Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
3.1
4.1
5.1
5.2
6.1
12.1
12.2
12.3
12.4
12.5
12.6
12.7
12.8
12.9
12.10
12.11
13.1
23.1
23.2
23.3
23.4
23.5
23.6
31.1
31.2
31.3
32.1
32.2
32.3
33.1

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

NZ_LIVV01000001.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | NAPAA | 358,062 | 397,821 | High | ε-Poly-L-lysine | NRPS:Type I
Region 1.2 | terpene,lanthipeptide-class-ii | 399,014 | 432,062 |
Region 1.3 | terpene | 707,686 | 729,884 | High | geosmin | terpene:Sesquiterpene
Region 1.4 | ectoine | 769,387 | 779,803 | High | ectoine | other:other
Region 1.5 | NRPS,T1PKS,terpene-precursor | 970,605 | 1,027,144 |
Region 1.6 | hydrogen-cyanide | 1,073,636 | 1,086,635 |  |
Region 1.7 | lanthipeptide-class-iii | 1,131,829 | 1,154,525 |
Region 1.8 | CDPS | 1,206,191 | 1,226,961 |  |
Region 1.9 | terpene | 1,274,403 | 1,295,293 |
Region 1.10 | T1PKS,NRPS-like | 1,375,525 | 1,441,490 |  |

NZ_LIVV01000011.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | CDPS | 1 | 18,194 |  |

NZ_LIVV01000012.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | lanthipeptide-class-iv,terpene | 147,661 | 172,935 |  |

NZ_LIVV01000013.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | terpene-precursor | 18,145 | 39,206 |  |
Region 5.2 | terpene | 51,239 | 78,823 | High | isorenieratene | terpene

NZ_LIVV01000014.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 6.1 | T1PKS,butyrolactone,NRPS-like,other,arylpolyene | 7,592 | 123,151 | Medium | C-1027 | PKS

NZ_LIVV01000002.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 12.1 | T2PKS,azole-containing-RiPP | 1 | 40,217 | Medium | alnumycin A/alnumycin B/alnumycin C/alnumycin P/prealnumycin/thalnumycin A/thalnumycin B/K1115A/1,6-dihydro-8-propylanthraquinone | PKS:Type II
Region 12.2 | terpene | 176,777 | 203,395 | High | hopene | terpene
Region 12.3 | RiPP-like | 249,283 | 260,149 |
Region 12.4 | lanthipeptide-class-iii | 282,580 | 305,225 | High | SapB | ribosomal:RiPP:Lanthipeptide
Region 12.5 | melanin | 467,765 | 478,157 | Low | melanin | other:other
Region 12.6 | NRP-metallophore,NRPS | 615,298 | 708,270 | Medium | peucechelin | NRPS:Type I
Region 12.7 | terpene,azole-containing-RiPP | 732,531 | 775,399 |  |
Region 12.8 | NRPS,T2PKS | 842,134 | 921,120 | High | spore pigment | PKS
Region 12.9 | NAPAA | 1,006,973 | 1,042,065 |  |
Region 12.10 | NRPS | 1,043,761 | 1,097,485 |  |
Region 12.11 | lanthipeptide-class-iv | 1,316,012 | 1,338,756 | High | venezuelin | ribosomal:RiPP:Lanthipeptide

NZ_LIVV01000020.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 13.1 | NRPS,T1PKS | 1 | 33,779 |

NZ_LIVV01000003.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 23.1 | NI-siderophore | 84,272 | 117,412 | Low | kinamycin | PKS
Region 23.2 | NRPS | 151,734 | 210,467 |  |
Region 23.3 | NRPS | 268,736 | 340,811 | Medium | pyrroloformamide A/pyrroloformamide B/pyrroloformamide D/pyrroloformamide C | NRPS:Type I+other:other
Region 23.4 | RiPP-like | 431,536 | 442,948 | Low | 14-hydroxyisochainin | PKS:Modular type I
Region 23.5 | butyrolactone | 554,273 | 565,220 | Low | coelimycin P1 | PKS:Type I
Region 23.6 | T1PKS,NRPS | 687,523 | 750,617 | Low | desulfoclethramycin/clethramycin | other:other

NZ_LIVV01000005.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 31.1 | melanin | 118,539 | 128,952 |  |
Region 31.2 | linaridin | 143,750 | 166,351 | High | cypemycin | ribosomal:RiPP:Linaridin
Region 31.3 | NRPS-like | 711,180 | 754,881 | Low | lankamycin | PKS

NZ_LIVV01000006.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 32.1 | terpene-precursor | 153,569 | 174,618 |  |
Region 32.2 | other,butyrolactone | 341,558 | 382,667 | High | A-factor | other:other
Region 32.3 | azole-containing-RiPP | 386,812 | 420,073 | Low | BD-12 | NRPS:Type I

NZ_LIVV01000007.1 (Streptomyces sp. CB02009)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 33.1 | NI-siderophore | 203,313 | 233,100 | High | desferrioxamin B | other:other

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | NAPAA | 358,062 | 397,821 | High | ε-Poly-L-lysine | NRPS:Type I
Region 1.2 | terpene,lanthipeptide-class-ii | 399,014 | 432,062 |
Region 1.3 | terpene | 707,686 | 729,884 | High | geosmin | terpene:Sesquiterpene
Region 1.4 | ectoine | 769,387 | 779,803 | High | ectoine | other:other
Region 1.5 | NRPS,T1PKS,terpene-precursor | 970,605 | 1,027,144 |
Region 1.6 | hydrogen-cyanide | 1,073,636 | 1,086,635 |  |
Region 1.7 | lanthipeptide-class-iii | 1,131,829 | 1,154,525 |
Region 1.8 | CDPS | 1,206,191 | 1,226,961 |  |
Region 1.9 | terpene | 1,274,403 | 1,295,293 |
Region 1.10 | T1PKS,NRPS-like | 1,375,525 | 1,441,490 |  |
Region 3.1 | CDPS | 1 | 18,194 |  |
Region 4.1 | lanthipeptide-class-iv,terpene | 147,661 | 172,935 |  |
Region 5.1 | terpene-precursor | 18,145 | 39,206 |  |
Region 5.2 | terpene | 51,239 | 78,823 | High | isorenieratene | terpene
Region 6.1 | T1PKS,butyrolactone,NRPS-like,other,arylpolyene | 7,592 | 123,151 | Medium | C-1027 | PKS
Region 12.1 | T2PKS,azole-containing-RiPP | 1 | 40,217 | Medium | alnumycin A/alnumycin B/alnumycin C/alnumycin P/prealnumycin/thalnumycin A/thalnumycin B/K1115A/1,6-dihydro-8-propylanthraquinone | PKS:Type II
Region 12.2 | terpene | 176,777 | 203,395 | High | hopene | terpene
Region 12.3 | RiPP-like | 249,283 | 260,149 |
Region 12.4 | lanthipeptide-class-iii | 282,580 | 305,225 | High | SapB | ribosomal:RiPP:Lanthipeptide
Region 12.5 | melanin | 467,765 | 478,157 | Low | melanin | other:other
Region 12.6 | NRP-metallophore,NRPS | 615,298 | 708,270 | Medium | peucechelin | NRPS:Type I
Region 12.7 | terpene,azole-containing-RiPP | 732,531 | 775,399 |  |
Region 12.8 | NRPS,T2PKS | 842,134 | 921,120 | High | spore pigment | PKS
Region 12.9 | NAPAA | 1,006,973 | 1,042,065 |  |
Region 12.10 | NRPS | 1,043,761 | 1,097,485 |  |
Region 12.11 | lanthipeptide-class-iv | 1,316,012 | 1,338,756 | High | venezuelin | ribosomal:RiPP:Lanthipeptide
Region 13.1 | NRPS,T1PKS | 1 | 33,779 |
Region 23.1 | NI-siderophore | 84,272 | 117,412 | Low | kinamycin | PKS
Region 23.2 | NRPS | 151,734 | 210,467 |  |
Region 23.3 | NRPS | 268,736 | 340,811 | Medium | pyrroloformamide A/pyrroloformamide B/pyrroloformamide D/pyrroloformamide C | NRPS:Type I+other:other
Region 23.4 | RiPP-like | 431,536 | 442,948 | Low | 14-hydroxyisochainin | PKS:Modular type I
Region 23.5 | butyrolactone | 554,273 | 565,220 | Low | coelimycin P1 | PKS:Type I
Region 23.6 | T1PKS,NRPS | 687,523 | 750,617 | Low | desulfoclethramycin/clethramycin | other:other
Region 31.1 | melanin | 118,539 | 128,952 |  |
Region 31.2 | linaridin | 143,750 | 166,351 | High | cypemycin | ribosomal:RiPP:Linaridin
Region 31.3 | NRPS-like | 711,180 | 754,881 | Low | lankamycin | PKS
Region 32.1 | terpene-precursor | 153,569 | 174,618 |  |
Region 32.2 | other,butyrolactone | 341,558 | 382,667 | High | A-factor | other:other
Region 32.3 | azole-containing-RiPP | 386,812 | 420,073 | Low | BD-12 | NRPS:Type I
Region 33.1 | NI-siderophore | 203,313 | 233,100 | High | desferrioxamin B | other:other

No secondary metabolite regions were found in these records:
  NZ_LIVV01000010.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000015.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000016.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000017.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000018.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000019.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000021.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000022.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000023.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000024.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000025.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000026.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000027.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000028.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000029.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000030.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000031.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000032.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000033.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000034.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000035.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000004.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000008.1 (Streptomyces sp. CB02009)
  NZ_LIVV01000009.1 (Streptomyces sp. CB02009)

Compact view
NZ_LIVV01000001.1 - Region 1 - NAPAA
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 358,062 - 397,821 nt. (total: 39,760 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: reductase
AMK27_RS01735: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: methyltransferase
AMK27_RS01690: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: ligase
AMK27_RS01740: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.59 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.98 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.72 out of 27.04
Confidence: medium
Additional weak hits (2):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.35 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.36 out of 21.55
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 358061 - 397821:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AMK27_RS01740: X
AMP-binding (20..492): 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:
    QAQLHVFGNALGASIFLWA-------ETVVATGR
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

AMK27_RS01755: X
AMP-binding (43..418): X
nrpys: (unknown)

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

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

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
DasR | N-acetylglucosamine dependent repressor

NZ_LIVV01000001.1 - Region 2 - lanthipeptide-class-ii,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: 399,014 - 432,062 nt. (total: 33,049 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)
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
Terpene
TFBS Finder
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
AMK27_RS01855: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: hydrolase
AMK27_RS01820: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Lyases: cyclase
AMK27_RS01860: Terpene synthase/cyclase metal-binding domain protein

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

AMK27_RS01905: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | terpene | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001181.4 |  |  | 0.93 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000518.3 |  |  | 0.25 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000908.3 |  |  | 0.24 | other (other) | melanin | Streptomyces avermitilis
BGC0001572.3 |  |  | 0.24 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000525.5 |  |  | 0.18 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000554.4 |  |  | 0.17 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0002434.2 |  |  | 0.16 | NRPS, PKS | clifednamide D, clifednamide E, clifednamide F, clifednamide G, clifednamide H, clifednamide I, clifednamide J | Kitasatospora sp.
BGC0001468.5 |  |  | 0.16 | other (trna-derived) | bicyclomycin | Streptomyces cinnamoneus
BGC0001441.5 |  |  | 0.16 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0001210.5 |  |  | 0.15 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.76 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000554.4 |  | 0.48 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001210.5 |  | 0.46 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000626.3 |  | 0.45 | ribosomal | thuricin | Bacillus thuringiensis
BGC0000516.4 |  | 0.45 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0000517.4 |  | 0.45 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0001910.4 |  | 0.44 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000527.5 |  | 0.44 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000518.3 |  | 0.44 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736

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

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.
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:
AMK27_RS01860: T1TS
Domain 1 (8 - 336): Type 1 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
Additional weak hits (12):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.96 out of 30.22
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.40 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.22 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.18 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.61 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.43 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.57 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.92 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.32 out of 27.78
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.87 out of 32.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.96 out of 29.65
Confidence: weak
Lanthipeptides
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LIVV01000001.1 - Region 3 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 707,686 - 729,884 nt. (total: 22,199 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
Lyases: cyclase hydratase
AMK27_RS03145: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

AMK27_RS03185: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: synthase
AMK27_RS03215: 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001972.4 |  | 0.33 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis
BGC0000711.5 |  | 0.32 | saccharide | neomycin | Streptomyces fradiae
BGC0000709.5 |  | 0.32 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000252.5 |  | 0.31 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0002196.2 |  | 0.30 | PKS | clavatol | Penicillium crustosum
BGC0000143.5 |  | 0.30 | PKS | salinomycin | Streptomyces albus
BGC0002657.2 |  | 0.27 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0000109.5 |  | 0.26 | PKS | LL-F28249α | Streptomyces cyaneogriseus subsp. noncyanogenus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0000658.3 |  | 0.56 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001972.4 |  | 0.33 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis
BGC0000711.5 |  | 0.32 | saccharide | neomycin | Streptomyces fradiae
BGC0000709.5 |  | 0.32 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000252.5 |  | 0.31 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0002196.2 |  | 0.30 | PKS | clavatol | Penicillium crustosum
BGC0000143.5 |  | 0.30 | PKS | salinomycin | Streptomyces albus
BGC0002657.2 |  | 0.27 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0000109.5 |  | 0.26 | PKS | LL-F28249α | Streptomyces cyaneogriseus subsp. noncyanogenus

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:
AMK27_RS03185: T1TS + T1TS
Domain 1 (2 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (335 - 695): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (4):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.63 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.75 out of 30.25
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.20 out of 27.04
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.10 out of 26.85
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
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_LIVV01000001.1 - Region 4 - 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: 769,387 - 779,803 nt. (total: 10,417 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
AMK27_RS03435: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

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

Reference | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.84 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.84 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000856.3 |  | 0.71 | other (other) | ectoine | Methylophaga thalassica
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
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 |  | 0.84 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.84 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000856.3 |  | 0.71 | other (other) | ectoine | Methylophaga thalassica
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 25.31
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):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LIVV01000001.1 - Region 5 - NRPS,T1PKS,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 970,605 - 1,027,144 nt. (total: 56,540 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))
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
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
AMK27_RS04370: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AMK27_RS04375: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: methyltransferase
AMK27_RS04540: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: protease
AMK27_RS04400: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

Isomerases: racemase
AMK27_RS04345: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

AMK27_RS04365: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: synthase synthetase
AMK27_RS04430: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AMK27_RS04510: 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 | NRPS | T1PKS | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  |  | 0.63 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  |  |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  |  |  | 0.59 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001160.5 |  |  |  | 0.52 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  |  | 0.52 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000677.5 |  |  |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002309.2 |  |  |  | 0.38 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000622.5 |  |  |  | 0.36 | ribosomal | megacin | Bacillus megaterium
BGC0001911.3 |  |  |  | 0.35 | terpene | raimonol | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.66 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.63 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.60 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000622.5 |  | 0.50 | ribosomal | megacin | Bacillus megaterium
BGC0000595.3 |  | 0.46 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0001161.5 |  | 0.46 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0001162.3 |  | 0.46 | PKS | 1-heptadecene | Moorea producens JHB

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
--- | --- | --- | --- | --- | ---
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:
AMK27_RS04510: PT_FPPS_like
Domain 1 (48 - 344): 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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26
Confidence: medium
Additional weak hits (10):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.49 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.07 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.64 out of 29.65
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: 19.90 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.78 out of 27.04
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
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.19 out of 23.43
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.65 out of 20.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.65 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
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 7, location 970604 - 1027144:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - ohmal - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 970604 - 1023804:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (fatty_acid - ohmal - 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).
AMK27_RS04430: fatty_acid - mal - X
CAL_domain (148..459): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 42.1
  NH2: 38.5
  shikimic_acid: 0.0
  Acetyl-CoA: 0.0
  AHBA: 0.0

PKS_AT (1355..1645): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 125.5
  Methylmalonyl-CoA: 72.3
  Methoxymalonyl-CoA: 67.9
  Ethylmalonyl-CoA: 47.3
  CHC-CoA: 45.4
  inactive: 42.0
  Propionyl-CoA: 36.5
  Isobutyryl-CoA: 30.3
  2-Methylbutyryl-CoA: 26.5
  trans-1,2-CPDA: 22.8
  fatty_acid: 22.5
  Benzoyl-CoA: 9.5
  Acetyl-CoA: 7.6
  3-Methylbutyryl-CoA: 4.4

AMP-binding (2834..3259): X
nrpys: Asp, Asn, Glu, Gln, Aad

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWAAFDASVRQASSHVGGEANLYGPTESTINATF
  Nearest Stachelhaus code(s):
    Gln DACSTGVINK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CRP | Cyclic AMP receptor protein
VqsM | Regulator of quorum-sensing signalling systems

NZ_LIVV01000001.1 - Region 6 - 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: 1,073,636 - 1,086,635 nt. (total: 13,000 nt) Show pHMM detection rules used
hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase reductase
AMK27_RS04780: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

AMK27_RS04790: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

AMK27_RS04805: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: acetyltransferase
AMK27_RS04810: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: deaminase
AMK27_RS04775: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

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
BGC0001739.3 |  | 0.33 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0001865.4 |  | 0.33 | PKS | elsinochrome C | Parastagonospora nodorum SN15
BGC0001057.4 |  | 0.32 | NRPS, PKS | zearalenone | Fusarium graminearum
BGC0001108.5 |  | 0.32 | NRPS, PKS | pederin, pseudopederin, pederone | Uncultured bacterium
BGC0002285.2 |  | 0.31 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002083.3 |  | 0.31 | PKS | gladiofungin A, gladiofungin B | Burkholderia gladioli
BGC0002169.3 |  | 0.31 | NRPS, PKS | acurin A | Aspergillus aculeatus ATCC 16872
BGC0000154.4 |  | 0.30 | PKS | stipitatic acid | Talaromyces stipitatus ATCC 10500
BGC0002556.2 |  | 0.30 | other (other) | cervinomycin B3, cervinomycin C1, cervinomycin C2, cervinomycin C3, cervinomycin C4 | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002345.2 |  | 0.54 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0001739.3 |  | 0.33 | other (other) | phosphonoacetic Acid | Streptomyces sp. NRRL F-525
BGC0001865.4 |  | 0.33 | PKS | elsinochrome C | Parastagonospora nodorum SN15
BGC0001057.4 |  | 0.32 | NRPS, PKS | zearalenone | Fusarium graminearum
BGC0001108.5 |  | 0.32 | NRPS, PKS | pederin, pseudopederin, pederone | Uncultured bacterium
BGC0002285.2 |  | 0.31 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0002083.3 |  | 0.31 | PKS | gladiofungin A, gladiofungin B | Burkholderia gladioli
BGC0002169.3 |  | 0.31 | NRPS, PKS | acurin A | Aspergillus aculeatus ATCC 16872
BGC0000154.4 |  | 0.30 | PKS | stipitatic acid | Talaromyces stipitatus ATCC 10500
BGC0002556.2 |  | 0.30 | other (other) | cervinomycin B3, cervinomycin C1, cervinomycin C2, cervinomycin C3, cervinomycin C4 | Streptomyces sp.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
Additional weak hits (7):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.30 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.06 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.29 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.28 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LIVV01000001.1 - Region 7 - lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,131,829 - 1,154,525 nt. (total: 22,697 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: deacetylase hydrolase
AMK27_RS05060: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

AMK27_RS05155: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: synthase
AMK27_RS05095: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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

Reference | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000757.3 |  | 0.47 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000756.3 |  | 0.46 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0002700.2 |  | 0.45 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000737.3 |  | 0.43 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000789.3 |  | 0.43 | saccharide | O-antigen | Escherichia coli
BGC0002111.3 |  | 0.42 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000519.4 |  | 0.41 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000752.3 |  | 0.40 | saccharide | capsular polysaccharide | Actinobacillus pleuropneumoniae serovar 6 str. Femo
BGC0002701.2 |  | 0.40 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0000739.3 |  | 0.40 | saccharide | capsular polysaccharide | Pasteurella multocida

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000757.3 |  | 0.47 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000756.3 |  | 0.46 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0002700.2 |  | 0.45 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000737.3 |  | 0.43 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000789.3 |  | 0.43 | saccharide | O-antigen | Escherichia coli
BGC0002111.3 |  | 0.42 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000519.4 |  | 0.41 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000752.3 |  | 0.40 | saccharide | capsular polysaccharide | Actinobacillus pleuropneumoniae serovar 6 str. Femo
BGC0002701.2 |  | 0.40 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0000739.3 |  | 0.40 | saccharide | capsular polysaccharide | Pasteurella multocida

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 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 (8):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.46 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.96 out of 27.78
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.68 out of 29.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.13 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.09 out of 30.98
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.65 out of 29.25
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.53 out of 26.85
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LIVV01000001.1 - Region 8 - CDPS
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: 1,206,191 - 1,226,961 nt. (total: 20,771 nt) Show pHMM detection rules used
CDPS: CDPS

#### 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 | CDPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000496.5 |  | 0.37 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000501.3 |  | 0.36 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0001862.4 |  | 0.35 | ribosomal | pallidocin | Aeribacillus pallidus
BGC0001864.3 |  | 0.34 | ribosomal | listeriocytocin | Listeria monocytogenes SLCC2540
BGC0000516.4 |  | 0.33 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0002116.3 |  | 0.32 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0001210.5 |  | 0.32 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000527.5 |  | 0.31 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001468.5 |  | 0.31 | other (trna-derived) | bicyclomycin | Streptomyces cinnamoneus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000496.5 |  | 0.37 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000501.3 |  | 0.36 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0001862.4 |  | 0.35 | ribosomal | pallidocin | Aeribacillus pallidus
BGC0001864.3 |  | 0.34 | ribosomal | listeriocytocin | Listeria monocytogenes SLCC2540
BGC0000516.4 |  | 0.33 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0002116.3 |  | 0.32 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0001210.5 |  | 0.32 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000527.5 |  | 0.31 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001468.5 |  | 0.31 | other (trna-derived) | bicyclomycin | Streptomyces cinnamoneus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (8):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.84 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.89 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.46 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.11 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.06 out of 28.14
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.52 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.28 out of 29.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LIVV01000001.1 - Region 9 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,274,403 - 1,295,293 nt. (total: 20,891 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
AMK27_RS05730: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase
AMK27_RS05755: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

AMK27_RS05760: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002218.2 |  | 0.38 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0001444.5 |  | 0.36 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0001850.4 |  | 0.36 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0001940.3 |  | 0.35 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0000101.5 |  | 0.35 | PKS | emodin, monodictyphenone, shamixanthone | Aspergillus nidulans FGSC A4
BGC0002062.2 |  | 0.34 | PKS | agnestin A, agnestin B | Paecilomyces divaricatus
BGC0002726.2 |  | 0.34 | PKS | 4-chloropinselin, pinselin, chloromonilinic acid B, chloromonilinic acid D, 4-hydroxyvertixanthone | Bipolaris sorokiniana
BGC0001596.3 |  | 0.33 | PKS | fluostatin M, fluostatin N, fluostatin O, fluostatin P, fluostatin Q | Streptomyces albus
BGC0000391.5 |  | 0.33 | NRPS | methylpendolmycin, pendolmycin | Marinactinospora thermotolerans
BGC0002477.3 |  | 0.32 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002218.2 |  | 0.38 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0001444.5 |  | 0.36 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0001850.4 |  | 0.36 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0001940.3 |  | 0.35 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax
BGC0000101.5 |  | 0.35 | PKS | emodin, monodictyphenone, shamixanthone | Aspergillus nidulans FGSC A4
BGC0002062.2 |  | 0.34 | PKS | agnestin A, agnestin B | Paecilomyces divaricatus
BGC0002726.2 |  | 0.34 | PKS | 4-chloropinselin, pinselin, chloromonilinic acid B, chloromonilinic acid D, 4-hydroxyvertixanthone | Bipolaris sorokiniana
BGC0001596.3 |  | 0.33 | PKS | fluostatin M, fluostatin N, fluostatin O, fluostatin P, fluostatin Q | Streptomyces albus
BGC0000391.5 |  | 0.33 | NRPS | methylpendolmycin, pendolmycin | Marinactinospora thermotolerans
BGC0002477.3 |  | 0.32 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072

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:
AMK27_RS05720: PT_phytoene_like
Domain 1 (16 - 272): 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.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.40 out of 20.97
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.11 out of 28.19
Confidence: medium
Additional weak hits (6):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.55 out of 33.14
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.33 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.92 out of 27.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.35 out of 26.06
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
--- | ---
CcpA | Catabolite control protein A
ZuR variant 1 | Zinc-responsive repressor

NZ_LIVV01000001.1 - Region 10 - 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: 1,375,525 - 1,441,490 nt. (total: 65,966 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: formyltransferase glycosyltransferase halogenase
AMK27_RS06200: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

AMK27_RS06225: halogenase

smcogs
  SMCOG1119: halogenase

AMK27_RS06235: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: esterase
AMK27_RS06285: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: synthase
AMK27_RS06245: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AMK27_RS41125: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

AMK27_RS43470: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001275.3 |  |  | 0.91 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  |  | 0.91 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  |  | 0.90 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002191.2 |  |  | 0.59 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001284.4 |  |  | 0.57 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002175.3 |  |  | 0.56 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0002154.2 |  |  | 0.56 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  |  | 0.56 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001164.3 |  |  | 0.55 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.55 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001275.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.75 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002175.3 |  | 0.63 | PKS | YWA1 | Aspergillus oryzae RIB40
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.13 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.28 out of 27.04
Confidence: medium
Additional weak hits (9):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.35 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.17 out of 29.38
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.66 out of 24.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.70 out of 26.85
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.03 out of 24.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.85 out of 35.63
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.66 out of 26.85
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 14, location 1375524 - 1441490:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AMK27_RS06235: Gly - mal
Search NORINE for peptide: strict or relaxed
AMP-binding (599..983): 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:
    FAITFDISLLELQALSGGEWNLYGPTEATIWAAA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

PKS_AT (2835..3125): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 123.3
  inactive: 64.2
  Methoxymalonyl-CoA: 58.4
  Methylmalonyl-CoA: 46.3
  fatty_acid: 34.6
  Propionyl-CoA: 31.3
  Ethylmalonyl-CoA: 27.0
  Isobutyryl-CoA: 22.5
  2-Methylbutyryl-CoA: 10.6
  Benzoyl-CoA: 10.2
  Acetyl-CoA: 5.8
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

AMK27_RS06245: mal
PKS_AT (1799..2091): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 66.7%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 117.8
  inactive: 58.5
  Methoxymalonyl-CoA: 51.1
  Methylmalonyl-CoA: 41.1
  fatty_acid: 34.2
  Propionyl-CoA: 28.8
  Ethylmalonyl-CoA: 26.5
  Isobutyryl-CoA: 17.2
  Acetyl-CoA: 11.0
  Benzoyl-CoA: 10.8
  2-Methylbutyryl-CoA: 9.1
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_LIVV01000011.1 - Region 1 - CDPS
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 - 18,194 nt. (total: 18,194 nt) Show pHMM detection rules used
Region on contig edge.
CDPS: CDPS

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase oxygenase
AMK27_RS34695: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

AMK27_RS34725: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: aminotransferase
AMK27_RS34720: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: dehalogenase
AMK27_RS34710: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

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

Reference | CDPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001986.3 |  | 0.58 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001948.3 |  | 0.51 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0002458.3 |  | 0.51 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002007.2 |  | 0.41 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0002482.2 |  | 0.40 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0002582.3 |  | 0.39 | NRPS | guanipiperazine A, guanipiperazine B | Streptomyces chrestomyceticus
BGC0002000.4 |  | 0.39 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001483.4 |  | 0.39 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001986.3 |  | 0.58 | other (other) | purincyclamide | Streptomyces chrestomyceticus
BGC0002631.2 |  | 0.53 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0001948.3 |  | 0.51 | other (other) | naseseazine C, C3-aryl pyrroloindolines | Streptomyces sp.
BGC0002458.3 |  | 0.51 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002007.2 |  | 0.41 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0002482.2 |  | 0.40 | other (other) | tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M | Symphyonema bifilamentata 97.28
BGC0002582.3 |  | 0.39 | NRPS | guanipiperazine A, guanipiperazine B | Streptomyces chrestomyceticus
BGC0002000.4 |  | 0.39 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0001483.4 |  | 0.39 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8

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: 16.67 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
Additional weak hits (10):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.68 out of 32.74
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.68 out of 39.62
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.41 out of 26.85
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
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.63 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.02 out of 20.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.72 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.93 out of 23.43
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.00 out of 32.38
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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein

NZ_LIVV01000012.1 - Region 1 - lanthipeptide-class-iv,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: 147,661 - 172,935 nt. (total: 25,275 nt) Show pHMM detection rules used
lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)
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
Lanthipeptides
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
Hydrolases: protease
AMK27_RS37060: 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 | lanthipeptide-class-iv | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000551.5 |  |  | 0.54 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000501.3 |  |  | 0.50 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000513.3 |  |  | 0.46 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  |  | 0.45 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000496.5 |  |  | 0.45 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000563.4 |  |  | 0.42 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  |  | 0.41 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000504.5 |  |  | 0.31 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000518.3 |  |  | 0.31 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000500.5 |  |  | 0.30 | ribosomal | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.60 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000501.3 |  | 0.59 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000513.3 |  | 0.56 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.56 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000496.5 |  | 0.55 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000563.4 |  | 0.53 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.53 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000518.3 |  | 0.47 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002306.2 |  | 0.47 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000504.5 |  | 0.46 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1

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 AMK27_RS37045

allorf_150684_150905
Leader:
MTLRIDVSRLLDVQAQSVPEDEDVRVAD
Core:
H S A L A V V A C H K T C M P R P T T A D R V R A R R V R L A P H I R P A S H A G P S G E
Core with dehydrations:
H Dha A L A V V A Cys H K Dhb Cys M P R P Dhb Dhb A D R V R A R R V R L A P H I R P A Dha H A G P Dha G E

#### antiSMASH-DB 4.0 matches for allorf_150684_150905

100.0%
NZ_LIVV01000012.1:
Lanthipeptides: allorf_150684_150905_lanthipeptide
1
H S A L A V V A C H K T C M P R P T T A D R V R A R R V R L A P H I R P A S H A G P S G E
45
H S A L A V V A C H K T C M P R P T T A D R V R A R R V R L A P H I R P A S H A G P S G E
1
H S A L A V V A C H K T C M P R P T T A D R V R A R R V R L A P H I R P A S H A G P S G E
45
22.2%
NZ_PUPX01000001.1:
Lanthipeptides: allorf_1091992_1092165_lanthipeptide
16
R P T T A D R V R A R R V R L A P H I R P A S H A G P S G
44
+P T R+ R+ I R P A P+G
5
Q P C T L G R L L I T V G R I K L I I R P A G D Q L P T G
33
20.0%
NZ_CP020570.1 and 15 others:
NZ_CP020570.1 Lanthipeptides: allorf_2516141_2516284_lanthipeptide NZ_CP020570.1 Lanthipeptides: allorf_2516141_2516284_lanthipeptide NZ_CP070242.1 Lanthipeptides: allorf_2528027_2528170_lanthipeptide NZ_CP070242.1 Lanthipeptides: allorf_2528027_2528170_lanthipeptide NZ_CP070242.1 Lanthipeptides: allorf_2528027_2528170_lanthipeptide NZ_CP070260.1 Lanthipeptides: allorf_5476524_5476667_lanthipeptide NZ_CP070260.1 Lanthipeptides: allorf_5476524_5476667_lanthipeptide NZ_CP070260.1 Lanthipeptides: allorf_5476524_5476667_lanthipeptide NZ_CP070260.1 Lanthipeptides: allorf_5476524_5476667_lanthipeptide NZ_JAJDST010000044.1 Lanthipeptides: allorf_029750_029893_lanthipeptide NZ_JAJDST010000044.1 Lanthipeptides: allorf_029750_029893_lanthipeptide NZ_JAJDST010000044.1 Lanthipeptides: allorf_029750_029893_lanthipeptide NZ_WWGL01000034.1 Lanthipeptides: allorf_1026403_1026546_lanthipeptide NZ_WWGL01000034.1 Lanthipeptides: allorf_1026403_1026546_lanthipeptide NZ_WWGL01000034.1 Lanthipeptides: allorf_1026403_1026546_lanthipeptide
Lanthipeptides: allorf_2516141_2516284_lanthipeptide
14
M P R P T T A D R V R A R R V R L A P H
33
M P R V R R++R+A P
1
M G A P G G F G R V R G R K M R V A P R
20
with 3 more sequence matches
20.0%
NZ_CP058556.1 and 4 others:
NZ_CP058556.1 Lanthipeptides: allorf_5603706_5603849_lanthipeptide NZ_CP058556.1 Lanthipeptides: allorf_5603706_5603849_lanthipeptide NZ_CP058556.1 Lanthipeptides: allorf_5603706_5603849_lanthipeptide NZ_CP059898.1 Lanthipeptides: allorf_2457020_2457163_lanthipeptide
Lanthipeptides: allorf_5603706_5603849_lanthipeptide
14
M P R P T T A D R V R A R R V R L A P H
33
M P R V R R++R A P
1
M G A P G G F G R V R G R K M R A A P R
20
15.6%
NZ_CP019687.1 and 1 other:
NZ_CP019717.1 Lanthipeptides: ERICV_RS20670_lanthipeptide
Lanthipeptides: BXP28_RS22835_lanthipeptide
1
H S A L A V V A C H K T C M P R
16
H A L V +K P R
12
H E A L E V K T A Y K D W F P R
27
15.0%
NZ_FNPT01000004.1:
Lanthipeptides: allorf_345034_345240_lanthipeptide
13
C M P R P T T A D R V R A R R V R L A P H I R P
36
C P R D + R V R+A + P
29
C P P R R V A P D T I T T E R V R I A S D L H P
52

#### Legend:

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene |  |  | C15 | C1-C6 | none
diterpene |  |  | C20 | C1-C6 | none
diterpene |  |  | C20 | C1-C7 + C6-C10 | none
sesterterpene |  |  | C25 | C1-C7 + C6-C10 | none

Genes with terpene domains:
AMK27_RS37055: TS_UbiA
Domain 1 (3 - 265): UbiA type terpene synthase

Reactions:
  FPP → sesquiterpene_C1-C6
  GGPP → diterpene_C1-C6
  GGPP → diterpene_C1-C7/C6-C10
  GFPP → sesterterpene_C1-C7/C6-C10

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
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
Additional weak hits (6):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.56 out of 29.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.22 out of 26.06
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
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.04 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Lanthipeptides
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

allorf_150684_150905 - Class III
  Cleavage pHMM score: -1.00
  RODEO score: 0
  Monoisotopic mass: 4727.5 Da
  Molecular weight: 4730.5 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4748.5 Da N = 1
    4766.5 Da N = 2
    4784.5 Da N = 3
    4802.5 Da N = 4

Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_LIVV01000013.1 - Region 1 - 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: 18,145 - 39,206 nt. (total: 21,062 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
AMK27_RS37340: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

AMK27_RS37360: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Ligases: synthetase
AMK27_RS37315: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

Translocases: transporter
AMK27_RS37290: 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-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000688.4 |  | 0.39 | terpene | copalyl diphosphate | Diaporthe amygdali
BGC0000678.5 |  | 0.39 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001910.4 |  | 0.38 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000664.5 |  | 0.38 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000688.4 |  | 0.39 | terpene | copalyl diphosphate | Diaporthe amygdali
BGC0000678.5 |  | 0.39 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001910.4 |  | 0.38 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000664.5 |  | 0.38 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488

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

No significant matches found.

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

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

Genes with terpene domains:
AMK27_RS37315: PT_FPPS_like
Domain 1 (62 - 349): 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:
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: 18.76 out of 23.05
Confidence: medium
Additional weak hits (6):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.48 out of 27.55
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.70 out of 21.55
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.42 out of 23.43
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.94 out of 32.74
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.75 out of 35.63
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
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production

NZ_LIVV01000013.1 - Region 2 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 51,239 - 78,823 nt. (total: 27,585 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
AMK27_RS37510: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
AMK27_RS37520: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
AMK27_RS37515: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.76 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.70 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.64 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.64 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0001456.3 |  | 0.63 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000646.5 |  | 0.51 | terpene | β-carotein | uncultured bacterium
BGC0000648.3 |  | 0.51 | terpene | carotenoid | Myxococcus xanthus
BGC0000640.3 |  | 0.51 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000639.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000641.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC416

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.76 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.70 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000633.3 |  | 0.64 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.64 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0001456.3 |  | 0.63 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000646.5 |  | 0.51 | terpene | β-carotein | uncultured bacterium
BGC0000648.3 |  | 0.51 | terpene | carotenoid | Myxococcus xanthus
BGC0000640.3 |  | 0.51 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000639.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000641.3 |  | 0.49 | terpene | carotenoid | Enterobacteriaceae bacterium DC416

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

No significant matches found.

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

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

Genes with terpene domains:
AMK27_RS37490: Lycopene_cycl
Domain 1 (4 - 379): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

AMK27_RS37505: PT_phytoene_like
Domain 1 (16 - 315): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

AMK27_RS37515: PT_FPPS_like
Domain 1 (48 - 359): 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 (9):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.37 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.12 out of 36.54
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.85 out of 26.12
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.03 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.79 out of 30.25
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.41 out of 36.53
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.67 out of 39.62
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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_LIVV01000014.1 - Region 1 - NRPS-like,T1PKS,arylpolyene,butyrolactone,other
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,592 - 123,151 nt. (total: 115,560 nt) Show pHMM detection rules used
Region on contig edge.
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
butyrolactone: AfsA
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase
AMK27_RS38015: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AMK27_RS38065: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

AMK27_RS38070: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

AMK27_RS38120: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

AMK27_RS38130: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

AMK27_RS38140: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

AMK27_RS38150: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

AMK27_RS38155: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

AMK27_RS38195: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

AMK27_RS38245: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

AMK27_RS38275: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

AMK27_RS38325: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

AMK27_RS38335: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

AMK27_RS38380: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

AMK27_RS38390: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

AMK27_RS38415: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

Transferases: acyltransferase methyltransferase
AMK27_RS38115: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

AMK27_RS38175: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

AMK27_RS38190: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

AMK27_RS38240: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase phosphatase
AMK27_RS38180: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

AMK27_RS38320: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

AMK27_RS38400: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: dehydratase lyase
AMK27_RS38285: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

AMK27_RS38300: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

AMK27_RS38305: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

AMK27_RS38315: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: isomerase
AMK27_RS38210: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
AMK27_RS38055: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AMK27_RS38160: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AMK27_RS38170: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AMK27_RS38215: carbamoyl phosphate synthase small subunit

smcogs
  SMCOG1249: carbamoyl phosphate synthase small subunit

AMK27_RS38265: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AMK27_RS38290: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

AMK27_RS38340: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AMK27_RS38345: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AMK27_RS38405: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

Translocases: transport transporter
AMK27_RS38185: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

AMK27_RS38230: 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 | butyrolactone | NRPS-like | other | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000849.4 |  |  |  |  |  | 0.95 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  |  |  |  |  | 0.67 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002347.3 |  |  |  |  |  | 0.60 | other (other) | cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D | Actinoalloteichus caeruleus WH1-2216-6
BGC0002031.3 |  |  |  |  |  | 0.55 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0001596.3 |  |  |  |  |  | 0.53 | PKS | fluostatin M, fluostatin N, fluostatin O, fluostatin P, fluostatin Q | Streptomyces albus
BGC0000274.5 |  |  |  |  |  | 0.53 | PKS | tetarimycin A, tetarimycin B | uncultured bacterium
BGC0002478.3 |  |  |  |  |  | 0.53 | PKS | rubiginone A2, rubiginone J, rubiginone K, rubiginone L, rubiginone M, rubiginone N, ochromycinone, rubiginone B2 | Streptomyces sp. CB02414
BGC0001335.5 |  |  |  |  |  | 0.53 | other (other) | borregomycin A, borregomycin B, borregomycin C, borregomycin D | uncultured bacterium
BGC0000279.5 |  |  |  |  |  | 0.51 | PKS | xantholipin | Streptomyces flavogriseus
BGC0000632.5 |  |  |  |  |  | 0.51 | saccharide, terpene | brasilicardin A | Nocardia terpenica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.77 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000056.3 |  | 0.70 | PKS | esperamicin | Actinomadura verrucosospora
BGC0000850.5 |  | 0.69 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.66 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.64 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.24 out of 19.26
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.81 out of 18.57
Confidence: medium
Additional weak hits (16):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.57 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.77 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.01 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.05 out of 20.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.88 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.98 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.43 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.88 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.96 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.29 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.76 out of 35.63
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.33 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.71 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 7591 - 123151:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 36230 - 78015:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpg)

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).
AMK27_RS38055: mal
PKS_AT (620..845): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  Propionyl-CoA: 58.3%
  inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 76.1
  Methoxymalonyl-CoA: 51.0
  Methylmalonyl-CoA: 47.0
  inactive: 34.5
  Isobutyryl-CoA: 28.0
  Ethylmalonyl-CoA: 20.4
  Propionyl-CoA: 20.0
  fatty_acid: 12.9
  trans-1,2-CPDA: 10.5
  2-Methylbutyryl-CoA: 9.1
  Benzoyl-CoA: 7.0
  CHC-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

AMK27_RS38170: Hpg
Search NORINE for peptide: strict or relaxed
AMP-binding (13..408): Hpg
nrpys: Hpg

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:
    LDSAFGVSTYEVHVLTGGDRAMYGATEVSSFAAY
  Nearest Stachelhaus code(s):
    ohMan NVYHLGMVFK (76% 8Å match)
    Hpg NVYHLGMLFK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMK27_RS38205: X
AMP-binding (102..333): 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:
    SRMPFGDVFTAGVCLVLGERALYGSQEALCIATG
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

AMK27_RS38220: X
AMP-binding (90..284): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    GSHA---FWGMAGLLAGAEFNAAGTTEFGGVFMF
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

AMK27_RS38265: X
AMP-binding (18..387): 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:
    SRMG------SFYSVVAGELNVYGTTEIGHALLA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

AMK27_RS38340: X
AMP-binding (101..353): 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:
    QATLYGYSVLSRDGGCGGDHDGYGLSEAGPNVAL
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
ToxT | Regulator of MSHA biosynthesis

NZ_LIVV01000002.1 - Region 1 - T2PKS,azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 40,217 nt. (total: 40,217 nt) Show pHMM detection rules used
Region on contig edge.
T2PKS: (t2ks and t2clf)
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
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
AMK27_RS07445: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AMK27_RS07465: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

AMK27_RS07485: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

AMK27_RS07590: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

AMK27_RS07600: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: PPTase acylase aminotransferase glycosyltransferase transferase
AMK27_RS07425: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

AMK27_RS07460: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

AMK27_RS07550: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

AMK27_RS07560: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

AMK27_RS07565: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

AMK27_RS07580: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: hydrolase
AMK27_RS07510: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: cyclase dehydratase
AMK27_RS07450: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

AMK27_RS07570: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

AMK27_RS07575: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
AMK27_RS07430: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AMK27_RS07435: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

AMK27_RS07595: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | T2PKS | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000195.5 |  |  | 0.47 | PKS | alnumycin A, alnumycin B, alnumycin C, alnumycin P, prealnumycin, thalnumycin A, thalnumycin B, K1115A, 1,6-dihydro-8-propylanthraquinone | Streptomyces sp. CM020
BGC0000813.3 |  |  | 0.40 | other (other) | K-252a | Nonomuraea longicatena
BGC0000277.5 |  |  | 0.40 | PKS | urdamycin | Streptomyces fradiae
BGC0000278.3 |  |  | 0.38 | PKS | urdamycin | Streptomyces fradiae
BGC0000827.3 |  |  | 0.38 | other (other) | staurosporine | Salinispora arenicola CNS-205
BGC0002361.3 |  |  | 0.37 | PKS, saccharide | baikalomycin B, baikalomycin A, baikalomycin C | Streptomyces sp. IB201691-2A2
BGC0000791.3 |  |  | 0.35 | saccharide | O-antigen | Cronobacter sakazakii
BGC0000790.3 |  |  | 0.35 | saccharide | O-antigen | Escherichia coli
BGC0000826.5 |  |  | 0.35 | other (other) | staurosporine | Streptomyces clavuligerus ATCC 27064
BGC0000825.5 |  |  | 0.35 | other (other) | staurosporine | Streptomyces sp. TP-A0274

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000278.3 |  | 0.71 | PKS | urdamycin | Streptomyces fradiae
BGC0000231.5 |  | 0.67 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001723.5 |  | 0.66 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000195.5 |  | 0.65 | PKS | alnumycin A, alnumycin B, alnumycin C, alnumycin P, prealnumycin, thalnumycin A, thalnumycin B, K1115A, 1,6-dihydro-8-propylanthraquinone | Streptomyces sp. CM020
BGC0002276.2 |  | 0.63 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0000272.3 |  | 0.61 | PKS | spore pigment | Streptomyces collinus
BGC0000234.5 |  | 0.61 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000253.4 |  | 0.58 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002000.4 |  | 0.58 | PKS | setomimycin | Streptomyces aurantiacus JA 4570

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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.79 out of 29.72
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
Additional weak hits (9):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.12 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.99 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.08 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.49 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.40 out of 28.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.49 out of 32.93
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.19 out of 28.14
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.
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
RREFinder
Type II PKS
TFBS Finder
Azole RiPPs
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).
AMK27_RS07425: mal
PKS_AT (8..297): 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: 84.0
  Methylmalonyl-CoA: 43.9
  Methoxymalonyl-CoA: 42.6
  inactive: 21.4
  Propionyl-CoA: 20.2
  Benzoyl-CoA: 8.4
  Ethylmalonyl-CoA: 7.1
  CHC-CoA: 4.1
  2-Methylbutyryl-CoA: 1.8
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (11946...34196)
AMK27_RS07530
  RRE type: Goadsporin_CD_RRE
  Location: 0 - 92
  Score: 48.1
  RRE type: Cyanobactin_D_RRE
  Location: 1 - 69
  Score: 46.6
  RRE type: NHLP_CD_RRE
  Location: 0 - 88
  Score: 41.6

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:
  0 to 40217
Starter unit(s):
  butyryl-CoA (Score: 696.0; E-value: 1.99e-172)
Malonyl elongations:
  7 (Score: 686.1; E-value: 3.1e-209)
Product class(es):
  benzoisochromanequinone
Product molecular weight(s):
  butyryl-CoA_7: 697 Da

AMK27_RS07420
  ACP (Score: 76.0; E-value: 4.1e-24)
AMK27_RS07425
  AT (Score: 372.5; E-value: 4.2e-114)
  AT AAC18106.1_Frenolicin_butyryl-CoA (Score: 223.0; E-value: 1.92e-73)
AMK27_RS07430
  KS (Score: 778.0; E-value: 4.7e-237)
AMK27_RS07435
  CLF 7 (Score: 686.1; E-value: 3.1e-209)
AMK27_RS07440
  ACP (Score: 100.9; E-value: 6.7e-32)
AMK27_RS07445
  KR C9 (Score: 460.5; E-value: 3.4e-141)
AMK27_RS07450
  CYC C7-C12 (Score: 316.8; E-value: 2.7e-97)
AMK27_RS07455
  CYC C5-C14 (Score: 448.8; E-value: 1.9e-137)
AMK27_RS07485
  KR (Score: 158.3; E-value: 6.5e-49)
AMK27_RS07550
  GT (Score: 413.3; E-value: 3e-126)
AMK27_RS07560
  GT (Score: 421.3; E-value: 1.1e-128)
AMK27_RS07595
  KSIII (Score: 414.8; E-value: 6.2e-127)
  KSIII ACI88883.1_Alnumycin_butyryl-CoA (Score: 473.0; E-value: 1.99e-172)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

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_LIVV01000002.1 - Region 2 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 176,777 - 203,395 nt. (total: 26,619 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
AMK27_RS08250: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

AMK27_RS08290: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: aminotransferase transferase
AMK27_RS08245: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

AMK27_RS08315: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Ligases: synthetase
AMK27_RS08295: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.71 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0001839.3 |  | 0.51 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.71 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0001839.3 |  | 0.51 | terpene | squalestatin S1 | Aspergillus sp. Z5
BGC0000656.5 |  | 0.50 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.49 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0000630.3 |  | 0.49 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

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

No significant matches found.

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

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

Genes with terpene domains:
AMK27_RS08280: PT_phytoene_like
Domain 1 (19 - 294): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

AMK27_RS08285: PT_phytoene_like
Domain 1 (17 - 305): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

AMK27_RS08295: PT_FPPS_like
Domain 1 (72 - 364): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

AMK27_RS08300: T2TS
Domain 1 (42 - 669): 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):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.69 out of 30.97
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.58 out of 24.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.90 out of 18.57
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.72 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.44 out of 23.43
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_LIVV01000002.1 - Region 3 - 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: 249,283 - 260,149 nt. (total: 10,867 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer
AMK27_RS08560: flavodoxin

smcogs
  SMCOG1134: flavodoxin

AMK27_RS08580: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: hydrolase
AMK27_RS08590: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000249.5 |  | 0.40 | PKS | nogalamycin | Streptomyces nogalater
BGC0000243.4 |  | 0.32 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0001188.3 |  | 0.32 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0001882.3 |  | 0.31 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0001137.5 |  | 0.30 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0001203.4 |  | 0.29 | NRPS, PKS | Clarexpoxcin A, Clarexpoxcin B, Clarexpoxcin C, Clarexpoxcin D, Clarexpoxcin E | uncultured bacterium AR_456
BGC0000335.4 |  | 0.26 | NRPS, PKS | cystomanamide A, cystomanamide B, cystomanamide C, cystomanamide D | Cystobacter fuscus
BGC0000981.3 |  | 0.25 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E6
BGC0001942.3 |  | 0.24 | NRPS, PKS | malonomycin | Streptomyces rimosus subsp. paromomycinus
BGC0001532.4 |  | 0.23 | NRPS | bogorol A | Brevibacillus laterosporus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000249.5 |  | 0.40 | PKS | nogalamycin | Streptomyces nogalater
BGC0000243.4 |  | 0.32 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0001188.3 |  | 0.32 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0001882.3 |  | 0.31 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0001137.5 |  | 0.30 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0001203.4 |  | 0.29 | NRPS, PKS | Clarexpoxcin A, Clarexpoxcin B, Clarexpoxcin C, Clarexpoxcin D, Clarexpoxcin E | uncultured bacterium AR_456
BGC0000335.4 |  | 0.26 | NRPS, PKS | cystomanamide A, cystomanamide B, cystomanamide C, cystomanamide D | Cystobacter fuscus
BGC0000981.3 |  | 0.25 | NRPS, PKS | cylindrospermopsin | Aphanizomenon sp. 10E6
BGC0001942.3 |  | 0.24 | NRPS, PKS | malonomycin | Streptomyces rimosus subsp. paromomycinus
BGC0001532.4 |  | 0.23 | NRPS | bogorol A | Brevibacillus laterosporus

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 (1):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.15 out of 30.25
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LIVV01000002.1 - Region 4 - lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 282,580 - 305,225 nt. (total: 22,646 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
AMK27_RS08710: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

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

Reference | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.83 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000496.5 |  | 0.69 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.60 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000553.3 |  | 0.58 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000546.3 |  | 0.55 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0000518.3 |  | 0.53 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000551.5 |  | 0.83 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000496.5 |  | 0.69 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.60 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000553.3 |  | 0.58 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0002276.2 |  | 0.55 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000546.3 |  | 0.55 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0000518.3 |  | 0.53 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai

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

No significant matches found.

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

#### Lanthipeptide(s) for AMK27_RS08705

AMK27_RS08700
Leader:
MNLFDLQSLETPKDEAIGDVE
Core:
T G S R A S L L L C G D S S L S V T T C N
Core with dehydrations:
Dhb G Dha R A Dha L L L Cys G D Dha Dha L Dha V Dhb Dhb Cys N

#### antiSMASH-DB 4.0 matches for AMK27_RS08700

100.0%
NC_018750.1 and 67 others:
NC_018750.1 Lanthipeptides: SVEN_RS32110_lanthipeptide NZ_BBNO01000003.1 Lanthipeptides: TU31_RS37940_lanthipeptide NZ_BMTO01000007.1 Lanthipeptides: IE136_RS15615_lanthipeptide NZ_BMUN01000001.1 Lanthipeptides: IE238_RS00740_lanthipeptide NZ_CP009754.1 Lanthipeptides: NI25_RS05015_lanthipeptide NZ_CP015866.1 Lanthipeptides: Spa2297_RS27800_lanthipeptide NZ_CP017157.1 Lanthipeptides: SL103_RS15895_lanthipeptide NZ_CP019457.1 Lanthipeptides: BXT88_RS03410_lanthipeptide NZ_CP019724.1 Lanthipeptides: B1H29_RS35355_lanthipeptide NZ_CP019779.1 Lanthipeptides: STRMOE7_RS03775_lanthipeptide NZ_CP023691.1 Lanthipeptides: CP981_RS03050_lanthipeptide NZ_CP023700.1 Lanthipeptides: CP969_RS04700_lanthipeptide NZ_CP027299.1 Lanthipeptides: C1N79_RS34970_lanthipeptide NZ_CP029042.1 Lanthipeptides: DDE74_RS03525_lanthipeptide NZ_CP029195.1 Lanthipeptides: DEJ45_RS04995_lanthipeptide NZ_CP029195.1 Lanthipeptides: DEJ45_RS04995_lanthipeptide NZ_CP029196.1 Lanthipeptides: DEJ44_RS30395_lanthipeptide NZ_CP029196.1 Lanthipeptides: DEJ44_RS30395_lanthipeptide NZ_CP029541.1 Lanthipeptides: DKG71_RS05245_lanthipeptide NZ_CP034353.1 Lanthipeptides: D1J63_RS04900_lanthipeptide NZ_CP039123.1 Lanthipeptides: E5N77_RS35250_lanthipeptide NZ_CP043317.1 Lanthipeptides: FYC74_RS09720_lanthipeptide NZ_CP046905.1 Lanthipeptides: GPZ77_RS32930_lanthipeptide NZ_CP047140.1 Lanthipeptides: GLX30_RS11420_lanthipeptide NZ_CP050976.1 Lanthipeptides: HEP86_RS04470_lanthipeptide NZ_CP054920.1 Lanthipeptides: HUT15_RS04615_lanthipeptide NZ_CP060825.1 Lanthipeptides: IAG43_RS32355_lanthipeptide NZ_CP074111.1 Lanthipeptides: KE639_RS31630_lanthipeptide NZ_CP084681.1 Lanthipeptides: KI385_RS00885_lanthipeptide NZ_CP085300.1 Lanthipeptides: LJA35_RS05220_lanthipeptide NZ_CP086217.1 Lanthipeptides: LJ741_RS03435_lanthipeptide NZ_CP094676.1 Lanthipeptides: L6J92_RS09690_lanthipeptide NZ_CP098437.1 Lanthipeptides: NCG97_RS34740_lanthipeptide NZ_CP099468.1 Lanthipeptides: NFX46_RS16770_lanthipeptide NZ_CP101137.1 Lanthipeptides: M6G08_RS24535_lanthipeptide NZ_CP102609.1 Lanthipeptides: NUT86_RS03980_lanthipeptide NZ_CP104697.1 Lanthipeptides: N6Q81_RS33560_lanthipeptide NZ_CP114202.1 Lanthipeptides: STRLI_RS35870_lanthipeptide NZ_CP114203.1 Lanthipeptides: STRNI_RS37360_lanthipeptide NZ_CP114205.1 Lanthipeptides: STRTU_RS33380_lanthipeptide NZ_JACHJE010000006.1 Lanthipeptides: FHS32_RS15850_lanthipeptide NZ_JACSCH020000032.1 Lanthipeptides: E0F75_RS38565_lanthipeptide NZ_JACSCH020000032.1 Lanthipeptides: E0F75_RS38565_lanthipeptide NZ_JACSCH020000032.1 Lanthipeptides: E0F75_RS38565_lanthipeptide NZ_JACWAA010000001.1 Lanthipeptides: ICA23_RS00800_lanthipeptide NZ_JAFEJA010000002.1 Lanthipeptides: JE024_RS34830_lanthipeptide NZ_JAGPYC010000033.1 Lanthipeptides: KBZ00_RS31440_lanthipeptide NZ_JAHLXF010000022.1 Lanthipeptides: KQY13_RS30555_lanthipeptide NZ_JAIHBQ010000001.1 Lanthipeptides: K4902_RS04515_lanthipeptide NZ_JAJJMU010000026.1 Lanthipeptides: LOC25_RS31275_lanthipeptide NZ_JAJNOJ010000002.1 Lanthipeptides: MBT42_RS06255_lanthipeptide NZ_JAJNOJ010000002.1 Lanthipeptides: MBT42_RS06255_lanthipeptide NZ_JAMGSL010000004.1 Lanthipeptides: M5362_RS09920_lanthipeptide NZ_JAMGSL010000004.1 Lanthipeptides: M5362_RS09920_lanthipeptide NZ_JAPKNL010000004.1 Lanthipeptides: OSI21_RS07750_lanthipeptide NZ_JH993790.1 Lanthipeptides: STRVIR_RS0131905_lanthipeptide NZ_KN039948.1 Lanthipeptides: FM21_RS29525_lanthipeptide NZ_LIPF01000004.1 Lanthipeptides: AMK11_RS16660_lanthipeptide NZ_LIVV01000002.1 Lanthipeptides: AMK27_RS08700_lanthipeptide NZ_LIVV01000002.1 Lanthipeptides: AMK27_RS08700_lanthipeptide NZ_LIVX01000004.1 Lanthipeptides: AMK29_RS15650_lanthipeptide NZ_LIWB01000010.1 Lanthipeptides: AMK33_RS24360_lanthipeptide NZ_MPOH02000012.1 Lanthipeptides: BM536_RS17150_lanthipeptide NZ_NNBP01000011.1 Lanthipeptides: CG747_RS19290_lanthipeptide NZ_NNBP01000011.1 Lanthipeptides: CG747_RS19290_lanthipeptide NZ_RAIF01000032.1 Lanthipeptides: EBH09_RS35480_lanthipeptide NZ_SOPG01000008.1 Lanthipeptides: E0I08_RS17090_lanthipeptide
Lanthipeptides: SVEN_RS32110_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
T G S R A S L L L C G D S S L S V T T C N
1
T G S R A S L L L C G D S S L S V T T C N
21
95.2%
NZ_BBOK01000011.1 and 23 others:
NZ_BEWD01000001.1 Lanthipeptides: Sru02f_RS01660_lanthipeptide NZ_BMSL01000016.1 Lanthipeptides: IE215_RS23330_lanthipeptide NZ_BMUC01000023.1 Lanthipeptides: IE172_RS32210_lanthipeptide NZ_BMVQ01000005.1 Lanthipeptides: IE283_RS17035_lanthipeptide NZ_BMWI01000025.1 Lanthipeptides: IE253_RS33945_lanthipeptide NZ_CP012382.1 Lanthipeptides: SAM23877_RS30085_lanthipeptide NZ_CP012949.1 Lanthipeptides: SAM40697_RS29010_lanthipeptide NZ_CP042324.1 Lanthipeptides: FQ762_RS34495_lanthipeptide NZ_CP043959.1 Lanthipeptides: F3L20_RS19105_lanthipeptide NZ_CP045547.1 Lanthipeptides: GEV49_RS05730_lanthipeptide NZ_CP054939.1 Lanthipeptides: HUT14_RS29815_lanthipeptide NZ_CP094918.1 Lanthipeptides: MTR79_RS16715_lanthipeptide NZ_GG657756.1 Lanthipeptides: SSPG_RS05020_lanthipeptide NZ_JAAIFS010000001.1 Lanthipeptides: GUR47_RS02255_lanthipeptide NZ_KZ195574.1 Lanthipeptides: B9W62_RS05695_lanthipeptide NZ_LT629768.1 Lanthipeptides: BLU60_RS34110_lanthipeptide NZ_MQUH01000025.1 Lanthipeptides: BSZ07_RS33280_lanthipeptide NZ_RAII01000001.1 Lanthipeptides: EBH12_RS10360_lanthipeptide NZ_RSEG01000006.1 Lanthipeptides: EIA57_RS12710_lanthipeptide NZ_SOAV01000001.1 Lanthipeptides: EV562_RS04520_lanthipeptide NZ_VIUV01000020.1 Lanthipeptides: FB570_RS34060_lanthipeptide NZ_WHZR01000001.1 Lanthipeptides: STPH1_RS04005_lanthipeptide NZ_WXVT01000001.1 Lanthipeptides: STPH2_RS03995_lanthipeptide
Lanthipeptides: APK71_RS25550_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
T G S R A S L L L C G D S S L S+T T C N
1
T G S R A S L L L C G D S S L S I T T C N
21
95.2%
NZ_BMSV01000002.1 and 18 others:
NZ_BMTP01000009.1 Lanthipeptides: IE109_RS18470_lanthipeptide NZ_CP007699.2 Lanthipeptides: T261_RS39185_lanthipeptide NZ_CP020042.1 Lanthipeptides: B4U46_RS32710_lanthipeptide NZ_CP023202.1 Lanthipeptides: SXIN_RS23100_lanthipeptide NZ_CP023692.1 Lanthipeptides: CP980_RS04735_lanthipeptide NZ_CP028158.1 Lanthipeptides: C6361_RS04660_lanthipeptide NZ_CP028159.1 Lanthipeptides: C6W10_RS01185_lanthipeptide NZ_CP034279.1 Lanthipeptides: EIZ62_RS28660_lanthipeptide NZ_CP102332.1 Lanthipeptides: NRO40_RS01140_lanthipeptide NZ_FNHI01000003.1 Lanthipeptides: BLT82_RS06465_lanthipeptide NZ_JADMLH010000003.1 Lanthipeptides: IT780_RS09875_lanthipeptide NZ_JAGGOI010000031.1 Lanthipeptides: J7E87_RS22160_lanthipeptide NZ_JAGPXX010000007.1 Lanthipeptides: KBZ10_RS10785_lanthipeptide NZ_JAPNLM010000003.1 Lanthipeptides: OTB16_RS07305_lanthipeptide NZ_LIVQ01000005.1 Lanthipeptides: AMK16_RS35205_lanthipeptide NZ_LIVQ01000005.1 Lanthipeptides: AMK16_RS35205_lanthipeptide NZ_LIYH01000004.1 Lanthipeptides: AMK26_RS17765_lanthipeptide NZ_NBCN01000003.1 Lanthipeptides: BKD26_RS06570_lanthipeptide
Lanthipeptides: IE106_RS06150_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
G S R A S L L L C G D S S L S V T T C N
1
G S R A S L L L C G D S S L S V T T C N
20
with 73 more sequence matches
Only the first 10 are displayed here.
95.2%
NZ_BMTU01000009.1 and 1 other:
NZ_JACHJI010000005.1 Lanthipeptides: FHS37_RS15430_lanthipeptide
Lanthipeptides: IE118_RS22890_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
+G S R A S L L L C G D S S L S V T T C N
1
S G S R A S L L L C G D S S L S V T T C N
21
95.2%
NZ_BNCA01000002.1 and 1 other:
NZ_CP049782.1 Lanthipeptides: G7Z12_RS34445_lanthipeptide
Lanthipeptides: IE314_RS02760_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
T G S R A S L L L C G D S S L S V+T C N
1
T G S R A S L L L C G D S S L S V S T C N
21
90.5%
NZ_CP048835.1:
Lanthipeptides: C8250_RS00390_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
G S R A S L L L C G+S S L S V T T C N
2
G S R A S L L L C G N S S L S V T T C N
21
90.5%
NZ_GG657758.1 and 1 other:
NZ_JACHEM010000005.1 Lanthipeptides: HNQ79_RS11445_lanthipeptide
Lanthipeptides: SSRG_RS03855_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
+G S R A S L L L C G D S S L S+T T C N
1
S G S R A S L L L C G D S S L S I T T C N
21
90.5%
NZ_QGGR01000008.1:
Lanthipeptides: BC793_RS19230_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
G S+A S L L L C G D S S L S V T T C N
2
G S Q A S L L L C G D S S L S V T T C N
21
85.7%
NZ_CP036455.1:
Lanthipeptides: EKD16_RS17975_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
G S A S L L L C G D S S L S+T T C N
2
G S E A S L L L C G D S S L S L T T C N
21
85.7%
NZ_CP077658.1:
Lanthipeptides: KQY30_RS33045_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
S R A S L L L C G D S S L S V T C N
1
A S R A S L L L C G D S S L S V V T C N
20
85.7%
NZ_CP092183.1:
Lanthipeptides: COUCH_RS09775_lanthipeptide
4
R A S L L L C G D S S L S V T T C N
21
R A S L L L C G D S S L S V T T C N
1
R A S L L L C G D S S L S V T T C N
18
85.7%
NZ_FOET01000001.1 and 2 others:
NZ_FOSG01000005.1 Lanthipeptides: BM237_RS08435_lanthipeptide NZ_PDKQ02000044.1 Lanthipeptides: BFM75_RS16855_lanthipeptide
Lanthipeptides: BMY40_RS02540_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
G S A S L L L C G D S S L S V T T C
2
G S E A S L L L C G D S S L S V T T C R
21
83.3%
NZ_CP007574.1 and 6 others:
NZ_CP007574.1 Lanthipeptides: DC74_RS36920_lanthipeptide NZ_CP026094.1 Lanthipeptides: SE95_RS37250_lanthipeptide NZ_CP104098.1 Lanthipeptides: N1H47_RS36625_lanthipeptide NZ_CP104098.1 Lanthipeptides: N1H47_RS36625_lanthipeptide NZ_CP119144.1 Lanthipeptides: P0D74_RS03260_lanthipeptide NZ_CP119144.1 Lanthipeptides: P0D74_RS03260_lanthipeptide
Lanthipeptides: DC74_RS36920_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
T G S R A S L L L C G D S S L S V T T C
4
T G S R A S L L L C G D S S L S V T T C K
24

#### MIBiG 4.0 matches for AMK27_RS08700

59.1%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
1
T G S R A S L L L C G D S S L S V T T C N
21
T G S+ S L L+C S S L S V C
1
T G S Q V S L L V C E Y S S L S V V L C T
21

#### Lanthipeptide(s) for AMK27_RS08715

AMK27_RS08700
Leader:
MNLFDLQSLETPKDEAIGDVE
Core:
T G S R A S L L L C G D S S L S V T T C N
Core with dehydrations:
Dhb G Dha R A Dha L L L Cys G D Dha Dha L Dha V Dhb Dhb Cys N

#### antiSMASH-DB 4.0 matches for AMK27_RS08700

100.0%
NC_018750.1 and 67 others:
NC_018750.1 Lanthipeptides: SVEN_RS32110_lanthipeptide NZ_BBNO01000003.1 Lanthipeptides: TU31_RS37940_lanthipeptide NZ_BMTO01000007.1 Lanthipeptides: IE136_RS15615_lanthipeptide NZ_BMUN01000001.1 Lanthipeptides: IE238_RS00740_lanthipeptide NZ_CP009754.1 Lanthipeptides: NI25_RS05015_lanthipeptide NZ_CP015866.1 Lanthipeptides: Spa2297_RS27800_lanthipeptide NZ_CP017157.1 Lanthipeptides: SL103_RS15895_lanthipeptide NZ_CP019457.1 Lanthipeptides: BXT88_RS03410_lanthipeptide NZ_CP019724.1 Lanthipeptides: B1H29_RS35355_lanthipeptide NZ_CP019779.1 Lanthipeptides: STRMOE7_RS03775_lanthipeptide NZ_CP023691.1 Lanthipeptides: CP981_RS03050_lanthipeptide NZ_CP023700.1 Lanthipeptides: CP969_RS04700_lanthipeptide NZ_CP027299.1 Lanthipeptides: C1N79_RS34970_lanthipeptide NZ_CP029042.1 Lanthipeptides: DDE74_RS03525_lanthipeptide NZ_CP029195.1 Lanthipeptides: DEJ45_RS04995_lanthipeptide NZ_CP029195.1 Lanthipeptides: DEJ45_RS04995_lanthipeptide NZ_CP029196.1 Lanthipeptides: DEJ44_RS30395_lanthipeptide NZ_CP029196.1 Lanthipeptides: DEJ44_RS30395_lanthipeptide NZ_CP029541.1 Lanthipeptides: DKG71_RS05245_lanthipeptide NZ_CP034353.1 Lanthipeptides: D1J63_RS04900_lanthipeptide NZ_CP039123.1 Lanthipeptides: E5N77_RS35250_lanthipeptide NZ_CP043317.1 Lanthipeptides: FYC74_RS09720_lanthipeptide NZ_CP046905.1 Lanthipeptides: GPZ77_RS32930_lanthipeptide NZ_CP047140.1 Lanthipeptides: GLX30_RS11420_lanthipeptide NZ_CP050976.1 Lanthipeptides: HEP86_RS04470_lanthipeptide NZ_CP054920.1 Lanthipeptides: HUT15_RS04615_lanthipeptide NZ_CP060825.1 Lanthipeptides: IAG43_RS32355_lanthipeptide NZ_CP074111.1 Lanthipeptides: KE639_RS31630_lanthipeptide NZ_CP084681.1 Lanthipeptides: KI385_RS00885_lanthipeptide NZ_CP085300.1 Lanthipeptides: LJA35_RS05220_lanthipeptide NZ_CP086217.1 Lanthipeptides: LJ741_RS03435_lanthipeptide NZ_CP094676.1 Lanthipeptides: L6J92_RS09690_lanthipeptide NZ_CP098437.1 Lanthipeptides: NCG97_RS34740_lanthipeptide NZ_CP099468.1 Lanthipeptides: NFX46_RS16770_lanthipeptide NZ_CP101137.1 Lanthipeptides: M6G08_RS24535_lanthipeptide NZ_CP102609.1 Lanthipeptides: NUT86_RS03980_lanthipeptide NZ_CP104697.1 Lanthipeptides: N6Q81_RS33560_lanthipeptide NZ_CP114202.1 Lanthipeptides: STRLI_RS35870_lanthipeptide NZ_CP114203.1 Lanthipeptides: STRNI_RS37360_lanthipeptide NZ_CP114205.1 Lanthipeptides: STRTU_RS33380_lanthipeptide NZ_JACHJE010000006.1 Lanthipeptides: FHS32_RS15850_lanthipeptide NZ_JACSCH020000032.1 Lanthipeptides: E0F75_RS38565_lanthipeptide NZ_JACSCH020000032.1 Lanthipeptides: E0F75_RS38565_lanthipeptide NZ_JACSCH020000032.1 Lanthipeptides: E0F75_RS38565_lanthipeptide NZ_JACWAA010000001.1 Lanthipeptides: ICA23_RS00800_lanthipeptide NZ_JAFEJA010000002.1 Lanthipeptides: JE024_RS34830_lanthipeptide NZ_JAGPYC010000033.1 Lanthipeptides: KBZ00_RS31440_lanthipeptide NZ_JAHLXF010000022.1 Lanthipeptides: KQY13_RS30555_lanthipeptide NZ_JAIHBQ010000001.1 Lanthipeptides: K4902_RS04515_lanthipeptide NZ_JAJJMU010000026.1 Lanthipeptides: LOC25_RS31275_lanthipeptide NZ_JAJNOJ010000002.1 Lanthipeptides: MBT42_RS06255_lanthipeptide NZ_JAJNOJ010000002.1 Lanthipeptides: MBT42_RS06255_lanthipeptide NZ_JAMGSL010000004.1 Lanthipeptides: M5362_RS09920_lanthipeptide NZ_JAMGSL010000004.1 Lanthipeptides: M5362_RS09920_lanthipeptide NZ_JAPKNL010000004.1 Lanthipeptides: OSI21_RS07750_lanthipeptide NZ_JH993790.1 Lanthipeptides: STRVIR_RS0131905_lanthipeptide NZ_KN039948.1 Lanthipeptides: FM21_RS29525_lanthipeptide NZ_LIPF01000004.1 Lanthipeptides: AMK11_RS16660_lanthipeptide NZ_LIVV01000002.1 Lanthipeptides: AMK27_RS08700_lanthipeptide NZ_LIVV01000002.1 Lanthipeptides: AMK27_RS08700_lanthipeptide NZ_LIVX01000004.1 Lanthipeptides: AMK29_RS15650_lanthipeptide NZ_LIWB01000010.1 Lanthipeptides: AMK33_RS24360_lanthipeptide NZ_MPOH02000012.1 Lanthipeptides: BM536_RS17150_lanthipeptide NZ_NNBP01000011.1 Lanthipeptides: CG747_RS19290_lanthipeptide NZ_NNBP01000011.1 Lanthipeptides: CG747_RS19290_lanthipeptide NZ_RAIF01000032.1 Lanthipeptides: EBH09_RS35480_lanthipeptide NZ_SOPG01000008.1 Lanthipeptides: E0I08_RS17090_lanthipeptide
Lanthipeptides: SVEN_RS32110_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
T G S R A S L L L C G D S S L S V T T C N
1
T G S R A S L L L C G D S S L S V T T C N
21
95.2%
NZ_BBOK01000011.1 and 23 others:
NZ_BEWD01000001.1 Lanthipeptides: Sru02f_RS01660_lanthipeptide NZ_BMSL01000016.1 Lanthipeptides: IE215_RS23330_lanthipeptide NZ_BMUC01000023.1 Lanthipeptides: IE172_RS32210_lanthipeptide NZ_BMVQ01000005.1 Lanthipeptides: IE283_RS17035_lanthipeptide NZ_BMWI01000025.1 Lanthipeptides: IE253_RS33945_lanthipeptide NZ_CP012382.1 Lanthipeptides: SAM23877_RS30085_lanthipeptide NZ_CP012949.1 Lanthipeptides: SAM40697_RS29010_lanthipeptide NZ_CP042324.1 Lanthipeptides: FQ762_RS34495_lanthipeptide NZ_CP043959.1 Lanthipeptides: F3L20_RS19105_lanthipeptide NZ_CP045547.1 Lanthipeptides: GEV49_RS05730_lanthipeptide NZ_CP054939.1 Lanthipeptides: HUT14_RS29815_lanthipeptide NZ_CP094918.1 Lanthipeptides: MTR79_RS16715_lanthipeptide NZ_GG657756.1 Lanthipeptides: SSPG_RS05020_lanthipeptide NZ_JAAIFS010000001.1 Lanthipeptides: GUR47_RS02255_lanthipeptide NZ_KZ195574.1 Lanthipeptides: B9W62_RS05695_lanthipeptide NZ_LT629768.1 Lanthipeptides: BLU60_RS34110_lanthipeptide NZ_MQUH01000025.1 Lanthipeptides: BSZ07_RS33280_lanthipeptide NZ_RAII01000001.1 Lanthipeptides: EBH12_RS10360_lanthipeptide NZ_RSEG01000006.1 Lanthipeptides: EIA57_RS12710_lanthipeptide NZ_SOAV01000001.1 Lanthipeptides: EV562_RS04520_lanthipeptide NZ_VIUV01000020.1 Lanthipeptides: FB570_RS34060_lanthipeptide NZ_WHZR01000001.1 Lanthipeptides: STPH1_RS04005_lanthipeptide NZ_WXVT01000001.1 Lanthipeptides: STPH2_RS03995_lanthipeptide
Lanthipeptides: APK71_RS25550_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
T G S R A S L L L C G D S S L S+T T C N
1
T G S R A S L L L C G D S S L S I T T C N
21
95.2%
NZ_BMSV01000002.1 and 18 others:
NZ_BMTP01000009.1 Lanthipeptides: IE109_RS18470_lanthipeptide NZ_CP007699.2 Lanthipeptides: T261_RS39185_lanthipeptide NZ_CP020042.1 Lanthipeptides: B4U46_RS32710_lanthipeptide NZ_CP023202.1 Lanthipeptides: SXIN_RS23100_lanthipeptide NZ_CP023692.1 Lanthipeptides: CP980_RS04735_lanthipeptide NZ_CP028158.1 Lanthipeptides: C6361_RS04660_lanthipeptide NZ_CP028159.1 Lanthipeptides: C6W10_RS01185_lanthipeptide NZ_CP034279.1 Lanthipeptides: EIZ62_RS28660_lanthipeptide NZ_CP102332.1 Lanthipeptides: NRO40_RS01140_lanthipeptide NZ_FNHI01000003.1 Lanthipeptides: BLT82_RS06465_lanthipeptide NZ_JADMLH010000003.1 Lanthipeptides: IT780_RS09875_lanthipeptide NZ_JAGGOI010000031.1 Lanthipeptides: J7E87_RS22160_lanthipeptide NZ_JAGPXX010000007.1 Lanthipeptides: KBZ10_RS10785_lanthipeptide NZ_JAPNLM010000003.1 Lanthipeptides: OTB16_RS07305_lanthipeptide NZ_LIVQ01000005.1 Lanthipeptides: AMK16_RS35205_lanthipeptide NZ_LIVQ01000005.1 Lanthipeptides: AMK16_RS35205_lanthipeptide NZ_LIYH01000004.1 Lanthipeptides: AMK26_RS17765_lanthipeptide NZ_NBCN01000003.1 Lanthipeptides: BKD26_RS06570_lanthipeptide
Lanthipeptides: IE106_RS06150_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
G S R A S L L L C G D S S L S V T T C N
1
G S R A S L L L C G D S S L S V T T C N
20
with 73 more sequence matches
Only the first 10 are displayed here.
95.2%
NZ_BMTU01000009.1 and 1 other:
NZ_JACHJI010000005.1 Lanthipeptides: FHS37_RS15430_lanthipeptide
Lanthipeptides: IE118_RS22890_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
+G S R A S L L L C G D S S L S V T T C N
1
S G S R A S L L L C G D S S L S V T T C N
21
95.2%
NZ_BNCA01000002.1 and 1 other:
NZ_CP049782.1 Lanthipeptides: G7Z12_RS34445_lanthipeptide
Lanthipeptides: IE314_RS02760_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
T G S R A S L L L C G D S S L S V+T C N
1
T G S R A S L L L C G D S S L S V S T C N
21
90.5%
NZ_CP048835.1:
Lanthipeptides: C8250_RS00390_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
G S R A S L L L C G+S S L S V T T C N
2
G S R A S L L L C G N S S L S V T T C N
21
90.5%
NZ_GG657758.1 and 1 other:
NZ_JACHEM010000005.1 Lanthipeptides: HNQ79_RS11445_lanthipeptide
Lanthipeptides: SSRG_RS03855_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
+G S R A S L L L C G D S S L S+T T C N
1
S G S R A S L L L C G D S S L S I T T C N
21
90.5%
NZ_QGGR01000008.1:
Lanthipeptides: BC793_RS19230_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
G S+A S L L L C G D S S L S V T T C N
2
G S Q A S L L L C G D S S L S V T T C N
21
85.7%
NZ_CP036455.1:
Lanthipeptides: EKD16_RS17975_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
G S A S L L L C G D S S L S+T T C N
2
G S E A S L L L C G D S S L S L T T C N
21
85.7%
NZ_CP077658.1:
Lanthipeptides: KQY30_RS33045_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
S R A S L L L C G D S S L S V T C N
1
A S R A S L L L C G D S S L S V V T C N
20
85.7%
NZ_CP092183.1:
Lanthipeptides: COUCH_RS09775_lanthipeptide
4
R A S L L L C G D S S L S V T T C N
21
R A S L L L C G D S S L S V T T C N
1
R A S L L L C G D S S L S V T T C N
18
85.7%
NZ_FOET01000001.1 and 2 others:
NZ_FOSG01000005.1 Lanthipeptides: BM237_RS08435_lanthipeptide NZ_PDKQ02000044.1 Lanthipeptides: BFM75_RS16855_lanthipeptide
Lanthipeptides: BMY40_RS02540_lanthipeptide
2
G S R A S L L L C G D S S L S V T T C N
21
G S A S L L L C G D S S L S V T T C
2
G S E A S L L L C G D S S L S V T T C R
21
83.3%
NZ_CP007574.1 and 6 others:
NZ_CP007574.1 Lanthipeptides: DC74_RS36920_lanthipeptide NZ_CP026094.1 Lanthipeptides: SE95_RS37250_lanthipeptide NZ_CP104098.1 Lanthipeptides: N1H47_RS36625_lanthipeptide NZ_CP104098.1 Lanthipeptides: N1H47_RS36625_lanthipeptide NZ_CP119144.1 Lanthipeptides: P0D74_RS03260_lanthipeptide NZ_CP119144.1 Lanthipeptides: P0D74_RS03260_lanthipeptide
Lanthipeptides: DC74_RS36920_lanthipeptide
1
T G S R A S L L L C G D S S L S V T T C N
21
T G S R A S L L L C G D S S L S V T T C
4
T G S R A S L L L C G D S S L S V T T C K
24

#### MIBiG 4.0 matches for AMK27_RS08700

59.1%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
1
T G S R A S L L L C G D S S L S V T T C N
21
T G S+ S L L+C S S L S V C
1
T G S Q V S L L V C E Y S S L S V V L C T
21

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (5):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.98 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.85 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.45 out of 21.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.62 out of 35.63
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

AMK27_RS08700 - Class III
  Cleavage pHMM score: 22.80
  RODEO score: 0
  Monoisotopic mass: 1940.0 Da
  Molecular weight: 1941.2 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1959.2 Da N = 1
    1977.2 Da N = 2
    1995.2 Da N = 3
    2013.2 Da N = 4
    2031.3 Da N = 5
    2049.3 Da N = 6
AMK27_RS08700 - Class III
  Cleavage pHMM score: 22.80
  RODEO score: 0
  Monoisotopic mass: 1940.0 Da
  Molecular weight: 1941.2 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1959.2 Da N = 1
    1977.2 Da N = 2
    1995.2 Da N = 3
    2013.2 Da N = 4
    2031.3 Da N = 5
    2049.3 Da N = 6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
VqsM | Regulator of quorum-sensing signalling systems

NZ_LIVV01000002.1 - Region 5 - 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: 467,765 - 478,157 nt. (total: 10,393 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

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

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

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

Reference | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.79 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000908.3 |  | 0.63 | other (other) | melanin | Streptomyces avermitilis
BGC0000909.3 |  | 0.63 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.61 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000911.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000662.5 |  | 0.40 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.40 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.38 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.38 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.79 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000908.3 |  | 0.63 | other (other) | melanin | Streptomyces avermitilis
BGC0000909.3 |  | 0.63 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.61 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000911.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000662.5 |  | 0.40 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.40 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.38 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.38 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.68 out of 30.12
Confidence: medium
Additional weak hits (2):
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.61 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.64 out of 32.93
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
OsdR | Development and stress management regulator

NZ_LIVV01000002.1 - Region 6 - 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: 615,298 - 708,270 nt. (total: 92,973 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase phosphate reductase
AMK27_RS10245: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AMK27_RS10320: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

AMK27_RS10385: N-acetyl-gamma-glutamyl-phosphate reductase

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

AMK27_RS10405: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AMK27_RS10410: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

AMK27_RS10415: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: PPTase aminotransferase formyltransferase kinase methyltransferase
AMK27_RS10225: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

AMK27_RS10305: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

AMK27_RS10315: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

AMK27_RS10370: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

AMK27_RS10375: acetylglutamate kinase

smcogs
  SMCOG1174: acetylglutamate kinase

Hydrolases: hydrolase
AMK27_RS10230: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase mutase
AMK27_RS10195: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

AMK27_RS10240: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
AMK27_RS10235: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AMK27_RS10250: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AMK27_RS10330: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002424.3 |  |  | 0.97 | NRPS | saccharochelin A, saccharochelin B, saccharochelin C, saccharochelin D, saccharochelin E, saccharochelin F, saccharochelin G, saccharochelin H | Saccharothrix sp.
BGC0001185.5 |  |  | 0.91 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0001758.4 |  |  | 0.90 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  | 0.88 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002071.2 |  |  | 0.87 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0002135.2 |  |  | 0.86 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  |  | 0.85 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000349.5 |  |  | 0.84 | NRPS | erythrochelin | Saccharopolyspora erythraea NRRL 2338
BGC0001128.4 |  |  | 0.83 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.83 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002424.3 |  | 0.78 | NRPS | saccharochelin A, saccharochelin B, saccharochelin C, saccharochelin D, saccharochelin E, saccharochelin F, saccharochelin G, saccharochelin H | Saccharothrix sp.
BGC0001185.5 |  | 0.76 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0001758.4 |  | 0.75 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002071.2 |  | 0.74 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000349.5 |  | 0.73 | NRPS | erythrochelin | Saccharopolyspora erythraea NRRL 2338
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.52 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.52 out of 30.11
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
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: 34.36 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 32.03 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 31.03 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.57 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.57 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.45 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.90 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.44 out of 36.53
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.73 out of 18.46
Confidence: medium
Additional weak hits (12):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.94 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.30 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.84 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.69 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.85 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.53 out of 36.53
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.30 out of 18.57
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.25 out of 36.53
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.00 out of 18.57
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.88 out of 39.62
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
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 615297 - 708270:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Fo-OH-Orn - Ser - OH-Orn - OH-Orn) + (Gly - Orn - Ser - D-Ser) + (Orn - 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).
AMK27_RS10235: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (66..477): diOH-Bz
nrpys: diOH-Bz

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    SGSLFPLSSPGGGLLVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPGLGVVNK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMK27_RS10250: Orn - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (473..880): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNHAFDTSWEQWDVLLGGEVNLYGPTEYTVDALA
  Nearest Stachelhaus code(s):
    Orn DTEDMGLVDK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1542..1953): 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:
    MNHVFDMSWEEWNVLLGGEYNLYGPTEYTINALG
  Nearest Stachelhaus code(s):
    OH-Orn DMENLGLINK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMK27_RS10255: Gly - Orn - Ser - Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (468..870): 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:
    FMQTFDIAALETQALVGGETNVYGPTEVTVWATS
  Nearest Stachelhaus code(s):
    Gly DILQLGVVWK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1535..1937): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDHAFDSSWEQWDVLLGGEVNYYGPTEFTVDALV
  Nearest Stachelhaus code(s):
    Orn DSEDLGFVDK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2605..3008): 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:
    RWMTFDVSVWEWHFVCSGEENLYGPTEAAVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3672..4075): 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:
    RWMTFDVSVWEWHFVCSGEENLYGPTEAAVDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMK27_RS10330: Fo-OH-Orn - Ser - OH-Orn - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (469..865): 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:
    LTAAFDVTVWDMILVVGTEVVAYGLTEATVNSTL
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DVWIIGAVNK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1504..1936): 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:
    RWMTFDVSVWEWHFFCSGEHNLYGPTEAAVDVTF
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2671..3091): 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 (3782..4182): OH-Orn
nrpys: 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:
    LTAAFDVFAFEMILLVGTEICAYGLTEATVNSTL
  Nearest Stachelhaus code(s):
    OH-Orn DVFILGAVNK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
CelR | Cellobiose uptake repressor
DmdR1 | Iron(II)-dependent repressor
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_LIVV01000002.1 - Region 7 - azole-containing-RiPP,terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 732,531 - 775,399 nt. (total: 42,869 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
AMK27_RS10555: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
AMK27_RS10575: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

Lyases: cyclase dehydratase
AMK27_RS10550: Terpene synthase/cyclase metal-binding domain protein

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

AMK27_RS10610: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

Translocases: permease
AMK27_RS10540: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | terpene | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000658.3 |  |  | 1.28 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  |  | 1.03 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  |  | 0.61 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001146.5 |  |  | 0.31 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0002584.2 |  |  | 0.31 | ribosomal | azolemycin B, azolemycin A, azolemycin D, azolemycin C | Streptomyces sp. FXJ1.264
BGC0001860.4 |  |  | 0.29 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0000613.5 |  |  | 0.29 | ribosomal | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0001174.4 |  |  | 0.29 | ribosomal | corynazolicin | Corynebacterium urealyticum DSM 7111
BGC0000603.5 |  |  | 0.28 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0000605.5 |  |  | 0.28 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.86 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.79 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  | 0.64 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0001146.5 |  | 0.53 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0001860.4 |  | 0.51 | ribosomal | thiomuracin | Thermobispora bispora DSM 43833
BGC0000613.5 |  | 0.51 | ribosomal | thiomuracin A | Nonomuraea sp. Bp3714-39
BGC0000603.5 |  | 0.50 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0000628.4 |  | 0.49 | ribosomal | lactocillin | Lactobacillus paragasseri JV-V03
BGC0001145.5 |  | 0.49 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001640.3 |  | 0.47 | ribosomal | kocurin | Kocuria rosea

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
--- | --- | --- | --- | --- | ---
monoterpene |  | 2-methylisoborneol | C11 | C1-C6 | OH
monoterpene |  | 2-methylenebornane | C11 | C1-C6 | none

Genes with terpene domains:
AMK27_RS10550: T1TS
Domain 1 (122 - 478): Type 1 terpene synthase
Subtype: 2-Methylisoborneol synthase type

Reactions:
  2-MeGPP → 2-methylisoborneol
  2-MeGPP → 2-methylenebornane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.16 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 26.03 out of 30.11
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.37 out of 27.04
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
Additional weak hits (10):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.56 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.55 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.58 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.96 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.23 out of 24.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.12 out of 27.04
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.62 out of 32.93
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
RREFinder
Terpene
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (740475...775399)
AMK27_RS10625
  RRE type: Thiopeptide_F_RRE
  Location: 11 - 89
  Score: 56.3
  RRE type: Heterocycloanthracin_C_RRE
  Location: 11 - 93
  Score: 34.7

Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
2-MeGPP | 2-methylgeranyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
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_LIVV01000002.1 - Region 8 - NRPS,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: 842,134 - 921,120 nt. (total: 78,987 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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 oxygenase
AMK27_RS10920: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

AMK27_RS10960: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

AMK27_RS10965: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AMK27_RS11060: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: carboxylase methyltransferase
AMK27_RS11020: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

AMK27_RS11075: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Hydrolases: amidase hydrolase
AMK27_RS11070: amidase

smcogs
  SMCOG1105: amidase

AMK27_RS11155: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: cyclase
AMK27_RS11025: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

AMK27_RS11030: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

Ligases: ligase synthase
AMK27_RS10990: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AMK27_RS10995: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AMK27_RS11000: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AMK27_RS11005: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AMK27_RS11040: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

AMK27_RS11045: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AMK27_RS11165: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

Translocases: permease
AMK27_RS11095: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | NRPS | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000271.5 |  |  | 1.01 | PKS | spore pigment | Streptomyces avermitilis
BGC0002075.3 |  |  | 0.88 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000272.3 |  |  | 0.88 | PKS | spore pigment | Streptomyces collinus
BGC0001249.5 |  |  | 0.84 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0000215.5 |  |  | 0.83 | PKS | curamycin | Streptomyces cyaneus
BGC0001132.4 |  |  | 0.83 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.82 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  | 0.81 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.78 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  | 0.77 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000271.5 |  | 0.79 | PKS | spore pigment | Streptomyces avermitilis
BGC0002075.3 |  | 0.75 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000272.3 |  | 0.75 | PKS | spore pigment | Streptomyces collinus
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0000215.5 |  | 0.73 | PKS | curamycin | Streptomyces cyaneus
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.72 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.71 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.14 out of 27.04
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (9):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.38 out of 26.85
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.99 out of 25.88
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.62 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.81 out of 27.04
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.00 out of 18.57
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.02 out of 31.73
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.86 out of 27.04
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
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 11, location 842133 - 921120:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly) + (Asp) + (Lys) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 12, location 842133 - 898006:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly) + (Asp) + (Lys) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 848607 - 921120:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly) + (Asp) + (Lys) + (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).
AMK27_RS10990: X
AMP-binding (12..397): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    GAHFTNAGQVMTFLNSSAAVNTYTSAEASPAQIS
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

AMK27_RS10995: Lys
Search NORINE for peptide: strict or relaxed
AMP-binding (474..970): Lys
nrpys: Lys

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:
    RWMAFDTHAEEPDLILGGSVNTYGPTEAAVIVTA
  Nearest Stachelhaus code(s):
    Lys DTEDIGSVIK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMK27_RS11000: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (510..949): Asp
nrpys: Asp

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

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

AMK27_RS11005: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (490..895): 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:
    LSFTFDISALELQALAGGEFNVYGPTETTIWSTC
  Nearest Stachelhaus code(s):
    Gly DILQLGVIWK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

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:
  848607 to 921120
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

AMK27_RS10965
  KR (Score: 177.4; E-value: 9.7e-55)
AMK27_RS11020
  MET C6|C8 (Score: 533.3; E-value: 4.4e-163)
AMK27_RS11025
  CYC C4-C21/C2-C23|C2-C19 (Score: 157.2; E-value: 2.7e-49)
AMK27_RS11030
  CYC C9-C14 (Score: 249.6; E-value: 2e-77)
AMK27_RS11035
  ACP (Score: 76.6; E-value: 2.6e-24)
AMK27_RS11040
  CLF (Score: 545.8; E-value: 1.3e-166)
AMK27_RS11045
  KS (Score: 728.7; E-value: 4.2e-222)
AMK27_RS11050
  CYC C5-C18 (Score: 214.9; E-value: 7e-67)
AMK27_RS11060
  OXY (Score: 288.1; E-value: 3.1e-88)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
DasR | N-acetylglucosamine dependent repressor

NZ_LIVV01000002.1 - Region 9 - NAPAA
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,006,973 - 1,042,065 nt. (total: 35,093 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidase oxygenase
AMK27_RS11715: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

AMK27_RS41770: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Hydrolases: deaminase
AMK27_RS11655: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: dehydratase
AMK27_RS11635: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
AMK27_RS11620: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

AMK27_RS11650: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

AMK27_RS11665: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.64 | NRPS | AM-toxin | Alternaria alternata
BGC0002174.2 |  | 0.63 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000357.5 |  | 0.60 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.64 | NRPS | AM-toxin | Alternaria alternata
BGC0002174.2 |  | 0.63 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000357.5 |  | 0.60 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
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:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
Additional weak hits (2):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.81 out of 27.78
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 14, location 1006972 - 1042065:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AMK27_RS11665: X
AMP-binding (243..647): X
nrpys: Dpr

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:
    HAKAFDISLWQAQVSVTGEVNAYGLTETSDDTHH
  Nearest Stachelhaus code(s):
    Dpr DIWQSTADDK (91% 8Å match)
    dnmeProp or Dab DIWQSTADDK (85% 8Å match)
    Asp DIWQSTADDK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
MexT | Global virulence regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_LIVV01000002.1 - Region 10 - 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: 1,043,761 - 1,097,485 nt. (total: 53,725 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
Transferases: acyltransferase
AMK27_RS11865: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: esterase
AMK27_RS11895: putative esterase

smcogs
  SMCOG1104: putative esterase

Ligases: ligase
AMK27_RS11835: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AMK27_RS11850: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AMK27_RS11855: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AMK27_RS11860: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRPS | 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 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001251.4 |  | 0.69 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.69 | NRPS | epichloenin A | Epichloe festucae
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti

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 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001251.4 |  | 0.69 | NRPS | epichloenin A | Epichloe festucae
BGC0001250.4 |  | 0.69 | NRPS | epichloenin A | Epichloe festucae
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.37 out of 30.12
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.75 out of 27.04
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
Additional weak hits (15):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.87 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.81 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.56 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.35 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.94 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
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.55 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.78 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.67 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.44 out of 35.63
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 15, location 1043760 - 1097485:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Ser) + (Gly)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AMK27_RS11850: Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (463..848): 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:
    VSLTFDISAVELQALTGGEVNVYGPTETTIWSTL
  Nearest Stachelhaus code(s):
    Gly DILQLGVIWK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMK27_RS11855: X
AMP-binding (25..411): 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:
    GRDFSNAGQTMNFVGSTAAVNYYTSTEAAPAQVT
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

AMK27_RS11860: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (527..922): 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:
    RWMTFDVSVWEWHFVCSGEANLYGPTEAAVDVSA
  Nearest Stachelhaus code(s):
    Ser DVWHVSLVDK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMK27_RS11865: X
AMP-binding (480..883): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMAFDTSAEEPDLILGADVNSYGPTETTIIATT
  Nearest Stachelhaus code(s):
    Lys DTEDIGSVIK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_LIVV01000002.1 - Region 11 - lanthipeptide-class-iv
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,316,012 - 1,338,756 nt. (total: 22,745 nt) Show pHMM detection rules used
lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
AMK27_RS12970: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
AMK27_RS12985: methyltransferase

smcogs
  SMCOG1089: methyltransferase

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

Reference | lanthipeptide-class-iv | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000563.4 |  | 0.86 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.84 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0001579.4 |  | 0.54 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0001660.3 |  | 0.53 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000503.5 |  | 0.48 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0002346.3 |  | 0.47 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0001779.5 |  | 0.46 | ribosomal | siamycin | Streptomyces nodosus
BGC0001364.3 |  | 0.43 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002635.2 |  | 0.41 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000888.5 |  | 0.41 | other (other) | bacilysin | Bacillus sp. CS93

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000563.4 |  | 0.86 | ribosomal | venezuelin | Streptomyces venezuelae ATCC 10712
BGC0001226.4 |  | 0.84 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0001579.4 |  | 0.54 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0001660.3 |  | 0.53 | ribosomal | mathermycin | Marinactinospora thermotolerans
BGC0000503.5 |  | 0.48 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0002346.3 |  | 0.47 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0001779.5 |  | 0.46 | ribosomal | siamycin | Streptomyces nodosus
BGC0001364.3 |  | 0.43 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0002635.2 |  | 0.41 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000888.5 |  | 0.41 | other (other) | bacilysin | Bacillus sp. CS93

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

No significant matches found.

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:
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.16 out of 20.01
Confidence: medium
Additional weak hits (6):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.35 out of 35.63
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
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.89 out of 29.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.21 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.26 out of 28.19
Confidence: weak
Lanthipeptides
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes

NZ_LIVV01000020.1 - Region 1 - 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: 1 - 33,779 nt. (total: 33,779 nt) Show pHMM detection rules used
Region on contig edge.
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
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: acyltransferase
AMK27_RS42560: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Ligases: synthase
AMK27_RS40410: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | NRPS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  |  | 0.71 | NRPS | enniatin | Fusarium equiseti
BGC0002286.3 |  |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  | 0.69 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.66 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.66 | 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.

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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.89 out of 18.16
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.70 out of 23.79
Confidence: medium
Additional weak hits (5):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.04 out of 21.84
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.69 out of 20.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.29 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.43 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 0 - 33779:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AMK27_RS40410: mal
PKS_AT (962..1242): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 74.3
  inactive: 22.1
  Methoxymalonyl-CoA: 17.1
  Propionyl-CoA: 10.3
  Methylmalonyl-CoA: 8.9
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

AMK27_RS42560: X - X
AMP-binding (19..401): 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:
    LQAFSDVAGMETVFMVGVEVNGYGPTETTVYSTF
  Nearest Stachelhaus code(s):
    meLeu DAMLWGGVYK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1060..1441): 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:
    LGAAFDLATFEAHLMVGGEVHCYGPAEGTVHTTY
  Nearest Stachelhaus code(s):
    Val DAFWLGCVFK (62% 8Å match)
    Hty DLGFTGCVTK (53% 8Å match)
    Asn DLTKMGEVGK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

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
MexT | Global virulence regulator
RpoN | Regulator of nitrogen assimilation and virulence

NZ_LIVV01000003.1 - Region 1 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 84,272 - 117,412 nt. (total: 33,141 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
AMK27_RS13510: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
AMK27_RS13460: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
AMK27_RS13525: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0001713.5 |  | 0.54 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002683.2 |  | 0.53 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0001572.3 |  | 0.52 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002470.2 |  | 0.52 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000295.5 |  | 0.52 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002633.2 |  | 0.52 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002305.2 |  | 0.51 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000939.5 |  | 0.51 | other (other) | aerobactin | Grimontia hollisae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0001713.5 |  | 0.54 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0002469.2 |  | 0.54 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0002683.2 |  | 0.53 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0001572.3 |  | 0.52 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002470.2 |  | 0.52 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0000295.5 |  | 0.52 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002633.2 |  | 0.52 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0002305.2 |  | 0.51 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000939.5 |  | 0.51 | other (other) | aerobactin | Grimontia hollisae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47
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: 16.26 out of 19.26
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.93 out of 27.18
Confidence: medium
Additional weak hits (7):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.12 out of 27.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.11 out of 23.43
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.53 out of 36.54
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
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.40 out of 20.01
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LIVV01000003.1 - Region 2 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 151,734 - 210,467 nt. (total: 58,734 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
Transferases: PPTase carbamoyltransferase
AMK27_RS13720: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

AMK27_RS13790: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: hydrolase
AMK27_RS13815: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: lyase
AMK27_RS13775: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

AMK27_RS13780: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
AMK27_RS13755: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AMK27_RS13760: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AMK27_RS13770: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

AMK27_RS13825: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.72 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.75 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001758.4 |  | 0.73 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.72 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.03 out of 27.04
Confidence: medium
Additional weak hits (11):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.08 out of 20.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.42 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.32 out of 30.25
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.88 out of 26.06
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.72 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.98 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.36 out of 23.43
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.39 out of 35.63
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.68 out of 29.25
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 151733 - 210467:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AMK27_RS13755: Val - X - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (32..448): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPSFDSSTYEVYFWTGGDVHAYGPTESTVFCSY
  Nearest Stachelhaus code(s):
    Cyc-D-Gly DAYLWGGVFK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1106..1509): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWWSFDSSTYEVYFWTGGDVHAYGPTESTVFCSY
  Nearest Stachelhaus code(s):
    Cyc-D-Gly DAYLWGGVFK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (2167..2562): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDTSFDATTYEAWLWTGGDVNAYGPTETTTFATS
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMK27_RS13760: Val - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (503..906): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDHSFDATTYEAWLWTGGDVNGYGPTETTTFATS
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1594..1991): X
nrpys: Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGPSWDAFALEGQMMTAGELNGYGPAESMGFTTV
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (2644..3041): X
nrpys: Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TGPSWDAFALEGQMMTAGELNGYGPAESMGFTTV
  Nearest Stachelhaus code(s):
    Val DALWMGGTFK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
VqsM | Regulator of quorum-sensing signalling systems

NZ_LIVV01000003.1 - Region 3 - 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: 268,736 - 340,811 nt. (total: 72,076 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase reductase
AMK27_RS14090: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

AMK27_RS14125: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AMK27_RS14160: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

AMK27_RS14185: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

AMK27_RS14195: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

AMK27_RS14225: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: methyltransferase
AMK27_RS14120: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

AMK27_RS14255: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase
AMK27_RS14200: thioesterase

smcogs
  SMCOG1004: thioesterase

AMK27_RS14260: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
AMK27_RS14135: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

AMK27_RS14150: 1-deoxy-D-xylulose-5-phosphate synthase

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

AMK27_RS14210: 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 | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002147.2 |  |  | 1.27 | NRPS | bohemamine A, bohemamine B, bohemamine C | Streptomyces sp. CB02009
BGC0002340.3 |  |  | 0.69 | NRPS, other (other) | pyrroloformamide A, pyrroloformamide B, pyrroloformamide D, pyrroloformamide C | Streptomyces sp. CB02980
BGC0001825.4 |  |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002286.3 |  |  | 0.65 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.62 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001641.4 |  |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002147.2 |  | 0.99 | NRPS | bohemamine A, bohemamine B, bohemamine C | Streptomyces sp. CB02009
BGC0002340.3 |  | 0.80 | NRPS, other (other) | pyrroloformamide A, pyrroloformamide B, pyrroloformamide D, pyrroloformamide C | Streptomyces sp. CB02980
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001534.3 |  | 0.72 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001873.3 |  | 0.71 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0001825.4 |  | 0.71 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001833.4 |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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: 18.31 out of 23.79
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
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.87 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 (17):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.91 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.37 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.60 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.16 out of 32.74
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.09 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.45 out of 30.25
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.66 out of 29.65
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.66 out of 26.85
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.10 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.03 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.93 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.72 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.07 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.72 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.25 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 3, location 268735 - 340811:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Cys) + (Ser - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 268735 - 315977:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 297466 - 340811:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Cys)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AMK27_RS14135: Ser - X
Search NORINE for peptide: strict or relaxed
AMP-binding (459..868): 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:
    RWMTFDVSVWEWHFFCSGEVNLYGPTEGTVDVTY
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1529..1931): X
nrpys: 5Me-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:
    YWQAFDVAFQESFMISSGEENQYGPTETHLLTHH
  Nearest Stachelhaus code(s):
    5Me-Pro DVQFISQLLK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMK27_RS14210: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (504..904): 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:
    TDIAFDLSVYDGNSLLSGDISLGGATEGSIWSIH
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (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
--- | ---
CRP | Cyclic AMP receptor protein
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator

NZ_LIVV01000003.1 - Region 4 - 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: 431,536 - 442,948 nt. (total: 11,413 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
AMK27_RS14640: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: deacetylase
AMK27_RS14690: 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
--- | --- | --- | --- | --- | ---
BGC0000513.3 |  | 0.36 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.36 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.36 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000351.5 |  | 0.32 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155
BGC0001311.5 |  | 0.32 | ribosomal | flavecins | Ruminococcus flavefaciens FD-1
BGC0000498.5 |  | 0.32 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0000561.5 |  | 0.32 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0000496.5 |  | 0.32 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002663.2 |  | 0.32 | ribosomal | amyloliquecidin GF610 | Bacillus amyloliquefaciens UMAF6639
BGC0001928.2 |  | 0.31 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000513.3 |  | 0.36 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.36 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.36 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000351.5 |  | 0.32 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155
BGC0001311.5 |  | 0.32 | ribosomal | flavecins | Ruminococcus flavefaciens FD-1
BGC0000498.5 |  | 0.32 | ribosomal | bovicin HJ50 | Streptococcus equinus
BGC0000561.5 |  | 0.32 | ribosomal | thermophilin 1277 | Streptococcus thermophilus
BGC0000496.5 |  | 0.32 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002663.2 |  | 0.32 | ribosomal | amyloliquecidin GF610 | Bacillus amyloliquefaciens UMAF6639
BGC0001928.2 |  | 0.31 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37

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

No significant matches found.

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):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.70 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.56 out of 29.38
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LIVV01000003.1 - Region 5 - 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: 554,273 - 565,220 nt. (total: 10,948 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
AMK27_RS15205: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

AMK27_RS15225: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: dehydratase
AMK27_RS15220: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

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

Reference | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.79 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.65 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000244.4 |  | 0.52 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0002578.2 |  | 0.48 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000706.3 |  | 0.43 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000003.3 |  | 0.40 | PKS | AF-toxin | Alternaria alternata
BGC0000207.5 |  | 0.40 | PKS | chartreusin | Streptomyces chartreusis
BGC0000783.3 |  | 0.40 | saccharide | O-antigen | Xanthomonas oryzae pv. oryzae
BGC0001928.2 |  | 0.40 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000849.4 |  | 0.79 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000850.5 |  | 0.65 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000244.4 |  | 0.52 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0002578.2 |  | 0.48 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000706.3 |  | 0.43 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000003.3 |  | 0.40 | PKS | AF-toxin | Alternaria alternata
BGC0000207.5 |  | 0.40 | PKS | chartreusin | Streptomyces chartreusis
BGC0000783.3 |  | 0.40 | saccharide | O-antigen | Xanthomonas oryzae pv. oryzae
BGC0001928.2 |  | 0.40 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37

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

No significant matches found.

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):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.30 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
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LIVV01000003.1 - Region 6 - 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: 687,523 - 750,617 nt. (total: 63,095 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
AMK27_RS15945: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
AMK27_RS15855: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

AMK27_RS15870: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

AMK27_RS15910: cobalamin synthesis protein/P47K family protein

smcogs
  SMCOG1178: cobalamin synthesis protein/P47K family protein

AMK27_RS43680: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  | 0.86 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.85 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.85 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000041.3 |  |  | 0.79 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001164.3 |  |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.62 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001758.4 |  |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001276.3 |  |  | 0.60 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001132.4 |  |  | 0.60 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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 |  | 0.72 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001164.3 |  | 0.66 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002192.3 |  | 0.64 | PKS | FR901512 | fungal sp. No.14919
BGC0001758.4 |  | 0.64 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001276.3 |  | 0.64 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.94 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.89 out of 23.79
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52
Confidence: medium
Additional weak hits (17):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.32 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.33 out of 30.97
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.94 out of 19.26
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.99 out of 27.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.49 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.82 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.92 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.99 out of 27.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.01 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
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.03 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.67 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.73 out of 29.65
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 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 8, location 687522 - 750617:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - redmal) + (Me-ccmal - Me-mal - Cys)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
AMK27_RS15855: X
AMP-binding (3..382): 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:
    HGVVFHANAWGSAAGCGGAVQGWGLTETSPLATF
  Nearest Stachelhaus code(s):
    Abu DAWFYGAPLK (38% 8Å match)
  Stachelhaus code match:
    60% (weak)

AMK27_RS15870: mmal - mmal - Cys
Search NORINE for peptide: strict or relaxed
PKS_AT (568..861): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 203.2
  Ethylmalonyl-CoA: 191.6
  Methoxymalonyl-CoA: 154.2
  2-Methylbutyryl-CoA: 141.6
  trans-1,2-CPDA: 98.6
  Propionyl-CoA: 96.6
  CHC-CoA: 94.5
  Malonyl-CoA: 84.3
  Isobutyryl-CoA: 74.6
  Benzoyl-CoA: 70.7
  fatty_acid: 37.1
  Acetyl-CoA: 32.2
  inactive: 31.4
  3-Methylbutyryl-CoA: 11.1

PKS_AT (2286..2579): 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: 205.6
  Ethylmalonyl-CoA: 197.6
  Methoxymalonyl-CoA: 155.6
  2-Methylbutyryl-CoA: 138.3
  trans-1,2-CPDA: 97.5
  Propionyl-CoA: 97.4
  CHC-CoA: 89.1
  Malonyl-CoA: 84.2
  Isobutyryl-CoA: 72.4
  Benzoyl-CoA: 72.0
  fatty_acid: 36.1
  inactive: 34.1
  Acetyl-CoA: 33.6
  3-Methylbutyryl-CoA: 11.1

AMP-binding (3568..3997): 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:
    TDISFDLSVYDGNSMMSGDWSLGGATEASIWSIL
  Nearest Stachelhaus code(s):
    Cys DLYNMSLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMK27_RS43680: mmal - mal
PKS_AT (583..879): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 198.8
  Ethylmalonyl-CoA: 191.6
  Methoxymalonyl-CoA: 170.8
  2-Methylbutyryl-CoA: 133.3
  Malonyl-CoA: 112.3
  trans-1,2-CPDA: 109.5
  Propionyl-CoA: 100.4
  CHC-CoA: 92.9
  Isobutyryl-CoA: 82.6
  Benzoyl-CoA: 62.5
  Acetyl-CoA: 44.2
  fatty_acid: 43.5
  3-Methylbutyryl-CoA: 32.5
  inactive: 27.4

PKS_AT (1601..1896): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 66.7%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 214.1
  inactive: 101.2
  Methoxymalonyl-CoA: 86.4
  Methylmalonyl-CoA: 76.9
  Propionyl-CoA: 47.5
  Isobutyryl-CoA: 44.5
  Acetyl-CoA: 34.5
  Ethylmalonyl-CoA: 32.0
  2-Methylbutyryl-CoA: 21.0
  fatty_acid: 20.6
  3-Methylbutyryl-CoA: 19.0
  CHC-CoA: 16.4
  Benzoyl-CoA: 13.2
  trans-1,2-CPDA: 5.7

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

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

NZ_LIVV01000005.1 - Region 1 - 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: 118,539 - 128,952 nt. (total: 10,414 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

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

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

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

Reference | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.79 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.79 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.64 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.47 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.31 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000662.5 |  | 0.31 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000889.5 |  | 0.31 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.30 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.24 | other (other) | iso-A82775C | Pestalotiopsis fici

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.79 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000911.3 |  | 0.79 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000909.3 |  | 0.64 | other (other) | melanin | Streptomyces avermitilis
BGC0000912.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.47 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.31 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000662.5 |  | 0.31 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000889.5 |  | 0.31 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.30 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.24 | other (other) | iso-A82775C | Pestalotiopsis fici

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (6):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.17 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.60 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.82 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.77 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.27 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LIVV01000005.1 - Region 2 - linaridin
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: 143,750 - 166,351 nt. (total: 22,602 nt) Show pHMM detection rules used
linaridin: (cypemycin or cypI)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
AMK27_RS20155: methyltransferase

smcogs
  SMCOG1248: methyltransferase

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

Reference | linaridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000582.4 |  | 0.90 | ribosomal | cypemycin | Streptomyces sp. OH-4156
BGC0002319.3 |  | 0.85 | ribosomal | salinipeptin A, salinipeptin B, salinipeptin C, salinipeptin D | Streptomyces sp.
BGC0000583.5 |  | 0.79 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001188.3 |  | 0.44 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0001521.3 |  | 0.38 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0002509.3 |  | 0.37 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0002294.3 |  | 0.36 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0002805.2 |  | 0.35 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001647.3 |  | 0.34 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0000700.5 |  | 0.31 | saccharide | istamycin | Streptomyces tenjimariensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000582.4 |  | 0.90 | ribosomal | cypemycin | Streptomyces sp. OH-4156
BGC0002319.3 |  | 0.85 | ribosomal | salinipeptin A, salinipeptin B, salinipeptin C, salinipeptin D | Streptomyces sp.
BGC0000583.5 |  | 0.79 | ribosomal | grisemycin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001188.3 |  | 0.44 | ribosomal | legonaridin | Streptomyces sp. CT34
BGC0001521.3 |  | 0.38 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0002509.3 |  | 0.37 | NRPS | montamide A, capsimycin, clifednamide A, frontalamide A, combamide A | Streptomyces sp.
BGC0002294.3 |  | 0.36 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0002805.2 |  | 0.35 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001647.3 |  | 0.34 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0000700.5 |  | 0.31 | saccharide | istamycin | Streptomyces tenjimariensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 20.76 out of 21.84
Confidence: strong
Additional weak hits (12):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.90 out of 33.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.55 out of 26.85
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.05 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.50 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.67 out of 30.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.07 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.32 out of 21.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.64 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.03 out of 29.65
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.19 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.81 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MexT | Global virulence regulator

NZ_LIVV01000005.1 - Region 3 - 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: 711,180 - 754,881 nt. (total: 43,702 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
AMK27_RS22880: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

AMK27_RS22935: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: acetyltransferase glycosyltransferase kinase methyltransferase sulfhydrylase
AMK27_RS22870: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

AMK27_RS22945: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

AMK27_RS22980: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

AMK27_RS23010: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

AMK27_RS23025: O-succinylhomoserine sulfhydrylase

smcogs
  SMCOG1168: O-succinylhomoserine sulfhydrylase

Hydrolases: esterase hydrolase
AMK27_RS22890: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

AMK27_RS22930: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

AMK27_RS22955: thioesterase

smcogs
  SMCOG1004: thioesterase

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
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.62 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.62 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.62 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.62 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.4 |  | 0.62 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  | 0.62 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.60 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 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
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 31.91 out of 32.38
Confidence: strong
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 29.76 out of 32.93
Confidence: medium
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 29.15 out of 32.38
Confidence: strong
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 26.96 out of 32.93
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.13 out of 20.47
Confidence: medium
Additional weak hits (10):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.93 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.94 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.37 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.22 out of 26.06
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.66 out of 25.88
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.12 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.80 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.48 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.30 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 3, location 711179 - 754881:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gln)

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).
AMK27_RS22955: Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (14..401): Gln
nrpys: Gln

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    QWMTFDAAQWEAQGYSGGEINLYGPTECTINASS
  Nearest Stachelhaus code(s):
    Gln DAWQFGLINK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CsoR | Copper-responsive repressor
RicR | Copper-responsive regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_LIVV01000006.1 - Region 1 - 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: 153,569 - 174,618 nt. (total: 21,050 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
AMK27_RS24640: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
AMK27_RS24570: 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
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002398.2 |  | 0.37 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001910.4 |  | 0.35 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

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
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002398.2 |  | 0.37 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001910.4 |  | 0.35 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus

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:
AMK27_RS24570: PT_FPPS_like
Domain 1 (59 - 342): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 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
Additional weak hits (7):
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.75 out of 32.93
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.69 out of 27.04
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.50 out of 33.14
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 25.07 out of 32.38
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.52 out of 32.93
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
ToxT | Regulator of MSHA biosynthesis

NZ_LIVV01000006.1 - Region 2 - butyrolactone,other
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 341,558 - 382,667 nt. (total: 41,110 nt) Show pHMM detection rules used
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)
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
Hydrolases: glucanase glucosidase
AMK27_RS25405: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

AMK27_RS25415: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

AMK27_RS25420: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

AMK27_RS25495: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

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

Reference | other | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000848.5 |  |  | 1.00 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  |  | 0.51 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  |  | 0.43 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  |  | 0.25 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001534.3 |  |  | 0.24 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001458.4 |  |  | 0.20 | other (aminocoumarin) | salinipostin G, Salinipostin G, Salinipostin A, Salinipostin B, Salinipostin C, Salinipostin D, Salinipostin E, Salinipostin F, Salinipostin H, Salinipostin I, Salinipostin J, Salinipostin K | Salinispora tropica CNB-440
BGC0000519.4 |  |  | 0.18 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002285.2 |  |  | 0.17 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001285.5 |  |  | 0.15 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001298.4 |  |  | 0.15 | PKS | 4-Z-annimycin, 4-E-annimycin | Streptomyces calvus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.79 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.59 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.55 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000519.4 |  | 0.49 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002285.2 |  | 0.49 | ribosomal | aborycin | Streptomyces sp. ZS0098
BGC0001285.5 |  | 0.46 | other (fatty acid) | pseudopyronine A, pseudopyronine B | Pseudomonas putida
BGC0001374.5 |  | 0.45 | other (other) | thienodolin | Streptomyces albogriseolus
BGC0000503.5 |  | 0.44 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0002064.2 |  | 0.43 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0002578.2 |  | 0.43 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (5):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.27 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.65 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.53 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.50 out of 21.55
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.31 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LIVV01000006.1 - Region 3 - 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: 386,812 - 420,073 nt. (total: 33,262 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
Ligases: ligase
AMK27_RS25570: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001146.5 |  | 0.54 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000606.5 |  | 0.53 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0002311.3 |  | 0.52 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0000662.5 |  | 0.52 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001640.3 |  | 0.51 | ribosomal | kocurin | Kocuria rosea
BGC0001145.5 |  | 0.51 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5 |  | 0.50 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0002826.2 |  | 0.50 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0000565.5 |  | 0.49 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000605.5 |  | 0.49 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001146.5 |  | 0.54 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000606.5 |  | 0.53 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0002311.3 |  | 0.52 | ribosomal | cutimycin | Cutibacterium acnes KPA171202
BGC0000662.5 |  | 0.52 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001640.3 |  | 0.51 | ribosomal | kocurin | Kocuria rosea
BGC0001145.5 |  | 0.51 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5 |  | 0.50 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0002826.2 |  | 0.50 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0000565.5 |  | 0.49 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000605.5 |  | 0.49 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.63 out of 27.04
Confidence: medium
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.62 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.38 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.17 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.31 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.57 out of 27.78
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.49 out of 27.78
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.15 out of 33.14
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 (386811...420073)
AMK27_RS25610
  RRE type: Thiopeptide_F_RRE
  Location: 5 - 87
  Score: 40.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_LIVV01000007.1 - Region 1 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
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Location: 203,313 - 233,100 nt. (total: 29,788 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
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Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
AMK27_RS27790: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

AMK27_RS27805: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: carboxylase transferase
AMK27_RS27815: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

AMK27_RS27820: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Hydrolases: hydrolase
AMK27_RS27765: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: decarboxylase
AMK27_RS27795: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: synthase
AMK27_RS27810: 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
--- | --- | --- | --- | --- | ---
BGC0000941.3 |  | 0.84 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.75 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000940.5 |  | 0.68 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.68 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.67 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.59 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002284.3 |  | 0.58 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002690.2 |  | 0.56 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0001531.5 |  | 0.53 | other (other) | bisucaberin B | Tenacibaculum mesophilum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000941.3 |  | 0.84 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001478.5 |  | 0.83 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.75 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000940.5 |  | 0.68 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0001453.5 |  | 0.68 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.67 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0002464.3 |  | 0.59 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002284.3 |  | 0.58 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0002690.2 |  | 0.56 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0001531.5 |  | 0.53 | other (other) | bisucaberin B | Tenacibaculum mesophilum

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
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 26.85
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 31.36 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.36 out of 36.53
Confidence: medium
Additional weak hits (7):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.10 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.16 out of 30.25
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.09 out of 27.04
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.71 out of 27.04
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.62 out of 29.65
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.56 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.37 out of 39.62
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
DmdR1 | Iron(II)-dependent repressor
RutR | Regulator of the pyrimidine and purine metabolism