcogs
  SMCOG1004: thioesterase

N6J21_RS29485: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

Lyases: cyclase hydratase
N6J21_RS29210: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

N6J21_RS29385: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

N6J21_RS29475: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
N6J21_RS29240: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

N6J21_RS29300: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS29350: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

N6J21_RS29375: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS29380: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

N6J21_RS29505: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | T1PKS | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000131.5 |  |  | 0.91 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0001160.5 |  |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001273.3 |  |  | 0.61 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  | 0.61 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  |  | 0.61 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.61 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002154.2 |  |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001258.3 |  |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000131.5 |  | 0.76 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0002341.2 |  | 0.76 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0000231.5 |  | 0.68 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001160.5 |  | 0.66 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002276.2 |  | 0.64 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001273.3 |  | 0.64 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.64 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001254.3 |  | 0.64 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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:
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 29.81 out of 35.63
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
Additional weak hits (12):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.37 out of 20.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.22 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.28 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.47 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.43 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.77 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 25.57 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.55 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Type II PKS
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 26, location 6458638 - 6548836:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (ccmal)
Non-colinear ordering:
  N6J21_RS29300 + N6J21_RS29305

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 27, location 6458638 - 6511333:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (ccmal)
Non-colinear ordering:
  N6J21_RS29300 + N6J21_RS29305

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 28, location 6476353 - 6548836:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (pk) + (ccmal)
Non-colinear ordering:
  N6J21_RS29300 + N6J21_RS29305

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).
N6J21_RS29240: NH2
CAL_domain (33..463): NH2
minowa: NH2

Prediction, score:
  NH2: 166.6
  Acetyl-CoA: 35.4
  fatty_acid: 21.5
  AHBA: 5.1
  shikimic_acid: 0.0

N6J21_RS29255: mal
PKS_AT (7..279): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 9.9
  2-Methylbutyryl-CoA: 7.4
  CHC-CoA: 6.8
  Methylmalonyl-CoA: 6.3
  trans-1,2-CPDA: 0.0
  inactive: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Methoxymalonyl-CoA: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

N6J21_RS29300: pk
PKS_AT (529..822): pk
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  Methylmalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 127.5
  Malonyl-CoA: 107.8
  Ethylmalonyl-CoA: 98.3
  Methoxymalonyl-CoA: 95.0
  trans-1,2-CPDA: 68.8
  Propionyl-CoA: 64.2
  Isobutyryl-CoA: 59.9
  2-Methylbutyryl-CoA: 46.3
  fatty_acid: 43.2
  CHC-CoA: 41.2
  inactive: 38.0
  Benzoyl-CoA: 34.6
  Acetyl-CoA: 23.0
  3-Methylbutyryl-CoA: 22.1

N6J21_RS29305: mal
PKS_AT (566..847): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 198.1
  inactive: 112.7
  Methoxymalonyl-CoA: 67.2
  Methylmalonyl-CoA: 57.1
  Isobutyryl-CoA: 38.3
  Propionyl-CoA: 34.5
  Ethylmalonyl-CoA: 26.2
  Benzoyl-CoA: 20.7
  CHC-CoA: 20.0
  Acetyl-CoA: 18.2
  2-Methylbutyryl-CoA: 16.3
  trans-1,2-CPDA: 8.3
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

N6J21_RS29350: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (12..396): 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:
    Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWAAFDLSVFDGYSLFAGELNWYGPTETNVCTSY
  Nearest Stachelhaus code(s):
    Pro DLFYLAWVCK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

N6J21_RS29505: X
AMP-binding (57..433): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    ITFPFGLGGLVPFTVSAGEINGIGATELLHIFVS
  Nearest Stachelhaus code(s):
    D-Hiv GALHVVGSIK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Cluster section:
  6476353 to 6548836
Starter unit(s):
  propionyl-CoA (Score: 186.8; E-value: 7.39e-37)
  butyryl-CoA (Score: 80.9; E-value: 6.48e-19)

N6J21_RS29300
  AT (Score: 188.2; E-value: 4.6e-58)
  AT AAC18106.1_Frenolicin_butyryl-CoA (Score: 80.9; E-value: 6.48e-19)
  AT ABC00730.1_Cosmomycin_propionyl-CoA (Score: 31.6; E-value: 0.003)
N6J21_RS29305
  AT (Score: 186.7; E-value: 1.3e-57)
  AT WP_100109099.1_Doxorubicin_propionyl-CoA (Score: 134.0; E-value: 7.39e-37)
  AT ABC00730.1_Cosmomycin_propionyl-CoA (Score: 21.2; E-value: 6.0)
N6J21_RS29315
  HAL (Score: 381.9; E-value: 9.2e-117)
N6J21_RS29320
  HAL (Score: 489.5; E-value: 2.1e-149)
N6J21_RS29325
  OXY (Score: 353.1; E-value: 6.1e-108)
N6J21_RS29330
  HAL (Score: 375.5; E-value: 8e-115)
N6J21_RS29335
  HAL (Score: 411.1; E-value: 1.3e-125)
N6J21_RS29340
  OXY (Score: 11.5; E-value: 0.00026)
N6J21_RS29375
  KS (Score: 708.8; E-value: 4.8e-216)
N6J21_RS29380
  CLF (Score: 573.1; E-value: 7e-175)
N6J21_RS29385
  CYC C7-C12 (Score: 314.3; E-value: 1.5e-96)
N6J21_RS29390
  KR (Score: 84.0; E-value: 3e-26)
N6J21_RS29405
  CYC C5-C14 (Score: 449.7; E-value: 1e-137)
N6J21_RS29480
  OXY (Score: 34.0; E-value: 3.9e-11)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
NrtR | NAD synthesis repressor

NZ_CP104794.1 - Region 21 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,643,095 - 6,654,378 nt. (total: 11,284 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
N6J21_RS29915: 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
--- | --- | --- | --- | --- | ---
BGC0002387.2 |  | 0.30 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001377.5 |  | 0.26 | PKS | uncialamycin | Streptomyces uncialis
BGC0002788.2 |  | 0.25 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0001060.5 |  | 0.24 | PKS | dynemicin A | Micromonospora chersina
BGC0001984.3 |  | 0.23 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0000241.5 |  | 0.20 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440
BGC0000029.5 |  | 0.20 | PKS | BE-14106 | Streptomyces sp. DSM 21069
BGC0001693.3 |  | 0.20 | PKS | nenestatin | Micromonospora echinospora
BGC0000240.5 |  | 0.20 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora pacifica
BGC0000233.5 |  | 0.19 | PKS | hedamycin | Streptomyces griseoruber

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002387.2 |  | 0.30 | PKS | yangpumicin A | Micromonospora yangpuensis
BGC0001377.5 |  | 0.26 | PKS | uncialamycin | Streptomyces uncialis
BGC0002788.2 |  | 0.25 | PKS | 14-hydroxyisochainin | Streptomyces peucetius subsp. caesius ATCC 27952
BGC0001060.5 |  | 0.24 | PKS | dynemicin A | Micromonospora chersina
BGC0001984.3 |  | 0.23 | NRPS | sarpeptin A, sarpeptin B | Streptomyces sp.
BGC0000241.5 |  | 0.20 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora tropica CNB-440
BGC0000029.5 |  | 0.20 | PKS | BE-14106 | Streptomyces sp. DSM 21069
BGC0001693.3 |  | 0.20 | PKS | nenestatin | Micromonospora echinospora
BGC0000240.5 |  | 0.20 | PKS, saccharide | lomaiviticin A, lomaiviticin C, lomaiviticin D, lomaiviticin E | Salinispora pacifica
BGC0000233.5 |  | 0.19 | PKS | hedamycin | Streptomyces griseoruber

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):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.89 out of 29.38
Confidence: weak
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
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.42 out of 27.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.28 out of 26.85
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP104794.1 - Region 22 - 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: 6,700,788 - 6,723,096 nt. (total: 22,309 nt) Show pHMM detection rules used
butyrolactone: AfsA
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
N6J21_RS30195: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: glucanase hydrolase peptidase protease
N6J21_RS30165: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

N6J21_RS30200: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

N6J21_RS30230: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

N6J21_RS30245: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

Lyases: cyclase
N6J21_RS30205: 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 | butyrolactone | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000850.5 |  |  | 1.16 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000849.4 |  |  | 1.00 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  |  | 0.95 | 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 |  |  | 0.32 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002031.3 |  |  | 0.30 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000595.3 |  |  | 0.26 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001485.4 |  |  | 0.24 | other (other) | chuangxinmycin | Actinoplanes tsinanensis

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 |  | 0.77 | 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
BGC0000595.3 |  | 0.43 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001285.5 |  | 0.42 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida

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:
N6J21_RS30205: T1TS + T1TS
Domain 1 (1 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (331 - 696): 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.
No hits above weak threshold.
Weak hits (4):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.70 out of 27.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.49 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.40 out of 30.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.92 out of 25.75
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
--- | ---

NZ_CP104794.1 - Region 23 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,868,904 - 6,899,999 nt. (total: 31,096 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
N6J21_RS30985: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase
N6J21_RS30910: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Isomerases: mutase
N6J21_RS30900: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.49 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000946.5 |  | 0.46 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000894.4 |  | 0.46 | other (other) | citrinin | Monascus aurantiacus
BGC0001206.5 |  | 0.42 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0000902.4 |  | 0.42 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0002584.2 |  | 0.42 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000204.5 |  | 0.41 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0001184.4 |  | 0.41 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000888.5 |  | 0.40 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000188.5 |  | 0.40 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.49 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0000946.5 |  | 0.46 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000894.4 |  | 0.46 | other (other) | citrinin | Monascus aurantiacus
BGC0001206.5 |  | 0.42 | other (other) | indolmycin | Streptomyces griseus subsp. griseus
BGC0000902.4 |  | 0.42 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0002584.2 |  | 0.42 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0000204.5 |  | 0.41 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0001184.4 |  | 0.41 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000888.5 |  | 0.40 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000188.5 |  | 0.40 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3

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

No significant matches found.

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:
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 22.40
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84
Confidence: medium
Additional weak hits (17):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.33 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.55 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.29 out of 27.04
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.52 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.96 out of 26.06
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.58 out of 20.01
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.68 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.44 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.71 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.89 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.68 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.95 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.91 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.81 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
HypR | L-hydroxyproline utilization repressor
MexT | Global virulence regulator

NZ_CP104794.1 - Region 24 - 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: 6,931,044 - 6,972,105 nt. (total: 41,062 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
N6J21_RS31190: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: methyltransferase
N6J21_RS31205: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase peptidase
N6J21_RS31120: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

N6J21_RS31165: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

N6J21_RS31250: gamma-glutamyltranspeptidase

smcogs
  SMCOG1274: gamma-glutamyltranspeptidase

N6J21_RS31260: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Ligases: synthase
N6J21_RS31175: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001905.4 |  | 0.46 | PKS | violapyrone B | Streptomyces somaliensis
BGC0001333.5 |  | 0.43 | other (other) | BE-54017 | uncultured bacterium AB1650
BGC0000821.5 |  | 0.43 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0001334.5 |  | 0.43 | other (other) | caldoniamide A, cladoniamide B, cladoniamide C7, cladoniamide D, cladoniamide E, cladoniamide F, cladoniamide G | Streptomyces uncialis
BGC0001831.3 |  | 0.42 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001223.5 |  | 0.42 | other (other) | hydroxysporine | uncultured bacterium
BGC0002514.3 |  | 0.42 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0002362.3 |  | 0.42 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0000602.5 |  | 0.42 | ribosomal | subtilosin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0001337.5 |  | 0.42 | other (other) | lazarimide A, lazarimide B, lazarimide C | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001905.4 |  | 0.46 | PKS | violapyrone B | Streptomyces somaliensis
BGC0001333.5 |  | 0.43 | other (other) | BE-54017 | uncultured bacterium AB1650
BGC0000821.5 |  | 0.43 | other (other) | rebeccamycin | Lechevalieria aerocolonigenes
BGC0001334.5 |  | 0.43 | other (other) | caldoniamide A, cladoniamide B, cladoniamide C7, cladoniamide D, cladoniamide E, cladoniamide F, cladoniamide G | Streptomyces uncialis
BGC0001831.3 |  | 0.42 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001223.5 |  | 0.42 | other (other) | hydroxysporine | uncultured bacterium
BGC0002514.3 |  | 0.42 | PKS | julichrome Q6.6 | Streptomyces sampsonii
BGC0002362.3 |  | 0.42 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0000602.5 |  | 0.42 | ribosomal | subtilosin A | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0001337.5 |  | 0.42 | other (other) | lazarimide A, lazarimide B, lazarimide C | 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.

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
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 25.31
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.38 out of 27.04
Confidence: medium
Additional weak hits (15):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.84 out of 32.74
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.29 out of 33.73
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.09 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.76 out of 26.06
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.13 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.92 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.14 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.11 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.84 out of 29.38
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.63 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.90 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.86 out of 28.14
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
DasR | N-acetylglucosamine dependent repressor

NZ_CP104794.1 - Region 25 - hydrogen-cyanide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,212,465 - 7,225,320 nt. (total: 12,856 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
N6J21_RS32310: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

N6J21_RS32320: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: PPTase
N6J21_RS32285: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

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
BGC0000571.3 |  | 0.41 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0002144.3 |  | 0.40 | ribosomal | phazolicin | Rhizobium sp. Pop5
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0002285.2 |  | 0.39 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001341.4 |  | 0.37 | NRPS | valinomycin | Rothia nasimurium
BGC0000897.5 |  | 0.34 | other (other) | dehydrophos | Streptomyces luridus
BGC0001364.3 |  | 0.34 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002465.2 |  | 0.33 | NRPS | amphibactin E, amphibactin H, amphibactin I | Alcanivorax borkumensis SK2
BGC0002494.3 |  | 0.33 | NRPS | vibriobactin | Vibrio cholerae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0000571.3 |  | 0.41 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0002144.3 |  | 0.40 | ribosomal | phazolicin | Rhizobium sp. Pop5
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0002285.2 |  | 0.39 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001341.4 |  | 0.37 | NRPS | valinomycin | Rothia nasimurium
BGC0000897.5 |  | 0.34 | other (other) | dehydrophos | Streptomyces luridus
BGC0001364.3 |  | 0.34 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002465.2 |  | 0.33 | NRPS | amphibactin E, amphibactin H, amphibactin I | Alcanivorax borkumensis SK2
BGC0002494.3 |  | 0.33 | NRPS | vibriobactin | Vibrio cholerae

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:
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 22.40
Confidence: strong
Additional weak hits (6):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.21 out of 20.01
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 17.67 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 out of 22.40
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
HypR | L-hydroxyproline utilization repressor

NZ_CP104794.1 - Region 26 - 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: 7,307,366 - 7,333,980 nt. (total: 26,615 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
N6J21_RS32745: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

N6J21_RS32780: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: aminotransferase transferase
N6J21_RS32740: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

N6J21_RS32815: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: dehydratase
N6J21_RS32730: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase synthetase
N6J21_RS32785: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

N6J21_RS32810: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.81 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.58 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000664.5 |  | 0.50 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0002736.2 |  | 0.49 | terpene | preaspterpenacid I | Aspergillus terreus NIH2624
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000651.5 |  | 0.49 | terpene | KS-505a | Streptomyces argenteolus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.81 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.58 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000664.5 |  | 0.50 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0002736.2 |  | 0.49 | terpene | preaspterpenacid I | Aspergillus terreus NIH2624
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000651.5 |  | 0.49 | terpene | KS-505a | Streptomyces argenteolus

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:
N6J21_RS32770: PT_phytoene_like
Domain 1 (19 - 278): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

N6J21_RS32775: PT_phytoene_like
Domain 1 (17 - 310): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

N6J21_RS32785: PT_FPPS_like
Domain 1 (82 - 376): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

N6J21_RS32790: T2TS
Domain 1 (28 - 652): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (6):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.90 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.18 out of 27.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.58 out of 26.12
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.68 out of 29.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 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
--- | ---

NZ_CP104794.1 - Region 27 - PKS-like,T1PKS,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: 7,464,895 - 7,683,158 nt. (total: 218,264 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
butyrolactone: AfsA
PKS-like: (t2pks2 or ksIII)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
N6J21_RS33405: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

N6J21_RS33420: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

N6J21_RS33425: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

N6J21_RS33505: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

N6J21_RS33565: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

N6J21_RS33570: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

N6J21_RS33635: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

N6J21_RS33645: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: PPTase acylase glycosyltransferase transferase
N6J21_RS33500: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

N6J21_RS33615: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

N6J21_RS33625: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

N6J21_RS33695: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

Hydrolases: esterase
N6J21_RS33705: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase hydratase
N6J21_RS33475: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

N6J21_RS33530: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

N6J21_RS33630: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

N6J21_RS33685: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
N6J21_RS33495: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS33575: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

N6J21_RS33580: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS33585: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS33590: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS33610: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS33650: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS33655: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS33660: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

N6J21_RS33665: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | T1PKS | butyrolactone | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001275.3 |  |  |  | 0.83 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  |  | 0.82 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002191.2 |  |  |  | 0.58 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002192.3 |  |  |  | 0.55 | PKS | FR901512 | fungal sp. No.14919
BGC0000016.4 |  |  |  | 0.49 | other (other) | amphotericin B | Streptomyces nodosus
BGC0000041.3 |  |  |  | 0.48 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002164.2 |  |  |  | 0.47 | NRPS | peramine | Epichloe festucae
BGC0001273.3 |  |  |  | 0.42 | PKS | asperlactone | Aspergillus ochraceus
BGC0000067.5 |  |  |  | 0.39 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0000850.5 |  |  |  | 0.38 | other (other) | γ-butyrolactone | Streptomyces acidiscabies

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.73 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000041.3 |  | 0.66 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0000067.5 |  | 0.61 | PKS | geldanamycin | Streptomyces hygroscopicus subsp. duamyceticus
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.57 out of 20.97
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (18):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.06 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.30 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.59 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.65 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.45 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.82 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.32 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.35 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.55 out of 30.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.97 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.21 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.48 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.82 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.89 out of 30.25
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.49 out of 19.26
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.42 out of 28.19
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.24 out of 32.38
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 37, location 7464894 - 7683158:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-ohmal - Me-ohmal) + (Me-ohmal - Me-ohmal - ccmal) + (mal - redmal - redmal - redmal) + (redmal - ccmal - ohmal) + (ccmal) + (ccmal - redmal) + (ohmal - ohmal - ohmal) + (ohmal - ohmal - mal - Me-ohmal - redmal) + (ohmal - redmal - ohmal) + (Me-ohmal - ccmal)
Non-colinear ordering:
  N6J21_RS33495 + N6J21_RS33500 + N6J21_RS33650 + N6J21_RS33655 + N6J21_RS33660 + N6J21_RS33575 + N6J21_RS33580 + N6J21_RS33585 + N6J21_RS33590 + N6J21_RS33610

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 38, location 7464894 - 7682029:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-ohmal - Me-ohmal) + (Me-ohmal - Me-ohmal - ccmal) + (mal - redmal - redmal - redmal) + (redmal - ccmal - ohmal) + (ccmal) + (ccmal - redmal) + (ohmal - ohmal - ohmal) + (ohmal - ohmal - mal - Me-ohmal - redmal) + (ohmal - redmal - ohmal) + (Me-ohmal - ccmal)
Non-colinear ordering:
  N6J21_RS33495 + N6J21_RS33500 + N6J21_RS33650 + N6J21_RS33655 + N6J21_RS33660 + N6J21_RS33575 + N6J21_RS33580 + N6J21_RS33585 + N6J21_RS33590 + N6J21_RS33610

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 39, location 7642099 - 7683158:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (redmal - ccmal - ohmal) + (ccmal)
Non-colinear ordering:
  N6J21_RS33655 + N6J21_RS33660

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).
N6J21_RS33495: mmal - mmal - mmal
PKS_AT (545..834): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 199.1
  Ethylmalonyl-CoA: 176.1
  Methoxymalonyl-CoA: 158.9
  2-Methylbutyryl-CoA: 118.7
  Propionyl-CoA: 102.2
  trans-1,2-CPDA: 99.2
  CHC-CoA: 82.0
  Malonyl-CoA: 77.0
  Benzoyl-CoA: 58.8
  Isobutyryl-CoA: 57.9
  Acetyl-CoA: 47.2
  fatty_acid: 24.3
  3-Methylbutyryl-CoA: 22.3
  inactive: 15.9

PKS_AT (1542..1829): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 202.3
  Ethylmalonyl-CoA: 180.0
  Methoxymalonyl-CoA: 164.4
  2-Methylbutyryl-CoA: 127.7
  trans-1,2-CPDA: 108.8
  Propionyl-CoA: 102.6
  Malonyl-CoA: 81.1
  CHC-CoA: 80.7
  Benzoyl-CoA: 55.0
  Isobutyryl-CoA: 52.3
  Acetyl-CoA: 38.8
  fatty_acid: 30.4
  3-Methylbutyryl-CoA: 25.3
  inactive: 21.3

PKS_AT (3081..3368): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.8
  Ethylmalonyl-CoA: 182.7
  Methoxymalonyl-CoA: 168.8
  2-Methylbutyryl-CoA: 131.6
  trans-1,2-CPDA: 111.5
  Propionyl-CoA: 103.5
  Malonyl-CoA: 82.6
  CHC-CoA: 81.4
  Isobutyryl-CoA: 54.7
  Benzoyl-CoA: 52.9
  Acetyl-CoA: 39.9
  fatty_acid: 30.5
  3-Methylbutyryl-CoA: 24.4
  inactive: 21.4

N6J21_RS33500: mmal - mmal - mal
PKS_AT (573..860): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.3
  Ethylmalonyl-CoA: 182.7
  Methoxymalonyl-CoA: 168.0
  2-Methylbutyryl-CoA: 123.1
  trans-1,2-CPDA: 105.0
  Propionyl-CoA: 103.8
  Malonyl-CoA: 85.0
  CHC-CoA: 80.2
  Benzoyl-CoA: 52.0
  Isobutyryl-CoA: 50.6
  Acetyl-CoA: 34.4
  fatty_acid: 23.9
  3-Methylbutyryl-CoA: 23.5
  inactive: 21.5

PKS_AT (2133..2420): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 205.6
  Ethylmalonyl-CoA: 186.1
  Methoxymalonyl-CoA: 168.0
  2-Methylbutyryl-CoA: 127.3
  trans-1,2-CPDA: 109.4
  Propionyl-CoA: 103.0
  Malonyl-CoA: 87.6
  CHC-CoA: 83.9
  Benzoyl-CoA: 54.6
  Isobutyryl-CoA: 51.2
  Acetyl-CoA: 39.0
  fatty_acid: 32.9
  3-Methylbutyryl-CoA: 27.1
  inactive: 22.4

PKS_AT (3672..3972): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 220.2
  inactive: 106.4
  Methoxymalonyl-CoA: 87.5
  Methylmalonyl-CoA: 78.1
  Isobutyryl-CoA: 48.8
  Ethylmalonyl-CoA: 47.6
  fatty_acid: 36.9
  Propionyl-CoA: 35.6
  Benzoyl-CoA: 30.2
  CHC-CoA: 27.5
  Acetyl-CoA: 23.3
  2-Methylbutyryl-CoA: 20.3
  trans-1,2-CPDA: 19.5
  3-Methylbutyryl-CoA: 0.0

N6J21_RS33575: mal - mal
PKS_AT (573..860): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 215.4
  inactive: 108.8
  Methylmalonyl-CoA: 63.0
  Methoxymalonyl-CoA: 60.9
  Propionyl-CoA: 41.9
  Isobutyryl-CoA: 27.0
  fatty_acid: 25.2
  Ethylmalonyl-CoA: 24.8
  Acetyl-CoA: 20.6
  2-Methylbutyryl-CoA: 18.5
  Benzoyl-CoA: 16.6
  CHC-CoA: 13.8
  trans-1,2-CPDA: 12.0
  3-Methylbutyryl-CoA: 8.5

PKS_AT (2278..2565): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 205.0
  inactive: 96.7
  Methoxymalonyl-CoA: 64.6
  Methylmalonyl-CoA: 46.7
  Propionyl-CoA: 26.0
  Isobutyryl-CoA: 22.7
  Acetyl-CoA: 20.6
  Benzoyl-CoA: 16.9
  Ethylmalonyl-CoA: 15.1
  fatty_acid: 12.7
  2-Methylbutyryl-CoA: 9.6
  CHC-CoA: 9.2
  trans-1,2-CPDA: 4.4
  3-Methylbutyryl-CoA: 0.0

N6J21_RS33580: mal - mal - mal
PKS_AT (563..856): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 216.7
  inactive: 109.8
  Methylmalonyl-CoA: 64.2
  Methoxymalonyl-CoA: 62.7
  Propionyl-CoA: 40.8
  fatty_acid: 26.8
  Isobutyryl-CoA: 26.4
  Ethylmalonyl-CoA: 23.4
  2-Methylbutyryl-CoA: 21.4
  Acetyl-CoA: 18.1
  Benzoyl-CoA: 16.6
  CHC-CoA: 14.2
  trans-1,2-CPDA: 6.5
  3-Methylbutyryl-CoA: 5.9

PKS_AT (2087..2383): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 184.1
  inactive: 82.6
  Methoxymalonyl-CoA: 50.7
  Methylmalonyl-CoA: 42.3
  Propionyl-CoA: 27.7
  Acetyl-CoA: 23.3
  Ethylmalonyl-CoA: 17.3
  Isobutyryl-CoA: 14.3
  Benzoyl-CoA: 14.0
  fatty_acid: 12.5
  2-Methylbutyryl-CoA: 11.1
  CHC-CoA: 9.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3626..3916): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 223.0
  inactive: 109.5
  Methoxymalonyl-CoA: 68.8
  Methylmalonyl-CoA: 67.2
  Propionyl-CoA: 41.6
  Isobutyryl-CoA: 29.6
  Ethylmalonyl-CoA: 27.5
  Acetyl-CoA: 22.8
  2-Methylbutyryl-CoA: 18.6
  CHC-CoA: 17.3
  Benzoyl-CoA: 16.8
  trans-1,2-CPDA: 13.6
  fatty_acid: 13.6
  3-Methylbutyryl-CoA: 0.0

N6J21_RS33585: mal - mal - mal - mmal - mal
PKS_AT (563..856): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 218.1
  inactive: 106.4
  Methylmalonyl-CoA: 64.2
  Methoxymalonyl-CoA: 60.4
  Propionyl-CoA: 40.1
  Isobutyryl-CoA: 28.5
  Ethylmalonyl-CoA: 27.5
  fatty_acid: 17.4
  Acetyl-CoA: 17.0
  Benzoyl-CoA: 15.5
  CHC-CoA: 13.2
  trans-1,2-CPDA: 10.3
  2-Methylbutyryl-CoA: 7.1
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2079..2362): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 217.4
  inactive: 103.4
  Methylmalonyl-CoA: 65.6
  Methoxymalonyl-CoA: 62.9
  Propionyl-CoA: 41.0
  Isobutyryl-CoA: 29.7
  Ethylmalonyl-CoA: 22.7
  Acetyl-CoA: 21.9
  fatty_acid: 21.2
  CHC-CoA: 17.2
  trans-1,2-CPDA: 16.7
  Benzoyl-CoA: 14.6
  2-Methylbutyryl-CoA: 12.4
  3-Methylbutyryl-CoA: 6.0

PKS_AT (3603..3884): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 225.0
  inactive: 110.1
  Methoxymalonyl-CoA: 64.6
  Methylmalonyl-CoA: 59.4
  Propionyl-CoA: 44.4
  Isobutyryl-CoA: 30.6
  2-Methylbutyryl-CoA: 26.2
  Acetyl-CoA: 22.2
  Ethylmalonyl-CoA: 18.4
  fatty_acid: 16.5
  Benzoyl-CoA: 12.8
  CHC-CoA: 11.1
  trans-1,2-CPDA: 3.6
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4915..5213): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 197.2
  Ethylmalonyl-CoA: 175.3
  Methoxymalonyl-CoA: 153.7
  2-Methylbutyryl-CoA: 151.6
  trans-1,2-CPDA: 127.2
  Propionyl-CoA: 100.5
  CHC-CoA: 90.7
  Isobutyryl-CoA: 62.8
  Malonyl-CoA: 58.6
  Benzoyl-CoA: 49.9
  3-Methylbutyryl-CoA: 42.2
  Acetyl-CoA: 39.9
  fatty_acid: 35.4
  inactive: 10.9

PKS_AT (6476..6766): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 223.3
  inactive: 107.6
  Methoxymalonyl-CoA: 75.0
  Methylmalonyl-CoA: 74.2
  Propionyl-CoA: 43.9
  Ethylmalonyl-CoA: 39.5
  Isobutyryl-CoA: 35.7
  2-Methylbutyryl-CoA: 21.6
  Acetyl-CoA: 20.9
  trans-1,2-CPDA: 17.3
  CHC-CoA: 15.6
  Benzoyl-CoA: 15.6
  fatty_acid: 15.1
  3-Methylbutyryl-CoA: 0.0

N6J21_RS33590: mal - mal - mal
PKS_AT (569..856): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 210.7
  inactive: 94.8
  Methoxymalonyl-CoA: 60.5
  Methylmalonyl-CoA: 46.2
  Propionyl-CoA: 40.1
  Benzoyl-CoA: 20.9
  Acetyl-CoA: 20.4
  2-Methylbutyryl-CoA: 20.4
  Ethylmalonyl-CoA: 17.5
  Isobutyryl-CoA: 17.4
  fatty_acid: 16.4
  CHC-CoA: 13.9
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2220..2510): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 214.9
  inactive: 90.6
  Methoxymalonyl-CoA: 61.7
  Methylmalonyl-CoA: 59.6
  Propionyl-CoA: 37.8
  Acetyl-CoA: 23.2
  Isobutyryl-CoA: 18.9
  Benzoyl-CoA: 16.4
  fatty_acid: 15.4
  CHC-CoA: 15.3
  Ethylmalonyl-CoA: 15.0
  2-Methylbutyryl-CoA: 13.4
  trans-1,2-CPDA: 7.7
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4252..4553): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 203.0
  inactive: 101.7
  Methoxymalonyl-CoA: 75.4
  Methylmalonyl-CoA: 59.9
  Isobutyryl-CoA: 39.7
  Propionyl-CoA: 27.0
  CHC-CoA: 22.9
  Benzoyl-CoA: 21.4
  2-Methylbutyryl-CoA: 20.8
  Acetyl-CoA: 19.7
  Ethylmalonyl-CoA: 19.1
  fatty_acid: 13.5
  trans-1,2-CPDA: 13.4
  3-Methylbutyryl-CoA: 7.6

N6J21_RS33610: mmal - mal
PKS_AT (565..863): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 214.5
  Ethylmalonyl-CoA: 211.0
  Methoxymalonyl-CoA: 176.0
  2-Methylbutyryl-CoA: 146.6
  trans-1,2-CPDA: 145.8
  Propionyl-CoA: 111.9
  Malonyl-CoA: 105.9
  CHC-CoA: 88.2
  Isobutyryl-CoA: 63.0
  Benzoyl-CoA: 58.0
  inactive: 38.9
  Acetyl-CoA: 38.6
  3-Methylbutyryl-CoA: 35.9
  fatty_acid: 28.2

PKS_AT (2146..2432): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.5
  inactive: 102.2
  Methoxymalonyl-CoA: 65.0
  Methylmalonyl-CoA: 62.2
  Propionyl-CoA: 41.7
  Ethylmalonyl-CoA: 28.2
  Isobutyryl-CoA: 27.2
  2-Methylbutyryl-CoA: 26.0
  Acetyl-CoA: 21.8
  fatty_acid: 14.8
  Benzoyl-CoA: 14.1
  CHC-CoA: 12.0
  trans-1,2-CPDA: 10.4
  3-Methylbutyryl-CoA: 0.0

N6J21_RS33650: mal - mal - mal - mal
PKS_AT (528..818): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 212.3
  inactive: 97.1
  Methoxymalonyl-CoA: 62.6
  Methylmalonyl-CoA: 58.8
  Propionyl-CoA: 39.1
  Isobutyryl-CoA: 24.6
  Ethylmalonyl-CoA: 24.4
  Benzoyl-CoA: 22.8
  2-Methylbutyryl-CoA: 20.7
  Acetyl-CoA: 20.5
  CHC-CoA: 18.4
  fatty_acid: 16.8
  trans-1,2-CPDA: 9.6
  3-Methylbutyryl-CoA: 0.0

PKS_AT (1541..1829): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 218.6
  inactive: 107.0
  Methylmalonyl-CoA: 67.9
  Methoxymalonyl-CoA: 65.6
  Isobutyryl-CoA: 32.8
  Propionyl-CoA: 31.8
  Ethylmalonyl-CoA: 23.3
  Acetyl-CoA: 18.7
  CHC-CoA: 13.4
  2-Methylbutyryl-CoA: 13.1
  fatty_acid: 13.0
  trans-1,2-CPDA: 12.4
  Benzoyl-CoA: 12.2
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3577..3866): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 214.2
  inactive: 107.8
  Methoxymalonyl-CoA: 54.4
  Methylmalonyl-CoA: 53.7
  Propionyl-CoA: 30.0
  Acetyl-CoA: 19.0
  fatty_acid: 18.1
  Isobutyryl-CoA: 15.6
  Benzoyl-CoA: 15.5
  CHC-CoA: 14.4
  Ethylmalonyl-CoA: 13.6
  trans-1,2-CPDA: 8.2
  2-Methylbutyryl-CoA: 7.8
  3-Methylbutyryl-CoA: 0.0

PKS_AT (5626..5917): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 212.9
  inactive: 101.2
  Methoxymalonyl-CoA: 53.8
  Methylmalonyl-CoA: 51.6
  Propionyl-CoA: 43.7
  Acetyl-CoA: 20.3
  Isobutyryl-CoA: 19.0
  Ethylmalonyl-CoA: 15.8
  Benzoyl-CoA: 15.5
  2-Methylbutyryl-CoA: 12.8
  CHC-CoA: 10.9
  fatty_acid: 10.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

N6J21_RS33655: mal - mal - mal
PKS_AT (572..861): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 75.0%
  2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 208.9
  inactive: 107.4
  Methoxymalonyl-CoA: 52.7
  Methylmalonyl-CoA: 48.7
  Propionyl-CoA: 22.9
  Acetyl-CoA: 17.9
  fatty_acid: 15.7
  Benzoyl-CoA: 15.5
  CHC-CoA: 13.5
  Isobutyryl-CoA: 13.1
  Ethylmalonyl-CoA: 13.0
  trans-1,2-CPDA: 8.5
  2-Methylbutyryl-CoA: 6.4
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2623..2917): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 217.2
  inactive: 98.3
  Methylmalonyl-CoA: 63.8
  Methoxymalonyl-CoA: 63.5
  Propionyl-CoA: 38.3
  Acetyl-CoA: 24.5
  Isobutyryl-CoA: 24.0
  Ethylmalonyl-CoA: 23.9
  2-Methylbutyryl-CoA: 18.9
  CHC-CoA: 18.8
  fatty_acid: 12.1
  Benzoyl-CoA: 11.4
  trans-1,2-CPDA: 10.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4397..4682): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 216.4
  inactive: 92.9
  Methylmalonyl-CoA: 59.5
  Methoxymalonyl-CoA: 57.3
  Propionyl-CoA: 38.7
  Isobutyryl-CoA: 22.6
  Acetyl-CoA: 20.4
  Ethylmalonyl-CoA: 19.7
  Benzoyl-CoA: 16.7
  2-Methylbutyryl-CoA: 15.6
  fatty_acid: 13.4
  CHC-CoA: 12.3
  trans-1,2-CPDA: 6.1
  3-Methylbutyryl-CoA: 0.0

N6J21_RS33660: mal
PKS_AT (571..854): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.7
  inactive: 109.1
  Methoxymalonyl-CoA: 59.5
  Methylmalonyl-CoA: 52.0
  Propionyl-CoA: 40.4
  Ethylmalonyl-CoA: 23.8
  Isobutyryl-CoA: 23.2
  Acetyl-CoA: 22.6
  CHC-CoA: 21.7
  Benzoyl-CoA: 16.8
  2-Methylbutyryl-CoA: 14.9
  fatty_acid: 10.7
  trans-1,2-CPDA: 9.7
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production
CcpA | Catabolite control protein A

NZ_CP104794.1 - Region 28 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,791,116 - 7,802,531 nt. (total: 11,416 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
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Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
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MIBiG comparison
KnownClusterBlast
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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
N6J21_RS34240: 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 |  | 0.48 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000844.5 |  | 0.43 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001224.5 |  | 0.39 | other (other) | reductasporine | uncultured bacterium
BGC0001485.4 |  | 0.38 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002825.2 |  | 0.34 | ribosomal | nocapeptin A | Nocardia terpenica IFM 0406
BGC0001336.5 |  | 0.34 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001483.4 |  | 0.33 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001223.5 |  | 0.33 | other (other) | hydroxysporine | uncultured bacterium
BGC0001605.3 |  | 0.32 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002482.2 |  | 0.31 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002631.2 |  | 0.48 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000844.5 |  | 0.43 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0001224.5 |  | 0.39 | other (other) | reductasporine | uncultured bacterium
BGC0001485.4 |  | 0.38 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002825.2 |  | 0.34 | ribosomal | nocapeptin A | Nocardia terpenica IFM 0406
BGC0001336.5 |  | 0.34 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001483.4 |  | 0.33 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001223.5 |  | 0.33 | other (other) | hydroxysporine | uncultured bacterium
BGC0001605.3 |  | 0.32 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002482.2 |  | 0.31 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31
Confidence: medium
Additional weak hits (3):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.57 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.74 out of 27.78
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP104794.1 - Region 29 - betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,811,537 - 7,845,820 nt. (total: 34,284 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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: carboxylase methyltransferase
N6J21_RS34405: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

N6J21_RS34410: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Ligases: ligase
N6J21_RS34355: 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 | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002193.2 |  | 0.56 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0000357.5 |  | 0.56 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001758.4 |  | 0.55 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.55 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.55 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.55 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000503.5 |  | 0.44 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000528.5 |  | 0.44 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.56 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002193.2 |  | 0.56 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0000357.5 |  | 0.56 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001758.4 |  | 0.55 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.55 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.55 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.55 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000503.5 |  | 0.44 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000528.5 |  | 0.44 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382

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: 19.29 out of 23.79
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (8):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.14 out of 30.22
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.04 out of 21.55
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.95 out of 27.55
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.85 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.12 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.44 out of 18.57
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.00 out of 21.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.67 out of 28.19
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism

NZ_CP104794.1 - Region 30 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,989,827 - 8,000,042 nt. (total: 10,216 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000518.3 |  | 0.52 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0001555.4 |  | 0.47 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.46 | ribosomal | microcin N | Escherichia coli
BGC0000588.5 |  | 0.45 | ribosomal | microcin L | Escherichia coli
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002698.2 |  | 0.41 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0001638.4 |  | 0.40 | ribosomal | klebsazolicin | Klebsiella pneumoniae subsp. ozaenae
BGC0000500.5 |  | 0.38 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0000617.5 |  | 0.38 | ribosomal | coagulin | Bacillus coagulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000518.3 |  | 0.52 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0001555.4 |  | 0.47 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000590.5 |  | 0.46 | ribosomal | microcin N | Escherichia coli
BGC0000588.5 |  | 0.45 | ribosomal | microcin L | Escherichia coli
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002698.2 |  | 0.41 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0001638.4 |  | 0.40 | ribosomal | klebsazolicin | Klebsiella pneumoniae subsp. ozaenae
BGC0000500.5 |  | 0.38 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum
BGC0000617.5 |  | 0.38 | ribosomal | coagulin | Bacillus coagulans

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.29 out of 23.79
Confidence: medium
Additional weak hits (4):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.11 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.45 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.38 out of 36.53
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.24 out of 29.25
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_CP104794.1 - Region 31 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,041,048 - 8,052,910 nt. (total: 11,863 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: oxidoreductase
N6J21_RS35400: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Hydrolases: protease
N6J21_RS35385: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002316.2 |  | 0.37 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001157.6 |  | 0.35 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0001387.5 |  | 0.35 | other (other) | nucleocidin | Streptomyces calvus
BGC0000468.5 |  | 0.35 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0000470.6 |  | 0.35 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0001810.3 |  | 0.34 | PKS | trehangelin | Polymorphospora rubra
BGC0001513.3 |  | 0.34 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000598.5 |  | 0.33 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0000469.6 |  | 0.33 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000662.5 |  | 0.33 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002316.2 |  | 0.37 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001157.6 |  | 0.35 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0001387.5 |  | 0.35 | other (other) | nucleocidin | Streptomyces calvus
BGC0000468.5 |  | 0.35 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0000470.6 |  | 0.35 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0001810.3 |  | 0.34 | PKS | trehangelin | Polymorphospora rubra
BGC0001513.3 |  | 0.34 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000598.5 |  | 0.33 | ribosomal | polytheonamide A, polytheonamide B | Candidatus Entotheonella factor
BGC0000469.6 |  | 0.33 | ribosomal | bottromycin A2 | Streptomyces sp. BC16019
BGC0000662.5 |  | 0.33 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (2):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.44 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP104794.1 - Region 32 - NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,237,717 - 8,308,417 nt. (total: 70,701 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
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
N6J21_RS36280: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

N6J21_RS36305: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

N6J21_RS36410: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

N6J21_RS36420: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

N6J21_RS36525: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: acylase
N6J21_RS36405: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase
N6J21_RS36375: thioesterase

smcogs
  SMCOG1004: thioesterase

N6J21_RS36490: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

Ligases: ligase synthase
N6J21_RS36295: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

N6J21_RS36390: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

N6J21_RS36395: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

N6J21_RS36400: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

N6J21_RS36415: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | T1PKS | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  | 1.26 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  | 1.23 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001164.3 |  |  |  | 1.23 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001132.4 |  |  |  | 1.21 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000342.4 |  |  |  | 1.20 | NRPS | enniatin | Fusarium equiseti
BGC0001135.5 |  |  |  | 1.20 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001160.5 |  |  |  | 1.20 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001128.4 |  |  |  | 1.19 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  |  | 1.17 | NRPS | AM-toxin | Alternaria alternata
BGC0001758.4 |  |  |  | 1.17 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001164.3 |  | 0.72 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.72 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.72 | NRPS | enniatin | Fusarium equiseti
BGC0001160.5 |  | 0.72 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001758.4 |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

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: 18.17 out of 23.79
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (10):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.90 out of 33.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.74 out of 28.14
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.40 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.36 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.39 out of 30.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.09 out of 21.55
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.00 out of 27.55
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 44, location 8237716 - 8308417:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Me-redmal) + (mal) + (Ser) + (ccmal) + (Ala - D-X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 45, location 8237716 - 8298388:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2 - Me-redmal) + (mal) + (Ser) + (ccmal) + (Ala - D-X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
N6J21_RS36390: NH2 - mmal
CAL_domain (27..466): NH2
minowa: NH2

Prediction, score:
  NH2: 150.5
  Acetyl-CoA: 71.0
  fatty_acid: 23.2
  AHBA: 8.0
  shikimic_acid: 0.0

PKS_AT (1228..1526): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 79.2%
  Malonyl-CoA: 75.0%
  Methoxymalonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 120.9
  Methoxymalonyl-CoA: 104.3
  Malonyl-CoA: 89.5
  Isobutyryl-CoA: 85.9
  Ethylmalonyl-CoA: 78.4
  Propionyl-CoA: 64.1
  3-Methylbutyryl-CoA: 63.4
  2-Methylbutyryl-CoA: 56.8
  Benzoyl-CoA: 54.8
  Acetyl-CoA: 42.5
  trans-1,2-CPDA: 41.7
  inactive: 26.3
  CHC-CoA: 25.3
  fatty_acid: 23.6

N6J21_RS36395: mal
PKS_AT (563..859): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 70.8%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 154.9
  inactive: 105.6
  Methoxymalonyl-CoA: 79.7
  Methylmalonyl-CoA: 68.1
  Propionyl-CoA: 43.1
  Isobutyryl-CoA: 38.3
  2-Methylbutyryl-CoA: 34.7
  Ethylmalonyl-CoA: 30.4
  CHC-CoA: 28.6
  Acetyl-CoA: 27.1
  Benzoyl-CoA: 25.0
  trans-1,2-CPDA: 21.8
  fatty_acid: 17.5
  3-Methylbutyryl-CoA: 7.0

N6J21_RS36400: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (495..893): 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:
    RWMTFDVSVWEWHFICSGEHNLYGPTEAAIDVTS
  Nearest Stachelhaus code(s):
    Ser DVWHISLIDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

N6J21_RS36405: mal
PKS_AT (535..824): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 79.2%
  2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 155.3
  inactive: 86.7
  Methoxymalonyl-CoA: 70.4
  Methylmalonyl-CoA: 68.3
  Propionyl-CoA: 46.3
  Ethylmalonyl-CoA: 36.6
  2-Methylbutyryl-CoA: 35.3
  CHC-CoA: 33.5
  Isobutyryl-CoA: 29.7
  Acetyl-CoA: 23.5
  trans-1,2-CPDA: 20.1
  Benzoyl-CoA: 19.8
  fatty_acid: 16.9
  3-Methylbutyryl-CoA: 8.0

N6J21_RS36415: Ala - X
Search NORINE for peptide: strict or relaxed
AMP-binding (496..888): 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:
    N/A

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

AMP-binding (1556..1946): X
nrpys: Val, Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRSFDASTYEAFFLSGGEYNIYGPTETTTFALL
  Nearest Stachelhaus code(s):
    Val DAYFLGGTFK (79% 8Å match)
    Val or aIle DAYFLGVTFK (74% 8Å match)
    Ile DAFFLGITFK (62% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
IolR | Regulator of the inositol catabolism

NZ_CP104794.1 - Region 33 - 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: 8,320,062 - 8,340,988 nt. (total: 20,927 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: oxidoreductase
N6J21_RS36600: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: glucosidase
N6J21_RS36585: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

Translocases: transporter
N6J21_RS36640: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002285.2 |  | 0.50 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001779.5 |  | 0.40 | ribosomal | siamycin | Streptomyces nodosus
BGC0001221.5 |  | 0.38 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0002284.3 |  | 0.37 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002110.3 |  | 0.37 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908
BGC0001810.3 |  | 0.37 | PKS | trehangelin | Polymorphospora rubra
BGC0001787.3 |  | 0.36 | ribosomal | suicin 3908 | Streptococcus suis
BGC0000541.5 |  | 0.36 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0001735.5 |  | 0.35 | other (other) | pentostatine, vidarabine | Streptomyces antibioticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002285.2 |  | 0.50 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001364.3 |  | 0.41 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001779.5 |  | 0.40 | ribosomal | siamycin | Streptomyces nodosus
BGC0001221.5 |  | 0.38 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0002284.3 |  | 0.37 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002110.3 |  | 0.37 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908
BGC0001810.3 |  | 0.37 | PKS | trehangelin | Polymorphospora rubra
BGC0001787.3 |  | 0.36 | ribosomal | suicin 3908 | Streptococcus suis
BGC0000541.5 |  | 0.36 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0001735.5 |  | 0.35 | other (other) | pentostatine, vidarabine | 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.

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
N6J21_RS36610: PT_phytoene_like
Domain 1 (19 - 295): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (9):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.98 out of 30.22
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.79 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.22 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.66 out of 29.65
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.95 out of 20.01
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.89 out of 29.25
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 23.65 out of 32.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.87 out of 28.14
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.99 out of 26.85
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_CP104794.1 - Region 34 - redox-cofactor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,471,485 - 8,494,191 nt. (total: 22,707 nt) Show pHMM detection rules used
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
N6J21_RS37315: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

N6J21_RS37330: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

N6J21_RS37345: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: ligase
N6J21_RS37335: 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 | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001137.5 |  | 0.44 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000906.3 |  | 0.42 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000632.5 |  | 0.42 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0000597.4 |  | 0.41 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000922.5 |  | 0.41 | PKS | 2-heptyl-3-hydroxy-4-quinolone, 2,4-Quinolinediol, 2-heptylquinolin-4(1H)-one | Pseudomonas aeruginosa PAO1
BGC0001444.5 |  | 0.41 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0002711.2 |  | 0.41 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000595.3 |  | 0.41 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000252.5 |  | 0.40 | PKS | nonactin | Streptomyces griseus subsp. griseus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001137.5 |  | 0.44 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000906.3 |  | 0.42 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000632.5 |  | 0.42 | saccharide, terpene | brasilicardin A | Nocardia terpenica
BGC0000597.4 |  | 0.41 | ribosomal | SWA-2138 | Streptomyces sp. e14
BGC0000922.5 |  | 0.41 | PKS | 2-heptyl-3-hydroxy-4-quinolone, 2,4-Quinolinediol, 2-heptylquinolin-4(1H)-one | Pseudomonas aeruginosa PAO1
BGC0001444.5 |  | 0.41 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0002711.2 |  | 0.41 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000595.3 |  | 0.41 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0000252.5 |  | 0.40 | PKS | nonactin | Streptomyces griseus subsp. 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.

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.58 out of 30.11
Confidence: medium
Additional weak hits (4):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.82 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.00 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.40 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.78 out of 28.19
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (8471484...8494191)
N6J21_RS37365
  RRE type: Mycofactocin_RRE
  Location: 13 - 90
  Score: 89.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CelR | Cellobiose uptake repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_CP104794.1 - Region 35 - 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: 8,501,235 - 8,583,210 nt. (total: 81,976 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
N6J21_RS37555: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Transferases: acyltransferase methyltransferase
N6J21_RS37535: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

N6J21_RS37595: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
N6J21_RS37620: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: ligase synthase
N6J21_RS37540: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

N6J21_RS37545: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

N6J21_RS37550: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

N6J21_RS37560: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.76 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002071.2 |  | 0.76 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.75 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.77 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.76 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.76 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.76 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002071.2 |  | 0.76 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.75 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
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
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.79 out of 21.84
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
Additional weak hits (15):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.72 out of 21.55
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.08 out of 28.14
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.05 out of 30.97
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.29 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.70 out of 26.85
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.59 out of 36.54
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.98 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.36 out of 32.93
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.67 out of 20.01
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.06 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.50 out of 27.04
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 48, location 8501234 - 8583210:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X - X - Ser) + (His - X - Thr - Cys) + (Thr - X) + (X - Gly - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
N6J21_RS37535: X - X - X - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (508..862): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQFFDGAVGEMVSIVVGEMNGYGPTEYTVYSHL
  Nearest Stachelhaus code(s):
    Val DGGQIAGVYK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1826..2200): X
nrpys: Ile, Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LPGAFDASTMEAFLLVGGDVHVYGPTETTTFALA
  Nearest Stachelhaus code(s):
    Ile or Val DAMFLGVTFK (71% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2854..3242): X
nrpys: OH-Asn, Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWASFDATVTSVKIVVGGEFNEYGPTEAVVGCVL
  Nearest Stachelhaus code(s):
    OH-Asn or Asn DATKVGEVGK (88% 8Å match)
    Asn DATKVGEVGK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3912..4300): 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:
    RWMTFDVSVWEWHFLCSGEHNLYGPTEAAVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHLSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

N6J21_RS37540: His - X - Thr - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (542..922): His
nrpys: His

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:
    SARSFDSSVAGGLCIVAGEVNEYGPTEACVWATA
  Nearest Stachelhaus code(s):
    His DSALIAEVWK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1543..1915): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    SARVFDAAAAAGICVVGGDVNEYGPTEATVWVTH
  Nearest Stachelhaus code(s):
    Trp DAAIIGEVWK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2553..2933): 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:
    LAAHFDFSVWEGSQVLGGELNMYGITEATVHVTV
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3571..3980): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGDSMMSGDHSYGGATEAAIWSVS
  Nearest Stachelhaus code(s):
    Cys DLYDMSMIWK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

N6J21_RS37545: Thr - X
Search NORINE for peptide: strict or relaxed
AMP-binding (542..922): 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:
    LAAHFDFSVWEGSQVLGGELNMYGITEATVHVTV
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1599..2030): X
nrpys: me-bAla

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWATFIDALTETTLVCSGEVNQYGSSEVAGDVTF
  Nearest Stachelhaus code(s):
    me-bAla LDTTVSLGDK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

N6J21_RS37550: X - Gly - X
Search NORINE for peptide: strict or relaxed
AMP-binding (19..376): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VAQAFDAFVFEMVLASAGDYNLYGPTEATIWSTV
  Nearest Stachelhaus code(s):
    Thr DMFVAGLIWK (50% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (994..1368): 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:
    VFFTFDIANLELQALSGGEWNVYGPTETTIWSTW
  Nearest Stachelhaus code(s):
    Gly DILQLGVIWK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2004..2405): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LHWSFDVSVLEAYLLVGVEVNAYGPTEATVLCTT
  Nearest Stachelhaus code(s):
    Ser DVGYLMAVLK (56% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems