Select genomic region:
Overview
1.1
1.2
1.3
1.4
2.1
3.1
3.2
3.3
8.1
11.1
12.1
12.2
12.3
12.4
12.5
17.1
23.1
23.2
23.3
23.4
23.5
23.6
23.7
23.8
23.9
23.10
23.11
23.12
23.13
23.14
24.1
24.2
24.3
24.4
24.5
24.6
24.7
24.8
25.1
25.2
26.1
26.2
26.3
26.4
26.5
26.6
27.1
27.2
27.3
27.4
28.1

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

NZ_LWKZ01000001.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | RRE-containing | 258,976 | 279,248 | Low | arginomycin | other:other
Region 1.2 | T1PKS | 305,402 | 351,689 |
Region 1.3 | terpene-precursor,lanthipeptide-class-ii,NRPS,PKS-like,NRPS-like | 397,806 | 524,755 | High | tyrobetaine | NRPS:Type I
Region 1.4 | triceptide | 541,231 | 562,800 |

NZ_LWKZ01000002.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | ectoine | 74,487 | 84,909 | High | ectoine | other:ectoine

NZ_LWKZ01000003.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | NI-siderophore | 59,183 | 93,535 |  |
Region 3.2 | NRPS,NRPS-like | 173,236 | 267,941 |  |
Region 3.3 | atropopeptide,NRP-metallophore,NRPS | 282,998 | 332,388 | High | griseobactin | NRPS:Type I

NZ_LWKZ01000008.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 8.1 | butyrolactone | 59,540 | 70,523 |  |

NZ_LWKZ01000011.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 11.1 | CDPS | 1 | 14,355 |

NZ_LWKZ01000012.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 12.1 | lassopeptide | 406 | 22,944 | Low | SSV-2083 | ribosomal:RiPP:Lanthipeptide
Region 12.2 | terpene | 560,342 | 581,568 |  |
Region 12.3 | NRPS | 652,370 | 703,532 | Medium | cephamycin C | NRPS:Type I
Region 12.4 | lanthipeptide-class-iii | 888,675 | 911,314 | High | SAL-2242 | ribosomal:RiPP:Lanthipeptide
Region 12.5 | terpene | 1,034,633 | 1,056,924 | High | geosmin | terpene:Sesquiterpene

NZ_LWKZ01000017.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 17.1 | terpene-precursor | 2,494 | 23,567 |  |

NZ_LWKZ01000023.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 23.1 | NRPS-like,T1PKS,NRPS | 58,908 | 129,402 | Low | deimino-antipain | NRPS:Type I
Region 23.2 | terpene | 153,782 | 174,846 |  |
Region 23.3 | NRPS-like,NRPS | 177,891 | 226,161 | High | antipain | NRPS:Type I
Region 23.4 | NRPS | 274,208 | 318,371 |
Region 23.5 | NRPS | 320,862 | 366,816 | Low | cyclofaulknamycin | PKS
Region 23.6 | terpene,NRPS | 455,258 | 501,047 | Low | paenibactin | NRPS:Type I
Region 23.7 | 2dos | 505,979 | 529,552 | Low | lividomycin | saccharide
Region 23.8 | T1PKS,NRPS-like | 544,254 | 659,113 | High | tetramycin B | PKS
Region 23.9 | arylpolyene,NRPS,NRPS-like,terpene | 684,085 | 763,671 |  |
Region 23.10 | RiPP-like | 776,960 | 788,867 |
Region 23.11 | azoxy-crosslink,T1PKS | 847,950 | 910,488 |  |
Region 23.12 | lassopeptide | 915,993 | 938,591 | High | lagmysin | ribosomal:RiPP
Region 23.13 | NRPS,terpene,T1PKS | 990,675 | 1,085,650 | High | isorenieratene | terpene
Region 23.14 | NRPS,NRPS-like,betalactone | 1,120,307 | 1,208,635 | Low | thiazostatin/watasemycin A/watasemycin B/2-hydroxyphenylthiazoline enantiopyochelin/isopyochelin | NRPS:Type I

NZ_LWKZ01000024.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 24.1 | terpene | 64,707 | 91,469 | High | hopene | terpene
Region 24.2 | NRPS | 223,501 | 299,315 | High | rimomycin A/rimomycin B/rimomycin C | NRPS:Type I
Region 24.3 | 2dos | 378,814 | 403,990 |
Region 24.4 | melanin | 448,221 | 459,495 |
Region 24.5 | other,NRPS-like,NRPS,indole,T1PKS | 576,411 | 687,835 | High | malonomycin | NRPS:Type I+PKS
Region 24.6 | RiPP-like | 895,022 | 906,371 |  |
Region 24.7 | butyrolactone | 1,009,432 | 1,020,418 |
Region 24.8 | T1PKS,NRPS-like | 1,053,292 | 1,104,206 | Low | sporolide A/sporolide B | NRPS:Type I+PKS:Enediyne type I

NZ_LWKZ01000025.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 25.1 | phosphonate,T1PKS,NRPS | 164,944 | 242,151 | Medium | pyridomycin | NRPS:Type I+PKS
Region 25.2 | terpene | 297,972 | 321,407 |

NZ_LWKZ01000026.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 26.1 | PKS-like,NRPS-like | 1 | 68,665 |  |
Region 26.2 | terpene,NRPS,NRPS-like,T1PKS | 118,036 | 239,487 |  |
Region 26.3 | nucleoside | 258,066 | 279,031 | High | tunicamycin B1 | other:nucleoside
Region 26.4 | NRPS | 293,287 | 358,492 |  |
Region 26.5 | NRPS-like,NAPAA | 371,860 | 450,754 |  |
Region 26.6 | arylpolyene,terpene | 565,828 | 622,128 |  |

NZ_LWKZ01000027.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 27.1 | terpene | 58,024 | 79,208 |
Region 27.2 | RiPP-like | 215,083 | 225,592 |  |
Region 27.3 | NI-siderophore | 597,755 | 629,626 | Low | peucechelin | NRPS:Type I
Region 27.4 | NI-siderophore | 703,191 | 721,891 | High | legonoxamine A/desferrioxamine B/legonoxamine B | other:other

NZ_LWKZ01000028.1 (Streptomyces sp. CB02923)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 28.1 | butyrolactone | 294,149 | 305,438 |  |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | RRE-containing | 258,976 | 279,248 | Low | arginomycin | other:other
Region 1.2 | T1PKS | 305,402 | 351,689 |
Region 1.3 | terpene-precursor,lanthipeptide-class-ii,NRPS,PKS-like,NRPS-like | 397,806 | 524,755 | High | tyrobetaine | NRPS:Type I
Region 1.4 | triceptide | 541,231 | 562,800 |
Region 2.1 | ectoine | 74,487 | 84,909 | High | ectoine | other:ectoine
Region 3.1 | NI-siderophore | 59,183 | 93,535 |  |
Region 3.2 | NRPS,NRPS-like | 173,236 | 267,941 |  |
Region 3.3 | atropopeptide,NRP-metallophore,NRPS | 282,998 | 332,388 | High | griseobactin | NRPS:Type I
Region 8.1 | butyrolactone | 59,540 | 70,523 |  |
Region 11.1 | CDPS | 1 | 14,355 |
Region 12.1 | lassopeptide | 406 | 22,944 | Low | SSV-2083 | ribosomal:RiPP:Lanthipeptide
Region 12.2 | terpene | 560,342 | 581,568 |  |
Region 12.3 | NRPS | 652,370 | 703,532 | Medium | cephamycin C | NRPS:Type I
Region 12.4 | lanthipeptide-class-iii | 888,675 | 911,314 | High | SAL-2242 | ribosomal:RiPP:Lanthipeptide
Region 12.5 | terpene | 1,034,633 | 1,056,924 | High | geosmin | terpene:Sesquiterpene
Region 17.1 | terpene-precursor | 2,494 | 23,567 |  |
Region 23.1 | NRPS-like,T1PKS,NRPS | 58,908 | 129,402 | Low | deimino-antipain | NRPS:Type I
Region 23.2 | terpene | 153,782 | 174,846 |  |
Region 23.3 | NRPS-like,NRPS | 177,891 | 226,161 | High | antipain | NRPS:Type I
Region 23.4 | NRPS | 274,208 | 318,371 |
Region 23.5 | NRPS | 320,862 | 366,816 | Low | cyclofaulknamycin | PKS
Region 23.6 | terpene,NRPS | 455,258 | 501,047 | Low | paenibactin | NRPS:Type I
Region 23.7 | 2dos | 505,979 | 529,552 | Low | lividomycin | saccharide
Region 23.8 | T1PKS,NRPS-like | 544,254 | 659,113 | High | tetramycin B | PKS
Region 23.9 | arylpolyene,NRPS,NRPS-like,terpene | 684,085 | 763,671 |  |
Region 23.10 | RiPP-like | 776,960 | 788,867 |
Region 23.11 | azoxy-crosslink,T1PKS | 847,950 | 910,488 |  |
Region 23.12 | lassopeptide | 915,993 | 938,591 | High | lagmysin | ribosomal:RiPP
Region 23.13 | NRPS,terpene,T1PKS | 990,675 | 1,085,650 | High | isorenieratene | terpene
Region 23.14 | NRPS,NRPS-like,betalactone | 1,120,307 | 1,208,635 | Low | thiazostatin/watasemycin A/watasemycin B/2-hydroxyphenylthiazoline enantiopyochelin/isopyochelin | NRPS:Type I
Region 24.1 | terpene | 64,707 | 91,469 | High | hopene | terpene
Region 24.2 | NRPS | 223,501 | 299,315 | High | rimomycin A/rimomycin B/rimomycin C | NRPS:Type I
Region 24.3 | 2dos | 378,814 | 403,990 |
Region 24.4 | melanin | 448,221 | 459,495 |
Region 24.5 | other,NRPS-like,NRPS,indole,T1PKS | 576,411 | 687,835 | High | malonomycin | NRPS:Type I+PKS
Region 24.6 | RiPP-like | 895,022 | 906,371 |  |
Region 24.7 | butyrolactone | 1,009,432 | 1,020,418 |
Region 24.8 | T1PKS,NRPS-like | 1,053,292 | 1,104,206 | Low | sporolide A/sporolide B | NRPS:Type I+PKS:Enediyne type I
Region 25.1 | phosphonate,T1PKS,NRPS | 164,944 | 242,151 | Medium | pyridomycin | NRPS:Type I+PKS
Region 25.2 | terpene | 297,972 | 321,407 |
Region 26.1 | PKS-like,NRPS-like | 1 | 68,665 |  |
Region 26.2 | terpene,NRPS,NRPS-like,T1PKS | 118,036 | 239,487 |  |
Region 26.3 | nucleoside | 258,066 | 279,031 | High | tunicamycin B1 | other:nucleoside
Region 26.4 | NRPS | 293,287 | 358,492 |  |
Region 26.5 | NRPS-like,NAPAA | 371,860 | 450,754 |  |
Region 26.6 | arylpolyene,terpene | 565,828 | 622,128 |  |
Region 27.1 | terpene | 58,024 | 79,208 |
Region 27.2 | RiPP-like | 215,083 | 225,592 |  |
Region 27.3 | NI-siderophore | 597,755 | 629,626 | Low | peucechelin | NRPS:Type I
Region 27.4 | NI-siderophore | 703,191 | 721,891 | High | legonoxamine A/desferrioxamine B/legonoxamine B | other:other
Region 28.1 | butyrolactone | 294,149 | 305,438 |  |

No secondary metabolite regions were found in these records:
  NZ_LWKZ01000004.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000005.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000006.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000007.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000009.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000010.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000013.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000014.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000015.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000016.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000018.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000019.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000020.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000021.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000022.1 (Streptomyces sp. CB02923)
  NZ_LWKZ01000029.1 (Streptomyces sp. CB02923)

Compact view
NZ_LWKZ01000001.1 - Region 1 - RRE-containing
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 258,976 - 279,248 nt. (total: 20,273 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
A6A06_RS01105: nucleotide sugar dehydrogenase

smcogs
  SMCOG1152: nucleotide sugar dehydrogenase

Lyases: decarboxylase dehydratase
A6A06_RS01060: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

A6A06_RS01125: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
A6A06_RS01050: 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 | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000883.5 |  | 0.52 | other (other) | arginomycin | Streptomyces arginensis
BGC0001778.5 |  | 0.42 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000757.3 |  | 0.40 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000754.3 |  | 0.40 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000755.3 |  | 0.40 | saccharide | capsular polysaccharide | Avibacterium paragallinarum 221
BGC0000756.3 |  | 0.40 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000737.3 |  | 0.40 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000739.3 |  | 0.37 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000868.5 |  | 0.34 | other (other) | teichuronic acid | Bacillus subtilis subsp. subtilis str. 168

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000883.5 |  | 0.52 | other (other) | arginomycin | Streptomyces arginensis
BGC0001778.5 |  | 0.42 | other (other) | showdomycin | Streptomyces showdoensis
BGC0000757.3 |  | 0.40 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000754.3 |  | 0.40 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000755.3 |  | 0.40 | saccharide | capsular polysaccharide | Avibacterium paragallinarum 221
BGC0000756.3 |  | 0.40 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000737.3 |  | 0.40 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000739.3 |  | 0.37 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000868.5 |  | 0.34 | other (other) | teichuronic acid | Bacillus subtilis subsp. subtilis str. 168

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.21 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
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: 17.28 out of 19.52
Confidence: medium
Additional weak hits (7):
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.93 out of 24.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.41 out of 27.04
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.10 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.37 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.36 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.84 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.75 out of 28.19
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (258975...279248)
A6A06_RS01090
  RRE type: Stand_Alone_Lasso_RRE
  Location: 2 - 73
  Score: 33.2

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
IolR | Regulator of the inositol catabolism

NZ_LWKZ01000001.1 - Region 2 - 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: 305,402 - 351,689 nt. (total: 46,288 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
A6A06_RS01385: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Lyases: lyase
A6A06_RS01405: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: synthase
A6A06_RS01380: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.67 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000107.3 |  | 0.60 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.67 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001284.4 |  | 0.62 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001254.3 |  | 0.61 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001257.3 |  | 0.60 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000107.3 |  | 0.60 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4

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 (15):
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: 15.64 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.09 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.36 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.51 out of 29.38
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.76 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.50 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.66 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.99 out of 32.74
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.86 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.22 out of 32.93
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.52 out of 36.53
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.76 out of 27.55
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.07 out of 35.63
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.35 out of 25.88
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 305401 - 351689:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal)

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).
A6A06_RS01380: mmal
PKS_AT (551..842): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 79.2%
  Malonyl-CoA: 70.8%
  Propionyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 129.1
  Methoxymalonyl-CoA: 106.5
  Ethylmalonyl-CoA: 104.4
  Malonyl-CoA: 85.4
  2-Methylbutyryl-CoA: 76.8
  Propionyl-CoA: 70.6
  Isobutyryl-CoA: 67.2
  trans-1,2-CPDA: 61.6
  fatty_acid: 44.2
  Acetyl-CoA: 42.5
  inactive: 31.6
  Benzoyl-CoA: 28.5
  CHC-CoA: 22.9
  3-Methylbutyryl-CoA: 13.9

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

Regulator | Description
--- | ---

NZ_LWKZ01000001.1 - Region 3 - NRPS,NRPS-like,PKS-like,lanthipeptide-class-ii,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: 397,806 - 524,755 nt. (total: 126,950 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)
lanthipeptide-class-ii: cds(LANC_like and DUF4135)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
PKS-like: (t2pks2 or ksIII)
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
Lanthipeptides
Terpene
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
A6A06_RS01770: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

A6A06_RS01945: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

A6A06_RS01955: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

A6A06_RS02005: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

A6A06_RS02030: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS02050: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: PPTase aminotransferase methyltransferase sulfotransferase
A6A06_RS01765: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

A6A06_RS01855: Sulfotransferase domain

extras
  Sulfotransfer_3: Sulfotransferase domain

A6A06_RS01920: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

A6A06_RS02025: methyltransferase

smcogs
  SMCOG1248: methyltransferase

Hydrolases: back translocase deaminase phosphatase
A6A06_RS01845: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

A6A06_RS01935: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

A6A06_RS02000: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: cyclase dehydratase
A6A06_RS01865: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

A6A06_RS41375: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase synthetase
A6A06_RS01800: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

A6A06_RS01915: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS01925: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS01940: 3-oxoacyl-(acyl carrier protein) synthase III

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

A6A06_RS01960: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS01980: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS01990: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS01995: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

A6A06_RS02010: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS02020: 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 | terpene-precursor | lanthipeptide-class-ii | NRPS | PKS-like | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001813.4 |  |  |  |  |  |  | 1.60 | NRPS | tyrobetaine | Streptomyces sp. NRRL WC-3703
BGC0002135.2 |  |  |  |  |  |  | 1.54 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  |  |  |  |  |  | 1.54 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  |  |  |  |  |  | 1.51 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0000342.4 |  |  |  |  |  |  | 1.50 | NRPS | enniatin | Fusarium equiseti
BGC0001135.5 |  |  |  |  |  |  | 1.49 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  |  |  |  |  |  | 1.46 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  |  |  |  |  | 1.45 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  |  |  |  |  |  | 1.45 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001833.4 |  |  |  |  |  |  | 1.42 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001813.4 |  | 0.80 | NRPS | tyrobetaine | Streptomyces sp. NRRL WC-3703
BGC0002286.3 |  | 0.75 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide 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
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000307.4 |  | 0.74 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lanthipeptide(s) for A6A06_RS01865

A6A06_RS41385
Leader:
MSTEAAAWKTGAQDVTNPAGANFGELSLADLREDQSAHM
Core:
I S S G Y F C T I T T E C F C
Core with dehydrations:
I Dha Dha G Y F Cys Dhb I Dhb Dhb E Cys F Cys

#### antiSMASH-DB 4.0 matches for A6A06_RS41385

100.0%
NZ_LWKZ01000001.1:
Lanthipeptides: A6A06_RS41385_lanthipeptide
1
I S S G Y F C T I T T E C F C
15
I S S G Y F C T I T T E C F C
1
I S S G Y F C T I T T E C F C
15
60.0%
NZ_JALMDK010000017.1:
Lanthipeptides: allorf_059288_059443_lanthipeptide
2
S S G Y F C T I T T E C F C
15
S G Y C T+T E C C
2
S G G Y I C T L T W E C N C
15
45.5%
NZ_CP034669.1:
Lanthipeptides: EJ065_RS32040_lanthipeptide
2
S S G Y F C T I T T E C F C
15
S G Y C T+T T E C C
9
S C G Y V C T L T T E C G C
22
with 99 more sequence matches
Only the first 10 are displayed here.
42.9%
NZ_AUBN01000022.1:
Lanthipeptides: G448_RS16025_lanthipeptide
2
S S G Y F C T I T T E C
13
S S G+F C T+T E C
2
S S G W F C T L T I E C
13
42.9%
NZ_CP086242.1 and 1 other:
NZ_CP086245.1 Lanthipeptides: LL037_RS25615_lanthipeptide
Lanthipeptides: LL038_RS25355_lanthipeptide
2
S S G Y F C T I T T E C
13
S S G C T T T E C
2
S S G A I C T A T T E C
13
40.0%
NZ_CP036455.1 and 4 others:
NZ_JAGPXN010000019.1 Lanthipeptides: KBX06_RS22045_lanthipeptide NZ_JAODUN010000003.1 Lanthipeptides: BXY51_RS10560_lanthipeptide NZ_KB895893.1 Lanthipeptides: C569_RS0129325_lanthipeptide NZ_KB900614.1 Lanthipeptides: SALPAC6_RS0114155_lanthipeptide
Lanthipeptides: EKD16_RS25235_lanthipeptide
2
S S G Y F C T I T T E C
13
S S G+ C T+T E C
1
S S G W V C T L T I E C
12
38.1%
NC_009480.1 and 12 others:
NZ_CP033724.1 Lanthipeptides: EFE39_RS10220_lanthipeptide NZ_CP047051.1 Lanthipeptides: GRD74_RS10365_lanthipeptide NZ_CP047054.1 Lanthipeptides: GRD61_RS10460_lanthipeptide NZ_CP053860.1 Lanthipeptides: DQP62_RS10825_lanthipeptide NZ_CP061274.1 Lanthipeptides: H9X71_RS09850_lanthipeptide NZ_CP076352.1 Lanthipeptides: KN218_RS09900_lanthipeptide NZ_CP085137.1 Lanthipeptides: LHJ48_RS10290_lanthipeptide NZ_CP085140.1 Lanthipeptides: LHJ47_RS10305_lanthipeptide NZ_CP095274.1 Lanthipeptides: MU580_RS10460_lanthipeptide NZ_JADKRR010000001.1 Lanthipeptides: ITJ40_RS10085_lanthipeptide NZ_PSTW01000024.1 Lanthipeptides: C5C03_RS09675_lanthipeptide NZ_SISU01000002.1 Lanthipeptides: EOG37_RS09890_lanthipeptide
Lanthipeptides: CMM_RS10575_lanthipeptide
2
S S G Y F C T I T T E C
13
S S G+ C T+T E C
2
S S G W L C T L T I E C
13
38.1%
NZ_CP015515.1 and 2 others:
NZ_CP028130.1 Lanthipeptides: C7V51_RS14690_lanthipeptide NZ_PSUO01000011.1 Lanthipeptides: C5C18_RS08595_lanthipeptide
Lanthipeptides: A6122_RS12855_lanthipeptide
2
S S G Y F C T I T T E C
13
S S G+ C T+T E C
2
S S G W M C T L T I E C
13
35.0%
NZ_CP022413.2 and 1 other:
NZ_JAQEYW010000009.1 Lanthipeptides: PG422_RS09400_lanthipeptide
Lanthipeptides: CGC63_RS01420_lanthipeptide
3
S G Y F C T I T T E C
13
S G C T I+ E C
1
S G V V C T I S V E C
11
31.8%
NC_004070.1 and 27 others:
NC_008024.1 Lanthipeptides: MGAS10750_RS08460_lanthipeptide NZ_CAAHHZ010000002.1 Lanthipeptides: E9518_RS02835_lanthipeptide NZ_CAAHIH010000002.1 Lanthipeptides: E9602_RS03585_lanthipeptide NZ_CAAHIO010000002.1 Lanthipeptides: E9584_RS04360_lanthipeptide NZ_CAAHJE010000002.1 Lanthipeptides: E9605_RS03435_lanthipeptide NZ_CAAHJS010000002.1 Lanthipeptides: E9628_RS02300_lanthipeptide NZ_CAAHKC010000012.1 Lanthipeptides: E9636_RS08085_lanthipeptide NZ_CAAHMR010000003.1 Lanthipeptides: E9727_RS05510_lanthipeptide NZ_CAAHQE010000003.1 Lanthipeptides: E9931_RS04945_lanthipeptide NZ_CAAHQG010000004.1 Lanthipeptides: E9903_RS05690_lanthipeptide NZ_CAAIFD010000008.1 Lanthipeptides: FAG63_RS07845_lanthipeptide NZ_CAAIJM010000014.1 Lanthipeptides: FAI23_RS09465_lanthipeptide NZ_CAAJDK010000010.1 Lanthipeptides: FAO79_RS08000_lanthipeptide NZ_CAAJFI010000003.1 Lanthipeptides: FAP60_RS03740_lanthipeptide NZ_CP008926.1 Lanthipeptides: DP15_RS03855_lanthipeptide NZ_CP035434.1 Lanthipeptides: ETT65_RS08240_lanthipeptide NZ_CP035435.1 Lanthipeptides: ETT64_RS07905_lanthipeptide NZ_CP035447.1 Lanthipeptides: ETT52_RS07920_lanthipeptide NZ_CP035449.1 Lanthipeptides: ETT50_RS08255_lanthipeptide NZ_CP035453.1 Lanthipeptides: ETT46_RS08220_lanthipeptide NZ_CP060646.1 Lanthipeptides: H7789_RS07920_lanthipeptide NZ_CP065054.1 Lanthipeptides: I2432_RS09105_lanthipeptide NZ_LRGW01000003.1 Lanthipeptides: AWU01_RS03260_lanthipeptide NZ_LS483298.1 Lanthipeptides: DQM39_RS08650_lanthipeptide NZ_LS483407.1 Lanthipeptides: DQM86_RS08100_lanthipeptide NZ_LS483425.1 Lanthipeptides: DQN36_RS07865_lanthipeptide NZ_LS483430.1 Lanthipeptides: DQN28_RS07600_lanthipeptide
Lanthipeptides: SPYM3_RS08605_lanthipeptide
3
S G Y F C T I T T E C
13
S G+F T I T +C
4
S G W F A T I T D D C
14
31.8%
NZ_CP061033.1 and 1 other:
NZ_CP061033.1 Lanthipeptides: IAU67_RS09320_lanthipeptide
Lanthipeptides: IAU67_RS09320_lanthipeptide
2
S S G Y F C T I T T E C
13
+ G F C T T E C
6
N E G N F C T G T I E C
17
30.8%
NZ_JALASB010000016.1 and 3 others:
NZ_JALASR010000012.1 Lanthipeptides: MOD87_RS16305_lanthipeptide NZ_JALAUW010000005.1 Lanthipeptides: MOE83_RS03160_lanthipeptide NZ_JALAXQ010000010.1 Lanthipeptides: MOF24_RS12150_lanthipeptide
Lanthipeptides: MOD42_RS18070_lanthipeptide
2
S S G Y F C T I T T E C F C
15
G C T I T+E C C
13
G G G G V C T I T S E C I C
26
30.4%
NZ_CP050134.2 and 3 others:
NZ_EQ973330.1 Lanthipeptides: CORMATOL_RS10565_lanthipeptide NZ_LR134504.1 Lanthipeptides: EL293_RS07240_lanthipeptide NZ_LR134504.1 Lanthipeptides: EL293_RS07240_lanthipeptide
Lanthipeptides: HBA49_RS00770_lanthipeptide
2
S S G Y F C T I T T E C F
14
++G +C T I T E C
7
N N G R W C T I T K E C M
19

#### MIBiG 4.0 matches for A6A06_RS41385

21.4%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
2
S S G Y F C T I T T E C F
14
+ G +C T+T E C
12
N K G A Y C T L T V E C M
24
20.0%
BGC0002110.3 (QKV49893.1):
Lanthipeptide: birimositide
2
S S G Y F C T I T T E C
13
++G +C T+T E C
14
N N G G W C T L T K E C
25
10.3%
BGC0001229.4 (SBI_06990):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
7
C T I T T E C
13
C T++ E C
28
C T L S K E C
34
A6A06_RS01895
Leader:
MRNVDLEGQMLNGV
Core:
M A E R G G T G A V V V P S A E A A P G P A G R P A D C P V E V P Q G V T V P R T G R T S G L R G E G
Core with dehydrations:
M A E R G G Dhb G A V V V P Dha A E A A P G P A G R P A D Cys P V E V P Q G V Dhb V P R Dhb G R Dhb Dha G L R G E G

#### antiSMASH-DB 4.0 matches for A6A06_RS01895

100.0%
NZ_LWKZ01000001.1:
Lanthipeptides: A6A06_RS01895_lanthipeptide
1
M A E R G G T G A V V V P S A E A A P G P A G R P A D C P V E V P Q G V T V P R T G R T S G L R G E G
51
M A E R G G T G A V V V P S A E A A P G P A G R P A D C P V E V P Q G V T V P R T G R T S G L R G E G
1
M A E R G G T G A V V V P S A E A A P G P A G R P A D C P V E V P Q G V T V P R T G R T S G L R G E G
51
17.6%
NZ_BBYJ01000013.1:
Lanthipeptides: allorf_220397_220594_lanthipeptide
1
M A E R G G T G A V V V P S A E A A P G P A G R P A D C
28
+ +R G T S+ + G G R P C
3
I G Q R G A T A G S T C A S S C N S Y G Q T G R P C R C
30
15.7%
NZ_CP116936.1:
Lanthipeptides: allorf_2868736_2868942_lanthipeptide
5
G G T G A V V V P S A E A A P G P A G R P A D C P V
30
G V P +A+ G R +D C +
15
G A D D G T W V P D T D A S T R S G G R L S D C S M
40
with 1 more sequence matches
13.7%
NZ_BCEZ01000027.1:
Thiopeptides: GOZ55_RS05270_thiopeptide
30
V E V P Q G V T V P R T G R T S G
46
V E+ + +P T T S G
2
V E I S E A T A L P E T A A T S G
18

#### MIBiG 4.0 matches for A6A06_RS01895

7.8%
BGC0002150.2 (MBO0654592.1):
Lasso peptide: triculamin
45
S G L R G E G
51
G+R G+G
8
D G I R G K G
14
allorf_0413819_0413920
Leader:
MCVFPRLHNGDGG
Core:
N A S S P C V R Y I F S R R G V R C E N
Core with dehydrations:
N A Dha Dha P Cys V R Y I F Dha R R G V R Cys E N

#### antiSMASH-DB 4.0 matches for allorf_0413819_0413920

100.0%
NZ_LWKZ01000001.1:
Lanthipeptides: allorf_0413819_0413920_lanthipeptide
1
N A S S P C V R Y I F S R R G V R C E N
20
N A S S P C V R Y I F S R R G V R C E N
1
N A S S P C V R Y I F S R R G V R C E N
20
30.0%
NZ_AP022613.1:
Lanthipeptides: allorf_4654794_4654925_lanthipeptide
6
C V R Y I F S R R G
15
C V Y+F R G
11
C V S Y V F H L R G
20
24.0%
NZ_QICS01000003.1:
Lanthipeptides: allorf_263557_263733_lanthipeptide
7
V R Y I F S R R G V
16
V Y+F+ R G V
5
V P Y L F A L R G V
14
with 2 more sequence matches
21.1%
NZ_LMGS01000001.1 and 1 other:
NZ_LMJF01000001.1 Lanthipeptides: ASE35_RS05580_lanthipeptide
Lanthipeptides: ASD69_RS05595_lanthipeptide
1
N A S S P C V R Y I F S R
13
N A S P +Y I F S+
14
N A S G P A Q Q Y I F S Q
26
14.0%
NZ_LMJO01000001.1:
Lanthipeptides: ASE43_RS02635_lanthipeptide
1
N A S S P C V R Y I F S R
13
N A S P +Y I F S
33
N A S G P A Q Q Y I F S E
45
allorf_0427142_0427354
Leader:
MKRRGDRWSGSRPVVRGSLCRLRIRAGG
Core:
T R V C G V A S P S G P C C V H V P H V I P A T Y P V T R P Y A G R G R G R T A P G
Core with dehydrations:
Dhb R V Cys G V A Dha P Dha G P Cys Cys V H V P H V I P A Dhb Y P V Dhb R P Y A G R G R G R Dhb A P G

#### antiSMASH-DB 4.0 matches for allorf_0427142_0427354

100.0%
NZ_LWKZ01000001.1:
Lanthipeptides: allorf_0427142_0427354_lanthipeptide
1
T R V C G V A S P S G P C C V H V P H V I P A T Y P V T R P Y A G R G R G R T A P G
42
T R V C G V A S P S G P C C V H V P H V I P A T Y P V T R P Y A G R G R G R T A P G
1
T R V C G V A S P S G P C C V H V P H V I P A T Y P V T R P Y A G R G R G R T A P G
42

#### MIBiG 4.0 matches for allorf_0427142_0427354

16.7%
BGC0002130.3 (QKI29070.1):
Lanthipeptide: cacaoidin
9
P S G P C C V H--V P H V I P A T
24
S P C ++ V I A T
1
S S A P C T I Y A S V S A S I S A T
18
9.5%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
4
C G V A S P S G P C C V H V P
18
C + + + C +H V
19
C N M K T A T C H C S I H V S
33
allorf_0427189_0427341
Leader:
MTGGPEAAPSFVVLCAVCASAQAAHVFAG
Core:
W Q V P L V H A V F T C L T S Y Q R R I P
Core with dehydrations:
W Q V P L V H A V F Dhb Cys L Dhb Dha Y Q R R I P

#### antiSMASH-DB 4.0 matches for allorf_0427189_0427341

100.0%
NZ_LWKZ01000001.1:
Lanthipeptides: allorf_0427189_0427341_lanthipeptide
1
W Q V P L V H A V F T C L T S Y Q R R I P
21
W Q V P L V H A V F T C L T S Y Q R R I P
1
W Q V P L V H A V F T C L T S Y Q R R I P
21
allorf_0428139_0428276
Leader:
MAGRAGDAWYGYAPAAEKALRAAAEGA
Core:
W R G R E P G C R P D D Y H R C G S
Core with dehydrations:
W R G R E P G Cys R P D D Y H R Cys G Dha

#### antiSMASH-DB 4.0 matches for allorf_0428139_0428276

100.0%
NZ_LWKZ01000001.1:
Lanthipeptides: allorf_0428139_0428276_lanthipeptide
1
W R G R E P G C R P D D Y H R C G S
18
W R G R E P G C R P D D Y H R C G S
1
W R G R E P G C R P D D Y H R C G S
18
25.0%
NZ_FMTS01000001.1:
Lassopeptides: BLO49_RS18320_lassopeptide
3
G R E P G C R P D
11
G P G R P D
1
G S T P G T R P D
9
16.7%
NZ_SLWS01000002.1 and 3 others:
NZ_SLWS01000002.1 Lanthipeptides: allorf_0484574_0484780_lanthipeptide NZ_SLWS01000002.1 Lanthipeptides: allorf_0484574_0484780_lanthipeptide NZ_SLWS01000002.1 Lanthipeptides: allorf_0484574_0484780_lanthipeptide
Lanthipeptides: allorf_0484574_0484780_lanthipeptide
9
R P D D Y H R C G S
18
+D H+C G S
15
N S N D S H Q C G S
24

#### 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 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:
A6A06_RS01800: PT_FPPS_like
Domain 1 (44 - 329): 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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.85 out of 20.97
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.63 out of 18.46
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.60 out of 29.72
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 29.30 out of 30.12
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.91 out of 27.04
Confidence: medium
Additional weak hits (16):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.53 out of 39.62
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.81 out of 31.73
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.11 out of 25.75
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.37 out of 25.75
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.94 out of 33.73
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.59 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.36 out of 26.85
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.37 out of 26.12
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.17 out of 29.51
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.02 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.09 out of 29.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.85 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.85 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.82 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.39 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
Lanthipeptides
NRPS/PKS products
NRPS/PKS substrates
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.

A6A06_RS41385 - Class II
  Cleavage pHMM score: -6.10
  RODEO score: 0
  Monoisotopic mass: 1583.7 Da
  Molecular weight: 1584.8 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1602.8 Da N = 1
    1620.9 Da N = 2
A6A06_RS01895 - Class II
  Cleavage pHMM score: -5.90
  RODEO score: 0
  Monoisotopic mass: 4815.5 Da
  Molecular weight: 4818.3 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4836.4 Da N = 1
    4854.4 Da N = 2
    4872.4 Da N = 3
    4890.4 Da N = 4
    4908.4 Da N = 5
allorf_0413819_0413920 - Class II
  Cleavage pHMM score: -5.20
  RODEO score: 0
  Monoisotopic mass: 2259.1 Da
  Molecular weight: 2260.5 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2278.6 Da N = 1
allorf_0427142_0427354 - Class II
  Cleavage pHMM score: -5.70
  RODEO score: 0
  Monoisotopic mass: 4191.2 Da
  Molecular weight: 4193.8 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4211.8 Da N = 1
    4229.9 Da N = 2
    4247.9 Da N = 3
allorf_0427189_0427341 - Class II
  Cleavage pHMM score: -4.60
  RODEO score: 0
  Monoisotopic mass: 2459.3 Da
  Molecular weight: 2460.9 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2478.9 Da N = 1
    2496.9 Da N = 2
allorf_0428139_0428276 - Class II
  Cleavage pHMM score: -6.30
  RODEO score: 0
  Monoisotopic mass: 2127.9 Da
  Molecular weight: 2129.3 Da
  Number of bridges: 1

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 397805 - 524755:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-Tyr - Tyr - X) + (X) + (NMe-Phe - NMe-X - NMe-X) + (NMe-Phe - Tyr - Phe - X - NMe-Gly - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 413721 - 464407:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-Tyr - Tyr - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 429327 - 470332:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-Phe - NMe-X - NMe-X) + (X) + (NMe-Tyr - Tyr - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 445796 - 488319:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (NMe-Phe - NMe-X - NMe-X) + (NMe-Phe - Tyr - Phe - X - NMe-Gly - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 448697 - 524755:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (NMe-Phe - NMe-X - NMe-X) + (NMe-Phe - Tyr - Phe - X - NMe-Gly - X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
A6A06_RS01915: Tyr - Tyr - X
Search NORINE for peptide: strict or relaxed
AMP-binding (14..389): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAHAFDASVAEVTLTVAGEVNAYGPTETTVCASV
  Nearest Stachelhaus code(s):
    Tyr DAATVAAVCK (88% 8Å match)
    Phe or Tyr DASTTAAVCK (76% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1478..1853): Tyr
nrpys: Tyr

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

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

AMP-binding (2525..2928): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDHAFDASTFDVLLWTGGEFNVYGPTEVTMSATY
  Nearest Stachelhaus code(s):
    3OH-Leu DAFLWGVMAK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

A6A06_RS01925: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (9..429): Ala
nrpys: Ala

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

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

A6A06_RS01990: X
AMP-binding (7..405): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    WWAAFDMTVIDVYSLFAGEMNLYGPTETTVCTAH
  Nearest Stachelhaus code(s):
    Pro DLLYLALVCK (76% 8Å match)
  Stachelhaus code match:
    80% (moderate)

A6A06_RS02010: X
AMP-binding (244..651): 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:
    HAKAFDISLWQGQVSATGEVNAYGLTETSDDTNH
  Nearest Stachelhaus code(s):
    Dpr DIWQSTADDK (91% 8Å match)
    dnmeProp or Dab DIWQSTADDK (79% 8Å match)
    Asp DIWQSTADDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS02020: Phe - X - X
Search NORINE for peptide: strict or relaxed
AMP-binding (580..955): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDAAWWEMTLALAGEVNAYGPTESTVCVSM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2003..2405): 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:
    NWMTFDSVGLEFQFWSSGESNLYGPTEMTIQVAS
  Nearest Stachelhaus code(s):
    Ala DILQISLIYK (53% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (3454..3826): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTQAFDAAVWEVLIVVGAEVNAYGPTESTVCVSM
  Nearest Stachelhaus code(s):
    Leu DAMLVGAVCK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

A6A06_RS02025: Phe - Tyr - Phe - X - Gly - X
Search NORINE for peptide: strict or relaxed
AMP-binding (470..845): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDAAWWEMTLALAGEVNAYGPTESTVCVSM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1898..2276): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDAAWAEMTLLVAGEVNAYGPTESTVCVSM
  Nearest Stachelhaus code(s):
    Tyr DASTLAAVCK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2938..3313): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDAAWWEMTLVLAGEVNAYGPTESTVCVSM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3979..4354): X
nrpys: OH-Asp, OMe-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:
    asn (Asn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWATFDLTVTGTKAILGGEVNAYGPTETTVNCTE
  Nearest Stachelhaus code(s):
    OH-Asp or OMe-Asp DLTKIGAVNK (91% 8Å match)
    Asp DLTKIGAVNK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5016..5425): 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:
    FAVTFDIAAVEAQALVGGEVNLYGPTEATVWVTT
  Nearest Stachelhaus code(s):
    Gly DILQLGLVWK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (6487..6872): 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:
    LHHV-APGAWDAATVLSGE--------TTRAYAV
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
CcpA | Catabolite control protein A
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_LWKZ01000001.1 - Region 4 - triceptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 541,231 - 562,800 nt. (total: 21,570 nt) Show pHMM detection rules used
triceptide: ((cds(PF04055 and (TIGR04085 or SPASM)) and triceptide_precursor) or triceptide_rSAM)

#### Legend:

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

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

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

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

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

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

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 (4):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.25 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.95 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.44 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.55 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LWKZ01000002.1 - Region 1 - ectoine
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 74,487 - 84,909 nt. (total: 10,423 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
A6A06_RS06680: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

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

Reference | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.88 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.85 | other (other) | ectoine | Streptomyces anulatus
BGC0000856.3 |  | 0.72 | other (other) | ectoine | Methylophaga thalassica
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002052.3 |  | 0.88 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000853.3 |  | 0.85 | other (other) | ectoine | Streptomyces anulatus
BGC0000856.3 |  | 0.72 | other (other) | ectoine | Methylophaga thalassica
BGC0000852.5 |  | 0.70 | other (other) | ectoine | Sporosarcina pasteurii
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000859.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000857.3 |  | 0.63 | other (other) | ectoine | Methylophaga alcalica
BGC0000860.3 |  | 0.63 | other (other) | ectoine | Methylarcula marina
BGC0000854.3 |  | 0.62 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.26 out of 27.18
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.62 out of 19.52
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.52 out of 19.26
Confidence: medium
Additional weak hits (4):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.23 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.79 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.66 out of 27.78
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
NrdR | Represses ribonucleotide reductase encoding genes

NZ_LWKZ01000003.1 - 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: 59,183 - 93,535 nt. (total: 34,353 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
A6A06_RS07610: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
A6A06_RS07555: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Hydrolases: amidase
A6A06_RS07605: amidase

smcogs
  SMCOG1105: amidase

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
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001478.5 |  | 0.53 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
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.

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
BGC0000942.4 |  | 0.54 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001478.5 |  | 0.53 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
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.

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: 19.35 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
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 25.29 out of 27.18
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.83 out of 27.18
Confidence: medium
Additional weak hits (8):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.49 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.88 out of 29.65
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
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
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.10 out of 30.11
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
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
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_LWKZ01000003.1 - Region 2 - NRPS,NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 173,236 - 267,941 nt. (total: 94,706 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
A6A06_RS08040: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

A6A06_RS08140: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS08150: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

A6A06_RS08195: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS42600: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

Transferases: acyltransferase halogenase
A6A06_RS08045: flavin-dependent trp 5 halogenase

halogenases
  flavin-dependent trp 5 halogenase
smcogs
  SMCOG1119: halogenase

A6A06_RS08120: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: amidase deaminase dehalogenase esterase
A6A06_RS08050: thioesterase

smcogs
  SMCOG1004: thioesterase

A6A06_RS08105: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

A6A06_RS08135: amidase

smcogs
  SMCOG1105: amidase

A6A06_RS08200: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: ligase synthase
A6A06_RS08025: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS08030: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS08100: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

A6A06_RS08125: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS08130: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease
A6A06_RS08160: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | NRPS | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  |  | 1.19 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  |  |  | 1.18 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  |  |  | 1.17 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  | 1.17 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  |  | 1.17 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  | 1.16 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  |  |  | 1.13 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  |  |  | 1.09 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001166.5 |  |  |  | 1.07 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001240.4 |  |  |  | 1.03 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.75 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
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
BGC0001133.4 |  | 0.73 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.54 out of 23.79
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.86 out of 18.57
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.05 out of 26.85
Confidence: medium
Additional weak hits (15):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.96 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.04 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.55 out of 18.57
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.90 out of 20.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.21 out of 20.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.92 out of 21.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.37 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.03 out of 32.74
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.65 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.90 out of 26.85
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.42 out of 30.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.29 out of 27.55
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.66 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.57 out of 26.12
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 173235 - 267941:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gln - X - Tyr) + (Gly - D-Val) + (Gly - X - Pro) + (X) + (Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 173235 - 217681:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 194984 - 238233:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gln - X - Tyr) + (Gly - D-Val) + (Gly - X - Pro) + (X) + (Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 199515 - 267941:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Gly - X - Pro) + (Gly - D-Val) + (Gln - X - Tyr)

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).
A6A06_RS08025: Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (473..872): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    VWQAFDVFFQESFLISSGEDNQYGPSETHVVTAE
  Nearest Stachelhaus code(s):
    Pro DVQFIAQVVK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

A6A06_RS08030: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (11..403): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LMTAWDAYALEGFLLTGGEINGYGPVESCVFATT
  Nearest Stachelhaus code(s):
    Val DALFLGGTFK (62% 8Å match)
  Stachelhaus code match:
    90% (moderate)

A6A06_RS42600: X
AMP-binding (155..558): 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:
    HAKAFDISLWQSQLSVTGEANAYGLTETSDDTNH
  Nearest Stachelhaus code(s):
    Dpr DIWQSTADDK (94% 8Å match)
    dnmeProp or Dab DIWQSTADDK (79% 8Å match)
    Asp DIWQSTADDK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS08120: Gly - X - Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (46..446): 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:
    FAMAFDIAGLDLQALVGAETNLYGPTETTVWSTL
  Nearest Stachelhaus code(s):
    Gly DILQLGLVWK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1106..1497): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FDMAFDASVLEMLVLTGGDHNAYGPTEATVWVTA
  Nearest Stachelhaus code(s):
    Leu DALLLGAVVK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (2811..3222): Pro
nrpys: Pro

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHTFDVATQESFASQGGEHNHYGPTETHLVTAY
  Nearest Stachelhaus code(s):
    4Me-Pro DVQFAGHAVK (88% 8Å match)
    Piz DVQFSAHVVK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

A6A06_RS08125: Gly - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (470..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:
    FAMTFDIAGLELQALVGGETNLYGPTETTIWSTL
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1531..1925): 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:
    N/A
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FDKSFDASVLELVLTVGGDFNGYGPTEATVWVTS
  Nearest Stachelhaus code(s):
    Val DALFTGGVFK (47% 8Å match)
  Stachelhaus code match:
    80% (moderate)

A6A06_RS08130: Gln - X - Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (465..870): 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:
    glu,gln (Glu, Gln)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    HWMTFDASVWELQFFVGGEHNLYGPTETTVQVTA
  Nearest Stachelhaus code(s):
    Gln DAWQFGLIQK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1531..1929): X
nrpys: OH-Asn

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

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

AMP-binding (2590..2982): Tyr
nrpys: Tyr

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    tyr (Tyr)

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

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

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
RutR | Regulator of the pyrimidine and purine metabolism
ToxT | Regulator of MSHA biosynthesis

NZ_LWKZ01000003.1 - Region 3 - NRP-metallophore,NRPS,atropopeptide
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: 282,998 - 332,388 nt. (total: 49,391 nt) Show pHMM detection rules used
Region on contig edge.
atropopeptide: atropopeptide_p450
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
A6A06_RS08315: Biaryl bond formation

MITE
  MITE0000172Biaryl bond formation (identity: 63.00%)
smcogs
  SMCOG1034: cytochrome P450

A6A06_RS08405: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase
A6A06_RS08360: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

Hydrolases: esterase hydrolase
A6A06_RS08375: amidohydrolase

smcogs
  SMCOG1244: amidohydrolase

A6A06_RS08395: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

A6A06_RS08420: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
A6A06_RS08410: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase oxygenase
A6A06_RS08315: Biaryl bond formation

MITE
  MITE0000172Biaryl bond formation (identity: 63.00%)
smcogs
  SMCOG1034: cytochrome P450

A6A06_RS08350: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

A6A06_RS08415: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS40720: 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 | atropopeptide | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000368.5 |  |  |  | 1.08 | NRPS | griseobactin | Streptomyces sp. ATCC 700974
BGC0000401.5 |  |  |  | 0.81 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001132.4 |  |  |  | 0.76 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001185.5 |  |  |  | 0.76 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0001833.4 |  |  |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000309.5 |  |  |  | 0.72 | NRPS | bacillibactin | Bacillus subtilis subsp. subtilis str. 168
BGC0001758.4 |  |  |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000343.5 |  |  |  | 0.71 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0002286.3 |  |  |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000368.5 |  | 0.79 | NRPS | griseobactin | Streptomyces sp. ATCC 700974
BGC0000401.5 |  | 0.72 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001185.5 |  | 0.70 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000309.5 |  | 0.69 | NRPS | bacillibactin | Bacillus subtilis subsp. subtilis str. 168
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000343.5 |  | 0.68 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0002286.3 |  | 0.68 | 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.21 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.19 out of 23.79
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.36 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.03 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.74 out of 36.53
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.38 out of 27.04
Confidence: medium
Additional weak hits (15):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 17.40 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.70 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.61 out of 28.14
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.97 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.63 out of 39.62
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
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.23 out of 27.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.88 out of 27.78
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: 16.72 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.57 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.81 out of 33.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.69 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.28 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.24 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 6, location 282997 - 332388:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Arg - Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 286653 - 332388:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Arg - Thr)

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).
A6A06_RS40720: Arg - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (526..977): Arg
nrpys: Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LGHAFDASWDPWDVVVGGEVNLYGPTETTVDAYY
  Nearest Stachelhaus code(s):
    Arg DADDVGLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1723..2135): Thr
nrpys: Thr

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

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

A6A06_RS08415: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (38..450): 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)

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

Regulator | Description
--- | ---
DasR | N-acetylglucosamine dependent repressor
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism

NZ_LWKZ01000008.1 - Region 1 - 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: 59,540 - 70,523 nt. (total: 10,984 nt) Show pHMM detection rules used
Region on contig edge.
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
Lyases: dehydratase
A6A06_RS10770: 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
--- | --- | --- | --- | --- | ---
BGC0001458.4 |  | 0.53 | 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
BGC0001151.5 |  | 0.34 | other (non-nrp beta-lactam) | valclavam, (-)-2-(2-hydroxyethyl)clavam | Streptomyces antibioticus
BGC0002443.3 |  | 0.32 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0002805.2 |  | 0.31 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0000248.5 |  | 0.31 | PKS | α naphtocyclinoic acid, fogacin | Streptomyces arenae DSM 40737
BGC0001495.3 |  | 0.30 | PKS | actinoallolide A | Actinoallomurus fulvus
BGC0001877.4 |  | 0.30 | PKS | cyphomycin | Streptomyces sp. ISID311
BGC0002386.2 |  | 0.29 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0002499.2 |  | 0.29 | NRPS, PKS | enteromycin | Streptomyces achromogenes subsp. streptozoticus
BGC0001302.5 |  | 0.29 | other (other) | lomofungin | Streptomyces lomondensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001458.4 |  | 0.53 | 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
BGC0001151.5 |  | 0.34 | other (non-nrp beta-lactam) | valclavam, (-)-2-(2-hydroxyethyl)clavam | Streptomyces antibioticus
BGC0002443.3 |  | 0.32 | PKS | mycemycin C, mycemycin A, mycemycin B | Streptomyces olivaceus
BGC0002805.2 |  | 0.31 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0000248.5 |  | 0.31 | PKS | α naphtocyclinoic acid, fogacin | Streptomyces arenae DSM 40737
BGC0001495.3 |  | 0.30 | PKS | actinoallolide A | Actinoallomurus fulvus
BGC0001877.4 |  | 0.30 | PKS | cyphomycin | Streptomyces sp. ISID311
BGC0002386.2 |  | 0.29 | NRPS, PKS | cyclo(n-Me-L-Leu-L-Val), cyclo(n-Me-L-Leu-L-Leu), cyclo(n-Me-L-Leu-L-Ile) | Sorangium cellulosum So0157-2
BGC0002499.2 |  | 0.29 | NRPS, PKS | enteromycin | Streptomyces achromogenes subsp. streptozoticus
BGC0001302.5 |  | 0.29 | other (other) | lomofungin | Streptomyces lomondensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (4):
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.79 out of 23.43
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.30 out of 20.97
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.07 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LWKZ01000011.1 - 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 - 14,355 nt. (total: 14,355 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
Hydrolases: hydrolase
A6A06_RS11480: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

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

Reference | CDPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001441.5 |  | 0.33 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0001778.5 |  | 0.32 | other (other) | showdomycin | Streptomyces showdoensis
BGC0001954.2 |  | 0.32 | NRPS, PKS | wortmanamide A, wortmanamide B | Talaromyces wortmannii
BGC0002058.3 |  | 0.31 | NRPS, PKS | mutanocyclin | Streptococcus mutans B04Sm5
BGC0002287.2 |  | 0.30 | NRPS | mutanocyclin, leuvalin, tyrvalin | Streptococcus mutans
BGC0001336.5 |  | 0.30 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001480.3 |  | 0.29 | other (other) | tundrenone | Methylobacter tundripaludum 21/22
BGC0002477.3 |  | 0.29 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0001736.3 |  | 0.27 | NRPS | pepteridine A, pepteridine B | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001441.5 |  | 0.33 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0001778.5 |  | 0.32 | other (other) | showdomycin | Streptomyces showdoensis
BGC0001954.2 |  | 0.32 | NRPS, PKS | wortmanamide A, wortmanamide B | Talaromyces wortmannii
BGC0002058.3 |  | 0.31 | NRPS, PKS | mutanocyclin | Streptococcus mutans B04Sm5
BGC0002287.2 |  | 0.30 | NRPS | mutanocyclin, leuvalin, tyrvalin | Streptococcus mutans
BGC0001336.5 |  | 0.30 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001480.3 |  | 0.29 | other (other) | tundrenone | Methylobacter tundripaludum 21/22
BGC0002477.3 |  | 0.29 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0001736.3 |  | 0.27 | NRPS | pepteridine A, pepteridine B | 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.

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 (5):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.41 out of 32.74
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.53 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.80 out of 26.06
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
--- | ---

NZ_LWKZ01000012.1 - Region 1 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 406 - 22,944 nt. (total: 22,539 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
A6A06_RS11745: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001539.4 |  | 0.73 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002053.3 |  | 0.72 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001507.3 |  | 0.68 | ribosomal | anantin C | Streptomyces olindensis
BGC0001549.3 |  | 0.67 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001493.5 |  | 0.66 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001551.4 |  | 0.65 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001889.2 |  | 0.65 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0002318.2 |  | 0.60 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0002064.2 |  | 0.60 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0002289.2 |  | 0.60 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001539.4 |  | 0.73 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002053.3 |  | 0.72 | ribosomal | ulleungdin | Streptomyces sp.
BGC0001507.3 |  | 0.68 | ribosomal | anantin C | Streptomyces olindensis
BGC0001549.3 |  | 0.67 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001493.5 |  | 0.66 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001551.4 |  | 0.65 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001889.2 |  | 0.65 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0002318.2 |  | 0.60 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0002064.2 |  | 0.60 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0002289.2 |  | 0.60 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.

#### Lassopeptide(s) for A6A06_RS11750

A6A06_RS11750
Leader:
MPDIQEQPESVEYEAPELAEAGDFAELTL
Full core:
G F H G H H W D T F G G R G H G W W
Putative macrolactam:
G F H G H H W D

#### antiSMASH-DB 4.0 matches for A6A06_RS11750

100.0%
NZ_LWKZ01000012.1:
Lassopeptides: A6A06_RS11750_lassopeptide
1
G F H G H H W D T F G G R G H G W W
18
G F H G H H W D T F G G R G H G W W
1
G F H G H H W D T F G G R G H G W W
18
42.1%
NZ_CP110636.1:
Lassopeptides: OJ254_RS13580_lassopeptide
1
G F H G H H W D T F G G R
13
G F G+H W D + G R
1
G F S G Y H W D G W A G R
13
36.8%
NZ_FQVL01000016.1:
Lassopeptides: BUB71_RS19780_lassopeptide
1
G F H G H H W D T F G G R
13
G G H+ D T F R
2
G K D G H N T D T F S T R
14
with 1 more sequence matches
26.1%
NZ_AULE01000001.1:
Lassopeptides: H509_RS27430_lassopeptide
4
G H H W D T F G G R G
14
G + D F G G R
5
G K Y T D V F G G R A
15

#### MIBiG 4.0 matches for A6A06_RS11750

19.0%
BGC0000581.6 (AAD28494.1):
Lasso peptide: microcin J25
11
G G R G H
15
G G G H
1
G G A G H
5

#### 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:
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.63 out of 24.78
Confidence: medium
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.96 out of 29.25
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.31 out of 26.85
Confidence: medium
Additional weak hits (8):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.63 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.76 out of 32.74
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.53 out of 35.63
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.63 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.48 out of 28.19
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

A6A06_RS11750 - Class II
  Cleavage pHMM score: 3.30
  RODEO score: 20
  Monoisotopic mass: 2114.9 Da
  Molecular weight: 2116.2 Da
  Number of bridges: 0

RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (405...22944)
A6A06_RS11740
  RRE type: Stand_Alone_Lasso_RRE
  Location: 1 - 84
  Score: 70.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
LexA variant 2 | Repressor of DNA damage response
RutR | Regulator of the pyrimidine and purine metabolism
SypG | Regulator of biofilm formation and host colonization

NZ_LWKZ01000012.1 - 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: 560,342 - 581,568 nt. (total: 21,227 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
A6A06_RS14020: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
A6A06_RS14045: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase
A6A06_RS14040: Terpene synthase/cyclase metal-binding domain protein

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

Translocases: permease transporter
A6A06_RS14005: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

A6A06_RS14095: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.81 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.63 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  | 0.62 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000923.3 |  | 0.40 | other (other) | paerucumarin | Pseudomonas aeruginosa PAO1
BGC0001928.2 |  | 0.40 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001197.5 |  | 0.40 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002493.3 |  | 0.38 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0000204.5 |  | 0.37 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0000218.5 |  | 0.36 | PKS | doxorubicin | Streptomyces peucetius
BGC0002138.2 |  | 0.36 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.81 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.63 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  | 0.62 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000923.3 |  | 0.40 | other (other) | paerucumarin | Pseudomonas aeruginosa PAO1
BGC0001928.2 |  | 0.40 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001197.5 |  | 0.40 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0002493.3 |  | 0.38 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0000204.5 |  | 0.37 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200
BGC0000218.5 |  | 0.36 | PKS | doxorubicin | Streptomyces peucetius
BGC0002138.2 |  | 0.36 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670

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:
A6A06_RS14040: T1TS
Domain 1 (51 - 402): 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.75 out of 23.79
Confidence: medium
Additional weak hits (9):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.50 out of 26.85
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.81 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.59 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.28 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.60 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.61 out of 30.25
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.16 out of 35.63
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.22 out of 30.98
Confidence: weak
Terpene
TFBS Finder
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
--- | ---
IolR | Regulator of the inositol catabolism

NZ_LWKZ01000012.1 - 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: 652,370 - 703,532 nt. (total: 51,163 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
A6A06_RS14470: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: aminotransferase methyltransferase
A6A06_RS14480: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

A6A06_RS14485: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

A6A06_RS14555: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: dehydratase
A6A06_RS14535: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase
A6A06_RS14490: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002164.2 |  | 0.66 | NRPS | peramine | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002164.2 |  | 0.66 | NRPS | peramine | Epichloe festucae

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:
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.67 out of 28.19
Confidence: medium
Additional weak hits (12):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.45 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.68 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.76 out of 20.97
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.98 out of 30.22
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.57 out of 29.65
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.99 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.23 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.82 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 3, location 652369 - 703532:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Aad - Cys - D-Val)

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).
A6A06_RS14490: Aad - Cys - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (238..653): Aad
nrpys: 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:
    aad (Aad)
  Single AA prediction:
    aad (Aad)

Stachelhaus prediction details:
  Stachelhaus sequence:
    SDLAFEPHLRQINALLVGEINEYAFTEAAFVTAV
  Nearest Stachelhaus code(s):
    Aad EPRNLVEFVK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1337..1745): 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:
    LSLSFDHFVEQDSGDAIGEINGYGPTEISITSHK
  Nearest Stachelhaus code(s):
    Cys DHESDIGITK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2428..2833): 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:
    FQVAFDFSVEQLSGLVAGESNAYGTTETAVYNTV
  Nearest Stachelhaus code(s):
    Val DFESLAAVYK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ZuR variant 1 | Zinc-responsive repressor

NZ_LWKZ01000012.1 - 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: 888,675 - 911,314 nt. (total: 22,640 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
A6A06_RS15600: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: glycosyltransferase methyltransferase
A6A06_RS15645: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

A6A06_RS15650: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
A6A06_RS15595: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

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

Reference | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.69 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.61 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000553.3 |  | 0.59 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000518.3 |  | 0.56 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000546.3 |  | 0.52 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002111.3 |  | 0.48 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.69 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.66 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.61 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000501.3 |  | 0.61 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000519.4 |  | 0.60 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000553.3 |  | 0.59 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000518.3 |  | 0.56 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0000546.3 |  | 0.52 | ribosomal | SAL-2242 | Streptomyces albidoflavus
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0002111.3 |  | 0.48 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139

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 A6A06_RS15615

A6A06_RS15620
Leader:
MALLDLQAMDAPEHGGGGGGS
Core:
E A S L L L C W S D A S I V L C L
Core with dehydrations:
E A Dha L L L Cys W Dha D A Dha I V L Cys L

#### antiSMASH-DB 4.0 matches for A6A06_RS15620

100.0%
NZ_LWKZ01000012.1:
Lanthipeptides: A6A06_RS15620_lanthipeptide
1
E A S L L L C W S D A S I V L C L
17
E A S L L L C W S D A S I V L C L
1
E A S L L L C W S D A S I V L C L
17
94.1%
NZ_JAFIQY010000032.1:
Lanthipeptides: JXZ78_RS28825_lanthipeptide
1
E A S L L L C W S D A S I V L C L
17
E A S L L L C W S+A S I V L C L
1
E A S L L L C W S E A S I V L C L
17
76.2%
NZ_CP022685.1 and 3 others:
NZ_CP023699.1 Lanthipeptides: CP970_RS30515_lanthipeptide NZ_CP029191.1 Lanthipeptides: DEJ49_RS10405_lanthipeptide NZ_CP029193.1 Lanthipeptides: DEJ47_RS10815_lanthipeptide
Lanthipeptides: KY5_RS12005_lanthipeptide
2
A S L L L C W S D A S I V L C L
17
A S L L L C W S D A S I V L C L
6
A S L L L C W S D A S I V L C L
21
with 50 more sequence matches
Only the first 10 are displayed here.
76.2%
NZ_CP029192.1 and 1 other:
NZ_CP101750.1 Lanthipeptides: NOO62_RS12495_lanthipeptide
Lanthipeptides: DEJ48_RS27490_lanthipeptide
1
E A S L L L C W S D A S I V L C L
17
+A S L L L C W S D A S I V L C L
5
Q A S L L L C W S D A S I V L C L
21
70.6%
NZ_CP023689.1 and 2 others:
NZ_CP056041.1 Lanthipeptides: HUT05_RS04385_lanthipeptide NZ_CP116353.1 Lanthipeptides: PGH47_RS39355_lanthipeptide
Lanthipeptides: CP983_RS02925_lanthipeptide
3
S L L L C W S D A S I V L C L
17
S L L L C S A S I L C L
3
S L L L C A S Q A S I S L C L
17
70.6%
NZ_KQ948929.1:
Lanthipeptides: AQJ67_RS21030_lanthipeptide
3
S L L L C W S D A S I V L C L
17
S L L L C S A S I L C L
1
S L L L C A S Q A S I T L C L
15
65.0%
NZ_BNBL01000010.1 and 1 other:
NZ_CP071595.1 Lanthipeptides: J3S04_RS21315_lanthipeptide
Lanthipeptides: IE295_RS24405_lanthipeptide
1
E A S L L L C W S D A S I V L C L
17
A S L L L C W S A S+ L C L
4
N A S L L L C W S T A S V A L C L
20
64.7%
NC_020504.1 and 2 others:
NZ_CP114413.1 Lanthipeptides: STRCI_RS37065_lanthipeptide NZ_KQ948993.1 Lanthipeptides: AQJ84_RS21420_lanthipeptide
Lanthipeptides: BN159_RS04910_lanthipeptide
3
S L L L C W S D A S I V L C L
17
S L L C S A S I L C L
3
S L L S C V S A A S I T L C L
17
64.7%
NZ_CM002285.1 and 2 others:
NZ_CP047020.1 Lanthipeptides: GQF42_RS39440_lanthipeptide NZ_VISR01000012.1 Lanthipeptides: FB157_RS21700_lanthipeptide
Lanthipeptides: M878_RS54195_lanthipeptide
3
S L L L C W S D A S I V L C L
17
S L L C S A S I+L C L
3
S L L S C V S A A S I L L C L
17
64.7%
NZ_CP011497.1 and 4 others:
NZ_CP017248.1 Lanthipeptides: BFF78_RS03720_lanthipeptide NZ_CP034687.1 Lanthipeptides: ELQ87_RS02805_lanthipeptide NZ_CP106795.1 Lanthipeptides: N8I86_RS33235_lanthipeptide NZ_LIWA01000002.1 Lanthipeptides: AMK32_RS11185_lanthipeptide
Lanthipeptides: ABB07_RS02975_lanthipeptide
1
E A S L L L C W S D A S I V L C L
17
A S L L C S A S++L C L
1
T A S L L S C V S A A S V L L C L
17
64.7%
NZ_CP013743.1 and 1 other:
NZ_JAJSBI010000005.1 Lanthipeptides: LJ657_RS12685_lanthipeptide
Lanthipeptides: AS200_RS06110_lanthipeptide
1
E A S L L L C W S D A S I V L C L
17
A S L L C S A S++L C L
1
T A S L L S C I S A A S V L L C L
17
64.7%
NZ_CP074380.1:
Lanthipeptides: KGS77_RS26180_lanthipeptide
3
S L L L C W S D A S I V L C L
17
S L L L C S A S+ L C L
3
S L L L C N S H A S V T L C L
17
63.2%
NZ_CP032402.1 and 1 other:
NZ_CP032402.1 Lanthipeptides: D3U04_RS17070_lanthipeptide
Lanthipeptides: D3U04_RS17070_lanthipeptide
2
A S L L L C--W S D A S I V L C L
17
A S L L L C S S V L C L
2
A S L L L C D K H S S Q S T V L C L
19

#### MIBiG 4.0 matches for A6A06_RS15620

40.9%
BGC0000553.3 (SSGG_RS09925):
Lanthipeptide: SRO15-2212
1
E A S L L L C-W S D A S I V L C
16
+ S L L+C +S S+V L C
4
Q V S L L V C E Y S S L S V V L C
20

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.51 out of 29.72
Confidence: medium
Additional weak hits (3):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.52 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.87 out of 30.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.98 out of 28.14
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.

A6A06_RS15620 - Class III
  Cleavage pHMM score: 20.60
  RODEO score: 0
  Monoisotopic mass: 1780.9 Da
  Molecular weight: 1782.1 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1800.1 Da N = 1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LWKZ01000012.1 - Region 5 - 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: 1,034,633 - 1,056,924 nt. (total: 22,292 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
A6A06_RS16220: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Lyases: cyclase
A6A06_RS16255: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: ligase
A6A06_RS16230: 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001164.3 |  | 0.53 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000667.3 |  | 0.51 | terpene | PR-toxin | Penicillium roqueforti FM164
BGC0001137.5 |  | 0.42 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000842.5 |  | 0.41 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0002493.3 |  | 0.39 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0000043.5 |  | 0.37 | PKS | curacin A | Moorea producens 19L
BGC0002316.2 |  | 0.36 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001909.3 |  | 0.35 | PKS | strobilurin A | Strobilurus tenacellus
BGC0000649.3 |  | 0.35 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.82 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001164.3 |  | 0.53 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000667.3 |  | 0.51 | terpene | PR-toxin | Penicillium roqueforti FM164
BGC0001137.5 |  | 0.42 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0000842.5 |  | 0.41 | other (non-nrp beta-lactam) | carbapenem MM4550 | Streptomyces argenteolus
BGC0002493.3 |  | 0.39 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0000043.5 |  | 0.37 | PKS | curacin A | Moorea producens 19L
BGC0002316.2 |  | 0.36 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0001909.3 |  | 0.35 | PKS | strobilurin A | Strobilurus tenacellus
BGC0000649.3 |  | 0.35 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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:
A6A06_RS16255: T1TS + T1TS
Domain 1 (1 - 309): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (327 - 691): 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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.31 out of 26.85
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.67 out of 19.26
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.18 out of 27.18
Confidence: medium
Additional weak hits (3):
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.90 out of 36.54
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.50 out of 21.55
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
--- | ---
CRP | Cyclic AMP receptor protein
NrdR | Represses ribonucleotide reductase encoding genes
RutR | Regulator of the pyrimidine and purine metabolism

NZ_LWKZ01000017.1 - 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: 2,494 - 23,567 nt. (total: 21,074 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Ligases: synthase synthetase
A6A06_RS18325: 1-deoxy-D-xylulose-5-phosphate synthase

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

A6A06_RS18335: 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
--- | --- | --- | --- | --- | ---
BGC0001361.3 |  | 0.45 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.45 | terpene | sodorifen | Serratia plymuthica
BGC0000677.5 |  | 0.39 | 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
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000666.5 |  | 0.35 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001911.3 |  | 0.35 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.34 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001456.3 |  | 0.34 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000668.5 |  | 0.33 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001361.3 |  | 0.45 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002283.2 |  | 0.45 | terpene | sodorifen | Serratia plymuthica
BGC0000677.5 |  | 0.39 | 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
BGC0002309.2 |  | 0.37 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000666.5 |  | 0.35 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999
BGC0001911.3 |  | 0.35 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.34 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001456.3 |  | 0.34 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000668.5 |  | 0.33 | other (other), terpene | 12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole | Hapalosiphon welwitschii UTEX B 1830

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:
A6A06_RS18335: PT_FPPS_like
Domain 1 (44 - 348): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.22 out of 23.79
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.29 out of 27.55
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.66 out of 30.12
Confidence: medium
Additional weak hits (4):
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.74 out of 25.31
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.76 out of 26.85
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.27 out of 25.88
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
--- | ---
GnfM | Regulator of nitrogen-fixation genes
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator

NZ_LWKZ01000023.1 - Region 1 - NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 58,908 - 129,402 nt. (total: 70,495 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)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
A6A06_RS19005: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

A6A06_RS19080: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS19090: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: aminotransferase methyltransferase
A6A06_RS18995: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

A6A06_RS19125: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
A6A06_RS19120: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Ligases: ligase synthase
A6A06_RS19010: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS19015: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS19025: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS19030: 3-oxoacyl-(acyl carrier protein) synthase III

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

A6A06_RS19035: 3-oxoacyl-(acyl carrier protein) synthase III

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

A6A06_RS19050: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS19085: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS19095: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS-like | T1PKS | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001261.3 |  |  |  |  | 1.35 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  |  |  |  | 1.30 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002135.2 |  |  |  |  | 1.28 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  |  |  |  | 1.27 | NRPS | enniatin | Fusarium equiseti
BGC0001128.4 |  |  |  |  | 1.26 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  |  |  |  | 1.23 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  |  |  |  | 1.17 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002276.2 |  |  |  |  | 1.01 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001023.5 |  |  |  |  | 0.98 | NRPS, PKS | myxochromide S1 | Stigmatella aurantiaca
BGC0002286.3 |  |  |  |  | 0.96 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.72 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002135.2 |  | 0.67 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.67 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  | 0.66 | NRPS | peramine | Epichloe festucae
BGC0000307.4 |  | 0.65 | NRPS | AbT1 | Aureobasidium pullulans

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.01 out of 27.18
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.63 out of 18.46
Confidence: medium
Additional weak hits (19):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.20 out of 26.12
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.40 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.74 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.87 out of 27.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.99 out of 36.53
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.30 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.36 out of 28.14
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.77 out of 31.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.05 out of 32.74
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.82 out of 23.43
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.78 out of 25.88
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.32 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.19 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.71 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.95 out of 30.25
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.86 out of 24.78
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.27 out of 26.85
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 58907 - 129402:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (ohmal) + (X) + (Arg) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 58907 - 105625:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (ohmal) + (X) + (Arg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 71573 - 125946:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (ohmal) + (X) + (Arg) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 87509 - 129402:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (Arg) + (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).
A6A06_RS19010: X
AMP-binding (30..417): 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:
    HVWSWDSAVQDAHSALGGDAGAYGSTECSCALLR
  Nearest Stachelhaus code(s):
    Phe DAGALGACAK (38% 8Å match)
    Leu DALHSGAVAK (35% 8Å match)
  Stachelhaus code match:
    60% (weak)

A6A06_RS19015: mal
PKS_AT (560..857): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 153.0
  inactive: 91.0
  Methoxymalonyl-CoA: 76.1
  Methylmalonyl-CoA: 62.1
  Propionyl-CoA: 57.5
  Ethylmalonyl-CoA: 38.7
  2-Methylbutyryl-CoA: 36.7
  Isobutyryl-CoA: 31.2
  CHC-CoA: 30.2
  trans-1,2-CPDA: 22.3
  Benzoyl-CoA: 18.0
  Acetyl-CoA: 14.7
  fatty_acid: 14.3
  3-Methylbutyryl-CoA: 10.9

A6A06_RS19050: X
AMP-binding (7..426): X
nrpys: Ile, Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LPTAWDAASLEGWLMVGGEVNGYGPAETTVFTTT
  Nearest Stachelhaus code(s):
    Ile or Val DALWMGGVFK (65% 8Å match)
    Val DALWMGGVFK (56% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS19085: Arg
Search NORINE for peptide: strict or relaxed
AMP-binding (483..897): Arg
nrpys: Arg

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:
    YAVAFDVSLEEPNLVLGGELNAYGITEATVTSTV
  Nearest Stachelhaus code(s):
    Arg DVENVGAVTK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS19095: X
AMP-binding (1..411): 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:
    FAYIFDAHLGDPIVFAGGDHNAYGPAEATVLCLT
  Nearest Stachelhaus code(s):
    Trp DAGIVGACAK (50% 8Å match)
    Val DAWMFAAVLK (47% 8Å match)
    aIle DALVFGVVLK (44% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
NrdR | Represses ribonucleotide reductase encoding genes
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_LWKZ01000023.1 - 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: 153,782 - 174,846 nt. (total: 21,065 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
A6A06_RS19360: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: methyltransferase
A6A06_RS19310: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase lyase
A6A06_RS19305: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

A6A06_RS19315: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.80 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.80 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  | 0.69 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002318.2 |  | 0.42 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0002645.3 |  | 0.40 | other (other) | fluopsin C | Pseudomonas aeruginosa PAO1
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001561.4 |  | 0.38 | NRPS | curacomycin | Streptomyces curacoi
BGC0001458.4 |  | 0.37 | 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
BGC0001221.5 |  | 0.37 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0001387.5 |  | 0.36 | other (other) | nucleocidin | Streptomyces calvus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000658.3 |  | 0.80 | terpene | 2-methylisoborneol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000659.3 |  | 0.80 | terpene | 2-methylisoborneol | Saccharopolyspora erythraea NRRL 2338
BGC0000657.5 |  | 0.69 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002318.2 |  | 0.42 | ribosomal | canucin A, canucin B | Streptomyces canus
BGC0002645.3 |  | 0.40 | other (other) | fluopsin C | Pseudomonas aeruginosa PAO1
BGC0000528.5 |  | 0.40 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001561.4 |  | 0.38 | NRPS | curacomycin | Streptomyces curacoi
BGC0001458.4 |  | 0.37 | 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
BGC0001221.5 |  | 0.37 | other (phenazine) | marinophenazine A, phenaziterpene A | Streptomyces sp. CNQ-509
BGC0001387.5 |  | 0.36 | other (other) | nucleocidin | Streptomyces calvus

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:
A6A06_RS19315: T1TS
Domain 1 (3 - 348): 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:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
Additional weak hits (7):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.02 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.94 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.19 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.32 out of 35.63
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.41 out of 18.57
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.06 out of 24.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.70 out of 35.63
Confidence: weak
Terpene
TFBS Finder
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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production

NZ_LWKZ01000023.1 - Region 3 - NRPS,NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 177,891 - 226,161 nt. (total: 48,271 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)
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
A6A06_RS19495: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

A6A06_RS19525: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase aminotransferase
A6A06_RS19385: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

A6A06_RS19595: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Lyases: dehydratase
A6A06_RS19480: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
A6A06_RS19395: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

A6A06_RS19485: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS19490: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS19500: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS19505: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS19600: 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-like | NRPS-like | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002051.2 |  |  |  | 1.38 | NRPS | antipain | Streptomyces sp.
BGC0001249.5 |  |  |  | 1.26 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  |  |  | 1.12 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  |  |  | 1.11 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  |  |  | 1.08 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  |  |  | 1.04 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  |  |  | 1.04 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  | 1.04 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  |  |  | 1.03 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2 |  |  |  | 1.01 | NRPS | peramine | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002051.2 |  | 0.76 | NRPS | antipain | Streptomyces sp.
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  | 0.68 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.68 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001239.3 |  | 0.67 | other (other) | biotin | Aspergillus nidulans

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.29 out of 23.79
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.84 out of 30.12
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.35 out of 18.57
Confidence: medium
Additional weak hits (24):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.04 out of 25.88
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.13 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.71 out of 31.73
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.38 out of 28.14
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.56 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.70 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.13 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.75 out of 31.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.43 out of 20.97
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.02 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.85 out of 29.38
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.54 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.34 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.48 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.11 out of 28.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.37 out of 29.65
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.25 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 6, location 177890 - 226161:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 177890 - 219789:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 179790 - 221695:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 182942 - 226161:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

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).
A6A06_RS19485: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (17..410): Val
nrpys: Val

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LRPSFDASAFEGVLLAGGEVNGYGPTEATTFATA
  Nearest Stachelhaus code(s):
    Val DAFWLGGTFK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

A6A06_RS19490: X
AMP-binding (42..443): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWYVFDPHVKEAVLVVGGDHNAYGPAEATVVTTV
  Nearest Stachelhaus code(s):
    Phe DPLVVGAVVK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

A6A06_RS19500: Arg
Search NORINE for peptide: strict or relaxed
AMP-binding (479..882): Arg
nrpys: Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    HATAFDVALEEPNLVLGGEFNAYGVTEAAITSTV
  Nearest Stachelhaus code(s):
    Arg DVENVGAITK (74% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
ToxT | Regulator of MSHA biosynthesis

NZ_LWKZ01000023.1 - Region 4 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 274,208 - 318,371 nt. (total: 44,164 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 oxidase
A6A06_RS19830: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

A6A06_RS19855: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

Hydrolases: deformylase
A6A06_RS19820: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Ligases: ligase synthase
A6A06_RS19900: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

A6A06_RS19905: 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 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004

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 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.63 | 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.

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.73 out of 23.79
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.61 out of 29.51
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.29 out of 29.51
Confidence: medium
Additional weak hits (7):
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
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
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.17 out of 26.85
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.04 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.97 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.49 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.35 out of 24.78
Confidence: weak
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 10, location 274207 - 318371:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).
A6A06_RS19905: Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (476..906): Orn
nrpys: Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDHAFDTAWEGFDLMVGGEYNYYGPTECTVDAVY
  Nearest Stachelhaus code(s):
    Orn DTEDMGYVDK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism

NZ_LWKZ01000023.1 - Region 5 - 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: 320,862 - 366,816 nt. (total: 45,955 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
A6A06_RS20015: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

A6A06_RS20050: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase
A6A06_RS20110: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase synthase
A6A06_RS20080: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS20085: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS20090: 3-oxoacyl-(acyl carrier protein) synthase III

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

Translocases: transporter
A6A06_RS20005: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

A6A06_RS20030: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.66 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.66 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.66 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (8):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.91 out of 27.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.29 out of 36.53
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.85 out of 35.63
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.24 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.19 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.45 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.85 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 11, location 320861 - 366816:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Hpg - X) + (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).
A6A06_RS20080: Hpg - X
Search NORINE for peptide: strict or relaxed
AMP-binding (454..831): 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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDPAFDASFLEVHLLTGGDRHLYGPTETTLCATV
  Nearest Stachelhaus code(s):
    Hpg DALHLGLLCK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1491..1872): 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:
    LALASGTALLEAFLVVGGEWNTHGTTECTMISTV
  Nearest Stachelhaus code(s):
    Dhpg DALSVGTVIK (50% 8Å match)
    bLys DTEDVGTMVK (47% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

Regulator | Description
--- | ---

NZ_LWKZ01000023.1 - Region 6 - NRPS,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: 455,258 - 501,047 nt. (total: 45,790 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)
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
Terpene
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
A6A06_RS20615: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

A6A06_RS20620: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS20680: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: aminotransferase
A6A06_RS20600: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: amidase esterase hydrolase
A6A06_RS20555: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

A6A06_RS20580: amidase

smcogs
  SMCOG1105: amidase

A6A06_RS20670: enterobactin/ferric enterobactin esterase

smcogs
  SMCOG1098: enterobactin/ferric enterobactin esterase

A6A06_RS20725: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Lyases: hydratase
A6A06_RS20695: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase
A6A06_RS20660: 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 | terpene | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001605.3 |  |  | 0.40 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000343.5 |  |  | 0.39 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0002173.2 |  |  | 0.39 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0001928.2 |  |  | 0.38 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000675.5 |  |  | 0.35 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0001758.4 |  |  | 0.35 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000677.5 |  |  | 0.35 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001833.4 |  |  | 0.35 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.34 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  |  | 0.34 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.64 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.63 | NRPS | AM-toxin | Alternaria alternata

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

No significant matches found.

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:
A6A06_RS20610: T2TS
Domain 1 (252 - 506): Type 2 terpene synthase
Subtype: unknown
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.56 out of 23.79
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: 28.73 out of 36.53
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (18):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.95 out of 30.97
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.60 out of 26.85
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.80 out of 19.26
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.71 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.49 out of 39.62
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.18 out of 18.57
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.34 out of 26.12
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.57 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.96 out of 33.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.57 out of 36.53
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.18 out of 27.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.13 out of 32.93
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.58 out of 29.65
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.96 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 12, location 455257 - 501047:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 14, location 457105 - 501047:
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).
A6A06_RS20660: X
AMP-binding (476..871): X
nrpys: Ala, 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:
    RWMTFDVSVWEWHFFCSGEHNLYGPTEAAVDVTH
  Nearest Stachelhaus code(s):
    Ala or Ser DVWHFSLVDK (100% 8Å match)
    Ser DVWHFSLVDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism

NZ_LWKZ01000023.1 - Region 7 - 2dos
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 505,979 - 529,552 nt. (total: 23,574 nt) Show pHMM detection rules used
2dos: ((DOIS or DHQ_synthase or ValA or salQ) and DegT_DnrJ_EryC1 and (LipV or ADSI-DH or cds(ADH_N and ADH_zinc_N)))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
A6A06_RS20780: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: aminotransferase glycosyltransferase
A6A06_RS20785: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

A6A06_RS20795: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Isomerases: mutase
A6A06_RS20820: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: synthase
A6A06_RS20790: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

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

Reference | 2dos | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000708.5 |  | 0.66 | saccharide | lividomycin | Streptomyces lividus
BGC0000711.5 |  | 0.65 | saccharide | neomycin | Streptomyces fradiae
BGC0000709.5 |  | 0.65 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000713.5 |  | 0.61 | saccharide | ribostamycin | Streptomyces ribosidificus
BGC0000712.5 |  | 0.51 | saccharide | paromomycin | Streptomyces rimosus subsp. paromomycinus
BGC0000513.3 |  | 0.50 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000719.5 |  | 0.50 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0000720.3 |  | 0.49 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000519.4 |  | 0.48 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000721.4 |  | 0.45 | saccharide | tobramycin | Streptoalloteichus tenebrarius

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000708.5 |  | 0.66 | saccharide | lividomycin | Streptomyces lividus
BGC0000711.5 |  | 0.65 | saccharide | neomycin | Streptomyces fradiae
BGC0000709.5 |  | 0.65 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0000713.5 |  | 0.61 | saccharide | ribostamycin | Streptomyces ribosidificus
BGC0000712.5 |  | 0.51 | saccharide | paromomycin | Streptomyces rimosus subsp. paromomycinus
BGC0000513.3 |  | 0.50 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000719.5 |  | 0.50 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0000720.3 |  | 0.49 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000519.4 |  | 0.48 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000721.4 |  | 0.45 | saccharide | tobramycin | Streptoalloteichus tenebrarius

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.64 out of 26.85
Confidence: medium
Additional weak hits (9):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.93 out of 29.38
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.97 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.54 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.08 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.08 out of 35.63
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.75 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.96 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
RutR | Regulator of the pyrimidine and purine metabolism

NZ_LWKZ01000023.1 - Region 8 - 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: 544,254 - 659,113 nt. (total: 114,860 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer oxygenase
A6A06_RS20885: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS20950: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS20980: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS21015: flavodoxin

smcogs
  SMCOG1134: flavodoxin

Transferases: aminotransferase glycosyltransferase
A6A06_RS20970: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

A6A06_RS20975: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: esterase hydrolase
A6A06_RS20910: thioesterase

smcogs
  SMCOG1004: thioesterase

A6A06_RS21005: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: dehydratase
A6A06_RS20905: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
A6A06_RS20935: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS20940: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS20945: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS20955: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS20990: 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
--- | --- | --- | --- | --- | --- | ---
BGC0000138.5 |  |  | 0.81 | PKS | rimocidin | Streptomyces diastaticus
BGC0001273.3 |  |  | 0.69 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  | 0.69 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0002106.3 |  |  | 0.66 | PKS | rimocidin | Streptomyces rimosus subsp. rimosus NRRL WC-3558
BGC0001164.3 |  |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  | 0.58 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002540.3 |  |  | 0.57 | PKS | tetramycin B | Streptomyces hygrospinosus subsp. beijingensis
BGC0001284.4 |  |  | 0.57 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001257.3 |  |  | 0.57 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002191.2 |  |  | 0.56 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002106.3 |  | 0.77 | PKS | rimocidin | Streptomyces rimosus subsp. rimosus NRRL WC-3558
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0000138.5 |  | 0.74 | PKS | rimocidin | Streptomyces diastaticus
BGC0002540.3 |  | 0.74 | PKS | tetramycin B | Streptomyces hygrospinosus subsp. beijingensis
BGC0001276.3 |  | 0.73 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  | 0.73 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0000016.4 |  | 0.71 | other (other) | amphotericin B | Streptomyces nodosus
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.21 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.35 out of 23.79
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 29.30 out of 30.12
Confidence: strong
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (14):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.47 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.42 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.07 out of 30.22
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.28 out of 29.51
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.20 out of 27.78
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.04 out of 27.04
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.68 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.37 out of 24.78
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.30 out of 32.93
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.30 out of 20.01
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.99 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.62 out of 26.06
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.99 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 16, location 544253 - 659113:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal - ohmal - Me-ohmal - ohmal - ohmal - ohmal) + (ccmal) + (ccmal) + (ohmal - ccmal - ccmal - ccmal) + (X - 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).
A6A06_RS20935: mal - mal - mmal - mal - mal - mal
PKS_AT (561..865): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 218.7
  inactive: 84.1
  Methoxymalonyl-CoA: 52.0
  Methylmalonyl-CoA: 46.7
  Propionyl-CoA: 27.7
  Acetyl-CoA: 26.8
  Isobutyryl-CoA: 14.5
  Ethylmalonyl-CoA: 13.6
  Benzoyl-CoA: 13.6
  CHC-CoA: 12.8
  2-Methylbutyryl-CoA: 8.7
  trans-1,2-CPDA: 8.4
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2321..2620): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 199.1
  inactive: 82.7
  Methoxymalonyl-CoA: 69.6
  Methylmalonyl-CoA: 63.6
  Isobutyryl-CoA: 44.3
  Benzoyl-CoA: 33.6
  Propionyl-CoA: 31.8
  Acetyl-CoA: 31.1
  Ethylmalonyl-CoA: 25.6
  2-Methylbutyryl-CoA: 23.0
  CHC-CoA: 22.1
  fatty_acid: 20.0
  trans-1,2-CPDA: 14.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3859..4156): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 210.0
  Ethylmalonyl-CoA: 195.1
  Methoxymalonyl-CoA: 175.3
  2-Methylbutyryl-CoA: 130.3
  trans-1,2-CPDA: 124.4
  Propionyl-CoA: 104.5
  CHC-CoA: 98.4
  Malonyl-CoA: 87.0
  Isobutyryl-CoA: 80.4
  Benzoyl-CoA: 60.4
  Acetyl-CoA: 39.9
  fatty_acid: 31.6
  3-Methylbutyryl-CoA: 29.0
  inactive: 18.3

PKS_AT (5393..5693): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 210.5
  inactive: 102.3
  Methoxymalonyl-CoA: 73.5
  Methylmalonyl-CoA: 61.4
  Isobutyryl-CoA: 44.9
  Propionyl-CoA: 25.5
  Ethylmalonyl-CoA: 21.1
  Benzoyl-CoA: 18.7
  fatty_acid: 18.1
  Acetyl-CoA: 17.9
  3-Methylbutyryl-CoA: 12.4
  2-Methylbutyryl-CoA: 10.6
  CHC-CoA: 10.5
  trans-1,2-CPDA: 8.2

PKS_AT (6913..7198): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 233.6
  inactive: 107.8
  Methoxymalonyl-CoA: 67.1
  Methylmalonyl-CoA: 63.0
  Propionyl-CoA: 33.3
  Isobutyryl-CoA: 24.3
  Acetyl-CoA: 22.4
  Ethylmalonyl-CoA: 21.1
  Benzoyl-CoA: 18.8
  2-Methylbutyryl-CoA: 16.5
  CHC-CoA: 7.6
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (8424..8717): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 231.9
  inactive: 109.1
  Methoxymalonyl-CoA: 74.4
  Methylmalonyl-CoA: 71.2
  Propionyl-CoA: 43.2
  Isobutyryl-CoA: 34.7
  Ethylmalonyl-CoA: 32.2
  Benzoyl-CoA: 25.6
  2-Methylbutyryl-CoA: 25.6
  CHC-CoA: 22.9
  Acetyl-CoA: 19.9
  fatty_acid: 16.8
  trans-1,2-CPDA: 13.5
  3-Methylbutyryl-CoA: 0.0

A6A06_RS20940: mal
PKS_AT (551..836): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 237.6
  inactive: 109.2
  Methoxymalonyl-CoA: 69.4
  Methylmalonyl-CoA: 65.0
  Propionyl-CoA: 35.5
  Acetyl-CoA: 25.6
  Isobutyryl-CoA: 24.2
  Benzoyl-CoA: 18.5
  Ethylmalonyl-CoA: 18.4
  2-Methylbutyryl-CoA: 16.6
  CHC-CoA: 4.7
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  3-Methylbutyryl-CoA: 0.0

A6A06_RS20945: mal
PKS_AT (547..834): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 236.7
  inactive: 108.6
  Methoxymalonyl-CoA: 70.4
  Methylmalonyl-CoA: 64.9
  Propionyl-CoA: 40.4
  Acetyl-CoA: 28.9
  Isobutyryl-CoA: 23.6
  2-Methylbutyryl-CoA: 19.4
  Benzoyl-CoA: 19.1
  Ethylmalonyl-CoA: 18.8
  fatty_acid: 7.7
  CHC-CoA: 7.1
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

A6A06_RS20955: mal - mal - mal - mal
PKS_AT (566..865): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 100.0%
  inactive: 83.3%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 215.2
  inactive: 111.5
  Methoxymalonyl-CoA: 69.3
  Methylmalonyl-CoA: 61.2
  Isobutyryl-CoA: 47.8
  Propionyl-CoA: 37.5
  Benzoyl-CoA: 23.3
  Ethylmalonyl-CoA: 22.8
  Acetyl-CoA: 22.3
  2-Methylbutyryl-CoA: 15.8
  trans-1,2-CPDA: 15.6
  fatty_acid: 10.2
  3-Methylbutyryl-CoA: 7.1
  CHC-CoA: 3.3

PKS_AT (2108..2407): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 91.7%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 231.3
  inactive: 109.4
  Methoxymalonyl-CoA: 50.1
  Methylmalonyl-CoA: 40.2
  Propionyl-CoA: 19.4
  Acetyl-CoA: 18.6
  Ethylmalonyl-CoA: 16.9
  Benzoyl-CoA: 15.1
  2-Methylbutyryl-CoA: 11.9
  fatty_acid: 11.5
  Isobutyryl-CoA: 9.4
  CHC-CoA: 3.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3845..4135): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 226.5
  inactive: 105.7
  Methoxymalonyl-CoA: 47.1
  Methylmalonyl-CoA: 37.0
  Acetyl-CoA: 23.9
  Propionyl-CoA: 22.8
  Benzoyl-CoA: 17.1
  fatty_acid: 13.2
  Ethylmalonyl-CoA: 12.0
  Isobutyryl-CoA: 11.9
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: -2.3

PKS_AT (5547..5836): mal
ATSignature: Malonyl-CoA, inactive

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 227.8
  inactive: 120.7
  Methoxymalonyl-CoA: 53.6
  Methylmalonyl-CoA: 44.5
  Acetyl-CoA: 24.6
  Propionyl-CoA: 22.8
  Ethylmalonyl-CoA: 20.3
  Benzoyl-CoA: 18.0
  2-Methylbutyryl-CoA: 13.9
  Isobutyryl-CoA: 13.5
  fatty_acid: 9.3
  CHC-CoA: 8.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

A6A06_RS20990: X - mal
AMP-binding (29..442): 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:
    TVTCHLFGLQAAFARTAGAVVVWGMSEIGTGTRT
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

PKS_AT (1190..1492): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 70.8%
  Methylmalonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 172.6
  inactive: 70.6
  Methoxymalonyl-CoA: 69.5
  Methylmalonyl-CoA: 63.7
  Propionyl-CoA: 36.4
  Isobutyryl-CoA: 35.2
  Ethylmalonyl-CoA: 30.3
  2-Methylbutyryl-CoA: 23.9
  Benzoyl-CoA: 23.1
  CHC-CoA: 22.8
  Acetyl-CoA: 19.8
  fatty_acid: 14.1
  3-Methylbutyryl-CoA: 8.6
  trans-1,2-CPDA: 6.1

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
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator

NZ_LWKZ01000023.1 - Region 9 - NRPS,NRPS-like,arylpolyene,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: 684,085 - 763,671 nt. (total: 79,587 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
A6A06_RS21160: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS21175: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

A6A06_RS21180: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

A6A06_RS21210: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

A6A06_RS21260: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

A6A06_RS21290: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS21370: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

A6A06_RS21390: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS21425: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS21435: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

Transferases: acylase aminotransferase methyltransferase
A6A06_RS21230: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

A6A06_RS21300: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

A6A06_RS21350: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase
A6A06_RS21295: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase hydratase
A6A06_RS21255: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

A6A06_RS21280: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

A6A06_RS21430: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: ligase synthase synthetase
A6A06_RS21235: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

A6A06_RS21240: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS21250: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS21270: 3-oxoacyl-(acyl carrier protein) synthase III

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

A6A06_RS21305: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS21315: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS21330: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS21365: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

A6A06_RS21405: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

A6A06_RS21470: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | arylpolyene | NRPS | NRPS-like | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001132.4 |  |  |  |  | 1.22 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  |  |  |  | 1.21 | NRPS | AM-toxin | Alternaria alternata
BGC0002135.2 |  |  |  |  | 1.18 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  |  |  |  | 1.17 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  |  | 1.17 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  |  |  | 1.13 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  |  |  | 1.13 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  |  |  |  | 1.12 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  |  |  | 1.09 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  |  |  |  | 1.05 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.72 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  | 0.68 | 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.
Location:
Identifier
Identity
Coverage
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

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

Genes with terpene domains:
A6A06_RS21365: PT_FPPS_like
Domain 1 (58 - 369): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

A6A06_RS21380: TS_Pyr4
Domain 1 (12 - 215): Pyr4 type terpene synthase
Subtype: unknown
A6A06_RS21405: PT_FPPS_like
Domain 1 (61 - 347): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

A6A06_RS21430: T1TS
Domain 1 (11 - 322): 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.48 out of 18.57
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.49 out of 24.78
Confidence: medium
Additional weak hits (8):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.61 out of 20.97
Confidence: weak
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
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.54 out of 26.06
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.28 out of 31.73
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.03 out of 30.12
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.30 out of 32.93
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.72 out of 33.14
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
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 17, location 684084 - 763671:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 18, location 684084 - 725395:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Asn - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 19, location 697651 - 744002:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 20, location 706134 - 748573:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Val) + (Asn - 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).
A6A06_RS21230: mal
PKS_AT (5..282): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 99.3
  inactive: 36.9
  Methoxymalonyl-CoA: 28.4
  Methylmalonyl-CoA: 28.3
  Propionyl-CoA: 15.9
  2-Methylbutyryl-CoA: 15.8
  CHC-CoA: 11.9
  trans-1,2-CPDA: 11.0
  Ethylmalonyl-CoA: 10.5
  fatty_acid: 8.9
  Isobutyryl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

A6A06_RS21315: Asn - X
Search NORINE for peptide: strict or relaxed
AMP-binding (468..870): Asn
nrpys: Asn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YRASFDITLTAGKAIVAGEINHYGPSEATCGCVD
  Nearest Stachelhaus code(s):
    Asp DLTKIGHIGK (62% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1533..1932): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQGFDAFLLEMTMVVAGEVNLYGPTEGSVITSW
  Nearest Stachelhaus code(s):
    Tyr DASTVAAVCK (65% 8Å match)
  Stachelhaus code match:
    70% (weak)

A6A06_RS21330: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (209..606): 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:
    LGPSFDASTIEALLLTGGETNGYGPTENTSFTTC
  Nearest Stachelhaus code(s):
    Leu DAILLGGIAK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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
--- | ---
LexA variant 2 | Repressor of DNA damage response
ToxT | Regulator of MSHA biosynthesis

NZ_LWKZ01000023.1 - Region 10 - 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: 776,960 - 788,867 nt. (total: 11,908 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
Transferases: methyltransferase
A6A06_RS21565: 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 | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.38 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002316.2 |  | 0.37 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000528.5 |  | 0.36 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000503.5 |  | 0.35 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000903.3 |  | 0.33 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0002346.3 |  | 0.32 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000468.5 |  | 0.31 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.31 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000470.6 |  | 0.31 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0001753.3 |  | 0.30 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001485.4 |  | 0.38 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0002316.2 |  | 0.37 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000528.5 |  | 0.36 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000503.5 |  | 0.35 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000903.3 |  | 0.33 | other (other) | fluorometabolite | Streptomyces cattleya
BGC0002346.3 |  | 0.32 | ribosomal | kyamicin | Saccharopolyspora sp.
BGC0000468.5 |  | 0.31 | ribosomal | bottromycin A2 | Streptomyces bottropensis DSM40262
BGC0001157.6 |  | 0.31 | ribosomal | bottromycin A2 | Streptomyces scabiei 87.22
BGC0000470.6 |  | 0.31 | ribosomal | bottromycin D | Streptomyces sp. WMMB272
BGC0001753.3 |  | 0.30 | ribosomal | radamycin, globimycin | Streptomyces globisporus subsp. globisporus

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.52 out of 23.79
Confidence: medium
Additional weak hits (1):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.52 out of 29.38
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LWKZ01000023.1 - Region 11 - T1PKS,azoxy-crosslink
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: 847,950 - 910,488 nt. (total: 62,539 nt) Show pHMM detection rules used
azoxy-crosslink: (azdH and LPG_synthase_C and azdO and vlmB)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer
A6A06_RS21845: flavodoxin

smcogs
  SMCOG1134: flavodoxin

A6A06_RS21870: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

A6A06_RS21875: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

A6A06_RS21965: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

A6A06_RS21985: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

A6A06_RS22050: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

A6A06_RS22080: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS22105: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase methyltransferase
A6A06_RS21880: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

A6A06_RS22100: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
A6A06_RS21990: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: dehydratase
A6A06_RS22055: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
A6A06_RS21900: 3-oxoacyl-(acyl carrier protein) synthase III

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

A6A06_RS21910: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS43545: 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 | azoxy-crosslink | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001160.5 |  |  | 0.49 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.49 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000041.3 |  |  | 0.38 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002711.2 |  |  | 0.34 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000882.5 |  |  | 0.33 | other (other) | mildiomycin | Streptomyces rimofaciens
BGC0002227.3 |  |  | 0.31 | NRPS | AKML B, AKML D, AKML A, AKML C | Aspergillus luchuensis IFO 4308
BGC0000272.3 |  |  | 0.30 | PKS | spore pigment | Streptomyces collinus
BGC0000234.5 |  |  | 0.29 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001161.5 |  |  | 0.29 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0001162.3 |  |  | 0.29 | PKS | 1-heptadecene | Moorea producens JHB

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002192.3 |  | 0.61 | PKS | FR901512 | fungal sp. No.14919
BGC0001160.5 |  | 0.61 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.61 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001268.4 |  | 0.60 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002154.2 |  | 0.60 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0000037.4 |  | 0.60 | PKS | cichorine | Aspergillus nidulans FGSC A4
BGC0000041.3 |  | 0.59 | PKS | oronofacic acid | Pseudomonas syringae
BGC0002227.3 |  | 0.52 | NRPS | AKML B, AKML D, AKML A, AKML C | Aspergillus luchuensis IFO 4308
BGC0002711.2 |  | 0.51 | PKS | nostovalerolactone, 9-dehydronostovalerolactone | Nostoc punctiforme PCC 73102
BGC0000919.5 |  | 0.51 | other (other) | phaseolotoxin | Pseudomonas syringae

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.92 out of 32.93
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.82 out of 30.11
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (12):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.44 out of 32.93
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.04 out of 30.11
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.83 out of 28.14
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.14 out of 32.93
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.86 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.46 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.75 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.01 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.75 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.57 out of 36.53
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 23, location 847949 - 910488:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 25, location 863654 - 910488:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-redmal)

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).
A6A06_RS43545: mmal
PKS_AT (532..825): mmal
ATSignature: Malonyl-CoA, Methylmalonyl-CoA

Top 3 matches:
  Malonyl-CoA: 70.8%
  Methylmalonyl-CoA: 70.8%
  Ethylmalonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 146.0
  Ethylmalonyl-CoA: 128.2
  Methoxymalonyl-CoA: 119.2
  Malonyl-CoA: 88.7
  2-Methylbutyryl-CoA: 81.4
  Propionyl-CoA: 73.8
  trans-1,2-CPDA: 69.5
  CHC-CoA: 62.6
  Isobutyryl-CoA: 60.1
  Benzoyl-CoA: 39.0
  inactive: 33.6
  Acetyl-CoA: 30.4
  3-Methylbutyryl-CoA: 16.4
  fatty_acid: 0.0

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
CelR | Cellobiose uptake repressor
LexA variant 3 | Repressor of DNA damage response
OsdR | Development and stress management regulator
RpoN | Regulator of nitrogen assimilation and virulence

NZ_LWKZ01000023.1 - Region 12 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 915,993 - 938,591 nt. (total: 22,599 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
A6A06_RS22205: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: synthase
A6A06_RS22245: 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 | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001645.3 |  | 0.73 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001551.4 |  | 0.71 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001552.3 |  | 0.65 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001634.3 |  | 0.63 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001550.3 |  | 0.62 | ribosomal | citrulassin D | Streptomyces katrae
BGC0000575.5 |  | 0.61 | ribosomal | lariatin | Rhodococcus jostii
BGC0001493.5 |  | 0.60 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001548.4 |  | 0.60 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001539.4 |  | 0.60 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001506.5 |  | 0.59 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001645.3 |  | 0.73 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001551.4 |  | 0.71 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001552.3 |  | 0.65 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001634.3 |  | 0.63 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001550.3 |  | 0.62 | ribosomal | citrulassin D | Streptomyces katrae
BGC0000575.5 |  | 0.61 | ribosomal | lariatin | Rhodococcus jostii
BGC0001493.5 |  | 0.60 | ribosomal | achromosin | Streptomyces achromogenes subsp. achromogenes
BGC0001548.4 |  | 0.60 | ribosomal | citrulassin A | Streptomyces albulus
BGC0001539.4 |  | 0.60 | ribosomal | cattlecin | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001506.5 |  | 0.59 | ribosomal | anantin B1, anantin B2 | Streptomyces sp. NRRL S-146

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.58 out of 20.97
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.68 out of 30.12
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 (5):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.43 out of 39.62
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.40 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.22 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.06 out of 35.63
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.43 out of 26.85
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (915992...938591)
A6A06_RS22200
  RRE type: Stand_Alone_Lasso_RRE
  Location: 0 - 84
  Score: 75.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CcpA | Catabolite control protein A
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_LWKZ01000023.1 - Region 13 - NRPS,T1PKS,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: 990,675 - 1,085,650 nt. (total: 94,976 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
A6A06_RS22520: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

A6A06_RS22700: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

A6A06_RS22750: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

A6A06_RS22810: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

A6A06_RS22815: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: acyltransferase aminotransferase
A6A06_RS22530: aminotransferase

smcogs
  SMCOG1019: aminotransferase

A6A06_RS22600: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

A6A06_RS22760: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: hydrolase
A6A06_RS22560: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: dehydratase hydratase
A6A06_RS22825: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

A6A06_RS22830: L-carnitine dehydratase/bile acid-inducible

smcogs
  SMCOG1189: L-carnitine dehydratase/bile acid-inducible

Ligases: synthase synthetase
A6A06_RS22705: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

A6A06_RS22720: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

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

Reference | NRPS | terpene | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000664.5 |  |  |  |  | 1.64 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  |  |  |  | 1.39 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  |  |  |  | 1.29 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  |  |  |  | 1.23 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  |  |  |  | 1.22 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0002135.2 |  |  |  |  | 1.03 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  |  | 1.01 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  |  |  |  | 0.99 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  |  |  |  | 0.99 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  |  | 0.98 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000664.5 |  | 0.73 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002075.3 |  | 0.73 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.72 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.71 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.71 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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

No significant matches found.

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:
A6A06_RS22675: Lycopene_cycl
Domain 1 (6 - 383): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

A6A06_RS41965: PT_phytoene_like
Domain 1 (16 - 307): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

A6A06_RS22705: PT_FPPS_like
Domain 1 (54 - 373): 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:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.27 out of 25.31
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
Additional weak hits (15):
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.04 out of 27.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.03 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.32 out of 29.38
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.85 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.71 out of 23.43
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.14 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.82 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.19 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.22 out of 26.12
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.98 out of 30.22
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.59 out of 18.57
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.30 out of 36.54
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.39 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
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 27, location 990674 - 1085650:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (mal) + (NMe-Ser - D-Ala - Tyr - Phe - Leu - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 28, location 990674 - 1052535:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NMe-Ser - D-Ala - Tyr - Phe - Leu - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 30, location 1034368 - 1077656:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 31, location 1037700 - 1085650:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
A6A06_RS22600: Ser - Ala - Tyr - Phe - Leu - X
Search NORINE for peptide: strict or relaxed
AMP-binding (29..449): 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSTHFDVSVWEGCQVLAGEVNMYGTTETTVHATY
  Nearest Stachelhaus code(s):
    Ser DVWNVAMVHK (82% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1539..1947): Ala
nrpys: Ala

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDAHFDLSVWEGHQELGAEVHAYGPTETTVFVVA
  Nearest Stachelhaus code(s):
    His DYWHFGAVDK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (3172..3576): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASVSDTKLAVAGEVNVYGPTEATVCVLM
  Nearest Stachelhaus code(s):
    Tyr DASTAAAVCK (76% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (4251..4656): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSQAFDASFWEMTLVVAGEVNAYGPTEATVCVLM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5335..5732): Leu
nrpys: Leu

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASVMEMLVVIGGEINAYGPTETTVCATL
  Nearest Stachelhaus code(s):
    Leu DAMLVGAVCK (76% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (6395..6802): X
nrpys: me-bAla

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWCTFIDGTTEGTVVTSGEVNLYGASEASGDSLH
  Nearest Stachelhaus code(s):
    me-bAla LDTTVSLGDK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

A6A06_RS22720: mal
PKS_AT (547..840): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 145.5
  inactive: 88.5
  Methylmalonyl-CoA: 73.1
  Isobutyryl-CoA: 66.8
  Methoxymalonyl-CoA: 64.7
  Propionyl-CoA: 59.3
  Ethylmalonyl-CoA: 46.4
  2-Methylbutyryl-CoA: 34.3
  Benzoyl-CoA: 30.6
  fatty_acid: 22.0
  Acetyl-CoA: 20.8
  CHC-CoA: 19.0
  trans-1,2-CPDA: 16.5
  3-Methylbutyryl-CoA: 10.0

A6A06_RS22725: X
AMP-binding (1487..1943): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWHCFDASVLEPILLLGGDVNVYGPTETTVLCTT
  Nearest Stachelhaus code(s):
    aIle DALVFGVVLK (65% 8Å match)
  Stachelhaus code match:
    80% (moderate)

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
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LWKZ01000023.1 - Region 14 - NRPS,NRPS-like,betalactone
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,120,307 - 1,208,635 nt. (total: 88,329 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
betalactone: (HMGL-like and AMP-binding)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
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
A6A06_RS23085: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

A6A06_RS23110: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

A6A06_RS23165: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS23240: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS43560: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Transferases: aminotransferase carbamoyltransferase methyltransferase
A6A06_RS23080: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

A6A06_RS23210: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

A6A06_RS23330: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: deaminase esterase hydrolase peptidase
A6A06_RS23145: thioesterase

smcogs
  SMCOG1004: thioesterase

A6A06_RS23150: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

A6A06_RS23230: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

A6A06_RS23295: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

A6A06_RS23310: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: dehydratase hydratase lyase
A6A06_RS23100: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

A6A06_RS23200: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

A6A06_RS23315: Nitrilase/cyanide hydratase and apolipoprotein

smcogs
  SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Ligases: ligase synthase
A6A06_RS23095: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS23115: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS23215: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS23220: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS23225: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

A6A06_RS23245: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS23275: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

A6A06_RS23285: 8-amino-7-oxononanoate synthase

smcogs
  SMCOG1109: 8-amino-7-oxononanoate synthase

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

Reference | NRPS | NRPS-like | NRPS-like | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002582.3 |  |  |  |  | 1.98 | NRPS | guanipiperazine A, guanipiperazine B | Streptomyces chrestomyceticus
BGC0002075.3 |  |  |  |  | 1.56 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  |  |  |  | 1.30 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  |  | 1.29 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  |  | 1.29 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  |  |  | 1.29 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  |  |  | 1.27 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001641.4 |  |  |  |  | 1.23 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  |  |  |  | 1.20 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  |  |  |  | 1.19 | NRPS | AbT1 | Aureobasidium pullulans

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002582.3 |  | 0.79 | NRPS | guanipiperazine A, guanipiperazine B | Streptomyces chrestomyceticus
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.67 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.67 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001641.4 |  | 0.66 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2 |  | 0.65 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26
Confidence: medium
Additional weak hits (16):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.76 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.46 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.79 out of 27.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.31 out of 26.85
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.08 out of 30.22
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.44 out of 25.88
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.89 out of 21.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.82 out of 30.98
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.44 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 32, location 1120306 - 1208635:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 33, location 1120306 - 1198219:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 34, location 1158298 - 1200173:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 35, location 1165308 - 1208635:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (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).
A6A06_RS23115: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (532..928): 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:
    TDIAFDLSVYDGNSLLSGDISLGGATEAAIWSIH
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS23140: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (575..964): 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:
    TAVSFDLSVWDGNSLLSGDVALGGATEASVWSNV
  Nearest Stachelhaus code(s):
    Cys DLWNLSLIWK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

A6A06_RS23215: X
AMP-binding (446..865): X
nrpys: (unknown)

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:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAMAFDASWQGLDGVIGGEFNVYGPTEFTVNATG
  Nearest Stachelhaus code(s):
    Dpr DAQDLAVVNK (65% 8Å match)
    Gln DAQDLGVVDK (62% 8Å match)
    Ile DAQDLGVVDK (59% 8Å match)
  Stachelhaus code match:
    80% (moderate)

A6A06_RS23220: X
AMP-binding (28..432): 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:
    GSMTFDPVLVDLQALCGGEWNIYGPTETTIWSTA
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (76% 8Å match)
  Stachelhaus code match:
    70% (weak)

A6A06_RS23245: X
AMP-binding (35..433): 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:
    LSDYSDASTIEGYLSAGGEVNFYGPTENAVVSTA
  Nearest Stachelhaus code(s):
    Leu DAWYLGNVVK (59% 8Å match)
    Leu or Ile DAIYLGVVLK (59% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

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

NZ_LWKZ01000024.1 - Region 1 - 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: 64,707 - 91,469 nt. (total: 26,763 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
A6A06_RS23790: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

A6A06_RS23825: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase
A6A06_RS23755: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

A6A06_RS23830: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: deformylase
A6A06_RS23745: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Ligases: synthase synthetase
A6A06_RS23760: 1-deoxy-D-xylulose-5-phosphate synthase

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

A6A06_RS23785: 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 |  | 0.75 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.51 | 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
BGC0002736.2 |  | 0.49 | terpene | preaspterpenacid I | Aspergillus terreus NIH2624
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.75 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002591.2 |  | 0.51 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.
BGC0000656.5 |  | 0.51 | 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
BGC0002736.2 |  | 0.49 | terpene | preaspterpenacid I | Aspergillus terreus NIH2624
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
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:
A6A06_RS23780: T2TS
Domain 1 (31 - 665): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

A6A06_RS23785: PT_FPPS_like
Domain 1 (57 - 346): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

A6A06_RS23795: PT_phytoene_like
Domain 1 (17 - 300): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

A6A06_RS23800: PT_phytoene_like
Domain 1 (30 - 295): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (7):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.54 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.28 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.27 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.86 out of 21.55
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.80 out of 36.54
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.72 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_LWKZ01000024.1 - 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: 223,501 - 299,315 nt. (total: 75,815 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: oxidase oxygenase reductase
A6A06_RS24485: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS24490: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS24560: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

A6A06_RS24580: alkyl hydroperoxide reductase subunit

smcogs
  SMCOG1176: alkyl hydroperoxide reductase subunit

Transferases: aminotransferase halogenase methyltransferase
A6A06_RS24465: aminotransferase

smcogs
  SMCOG1019: aminotransferase

A6A06_RS24495: flavin-dependent tyrosine-like hpg halogenase

halogenases
  flavin-dependent tyrosine-like hpg halogenase
MITE
  MITE0000028Halogenation (identity: 73.90%)
smcogs
  SMCOG1119: halogenase

A6A06_RS24585: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: dehydratase
A6A06_RS24565: L-carnitine dehydratase/bile acid-inducible

smcogs
  SMCOG1189: L-carnitine dehydratase/bile acid-inducible

Ligases: ligase
A6A06_RS24510: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS24520: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS41070: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease
A6A06_RS24445: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002637.3 |  | 0.79 | NRPS | rimomycin A, rimomycin B, rimomycin C | Streptomyces sp. WAC 06783
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002608.2 |  | 0.76 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0000326.5 |  | 0.75 | NRPS | isocomplestatin | Streptomyces lavendulae
BGC0001133.4 |  | 0.65 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000351.5 |  | 0.65 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002637.3 |  | 0.79 | NRPS | rimomycin A, rimomycin B, rimomycin C | Streptomyces sp. WAC 06783
BGC0002341.2 |  | 0.77 | other (other) | 3,5-dibromo-p-anisic acid | Planctomycetales bacterium 10988
BGC0002608.2 |  | 0.76 | NRPS, PKS | ochratoxin A | Aspergillus steynii
BGC0000326.5 |  | 0.75 | NRPS | isocomplestatin | Streptomyces lavendulae
BGC0001133.4 |  | 0.65 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.65 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  | 0.65 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.65 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000351.5 |  | 0.65 | NRPS | exochelin | Mycolicibacterium smegmatis MC2 155

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (28):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.39 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.38 out of 30.25
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.91 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.11 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.49 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.35 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.40 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.34 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.44 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.28 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.08 out of 20.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.02 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.47 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.88 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.28 out of 36.54
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.23 out of 35.63
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.68 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.56 out of 32.93
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: 15.91 out of 33.14
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.09 out of 32.93
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 12.94 out of 18.57
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.93 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.51 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 223500 - 299315:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Hpg - D-Trp) + (D-Hpg) + (D-Hpg - D-Hpg - D-NMe-Tyr) + (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).
A6A06_RS24510: Hpg - X
Search NORINE for peptide: strict or relaxed
AMP-binding (466..862): 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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDLAFDASLFEVHLLTGGDRHLYGPTETTLCATW
  Nearest Stachelhaus code(s):
    Hpg DAFHLGLLCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1526..1903): X
nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    QYRV------PALVVSAGP---------TVVTGH
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

A6A06_RS24515: Hpg - Hpg - Tyr
Search NORINE for peptide: strict or relaxed
AMP-binding (462..865): 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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LERAFDVSLFEAHVLTGGDRHLYGPTEVTLCATW
  Nearest Stachelhaus code(s):
    Hpg DVFHLGLLCK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2000..2407): 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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LERAFDASLYEAHLLTGGDRHLYGPTETTLCATW
  Nearest Stachelhaus code(s):
    Hpg DAYHLGLLCK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3545..3943): Tyr
nrpys: Tyr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDAAVSEMTVTVAGEVNAYGPTETTVCAAM
  Nearest Stachelhaus code(s):
    Tyr DASTTAAVCK (100% 8Å match)
    Phe or Tyr DASTTAAVCK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS24520: Hpg
Search NORINE for peptide: strict or relaxed
AMP-binding (474..872): 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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LERAFDASLFEVHLLTGGDRHLYGPTEATLSATW
  Nearest Stachelhaus code(s):
    Hpg DAFHLGLLSK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS41070: Hpg - Trp
Search NORINE for peptide: strict or relaxed
AMP-binding (464..861): 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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LQRAFDASLFEVHLLTGGDRHLYGPTEAALCATW
  Nearest Stachelhaus code(s):
    Hpg DAFHLGLLCK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2074..2481): Trp
nrpys: Trp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDRVFDVSMGDPALVTGGEFNEYGVTEATVTSTV
  Nearest Stachelhaus code(s):
    Trp DVGVVGEVTK (97% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---

NZ_LWKZ01000024.1 - Region 3 - 2dos
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 378,814 - 403,990 nt. (total: 25,177 nt) Show pHMM detection rules used
2dos: ((DOIS or DHQ_synthase or ValA or salQ) and DegT_DnrJ_EryC1 and (LipV or ADSI-DH or cds(ADH_N and ADH_zinc_N)))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
A6A06_RS25000: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acyltransferase aminotransferase methyltransferase
A6A06_RS24980: methyltransferase

smcogs
  SMCOG1089: methyltransferase

A6A06_RS25015: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

A6A06_RS25025: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

A6A06_RS25030: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Isomerases: racemase
A6A06_RS24950: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: synthase
A6A06_RS25010: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

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

Reference | 2dos | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001616.3 |  | 0.51 | NRPS, PKS | himeic acid A | Aspergillus japonicus
BGC0000701.5 |  | 0.47 | saccharide | jinggangmycin | Streptomyces hygroscopicus subsp. yingchengensis
BGC0000719.5 |  | 0.45 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0000720.3 |  | 0.45 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000041.3 |  | 0.42 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000772.5 |  | 0.41 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0000709.5 |  | 0.40 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0001774.5 |  | 0.40 | other (other) | spicamycin | Streptomyces fimbriatus
BGC0000711.5 |  | 0.40 | saccharide | neomycin | Streptomyces fradiae
BGC0000353.5 |  | 0.39 | NRPS | tacrolimus | Streptomyces sp. MA6548

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001616.3 |  | 0.51 | NRPS, PKS | himeic acid A | Aspergillus japonicus
BGC0000701.5 |  | 0.47 | saccharide | jinggangmycin | Streptomyces hygroscopicus subsp. yingchengensis
BGC0000719.5 |  | 0.45 | saccharide | tobramycin | Streptoalloteichus hindustanus
BGC0000720.3 |  | 0.45 | saccharide | tobramycin | Streptoalloteichus tenebrarius
BGC0000041.3 |  | 0.42 | PKS | oronofacic acid | Pseudomonas syringae
BGC0000772.5 |  | 0.41 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0000709.5 |  | 0.40 | saccharide | neomycin | Streptomyces fradiae ATCC 10745 = DSM 40063
BGC0001774.5 |  | 0.40 | other (other) | spicamycin | Streptomyces fimbriatus
BGC0000711.5 |  | 0.40 | saccharide | neomycin | Streptomyces fradiae
BGC0000353.5 |  | 0.39 | NRPS | tacrolimus | Streptomyces sp. MA6548

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
Additional weak hits (17):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.88 out of 27.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.85 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.66 out of 20.01
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.24 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.66 out of 27.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.00 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.84 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.06 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.10 out of 25.88
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
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.30 out of 26.85
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.58 out of 26.85
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.74 out of 29.65
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LWKZ01000024.1 - Region 4 - 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: 448,221 - 459,495 nt. (total: 11,275 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
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
A6A06_RS25285: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

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
--- | --- | --- | --- | --- | ---
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000911.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.59 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.53 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.48 | other (other) | melanin | Streptomyces avermitilis
BGC0000662.5 |  | 0.39 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.39 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.38 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.37 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.36 | other (other) | iso-A82775C | Pestalotiopsis fici

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000912.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000911.3 |  | 0.59 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000910.3 |  | 0.59 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.53 | other (other) | melanin | Streptomyces avermitilis
BGC0000908.3 |  | 0.48 | other (other) | melanin | Streptomyces avermitilis
BGC0000662.5 |  | 0.39 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000885.3 |  | 0.39 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000889.5 |  | 0.38 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.37 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.36 | 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.

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.

NZ_LWKZ01000024.1 - Region 5 - NRPS,NRPS-like,T1PKS,indole,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: 576,411 - 687,835 nt. (total: 111,425 nt) Show pHMM detection rules used
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
indole: (indsynth or dmat or indole_PTase)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
A6A06_RS25880: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

A6A06_RS25980: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS26060: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

A6A06_RS26115: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

A6A06_RS42075: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

Transferases: aminotransferase methyltransferase
A6A06_RS25945: methyltransferase

smcogs
  SMCOG1089: methyltransferase

A6A06_RS25975: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: amidase deaminase esterase hydrolase
A6A06_RS25820: amidase

smcogs
  SMCOG1105: amidase

A6A06_RS26015: thioesterase

smcogs
  SMCOG1004: thioesterase

A6A06_RS26035: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

A6A06_RS26065: thioesterase

smcogs
  SMCOG1004: thioesterase

A6A06_RS26190: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Lyases: lyase
A6A06_RS25940: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase
A6A06_RS25920: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

A6A06_RS26005: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS26010: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS26030: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

A6A06_RS26045: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS26050: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS26090: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS26110: 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 | other | NRPS-like | NRPS | indole | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001261.3 |  |  |  |  |  | 1.52 | NRPS | AM-toxin | Alternaria alternata
BGC0001132.4 |  |  |  |  |  | 1.50 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  |  |  |  | 1.48 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  |  |  |  | 1.47 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  |  |  | 1.47 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  |  |  |  | 1.45 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  |  |  |  | 1.40 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001825.4 |  |  |  |  |  | 1.36 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  |  |  |  | 1.34 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001166.5 |  |  |  |  |  | 1.33 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001942.3 |  | 0.77 | NRPS, PKS | malonomycin | Streptomyces rimosus subsp. paromomycinus
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.74 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001249.5 |  | 0.73 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0001166.5 |  | 0.71 | 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: 17.92 out of 20.47
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.06 out of 19.26
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.25 out of 29.72
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.35 out of 24.78
Confidence: medium
Additional weak hits (25):
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.63 out of 29.51
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.07 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.76 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.47 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.56 out of 28.14
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.89 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.36 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.33 out of 29.65
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.16 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.74 out of 23.43
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.33 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.28 out of 27.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.04 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.88 out of 26.06
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.47 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.94 out of 27.78
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.27 out of 29.65
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.05 out of 25.88
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.60 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 5, location 576410 - 687835:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu) + (Val) + (Ser - Asp) + (mal - X) + (Val - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 603073 - 644834:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu) + (Val) + (Ser - Asp) + (mal - X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 604937 - 687835:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Leu) + (Val) + (Ser - Asp) + (mal - X) + (Val - 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).
A6A06_RS26005: Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (13..409): Leu
nrpys: Leu

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    leu (Leu)

Stachelhaus prediction details:
  Stachelhaus sequence:
    FNPSFDAFHFESVVGAGGDYNCYGPAEITTGCTA
  Nearest Stachelhaus code(s):
    Val DAFWLGCTFK (50% 8Å match)
  Stachelhaus code match:
    70% (weak)

A6A06_RS26010: Val
Search NORINE for peptide: strict or relaxed
AMP-binding (24..417): 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:
    TDCAWDGLSLEAWLLVGGEVNGYGPAEATIFATH
  Nearest Stachelhaus code(s):
    Val DALWLGGTFK (62% 8Å match)
  Stachelhaus code match:
    80% (moderate)

A6A06_RS26045: Ser - Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (497..893): Ser
nrpys: Ser

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

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

AMP-binding (1554..1958): Asp
nrpys: Asp

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWQTFDVMLRDLHAFLAGEVNLYGPTETTMAKFA
  Nearest Stachelhaus code(s):
    Asp DVRHFALMAK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS26050: X
AMP-binding (1318..1726): X
nrpys: Dpr

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:
    HAKAFDISLWQAEVMVTGEVNAYGPTEASDDVTH
  Nearest Stachelhaus code(s):
    Dpr DIWEMTADDK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS26090: Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (10..412): Thr
nrpys: Thr

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LATHFDFSVWEGNQVFGGEVNMYGITETTVHATF
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS26110: Val - mal
Search NORINE for peptide: strict or relaxed
AMP-binding (1..394): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    FWCTFDAAILDAFLVTGGELQIYGPTECTVCVAT
  Nearest Stachelhaus code(s):
    Val DALFVGIVLK (68% 8Å match)
  Stachelhaus code match:
    90% (moderate)

PKS_AT (1674..1969): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 90.7
  Methoxymalonyl-CoA: 58.6
  inactive: 57.1
  Methylmalonyl-CoA: 38.8
  Ethylmalonyl-CoA: 30.0
  fatty_acid: 27.0
  Isobutyryl-CoA: 21.5
  Propionyl-CoA: 17.1
  Acetyl-CoA: 15.4
  2-Methylbutyryl-CoA: 14.4
  CHC-CoA: 13.5
  Benzoyl-CoA: 13.5
  trans-1,2-CPDA: 12.7
  3-Methylbutyryl-CoA: 9.2

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
LexA variant 2 | Repressor of DNA damage response
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_LWKZ01000024.1 - Region 6 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 895,022 - 906,371 nt. (total: 11,350 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000843.5 |  | 0.26 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0001650.4 |  | 0.25 | NRPS | Le-pyrrolopyrazines | Lysobacter enzymogenes
BGC0000847.4 |  | 0.23 | other (non-nrp beta-lactam) | thienamycin | Streptomyces cattleya
BGC0000700.5 |  | 0.20 | saccharide | istamycin | Streptomyces tenjimariensis
BGC0001690.5 |  | 0.19 | PKS | natamycin | Streptomyces gilvosporeus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000843.5 |  | 0.26 | other (non-nrp beta-lactam) | alanylclavam, 2-hydroxymethylclavam, 2-formyloxymethylclavam, clavam-2-carboxylate | Streptomyces clavuligerus ATCC 27064
BGC0001650.4 |  | 0.25 | NRPS | Le-pyrrolopyrazines | Lysobacter enzymogenes
BGC0000847.4 |  | 0.23 | other (non-nrp beta-lactam) | thienamycin | Streptomyces cattleya
BGC0000700.5 |  | 0.20 | saccharide | istamycin | Streptomyces tenjimariensis
BGC0001690.5 |  | 0.19 | PKS | natamycin | Streptomyces gilvosporeus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.17 out of 23.43
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.67 out of 23.43
Confidence: medium
Additional weak hits (1):
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.70 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator

NZ_LWKZ01000024.1 - Region 7 - 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: 1,009,432 - 1,020,418 nt. (total: 10,987 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 oxygenase
A6A06_RS27640: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

A6A06_RS27655: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Hydrolases: hydrolase
A6A06_RS27620: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: hydratase
A6A06_RS27645: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

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
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.68 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.62 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.46 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001633.3 |  | 0.40 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001386.5 |  | 0.36 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77
BGC0000847.4 |  | 0.36 | other (non-nrp beta-lactam) | thienamycin | Streptomyces cattleya
BGC0001304.3 |  | 0.36 | PKS | aflavarin | Aspergillus flavus NRRL3357
BGC0001625.5 |  | 0.35 | PKS | Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F | Streptomyces sp. CB01883
BGC0000194.5 |  | 0.35 | PKS | actinorhodin | Streptomyces coelicolor A3(2)

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.78 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.68 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.62 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.46 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0001633.3 |  | 0.40 | other (other) | ketomemicin B3, ketomemicin B4 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0001386.5 |  | 0.36 | PKS | JBIR-76, JBIR-77 | Streptomyces sp. RI-77
BGC0000847.4 |  | 0.36 | other (non-nrp beta-lactam) | thienamycin | Streptomyces cattleya
BGC0001304.3 |  | 0.36 | PKS | aflavarin | Aspergillus flavus NRRL3357
BGC0001625.5 |  | 0.35 | PKS | Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F | Streptomyces sp. CB01883
BGC0000194.5 |  | 0.35 | PKS | actinorhodin | Streptomyces coelicolor A3(2)

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

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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.37 out of 30.12
Confidence: medium
Additional weak hits (5):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.13 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.59 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.56 out of 23.43
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.88 out of 33.73
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LWKZ01000024.1 - Region 8 - 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: 1,053,292 - 1,104,206 nt. (total: 50,915 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase
A6A06_RS27865: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

A6A06_RS27915: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

A6A06_RS27920: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS27935: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

A6A06_RS27940: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS27945: acyl-CoA dehydrogenase type 2

smcogs
  SMCOG1191: acyl-CoA dehydrogenase type 2

A6A06_RS27955: monooxygenase FAD-binding

smcogs
  SMCOG1246: monooxygenase FAD-binding

Transferases: methyltransferase
A6A06_RS27910: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: ligase synthase
A6A06_RS27875: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS27890: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter
A6A06_RS27970: 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 | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000056.3 |  |  | 0.75 | PKS | esperamicin | Actinomadura verrucosospora
BGC0001261.3 |  |  | 0.61 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  |  | 0.58 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  |  | 0.57 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  |  | 0.56 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001284.4 |  |  | 0.56 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001641.4 |  |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.54 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000056.3 |  | 0.70 | PKS | esperamicin | Actinomadura verrucosospora
BGC0001261.3 |  | 0.64 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.62 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001240.4 |  | 0.62 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.31 out of 23.79
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
Additional weak hits (12):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.20 out of 30.22
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.71 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.36 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.60 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.74 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.71 out of 30.25
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.85 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.04 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.49 out of 20.97
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.65 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.44 out of 32.93
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 12, location 1053291 - 1104206:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 1053291 - 1099195:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 14, location 1062394 - 1104206:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
A6A06_RS27875: mal
PKS_AT (622..849): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 99.7
  Methylmalonyl-CoA: 55.6
  Methoxymalonyl-CoA: 54.3
  inactive: 45.5
  Propionyl-CoA: 33.1
  Ethylmalonyl-CoA: 30.1
  Isobutyryl-CoA: 27.7
  fatty_acid: 22.9
  trans-1,2-CPDA: 15.0
  2-Methylbutyryl-CoA: 5.3
  Acetyl-CoA: 3.1
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  CHC-CoA: -1.4

A6A06_RS27890: X
AMP-binding (30..424): X
nrpys: ohMan

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:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    val (Val)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDSAFNVSTYEVHVLTGGDRAMYGATEATVFSTH
  Nearest Stachelhaus code(s):
    ohMan NVYHLGMVFK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_LWKZ01000025.1 - Region 1 - NRPS,T1PKS,phosphonate
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 164,944 - 242,151 nt. (total: 77,208 nt) Show pHMM detection rules used
phosphonate: (phosphonates and minimum(1, [2-Hacid_dh_C, Aldedh, Aminotran_1_2, Aminotran_5, AurF, CTP_transf_like, DUF4992, Fe-ADH, HMGL-like, Metallophos_2, NTP_transf_3, NTP_transf_5, PALP, PEP_mutase, TPP_enzyme_C, TPP_enzyme_N, phosphonates]) and not (phosphonatesHydrolase or phosphonatesMeIsocitrateLyase))
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase synthase
A6A06_RS28920: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

A6A06_RS28940: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

A6A06_RS28960: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS29020: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

A6A06_RS29030: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

A6A06_RS29040: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS29080: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

A6A06_RS29105: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS29115: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

A6A06_RS29165: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: PPTase acyltransferase aminotransferase
A6A06_RS28935: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

A6A06_RS28955: acyltransferase

smcogs
  SMCOG1141: acyltransferase

A6A06_RS29060: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

A6A06_RS29095: polyketide synthase associated protein papA3

smcogs
  SMCOG1209: polyketide synthase associated protein papA3

A6A06_RS29110: aminotransferase

smcogs
  SMCOG1019: aminotransferase

A6A06_RS43100: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase phosphatase synthase
A6A06_RS28920: riboflavin biosynthesis protein RibD

smcogs
  SMCOG1240: riboflavin biosynthesis protein RibD

A6A06_RS28975: thioesterase

smcogs
  SMCOG1004: thioesterase

A6A06_RS29035: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Ligases: ligase synthase
A6A06_RS28990: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS29015: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS29065: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS29085: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS29090: 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 | phosphonate | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001039.5 |  |  |  | 0.85 | NRPS, PKS | pyridomycin | Streptomyces pyridomyceticus
BGC0002135.2 |  |  |  | 0.81 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  |  | 0.77 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  | 0.75 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  |  |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  |  |  | 0.74 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  |  |  | 0.74 | NRPS | AM-toxin | Alternaria alternata
BGC0002286.3 |  |  |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.71 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001039.5 |  | 0.70 | NRPS, PKS | pyridomycin | Streptomyces pyridomyceticus
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001135.5 |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
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

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.16 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.60 out of 19.26
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.19 out of 23.79
Confidence: medium
Additional weak hits (11):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.23 out of 26.85
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.84 out of 26.33
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.57 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.03 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.27 out of 29.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.46 out of 30.25
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.21 out of 30.22
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.09 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.52 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 1, location 164943 - 242151:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal) + (Thr - X) + (Me-mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 166453 - 242151:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (ccmal) + (Thr - X) + (Me-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).
A6A06_RS28990: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (34..463): 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:
    VSALFVFGHPGGALQVGGAQQVYGMSEGLLNFTR
  Nearest Stachelhaus code(s):
    Sal PLPAQGVLNK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

A6A06_RS29015: mal
PKS_AT (542..850): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 140.3
  inactive: 95.4
  Methoxymalonyl-CoA: 65.2
  Methylmalonyl-CoA: 48.0
  Ethylmalonyl-CoA: 29.4
  Isobutyryl-CoA: 28.2
  Propionyl-CoA: 27.7
  fatty_acid: 19.4
  Acetyl-CoA: 14.4
  Benzoyl-CoA: 14.1
  2-Methylbutyryl-CoA: 11.2
  CHC-CoA: 11.0
  3-Methylbutyryl-CoA: 8.4
  trans-1,2-CPDA: 0.0

A6A06_RS29065: X
AMP-binding (33..441): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    QAALFTWGCPGGSCQIGSAQQVFGMAEGLLTFTR
  Nearest Stachelhaus code(s):
    Hpa TWPSQGVLCK (91% 8Å match)
  Stachelhaus code match:
    90% (moderate)

A6A06_RS29085: Thr - X
Search NORINE for peptide: strict or relaxed
AMP-binding (452..866): Thr
nrpys: Thr

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

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

AMP-binding (1526..1924): X
nrpys: pyrAla

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNQAFDAAFWDMTLVVAGEVNSYGPTEITVSCAI
  Nearest Stachelhaus code(s):
    pyrAla DAWTVASVSK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS29090: mal
PKS_AT (534..810): mal
ATSignature: (unknown)
No matches above 50%
minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 89.8
  Methoxymalonyl-CoA: 50.3
  inactive: 39.6
  Methylmalonyl-CoA: 35.8
  Propionyl-CoA: 25.6
  Ethylmalonyl-CoA: 11.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Isobutyryl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

A6A06_RS29095: X - fatty_acid
AMP-binding (509..858): 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:
    RRLAQERAVWELIALCLAP--------VLRWVYA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

CAL_domain (1065..1480): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 17.5
  Acetyl-CoA: 13.2
  NH2: 12.3
  shikimic_acid: 0.0
  AHBA: 0.0

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism

NZ_LWKZ01000025.1 - 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: 297,972 - 321,407 nt. (total: 23,436 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
A6A06_RS29530: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
A6A06_RS29545: 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
--- | --- | --- | --- | --- | ---
BGC0002173.2 |  | 0.47 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000502.5 |  | 0.37 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001173.5 |  | 0.36 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0000569.5 |  | 0.36 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001391.3 |  | 0.36 | ribosomal | thusin | Bacillus thuringiensis serovar rongseni
BGC0000594.5 |  | 0.35 | ribosomal | microviridin K | Planktothrix agardhii NIVA-CYA 126/8
BGC0001227.3 |  | 0.35 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0001170.5 |  | 0.34 | ribosomal | clostridiolysin S | Clostridium sporogenes ATCC 15579
BGC0000564.5 |  | 0.34 | ribosomal | clostridiolysin S | Clostridium botulinum A str. ATCC 3502

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002173.2 |  | 0.47 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163
BGC0000616.4 |  | 0.40 | ribosomal | amylocyclicin | Bacillus velezensis FZB42
BGC0000502.5 |  | 0.37 | ribosomal | cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7 | Bacillus cereus
BGC0001173.5 |  | 0.36 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0000569.5 |  | 0.36 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001391.3 |  | 0.36 | ribosomal | thusin | Bacillus thuringiensis serovar rongseni
BGC0000594.5 |  | 0.35 | ribosomal | microviridin K | Planktothrix agardhii NIVA-CYA 126/8
BGC0001227.3 |  | 0.35 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0001170.5 |  | 0.34 | ribosomal | clostridiolysin S | Clostridium sporogenes ATCC 15579
BGC0000564.5 |  | 0.34 | ribosomal | clostridiolysin S | Clostridium botulinum A str. ATCC 3502

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
A6A06_RS29545: PT_FPPS_like
Domain 1 (87 - 376): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

A6A06_RS29550: T2TS
Domain 1 (31 - 657): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
Additional weak hits (7):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.17 out of 26.06
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.90 out of 30.22
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.09 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.27 out of 29.65
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
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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
MexT | Global virulence regulator
OsdR | Development and stress management regulator
ToxT | Regulator of MSHA biosynthesis

NZ_LWKZ01000026.1 - Region 1 - NRPS-like,PKS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 68,665 nt. (total: 68,665 nt) Show pHMM detection rules used
Region on contig edge.
PKS-like: (t2pks2 or ksIII)
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 oxygenase
A6A06_RS31870: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

A6A06_RS31965: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

A6A06_RS32105: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: amidase dehalogenase hydrolase
A6A06_RS31935: amidase

smcogs
  SMCOG1105: amidase

A6A06_RS32075: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

A6A06_RS32095: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: ligase
A6A06_RS32040: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | PKS-like | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001135.5 |  |  | 0.28 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  |  | 0.27 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002174.2 |  |  | 0.27 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001641.4 |  |  | 0.27 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  |  | 0.27 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  |  | 0.27 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  |  | 0.27 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001128.4 |  |  | 0.27 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.27 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  |  | 0.26 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002174.2 |  | 0.61 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001641.4 |  | 0.60 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  | 0.60 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001128.4 |  | 0.60 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.60 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.11 out of 25.31
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.07 out of 25.31
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
Additional weak hits (13):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.97 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.68 out of 27.78
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.50 out of 20.97
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.11 out of 26.06
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.14 out of 27.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.89 out of 30.22
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.92 out of 36.54
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.49 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.68 out of 29.65
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.57 out of 30.98
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.37 out of 32.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75
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 - 68665:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 25566 - 68665:
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).
A6A06_RS32040: X
AMP-binding (31..431): 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:
    LNTTFDISCLEAWLIAGGDINGYGPTEASSLVTA
  Nearest Stachelhaus code(s):
    Val DALWIGGTFK (68% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CatR | H2O2-responsive repressor
MexT | Global virulence regulator

NZ_LWKZ01000026.1 - Region 2 - NRPS,NRPS-like,T1PKS,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: 118,036 - 239,487 nt. (total: 121,452 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)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
A6A06_RS32420: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS32635: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS32645: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS32650: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

A6A06_RS32680: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS32730: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: methyltransferase
A6A06_RS32415: methyltransferase

smcogs
  SMCOG1089: methyltransferase

A6A06_RS32595: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: glucosidase hydrolase
A6A06_RS32530: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

A6A06_RS32555: HAD-superfamily hydrolase, subfamily IA, variant

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

A6A06_RS32585: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: cyclase
A6A06_RS32410: Terpene synthase/cyclase metal-binding domain protein

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

Ligases: ligase synthase synthetase
A6A06_RS32425: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

A6A06_RS32430: 1-deoxy-D-xylulose-5-phosphate synthase

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

A6A06_RS32475: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS32480: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

A6A06_RS32485: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS32570: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS32625: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS32630: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS32640: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | terpene | NRPS | NRPS-like | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0001181.4 |  |  |  |  | 0.93 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001273.3 |  |  |  |  | 0.87 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  |  |  |  | 0.87 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  |  |  | 0.87 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001160.5 |  |  |  |  | 0.78 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001276.3 |  |  |  |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002099.3 |  |  |  |  | 0.71 | ribosomal | biarylitide YFH | Planomonospora sp. ID107089
BGC0002084.4 |  |  |  |  | 0.70 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0000041.3 |  |  |  |  | 0.68 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001050.5 |  |  |  |  | 0.68 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.76 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
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
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001833.4 |  | 0.73 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001133.4 |  | 0.71 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0001050.5 |  | 0.71 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis

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

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

Genes with terpene domains:
A6A06_RS32410: T1TS + T1TS
Domain 1 (98 - 401): Type 1 terpene synthase
Subtype: unknown
Domain 2 (447 - 787): Type 1 terpene synthase
Subtype: unknown
A6A06_RS32425: PT_FPPS_like
Domain 1 (63 - 376): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.98 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.14 out of 23.79
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
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 (33):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.50 out of 29.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.79 out of 30.97
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.06 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.50 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.09 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.05 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.24 out of 29.38
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.00 out of 27.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.74 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.82 out of 30.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.33 out of 30.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.93 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.62 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.00 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.13 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.16 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.43 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.59 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.96 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.22 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.31 out of 36.54
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.34 out of 27.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 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
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.18 out of 27.78
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.32 out of 32.74
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.64 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.85 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.70 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.26 out of 26.06
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.82 out of 30.98
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
Terpene
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 4, location 118035 - 239487:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk - ohmal) + (ccmal) + (X) + (Hpg - Hpg - D-Hpg) + (Hpg - D-Hpg) + (Hpg)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 122765 - 185695:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 165657 - 209230:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 179149 - 239487:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (pk - ohmal) + (ccmal) + (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).
A6A06_RS32475: Hpg
Search NORINE for peptide: strict or relaxed
AMP-binding (463..841): Hpg
nrpys: Hpg

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:
    LDTAFDASTLEVHLLTGGDGHLYGPTETTLCATT
  Nearest Stachelhaus code(s):
    Hpg DALHLGLLCK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS32480: Hpg - Hpg
Search NORINE for peptide: strict or relaxed
AMP-binding (464..842): 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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDSAFDASTFEVHVLTGGDRHLYGPTETTLCATT
  Nearest Stachelhaus code(s):
    Hpg DAFHLGLLCK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1491..1868): 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:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDAAFDASAFEVHVLTGGDHHLYGPTETTLCATT
  Nearest Stachelhaus code(s):
    Hpg DAFHLGLLCK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS32485: Hpg - Hpg - Hpg
Search NORINE for peptide: strict or relaxed
AMP-binding (472..852): 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:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDTAFDASTFEVHVLTGGDHHLYGPTEITLCATT
  Nearest Stachelhaus code(s):
    Hpg DAFHLGLLCK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1507..1880): 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:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDSAFDASTFEVHLLTGGDRHLYGPTETTLCATT
  Nearest Stachelhaus code(s):
    Hpg DAFHLGLLCK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2535..2913): 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:
    Polar, uncharged (hydroxy-phenyl) (Dhpg, Hpg)
  Single AA prediction:
    hpg (Hpg)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAPAFDASTLEVHVLTGGDHHLYGPTETTLCATT
  Nearest Stachelhaus code(s):
    Hpg DALHLGLLCK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

A6A06_RS32570: X
AMP-binding (88..526): 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:
    FGFMHMMGRGVGIMWTVSALDGYGSTEAGIVSLD
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

A6A06_RS32630: mal
PKS_AT (569..860): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 195.4
  inactive: 87.8
  Methoxymalonyl-CoA: 52.5
  Methylmalonyl-CoA: 51.6
  Propionyl-CoA: 28.8
  Isobutyryl-CoA: 23.6
  Ethylmalonyl-CoA: 22.1
  Benzoyl-CoA: 17.9
  Acetyl-CoA: 17.1
  2-Methylbutyryl-CoA: 15.1
  CHC-CoA: 14.1
  fatty_acid: 11.3
  trans-1,2-CPDA: 6.7
  3-Methylbutyryl-CoA: 0.0

A6A06_RS32640: pk - mal
PKS_AT (567..864): pk
ATSignature: Methylmalonyl-CoA

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

minowa: Ethylmalonyl-CoA

Prediction, score:
  Ethylmalonyl-CoA: 208.0
  Methylmalonyl-CoA: 205.9
  2-Methylbutyryl-CoA: 171.9
  Methoxymalonyl-CoA: 169.8
  Propionyl-CoA: 128.6
  trans-1,2-CPDA: 124.5
  Malonyl-CoA: 110.9
  CHC-CoA: 110.1
  Isobutyryl-CoA: 65.5
  Benzoyl-CoA: 55.4
  Acetyl-CoA: 43.4
  fatty_acid: 39.5
  3-Methylbutyryl-CoA: 27.0
  inactive: 25.4

PKS_AT (2228..2511): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 79.2%
  inactive: 70.8%
  Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 170.9
  Methoxymalonyl-CoA: 87.7
  Methylmalonyl-CoA: 80.4
  inactive: 52.9
  Propionyl-CoA: 49.3
  Ethylmalonyl-CoA: 43.7
  Isobutyryl-CoA: 33.8
  fatty_acid: 30.1
  2-Methylbutyryl-CoA: 25.3
  CHC-CoA: 16.0
  Acetyl-CoA: 12.4
  trans-1,2-CPDA: 11.1
  Benzoyl-CoA: 7.5
  3-Methylbutyryl-CoA: 0.0

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

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_LWKZ01000026.1 - Region 3 - nucleoside
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: 258,066 - 279,031 nt. (total: 20,966 nt) Show pHMM detection rules used
nucleoside: (LipM or LipV or LipU or TunD or pur6 or pur10 or nikJ or nikO or truD)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
A6A06_RS32815: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS32840: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

A6A06_RS32845: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: glycosyltransferase
A6A06_RS32830: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

A6A06_RS32865: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Lyases: dehydratase
A6A06_RS32835: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

A6A06_RS32850: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

A6A06_RS32875: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: mutase
A6A06_RS32880: 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 | nucleoside | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000880.4 |  | 0.81 | other (nucleoside) | tunicamycin B1 | Streptomyces chartreusis NRRL 3882
BGC0000786.3 |  | 0.48 | saccharide | O-antigen | Edwardsiella ictaluri 93-146
BGC0000866.5 |  | 0.46 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000888.5 |  | 0.46 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001927.4 |  | 0.45 | other (other) | A-94964 | Streptomyces sp.
BGC0000231.5 |  | 0.45 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000707.5 |  | 0.45 | saccharide | kasugamycin | Streptomyces kasugaensis
BGC0000777.3 |  | 0.45 | saccharide | lipopolysaccharide | Escherichia coli
BGC0000790.3 |  | 0.45 | saccharide | O-antigen | Escherichia coli
BGC0000916.5 |  | 0.45 | other (other) | molybdenum cofactor | Staphylococcus carnosus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000880.4 |  | 0.81 | other (nucleoside) | tunicamycin B1 | Streptomyces chartreusis NRRL 3882
BGC0000786.3 |  | 0.48 | saccharide | O-antigen | Edwardsiella ictaluri 93-146
BGC0000866.5 |  | 0.46 | other (other) | polyhydroxyalkanoate | Burkholderia sp. DSM 9242
BGC0000888.5 |  | 0.46 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001927.4 |  | 0.45 | other (other) | A-94964 | Streptomyces sp.
BGC0000231.5 |  | 0.45 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000707.5 |  | 0.45 | saccharide | kasugamycin | Streptomyces kasugaensis
BGC0000777.3 |  | 0.45 | saccharide | lipopolysaccharide | Escherichia coli
BGC0000790.3 |  | 0.45 | saccharide | O-antigen | Escherichia coli
BGC0000916.5 |  | 0.45 | other (other) | molybdenum cofactor | Staphylococcus carnosus

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.46 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31
Confidence: medium
Additional weak hits (3):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.49 out of 26.85
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.70 out of 29.38
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CatR | H2O2-responsive repressor
IolR | Regulator of the inositol catabolism

NZ_LWKZ01000026.1 - Region 4 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 293,287 - 358,492 nt. (total: 65,206 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
A6A06_RS33035: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS33075: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS33135: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

A6A06_RS33140: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: dehalogenase
A6A06_RS32990: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Ligases: ligase
A6A06_RS33085: 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
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001240.4 |  | 0.67 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001833.4 |  | 0.71 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.71 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti
BGC0001240.4 |  | 0.67 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.37 out of 20.47
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.71 out of 26.33
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 (15):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.75 out of 29.38
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.44 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.61 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.68 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.79 out of 30.22
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.11 out of 32.93
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.18 out of 29.25
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.76 out of 29.25
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.36 out of 28.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.26 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.15 out of 23.43
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.57 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.45 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 10, location 293286 - 358492:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (D-Thr - Ser - Tyr - D-NMe-Trp - Gly - NMe-Phe)

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).
A6A06_RS33085: Thr - Ser - Tyr - Trp - Gly - Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (463..878): Thr
nrpys: Thr

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

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

AMP-binding (2034..2436): 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:
    RWMTFDVSVWEWHFVTSGEYNLYGPTETTIDVTA
  Nearest Stachelhaus code(s):
    Ser DVWHVSLIDK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3099..3495): Tyr
nrpys: Tyr

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

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

AMP-binding (4155..4526): Trp
nrpys: Trp

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:
    LAHVFDVSFSETMLVVGGDINAYGPTEFTVCATM
  Nearest Stachelhaus code(s):
    Trp DVAMVGAVCK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (6096..6497): 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:
    FAMTFDIAALELQALVGGETNLYGPTETTIWSTV
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (7157..7529): Phe
nrpys: Phe

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LAQAFDASFWEMTLVVAGEFNAYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_LWKZ01000026.1 - Region 5 - NAPAA,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: 371,860 - 450,754 nt. (total: 78,895 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)
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: oxidoreductase oxygenase
A6A06_RS33225: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

A6A06_RS33290: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS33430: Dioxygenase TauD/TfdA

smcogs
  SMCOG1046: Dioxygenase TauD/TfdA

A6A06_RS33470: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

A6A06_RS33480: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

A6A06_RS33490: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Transferases: acetyltransferase methyltransferase
A6A06_RS33270: methyltransferase

smcogs
  SMCOG1089: methyltransferase

A6A06_RS33280: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: deaminase glucosidase hydrolase
A6A06_RS33265: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

A6A06_RS33340: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

A6A06_RS33365: Alpha-glucosidase

smcogs
  SMCOG1257: Alpha-glucosidase

A6A06_RS33425: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: dehydratase
A6A06_RS43280: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
A6A06_RS33260: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

A6A06_RS33275: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

A6A06_RS33415: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

A6A06_RS33420: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

A6A06_RS33435: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

Translocases: transporter
A6A06_RS33350: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | NRPS-like | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002164.2 |  |  | 0.59 | NRPS | peramine | Epichloe festucae
BGC0001132.4 |  |  | 0.58 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  |  | 0.58 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.57 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001128.4 |  |  | 0.57 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002174.2 |  |  | 0.57 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001261.3 |  |  | 0.56 | NRPS | AM-toxin | Alternaria alternata
BGC0000307.4 |  |  | 0.56 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002135.2 |  |  | 0.55 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  |  | 0.55 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001249.5 |  | 0.71 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002164.2 |  | 0.67 | NRPS | peramine | Epichloe festucae
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
BGC0001261.3 |  | 0.64 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0002174.2 |  | 0.64 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002285.2 |  | 0.63 | ribosomal | aborycin | Streptomyces sp. ZS0098

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.06 out of 23.43
Confidence: medium
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.31 out of 18.57
Confidence: medium
Additional weak hits (24):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.59 out of 30.22
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.14 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.02 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.34 out of 21.55
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.81 out of 18.57
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.45 out of 31.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.67 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.49 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.56 out of 30.22
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.70 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.66 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.20 out of 26.12
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.99 out of 31.73
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.93 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.42 out of 29.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.61 out of 20.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.13 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.57 out of 36.53
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.06 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.96 out of 35.63
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.82 out of 23.43
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.55 out of 29.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.15 out of 33.14
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.64 out of 24.78
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 11, location 371859 - 450754:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 12, location 371859 - 415147:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 13, location 414903 - 450754:
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).
A6A06_RS33260: X
AMP-binding (28..423): 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:
    -DMTHVAGIADAWLTYGGCFGGYGQSEAGHITVI
  Nearest Stachelhaus code(s):
    Val DAAWWGGTFK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

A6A06_RS43280: X
AMP-binding (33..436): X
nrpys: Gly, Ala, Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LSAYSDASTIETFLSAGGEVNFYGPTENSVVSSA
  Nearest Stachelhaus code(s):
    Leu DAWFLGHVVK (59% 8Å match)
  Stachelhaus code match:
    70% (weak)

A6A06_RS33435: X
AMP-binding (255..661): 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:
    HAKAFDISLWQAQVSATGEVNAYGLTETSDDTNH
  Nearest Stachelhaus code(s):
    Dpr DIWQSTADDK (91% 8Å match)
    dnmeProp or Dab DIWQSTADDK (82% 8Å match)
    Asp DIWQSTADDK (82% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
BldD | Development and antibiotic global regulator
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis

NZ_LWKZ01000026.1 - Region 6 - arylpolyene,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: 565,828 - 622,128 nt. (total: 56,301 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Terpene
TFBS Finder
NRPS/PKS 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
A6A06_RS34040: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

A6A06_RS34085: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

A6A06_RS34145: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

A6A06_RS34150: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

A6A06_RS34160: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

A6A06_RS34175: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

A6A06_RS34185: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: kinase methyltransferase
A6A06_RS34050: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

A6A06_RS34055: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

A6A06_RS34195: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: dehalogenase
A6A06_RS34200: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: cyclase
A6A06_RS34190: Terpene synthase/cyclase metal-binding domain protein

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

Isomerases: mutase
A6A06_RS34045: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: ligase synthase
A6A06_RS34080: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

A6A06_RS34090: 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 | arylpolyene | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001160.5 |  |  | 0.45 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  |  | 0.45 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001364.3 |  |  | 0.27 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001778.5 |  |  | 0.26 | other (other) | showdomycin | Streptomyces showdoensis
BGC0001610.5 |  |  | 0.24 | other (other) | gougerotin | Streptomyces ahygroscopicus subsp. wuzhouensis
BGC0002194.3 |  |  | 0.24 | PKS | epipyrone A | Epicoccum nigrum
BGC0000194.5 |  |  | 0.24 | PKS | actinorhodin | Streptomyces coelicolor A3(2)
BGC0001137.5 |  |  | 0.24 | other (other) | marinacarboline A, marinacarboline B, marinacarboline C, marinacarboline D | Marinactinospora thermotolerans
BGC0001858.2 |  |  | 0.23 | PKS | alternapyrone B, alternapyrone C, alternapyrone D, alternapyrone E, alternapyrone F | Parastagonospora nodorum SN15
BGC0001166.5 |  |  | 0.23 | NRPS | HC-toxin | Alternaria jesenskae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001160.5 |  | 0.59 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.58 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001166.5 |  | 0.56 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001261.3 |  | 0.55 | NRPS | AM-toxin | Alternaria alternata
BGC0002260.3 |  | 0.50 | terpene | trichobrasilenol, xylarenic acid B, brasilane A, brasilane F, brasilane E, brasilane D | Annulohypoxylon truncatum
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001336.5 |  | 0.47 | other (other) | erdasporine A, erdasporine B, erdasporine C | uncultured bacterium
BGC0001965.4 |  | 0.46 | other (other) | nybomycin | Streptomyces albus subsp. chlorinus
BGC0002493.3 |  | 0.46 | NRPS | parabactin | Paracoccus denitrificans PD1222

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
A6A06_RS34190: T1TS
Domain 1 (5 - 311): 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:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 25.31
Confidence: medium
Additional weak hits (17):
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.25 out of 20.01
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.68 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.61 out of 20.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.91 out of 29.38
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.67 out of 23.43
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.11 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.91 out of 18.57
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.09 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.41 out of 26.06
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.45 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.84 out of 32.74
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.25 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.53 out of 27.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.55 out of 30.25
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.66 out of 30.98
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.96 out of 27.18
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
Terpene
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
A6A06_RS34090: X
AMP-binding (11..434): X
nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

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:
    AVLAHAAALMQPFGVCGGARQGYGMTEAAPGVLL
  Nearest Stachelhaus code(s):
    Val DAMFVGGVFK (41% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
CatR | H2O2-responsive repressor

NZ_LWKZ01000027.1 - Region 1 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 58,024 - 79,208 nt. (total: 21,185 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
A6A06_RS35105: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Lyases: cyclase
A6A06_RS35100: Terpene synthase/cyclase metal-binding domain protein

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001475.4 |  | 0.49 | terpene | aspterric acid | Aspergillus terreus NIH2624
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.47 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000674.5 |  | 0.45 | terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064
BGC0001911.3 |  | 0.41 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.40 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001679.3 |  | 0.39 | NRPS | N-Acetyltryptophan | Aspergillus nidulans FGSC A4
BGC0002651.2 |  | 0.38 | terpene | sordaricin B | Rosellinia necatrix
BGC0001375.4 |  | 0.38 | terpene | penitrem A, penitrem B, penitrem C, penitrem D, penitrem E, penitrem F | Penicillium simplicissimum
BGC0000678.5 |  | 0.37 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001475.4 |  | 0.49 | terpene | aspterric acid | Aspergillus terreus NIH2624
BGC0000675.5 |  | 0.49 | terpene | (+)-T-muurolol | Streptomyces clavuligerus ATCC 27064
BGC0000677.5 |  | 0.47 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000674.5 |  | 0.45 | terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064
BGC0001911.3 |  | 0.41 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.40 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001679.3 |  | 0.39 | NRPS | N-Acetyltryptophan | Aspergillus nidulans FGSC A4
BGC0002651.2 |  | 0.38 | terpene | sordaricin B | Rosellinia necatrix
BGC0001375.4 |  | 0.38 | terpene | penitrem A, penitrem B, penitrem C, penitrem D, penitrem E, penitrem F | Penicillium simplicissimum
BGC0000678.5 |  | 0.37 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

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

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:
No product predictions
Genes with terpene domains:
A6A06_RS35100: T1TS
Domain 1 (17 - 349): 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.19 out of 20.47
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.83 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.96 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.18 out of 23.79
Confidence: medium
Additional weak hits (6):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.26 out of 26.85
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.67 out of 25.88
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.08 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.13 out of 24.78
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LWKZ01000027.1 - Region 2 - 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: 215,083 - 225,592 nt. (total: 10,510 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: hydrolase
A6A06_RS35820: HAD-superfamily hydrolase, subfamily IA, variant

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

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002657.2 |  | 0.32 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0001782.3 |  | 0.28 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0001927.4 |  | 0.25 | other (other) | A-94964 | Streptomyces sp.
BGC0002129.4 |  | 0.20 | PKS | metathramycin, premetathramycin | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002657.2 |  | 0.32 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0001782.3 |  | 0.28 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032
BGC0001927.4 |  | 0.25 | other (other) | A-94964 | Streptomyces sp.
BGC0002129.4 |  | 0.20 | PKS | metathramycin, premetathramycin | uncultured bacterium

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (7):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.26 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.01 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.07 out of 24.78
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.70 out of 29.25
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.72 out of 30.98
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_LWKZ01000027.1 - Region 3 - 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: 597,755 - 629,626 nt. (total: 31,872 nt) Show pHMM detection rules used
NI-siderophore: IucA_IucC

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
A6A06_RS37665: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase
A6A06_RS37610: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: decarboxylase lyase
A6A06_RS37620: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

A6A06_RS37635: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002527.2 |  | 0.61 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001408.5 |  | 0.60 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0000946.5 |  | 0.59 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000947.5 |  | 0.49 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000885.3 |  | 0.48 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000942.4 |  | 0.47 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001880.3 |  | 0.45 | ribosomal | scytodecamide | Scytonema sp. UIC 10036
BGC0000846.5 |  | 0.42 | other (other) | tabtoxin | Pseudomonas syringae
BGC0000888.5 |  | 0.41 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000671.3 |  | 0.41 | terpene | momilactone B | Oryza sativa Japonica Group

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002527.2 |  | 0.61 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001408.5 |  | 0.60 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0000946.5 |  | 0.59 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0000947.5 |  | 0.49 | other (other) | vibrioferrin | Vibrio alginolyticus
BGC0000885.3 |  | 0.48 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000942.4 |  | 0.47 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0001880.3 |  | 0.45 | ribosomal | scytodecamide | Scytonema sp. UIC 10036
BGC0000846.5 |  | 0.42 | other (other) | tabtoxin | Pseudomonas syringae
BGC0000888.5 |  | 0.41 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000671.3 |  | 0.41 | terpene | momilactone B | Oryza sativa Japonica Group

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.11 out of 23.79
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.90 out of 36.53
Confidence: medium
Additional weak hits (8):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.96 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.55 out of 27.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.70 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.27 out of 36.53
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.23 out of 26.06
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.02 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.13 out of 24.78
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.91 out of 24.78
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism

NZ_LWKZ01000027.1 - Region 4 - 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: 703,191 - 721,891 nt. (total: 18,701 nt) Show pHMM detection rules used
Region on contig edge.
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
A6A06_RS38060: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Lyases: decarboxylase
A6A06_RS38055: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.85 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.80 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000941.3 |  | 0.79 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001453.5 |  | 0.72 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000940.5 |  | 0.66 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0002464.3 |  | 0.61 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0001531.5 |  | 0.54 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002690.2 |  | 0.54 | other (other) | FW0622 | Verrucosispora sp. FIM060022

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001478.5 |  | 0.85 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0002305.2 |  | 0.80 | other (other) | legonoxamine A, desferrioxamine B, legonoxamine B | Streptomyces sp.
BGC0000941.3 |  | 0.79 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001453.5 |  | 0.72 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0001572.3 |  | 0.70 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000940.5 |  | 0.66 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0002464.3 |  | 0.61 | other (other) | alcaligin | Bordetella pertussis Tohama I
BGC0002620.2 |  | 0.55 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0001531.5 |  | 0.54 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002690.2 |  | 0.54 | other (other) | FW0622 | Verrucosispora sp. FIM060022

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 33.62 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.03 out of 36.53
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.17 out of 23.79
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
Additional weak hits (4):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.21 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.34 out of 30.25
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.88 out of 30.97
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
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism

NZ_LWKZ01000028.1 - Region 1 - 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: 294,149 - 305,438 nt. (total: 11,290 nt) Show pHMM detection rules used
Region on contig edge.
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
Lyases: dehydratase
A6A06_RS39405: 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
--- | --- | --- | --- | --- | ---
BGC0000850.5 |  | 0.65 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000849.4 |  | 0.59 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0002578.2 |  | 0.38 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000914.5 |  | 0.29 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000019.5 |  | 0.28 | PKS | angolamycin | Streptomyces eurythermus
BGC0000112.5 |  | 0.27 | PKS | neocarzinostatin | Streptomyces carzinostaticus subsp. neocarzinostaticus
BGC0002642.2 |  | 0.26 | other (other) | clipibycyclene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000262.5 |  | 0.26 | PKS, saccharide | prejadomycin, rabelomycin, gaudimycin C, gaudimycin D, UWM6, gaudimycin A | Streptomyces sp. PGA64
BGC0001083.5 |  | 0.25 | PKS, terpene | merochlorin A, merochlorin B, deschloro-merochlorin A, deschloro-merochlorin B, isochloro-merochlorin B, dichloro-merochlorin B, merochlorin D, merochlorin C | Streptomyces sp. CNH189
BGC0002078.2 |  | 0.25 | NRPS | omnipeptin | uncultured bacterium

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000850.5 |  | 0.65 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0000849.4 |  | 0.59 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0002578.2 |  | 0.38 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000914.5 |  | 0.29 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0000019.5 |  | 0.28 | PKS | angolamycin | Streptomyces eurythermus
BGC0000112.5 |  | 0.27 | PKS | neocarzinostatin | Streptomyces carzinostaticus subsp. neocarzinostaticus
BGC0002642.2 |  | 0.26 | other (other) | clipibycyclene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000262.5 |  | 0.26 | PKS, saccharide | prejadomycin, rabelomycin, gaudimycin C, gaudimycin D, UWM6, gaudimycin A | Streptomyces sp. PGA64
BGC0001083.5 |  | 0.25 | PKS, terpene | merochlorin A, merochlorin B, deschloro-merochlorin A, deschloro-merochlorin B, isochloro-merochlorin B, dichloro-merochlorin B, merochlorin D, merochlorin C | Streptomyces sp. CNH189
BGC0002078.2 |  | 0.25 | NRPS | omnipeptin | uncultured bacterium

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.15 out of 27.04
Confidence: medium
Additional weak hits (12):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.55 out of 18.57
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.42 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.36 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.26 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.63 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.94 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.14 out of 26.06
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.02 out of 24.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.26 out of 26.06
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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