Select genomic region:
Overview
1.1
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
1.11
1.12
1.13
1.14
1.15
1.16
1.17
1.18
1.19
1.20
1.21
1.22
1.23
1.24
1.25
1.26
1.27
1.28
1.29
1.30
1.31
1.32
1.33
1.34
3.1

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

NZ_AP018365.1 (Streptomyces sp. SN-593)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | lanthipeptide-class-ii | 22,672 | 46,121 |  |
Region 1.2 | terpene,t3nrps-iterative,NRPS | 216,151 | 316,729 | High | isorenieratene | terpene
Region 1.3 | T3PKS | 317,963 | 359,036 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 1.4 | RiPP-like | 651,404 | 662,222 |
Region 1.5 | lanthipeptide-class-iii | 726,609 | 749,260 |  |
Region 1.6 | azole-containing-RiPP | 1,036,781 | 1,060,759 |
Region 1.7 | T3PKS | 1,159,768 | 1,200,952 |  |
Region 1.8 | terpene | 1,216,732 | 1,237,760 |  |
Region 1.9 | T2PKS | 1,352,155 | 1,424,634 | Medium | nenestatin | PKS
Region 1.10 | T1PKS | 1,429,832 | 1,474,994 |  |
Region 1.11 | terpene-precursor | 1,482,777 | 1,503,805 |  |
Region 1.12 | thioamide-NRP,HR-T2PKS | 1,747,500 | 1,803,059 |  |
Region 1.13 | terpene | 1,887,695 | 1,909,971 | High | geosmin | terpene:Sesquiterpene
Region 1.14 | lanthipeptide-class-i | 1,998,428 | 2,024,872 |  |
Region 1.15 | T1PKS | 2,275,676 | 2,383,532 | Low | lydicamycin | NRPS:Type I+PKS:Type I
Region 1.16 | T2PKS | 2,483,008 | 2,555,514 | High | kinanthraquinone B/kinanthraquinone | PKS
Region 1.17 | T2PKS | 2,872,734 | 2,945,294 | High | spore pigment | PKS
Region 1.18 | butyrolactone | 3,425,894 | 3,436,811 |
Region 1.19 | T3PKS,terpene-precursor,other | 3,541,570 | 3,597,532 | High | furaquinocin B | terpene+PKS
Region 1.20 | indole | 3,680,693 | 3,701,850 | Low | Azodyrecin A/Azodyrecin B/Azodyrecin C | other:other
Region 1.21 | melanin | 4,108,974 | 4,119,402 |  |
Region 1.22 | lanthipeptide-class-i | 4,670,936 | 4,696,228 |
Region 1.23 | linaridin | 5,109,216 | 5,129,791 |
Region 1.24 | benzoxazole,hglE-KS | 5,858,552 | 5,927,828 | High | A33853 | other:other
Region 1.25 | NI-siderophore | 6,500,719 | 6,533,241 | Low | kinamycin | PKS
Region 1.26 | terpene | 7,083,210 | 7,110,057 | Medium | hopene | terpene
Region 1.27 | T1PKS,terpene | 7,145,500 | 7,279,965 | High | reveromycin A | PKS
Region 1.28 | T1PKS | 7,316,223 | 7,443,763 | Low | akaeolide | PKS
Region 1.29 | T2PKS | 7,450,327 | 7,522,815 | High | WS-5995 D/WS-5995 B/WS-5995 C/SEK 43 | PKS
Region 1.30 | lanthipeptide-class-ii,lanthipeptide-class-iv | 7,986,833 | 8,018,583 |
Region 1.31 | NRPS,T1PKS | 8,044,760 | 8,100,439 |
Region 1.32 | NRPS,T1PKS | 8,126,442 | 8,210,090 |  |
Region 1.33 | T1PKS,NRPS,NRPS-like | 8,439,228 | 8,740,152 | Medium | bafilomycin B1 | PKS:Type I
Region 1.34 | NRP-metallophore,NRPS,T1PKS,betalactone | 8,753,029 | 8,819,825 |  |

NZ_AP018367.1 (Streptomyces sp. SN-593)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | T3PKS | 1 | 32,347 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | lanthipeptide-class-ii | 22,672 | 46,121 |  |
Region 1.2 | terpene,t3nrps-iterative,NRPS | 216,151 | 316,729 | High | isorenieratene | terpene
Region 1.3 | T3PKS | 317,963 | 359,036 | High | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone/2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | PKS:Type III
Region 1.4 | RiPP-like | 651,404 | 662,222 |
Region 1.5 | lanthipeptide-class-iii | 726,609 | 749,260 |  |
Region 1.6 | azole-containing-RiPP | 1,036,781 | 1,060,759 |
Region 1.7 | T3PKS | 1,159,768 | 1,200,952 |  |
Region 1.8 | terpene | 1,216,732 | 1,237,760 |  |
Region 1.9 | T2PKS | 1,352,155 | 1,424,634 | Medium | nenestatin | PKS
Region 1.10 | T1PKS | 1,429,832 | 1,474,994 |  |
Region 1.11 | terpene-precursor | 1,482,777 | 1,503,805 |  |
Region 1.12 | thioamide-NRP,HR-T2PKS | 1,747,500 | 1,803,059 |  |
Region 1.13 | terpene | 1,887,695 | 1,909,971 | High | geosmin | terpene:Sesquiterpene
Region 1.14 | lanthipeptide-class-i | 1,998,428 | 2,024,872 |  |
Region 1.15 | T1PKS | 2,275,676 | 2,383,532 | Low | lydicamycin | NRPS:Type I+PKS:Type I
Region 1.16 | T2PKS | 2,483,008 | 2,555,514 | High | kinanthraquinone B/kinanthraquinone | PKS
Region 1.17 | T2PKS | 2,872,734 | 2,945,294 | High | spore pigment | PKS
Region 1.18 | butyrolactone | 3,425,894 | 3,436,811 |
Region 1.19 | T3PKS,terpene-precursor,other | 3,541,570 | 3,597,532 | High | furaquinocin B | terpene+PKS
Region 1.20 | indole | 3,680,693 | 3,701,850 | Low | Azodyrecin A/Azodyrecin B/Azodyrecin C | other:other
Region 1.21 | melanin | 4,108,974 | 4,119,402 |  |
Region 1.22 | lanthipeptide-class-i | 4,670,936 | 4,696,228 |
Region 1.23 | linaridin | 5,109,216 | 5,129,791 |
Region 1.24 | benzoxazole,hglE-KS | 5,858,552 | 5,927,828 | High | A33853 | other:other
Region 1.25 | NI-siderophore | 6,500,719 | 6,533,241 | Low | kinamycin | PKS
Region 1.26 | terpene | 7,083,210 | 7,110,057 | Medium | hopene | terpene
Region 1.27 | T1PKS,terpene | 7,145,500 | 7,279,965 | High | reveromycin A | PKS
Region 1.28 | T1PKS | 7,316,223 | 7,443,763 | Low | akaeolide | PKS
Region 1.29 | T2PKS | 7,450,327 | 7,522,815 | High | WS-5995 D/WS-5995 B/WS-5995 C/SEK 43 | PKS
Region 1.30 | lanthipeptide-class-ii,lanthipeptide-class-iv | 7,986,833 | 8,018,583 |
Region 1.31 | NRPS,T1PKS | 8,044,760 | 8,100,439 |
Region 1.32 | NRPS,T1PKS | 8,126,442 | 8,210,090 |  |
Region 1.33 | T1PKS,NRPS,NRPS-like | 8,439,228 | 8,740,152 | Medium | bafilomycin B1 | PKS:Type I
Region 1.34 | NRP-metallophore,NRPS,T1PKS,betalactone | 8,753,029 | 8,819,825 |  |
Region 3.1 | T3PKS | 1 | 32,347 |

No secondary metabolite regions were found in these records:
  NZ_AP018366.1 (Streptomyces sp. SN-593)

Compact view
NZ_AP018365.1 - Region 1 - lanthipeptide-class-ii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 22,672 - 46,121 nt. (total: 23,450 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
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
RVR_RS00110: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

RVR_RS00120: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS00155: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Hydrolases: esterase
RVR_RS00140: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: cyclase
RVR_RS00135: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Translocases: transporter
RVR_RS00180: 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 | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000528.5 |  | 0.48 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002704.2 |  | 0.47 | ribosomal | archalan β | Halorussus salinus
BGC0002496.3 |  | 0.46 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000503.5 |  | 0.45 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000888.5 |  | 0.44 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001364.3 |  | 0.43 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001579.4 |  | 0.43 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000554.4 |  | 0.43 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001576.3 |  | 0.43 | ribosomal | divamide A | Prochloron didemni

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000525.5 |  | 0.50 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000528.5 |  | 0.48 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002704.2 |  | 0.47 | ribosomal | archalan β | Halorussus salinus
BGC0002496.3 |  | 0.46 | NRPS | serratiochelin A, serratiochelin C, serratiochelin B | Serratia plymuthica
BGC0000503.5 |  | 0.45 | ribosomal | cinnamycin | Streptomyces cinnamoneus
BGC0000888.5 |  | 0.44 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001364.3 |  | 0.43 | ribosomal | cinnamycin B | Actinomadura atramentaria DSM 43919
BGC0001579.4 |  | 0.43 | ribosomal | duramycin | Streptomyces cinnamoneus
BGC0000554.4 |  | 0.43 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001576.3 |  | 0.43 | ribosomal | divamide A | Prochloron didemni

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 RVR_RS00135

RVR_RS00125
Leader:
MENDIVRAWKAYAEPGVAGGGPLQALDVQDVVQGG
Core:
S V V A S W Q G S F S C C D T T L C S D C S I N
Core with dehydrations:
Dha V V A Dha W Q G Dha F Dha Cys Cys D Dhb Dhb L Cys Dha D Cys Dha I N

#### antiSMASH-DB 4.0 matches for RVR_RS00125

100.0%
NZ_AP018365.1:
Lanthipeptides: RVR_RS00125_lanthipeptide
1
S V V A S W Q G S F S C C D T T L C S D C S I N
24
S V V A S W Q G S F S C C D T T L C S D C S I N
1
S V V A S W Q G S F S C C D T T L C S D C S I N
24
79.2%
NZ_FONG01000023.1 and 4 others:
NZ_FONG01000023.1 Lanthipeptides: BM076_RS29665_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: BM076_RS29665_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: BM076_RS29665_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: BM076_RS29665_lanthipeptide
Lanthipeptides: BM076_RS29665_lanthipeptide
2
V V A S W Q G S F S C C D T T L C S D C S I N
24
+ S W Q S F S C C D T T L C S D C S I N
2
I G G S W Q W S F S C C D T T L C S D C S I N
24
54.2%
NZ_AP018365.1:
Lanthipeptides: RVR_RS00130_lanthipeptide
1
S V V A S W Q G S F S C C D T T L C S D C S
22
V+ S W+G+F S C C D T T+C+ C+
1
G V I G S W E G T F S C C D T T I C A G C T
22
with 13 more sequence matches
Only the first 10 are displayed here.
25.0%
NZ_CP031746.1:
Lanthipeptides: DCC27_RS08165_lanthipeptide
3
V A S W Q G S F S C C
13
+ S W Q G +C C
13
M N S W Q G L L T C C
23
25.0%
NZ_MSRJ01000005.1:
Lanthipeptides: BKH06_RS03755_lanthipeptide
5
S W Q G S F S C C
13
S W Q F+C C
15
S W Q F I F T C C
23
24.0%
NZ_FOGI01000013.1 and 1 other:
NZ_RCDD01000003.1 Lanthipeptides: CLV68_RS20325_lanthipeptide
Lanthipeptides: BMY07_RS27390_lanthipeptide
1
S V V A S W Q G S F S C C
13
+V W G S +C C
8
A V A F D W P G S T T C C
20
24.0%
NZ_GL882519.1:
Lanthipeptides: HMPREF9056_RS03330_lanthipeptide
3
V A S W Q G S F S C C
13
+ S W Q F+C C
14
M N S W Q F I F T C C
24
24.0%
NZ_JAEEGA010000010.1:
Lanthipeptides: I6N95_RS15660_lanthipeptide
3
V A S W Q G S F S C C
13
+ S W Q F+C C
14
M N S W Q W I F T C C
24
24.0%
NZ_JH792236.1 and 1 other:
NZ_JH792236.1 Lanthipeptides: IIM_RS26240_lanthipeptide
Lanthipeptides: IIM_RS26245_lanthipeptide
5
S W Q G S F S C C
13
S W Q F+C C
16
S W Q A I F T C C
24
23.1%
NC_012470.1 and 15 others:
NC_012470.1 Lanthipeptides: SZO_RS04065_lanthipeptide NZ_CABY01000005.1 Lanthipeptides: SZBHS5_RS06485_lanthipeptide NZ_CABY01000005.1 Lanthipeptides: SZBHS5_RS06490_lanthipeptide NZ_CP026729.1 Lanthipeptides: BKKJ1_RS07010_lanthipeptide NZ_CP029398.1 Lanthipeptides: DF184_RS05185_lanthipeptide NZ_CP029398.1 Lanthipeptides: DF184_RS05180_lanthipeptide NZ_CP078012.1 Lanthipeptides: KV238_RS09835_lanthipeptide NZ_CP078012.1 Lanthipeptides: KV238_RS09830_lanthipeptide NZ_CP078012.1 Lanthipeptides: KV238_RS09840_lanthipeptide NZ_JAFLMI010000009.1 Lanthipeptides: J0638_RS05350_lanthipeptide NZ_JAFLMI010000009.1 Lanthipeptides: J0638_RS05345_lanthipeptide NZ_LR738724.1 Lanthipeptides: GPW69_RS05065_lanthipeptide NZ_LR738724.1 Lanthipeptides: GPW69_RS05060_lanthipeptide NZ_VZNS01000007.1 Lanthipeptides: F6P79_RS05580_lanthipeptide NZ_VZNS01000007.1 Lanthipeptides: F6P79_RS05575_lanthipeptide
Lanthipeptides: SZO_RS04070_lanthipeptide
3
V A S W Q G S F S C C
13
+ S W Q F+C C
15
M N S W Q F L F T C C
25
22.2%
NZ_CP044492.1 and 1 other:
NZ_CP066294.2 Lanthipeptides: IGS65_RS08185_lanthipeptide
Lanthipeptides: FSA31_RS00605_lanthipeptide
5
S W Q G S F S C C
13
S W Q F+C C
19
S W Q H V F T C C
27
22.2%
NZ_CP046629.1 and 4 others:
NZ_FNJX01000002.1 Lanthipeptides: BLR40_RS05025_lanthipeptide NZ_FNZS01000001.1 Lanthipeptides: BMX70_RS03125_lanthipeptide NZ_FOLK01000002.1 Lanthipeptides: BM262_RS05670_lanthipeptide NZ_VDNV01000006.1 Lanthipeptides: FSV44_RS08765_lanthipeptide
Lanthipeptides: GPA00_RS05740_lanthipeptide
5
S W Q G S F S C C
13
S W Q F+C C
18
S W Q F L F T C C
26
22.2%
NZ_CP069183.1 and 4 others:
NZ_JAHBEV010000004.1 Lanthipeptides: KII98_RS01100_lanthipeptide NZ_JAHBEX010000010.1 Lanthipeptides: KII86_RS06785_lanthipeptide NZ_JAHBFD010000039.1 Lanthipeptides: KIJ16_RS07340_lanthipeptide NZ_LN890331.1 Lanthipeptides: LEKG_RS02295_lanthipeptide
Lanthipeptides: LLNCDO700_RS13730_lanthipeptide
5
S W Q G S F S C C
13
S W Q F+C C
18
S W Q F V F T C C
26

#### MIBiG 4.0 matches for RVR_RS00125

10.8%
BGC0001229.4 (SBI_06989)and 1 other:
BGC0002110.3 (QKV49894.1) Lanthipeptide: birimositide
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
13
C D T T L C S
19
C T T C+
28
C P T T K C T
34
RVR_RS00130
Leader:
MENDIVRAWKAYAEPGVAVSGPLEALDVRDVVKGG
Core:
G V I G S W E G T F S C C D T T I C A G C T G F
Core with dehydrations:
G V I G Dha W E G Dhb F Dha Cys Cys D Dhb Dhb I Cys A G Cys Dhb G F

#### antiSMASH-DB 4.0 matches for RVR_RS00130

100.0%
NZ_AP018365.1:
Lanthipeptides: RVR_RS00130_lanthipeptide
1
G V I G S W E G T F S C C D T T I C A G C T G F
24
G V I G S W E G T F S C C D T T I C A G C T G F
1
G V I G S W E G T F S C C D T T I C A G C T G F
24
54.2%
NZ_AP018365.1:
Lanthipeptides: RVR_RS00125_lanthipeptide
1
G V I G S W E G T F S C C D T T I C A G C T
22
V+ S W+G+F S C C D T T+C+ C+
1
S V V A S W Q G S F S C C D T T L C S D C S
22
50.0%
NZ_FONG01000023.1 and 4 others:
NZ_FONG01000023.1 Lanthipeptides: BM076_RS29665_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: BM076_RS29665_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: BM076_RS29665_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: BM076_RS29665_lanthipeptide
Lanthipeptides: BM076_RS29665_lanthipeptide
4
G S W E G T F S C C D T T I C A G C T
22
G S W+ +F S C C D T T+C+ C+
4
G S W Q W S F S C C D T T L C S D C S
22
with 15 more sequence matches
Only the first 10 are displayed here.
32.1%
NZ_CP048397.1:
Lanthipeptides: SSPS47_RS33185_lanthipeptide
3
I G S W E G T F S C C D T T I--C A G C T
22
+ W S C C+ T+ C G C T
4
L P D W L Y P T S C C E L T V V T C F G C T
25
29.2%
NZ_CP095474.1:
Lanthipeptides: MW084_RS10260_lanthipeptide
12
C C D T T I C A G C T G F
24
C T+ G C T G F
7
C T S T S A S T G C T G F
19
28.0%
NC_010612.1 and 5 others:
NC_020133.1 Lanthipeptides: MULP_RS31530_lanthipeptide NZ_AP017635.1 Lanthipeptides: CPZ18_RS26105_lanthipeptide NZ_AP018410.1 Lanthipeptides: MPSD_RS28020_lanthipeptide NZ_CP024190.1 Lanthipeptides: CCUG20998_RS27770_lanthipeptide NZ_CP058277.1 Lanthipeptides: HXW97_RS10835_lanthipeptide
Lanthipeptides: MMAR_RS29665_lanthipeptide
6
W E G T F S C C D T T I C A G C T G F
24
G C D + A C G F
3
M N G L G P C V D Q A L T A P C L G F
21
28.0%
NZ_CP118910.1:
Lanthipeptides: PQR73_RS04430_lanthipeptide
6
W E G T F S C C D T T I C A G C T G F
24
G C D + A C G F
3
M S G L G P C V D Q A L T A P C L G F
21
20.8%
NZ_CP031746.1:
Lanthipeptides: DCC27_RS08165_lanthipeptide
3
I G S W E G T F S C C
13
+ S W+G +C C
13
M N S W Q G L L T C C
23
20.8%
NZ_MSRJ01000005.1:
Lanthipeptides: BKH06_RS03755_lanthipeptide
3
I G S W E G T F S C C
13
+ S W+ F+C C
13
M N S W Q F I F T C C
23
20.0%
NZ_CP026729.1 and 4 others:
NZ_CP046629.1 Lanthipeptides: GPA00_RS05740_lanthipeptide NZ_FNJX01000002.1 Lanthipeptides: BLR40_RS05025_lanthipeptide NZ_FNZS01000001.1 Lanthipeptides: BMX70_RS03125_lanthipeptide NZ_FOLK01000002.1 Lanthipeptides: BM262_RS05670_lanthipeptide
Lanthipeptides: BKKJ1_RS07010_lanthipeptide
3
I G S W E G T F S C C
13
+ S W+ F+C C
14
M N S W Q F L F T C C
24
20.0%
NZ_GL882519.1:
Lanthipeptides: HMPREF9056_RS03330_lanthipeptide
3
I G S W E G T F S C C D
14
+ S W+ F+C C
14
M N S W Q F I F T C C S
25
20.0%
NZ_JAEEGA010000010.1:
Lanthipeptides: I6N95_RS15660_lanthipeptide
3
I G S W E G T F S C C D
14
+ S W+ F+C C
14
M N S W Q W I F T C C S
25
20.0%
NZ_JH792236.1 and 1 other:
NZ_JH792236.1 Lanthipeptides: IIM_RS26240_lanthipeptide
Lanthipeptides: IIM_RS26245_lanthipeptide
3
I G S W E G T F S C C D
14
+ S W+ F+C C
14
M N S W Q A I F T C C S
25

#### MIBiG 4.0 matches for RVR_RS00130

15.4%
BGC0002110.3 (QKV49894.1):
Lanthipeptide: birimositide
13
C D T T I C A G
20
C T T C
17
C P T T K C T S
24
10.8%
BGC0001229.4 (SBI_06989):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
13
C D T T I C
18
C T T C
28
C P T T K C
33
allorf_0023444_0023620
Leader:
MATRARGDPGDAGQGDPAESGRARAFLAG
Core:
P V P E R R G D P R G A R G P L A G R L P G C G S A R P R
Core with dehydrations:
P V P E R R G D P R G A R G P L A G R L P G Cys G Dha A R P R

#### antiSMASH-DB 4.0 matches for allorf_0023444_0023620

100.0%
NZ_AP018365.1:
Lanthipeptides: allorf_0023444_0023620_lanthipeptide
1
P V P E R R G D P R G A R G P L A G R L P G C G S A R P R
29
P V P E R R G D P R G A R G P L A G R L P G C G S A R P R
1
P V P E R R G D P R G A R G P L A G R L P G C G S A R P R
29
32.4%
NZ_CP102512.1:
Lanthipeptides: allorf_05043013_05043189_lanthipeptide
3
P E R R G D P R G A R G P L A G R L P G C G S A R P R
29
E R+ R G A G+ P G C G+ R
1
S E R Q R P H R G T V A V S A G Q A P G C G A V L T R
27
23.5%
NZ_CP084058.1:
Lanthipeptides: allorf_08395906_08396046_lanthipeptide
5
R R G D P R G A R G P L A G R L P G C
23
R R P R P++G R+ C
11
R R P S P R S I S C P I S G R M L A C
29
with 3 more sequence matches
20.7%
NC_013729.1:
Lanthipeptides: KFLA_RS37060_lanthipeptide
22
G C G S A R P R
29
G C G S A+P
11
G C G S A K P S
18
17.1%
NZ_QOCT01000001.1:
Lanthipeptides: DS833_RS00365_lanthipeptide
14
G P L A G R L P G C G S
25
G + G R L G C S
10
G C I T G R L M G C N S
21
15.4%
NZ_AP019008.1 and 2 others:
NZ_BDDX01000012.1 Lanthipeptides: FF306_RS05510_lanthipeptide NZ_JXCW01000008.1 Lanthipeptides: RZ55_RS07215_lanthipeptide
Lanthipeptides: FF306_RS00060_lanthipeptide
14
G P L A G R L P G C G S
25
G + G R L G C +
10
G C I T G R L M G C N N
21

#### MIBiG 4.0 matches for allorf_0023444_0023620

17.2%
BGC0000580.3 (EGD17354.1)and 1 other:
BGC0000580.3 (EGD17355.1) Lasso peptide: xanthomonin II or xanthomonin I
Lasso peptide: xanthomonin II or xanthomonin I
14
G P L A G R
19
G P L A G
2
G P L A G E
7
allorf_0038677_0038835
Leader:
MCHGPPVRGRRLSRTPAVPAA
Core:
A S R T P V P A A P R C R V P V S A T G G H R C A G R A V T W
Core with dehydrations:
A Dha R Dhb P V P A A P R Cys R V P V Dha A Dhb G G H R Cys A G R A V Dhb W

#### antiSMASH-DB 4.0 matches for allorf_0038677_0038835

100.0%
NZ_AP018365.1:
Lanthipeptides: allorf_0038677_0038835_lanthipeptide
1
A S R T P V P A A P R C R V P V S A T G G H R C A G R A V T W
31
A S R T P V P A A P R C R V P V S A T G G H R C A G R A V T W
1
A S R T P V P A A P R C R V P V S A T G G H R C A G R A V T W
31
25.0%
NZ_JAPTYM010000001.1:
Lanthipeptides: allorf_00301141_00301338_lanthipeptide
6
V P A A P R C R V P V S----A T G G H R C A G
26
V A R C R P V+ T G H R +G
13
V R A G W R C R E P V N L S G H G T G R H R T S G
37
20.5%
NZ_QRDO01000002.1:
Lanthipeptides: allorf_1072387_1072554_lanthipeptide
7
P A A P R C R V P V S
17
P A R C R V P S
6
P K A A R C R V P Q S
16
with 3 more sequence matches
19.4%
NZ_CP011130.1 and 4 others:
NZ_CP023465.1 Lanthipeptides: CNO08_RS25790_lanthipeptide NZ_CP076103.1 Lanthipeptides: KME82_RS10615_lanthipeptide NZ_CP094357.1 Lanthipeptides: IEQ11_RS10290_lanthipeptide NZ_KQ061217.1 Lanthipeptides: WN54_RS27350_lanthipeptide
Lanthipeptides: LC55x_RS27745_lanthipeptide
12
C R V P V S A T G G H R C A G R
27
C S+ G G C+G
8
C N C S T S S N G G C L C S G E
23
17.9%
NZ_BMLN01000009.1:
Lanthipeptides: allorf_125527_125676_lanthipeptide
3
R T P V P A A P R C R V P V S
17
R P P+A P R+ +S
24
R N P S P S A P Y N R L T I S
38
14.0%
NZ_CP068102.1 and 1 other:
NZ_CP068102.1 Lanthipeptides: allorf_1176709_1176894_lanthipeptide
Lanthipeptides: allorf_1176709_1176894_lanthipeptide
13
R V P V S A T G G H R C
24
R P+S A G R C
27
R S P I S A F G S S R C
38

#### MIBiG 4.0 matches for allorf_0038677_0038835

9.8%
BGC0002120.3 (NQE92413.1):
Lanthipeptide: nocathioamide A
7
P A A P R C
12
P A A P C
35
P A A P A C
40

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (5):
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
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.51 out of 30.22
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.73 out of 32.93
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 20.70 out of 36.53
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
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.

RVR_RS00125 - Class II
  Cleavage pHMM score: -2.20
  RODEO score: 0
  Monoisotopic mass: 2370.0 Da
  Molecular weight: 2371.6 Da
  Number of bridges: 4
  Additional modifications: Lac
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2389.6 Da N = 1
    2407.6 Da N = 2
    2425.7 Da N = 3
    2443.7 Da N = 4
RVR_RS00130 - Class II
  Cleavage pHMM score: -3.80
  RODEO score: 0
  Monoisotopic mass: 2306.0 Da
  Molecular weight: 2307.6 Da
  Number of bridges: 4
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2325.6 Da N = 1
    2343.6 Da N = 2
allorf_0023444_0023620 - Class II
  Cleavage pHMM score: -5.20
  RODEO score: 0
  Monoisotopic mass: 2989.6 Da
  Molecular weight: 2991.4 Da
  Number of bridges: 1
allorf_0038677_0038835 - Class II
  Cleavage pHMM score: -6.20
  RODEO score: 0
  Monoisotopic mass: 3096.7 Da
  Molecular weight: 3098.6 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3116.6 Da N = 1
    3134.6 Da N = 2
    3152.6 Da N = 3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_AP018365.1 - Region 2 - NRPS,t3nrps-iterative,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: 216,151 - 316,729 nt. (total: 100,579 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)
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### 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
RVR_RS01075: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

RVR_RS01190: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

RVR_RS01275: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

RVR_RS01325: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

Transferases: methyltransferase
RVR_RS01055: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: dehalogenase hydrolase
RVR_RS01090: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

RVR_RS01260: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

RVR_RS01320: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

Lyases: decarboxylase
RVR_RS01250: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase synthetase
RVR_RS01080: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

RVR_RS01200: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

RVR_RS01235: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | terpene | t3nrps-iterative | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  |  | 0.87 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  |  |  | 0.86 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  |  |  | 0.86 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  |  |  | 0.84 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 0.82 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  |  | 0.82 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  |  |  | 0.82 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  |  | 0.82 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001261.3 |  |  |  | 0.74 | NRPS | AM-toxin | Alternaria alternata
BGC0001641.4 |  |  |  | 0.73 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.82 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000649.3 |  | 0.77 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.75 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001833.4 |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.74 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  | 0.73 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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

No significant matches found.

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:
RVR_RS01050: Lycopene_cycl
Domain 1 (6 - 383): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

RVR_RS01070: PT_phytoene_like
Domain 1 (16 - 319): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

RVR_RS01080: PT_FPPS_like
Domain 1 (136 - 414): 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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
Additional weak hits (16):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.12 out of 25.88
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.87 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.83 out of 29.38
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.08 out of 19.26
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.36 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.52 out of 29.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.91 out of 21.55
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.11 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.22 out of 29.38
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.12 out of 29.65
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 27.04
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.26 out of 29.38
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.29 out of 29.38
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
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 2, location 216150 - 316729:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Thr - Tyr - Pro - Phe - NMe-Tyr - Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 239278 - 316729:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Thr - Tyr - Pro - Phe - NMe-Tyr - 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).
RVR_RS01200: X - Thr - Tyr - Pro - Phe - Tyr - Val
Search NORINE for peptide: strict or relaxed
AMP-binding (469..870): X
nrpys: Orn, Lys, Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDHTFDASWNQMEAAAGGELNFYGPSECTVNTVA
  Nearest Stachelhaus code(s):
    OH-Orn DAQEGGLVDK (59% 8Å match)
    Lys DADDAGTVDK (53% 8Å match)
  Stachelhaus code match:
    60% (weak)

AMP-binding (1540..1943): 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:
    LTTHFDFSVWEGNQVFGGEVNMYGITETTVHVTY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2604..3002): Tyr
nrpys: Tyr

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:
    tyr (Tyr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    LNQTFDASCDQAGGALGGELNFYGPSECTVDSVH
  Nearest Stachelhaus code(s):
    Lys DADDAGTVDK (59% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (3666..4053): 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:
    LWHTFDVSVQESFAAQAGEHNHYGPAETHVITAY
  Nearest Stachelhaus code(s):
    Pro DVQFAAHVVK (91% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (4706..5075): 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:
    LEQAFDASFWDGTLVVAGEINAYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (5730..6098): 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:
    LGQAFDASVSETTVVVAGEINAYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Tyr DASTVAAVCK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (7164..7546): 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:
    LSPSFDLSTYEVWLWTGGDVNGYGPTEATTLATR
  Nearest Stachelhaus code(s):
    Val DAYWWGGTFK (85% 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
--- | ---
RpoN | Regulator of nitrogen assimilation and virulence

NZ_AP018365.1 - Region 3 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 317,963 - 359,036 nt. (total: 41,074 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase electron transfer oxidase oxidoreductase
RVR_RS01455: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

RVR_RS01460: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

RVR_RS01500: flavodoxin

smcogs
  SMCOG1134: flavodoxin

RVR_RS01520: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

RVR_RS01525: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase methyltransferase
RVR_RS01435: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

RVR_RS01450: Methylation

MITE
  MITE0000155Methylation (identity: 70.60%)
smcogs
  SMCOG1150: isoprenylcysteine carboxyl methyltransferase

Hydrolases: esterase
RVR_RS38510: putative esterase

smcogs
  SMCOG1104: putative esterase

Lyases: dehydratase
RVR_RS01365: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
RVR_RS01360: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

RVR_RS01445: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.82 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002276.2 |  | 0.56 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001831.3 |  | 0.53 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000528.5 |  | 0.46 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001964.2 |  | 0.45 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0002362.3 |  | 0.45 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0000249.5 |  | 0.44 | PKS | nogalamycin | Streptomyces nogalater
BGC0001647.3 |  | 0.43 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0002315.2 |  | 0.41 | PKS | accramycin A | Streptomyces sp.
BGC0000786.3 |  | 0.41 | saccharide | O-antigen | Edwardsiella ictaluri 93-146

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.82 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002276.2 |  | 0.56 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001831.3 |  | 0.53 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0000528.5 |  | 0.46 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001964.2 |  | 0.45 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0002362.3 |  | 0.45 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0000249.5 |  | 0.44 | PKS | nogalamycin | Streptomyces nogalater
BGC0001647.3 |  | 0.43 | PKS | lagunapyrone A, lagunapyrone B, lagunapyrone C | Streptomyces sp. MP131-18
BGC0002315.2 |  | 0.41 | PKS | accramycin A | Streptomyces sp.
BGC0000786.3 |  | 0.41 | saccharide | O-antigen | Edwardsiella ictaluri 93-146

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.

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
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.32 out of 23.79
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.03 out of 36.53
Confidence: medium
Additional weak hits (13):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.77 out of 26.06
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.60 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.23 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.02 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.03 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.45 out of 26.33
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.91 out of 19.26
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.11 out of 21.55
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.15 out of 29.65
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.00 out of 28.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.20 out of 33.14
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.25 out of 33.14
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.41 out of 36.53
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
--- | ---
DmdR1 | Iron(II)-dependent repressor
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP018365.1 - Region 4 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 651,404 - 662,222 nt. (total: 10,819 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
--- | --- | --- | --- | --- | ---
BGC0001882.3 |  | 0.22 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0002805.2 |  | 0.20 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001755.5 |  | 0.20 | PKS | reedsmycin A, reedsmycin B, reedsmycin C, reedsmycin D, reedsmycin E | Streptomyces sp.
BGC0000495.5 |  | 0.20 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0000266.5 |  | 0.19 | PKS | collinomycin | Streptomyces collinus
BGC0002288.2 |  | 0.19 | NRPS | ashimide A, ashimide B | Streptomyces sp. NA03103

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001882.3 |  | 0.22 | PKS | chrysoxanthone A, chrysoxanthone B, chrysoxanthone C | Penicillium rubens Wisconsin 54-1255
BGC0002805.2 |  | 0.20 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0001755.5 |  | 0.20 | PKS | reedsmycin A, reedsmycin B, reedsmycin C, reedsmycin D, reedsmycin E | Streptomyces sp.
BGC0000495.5 |  | 0.20 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0000266.5 |  | 0.19 | PKS | collinomycin | Streptomyces collinus
BGC0002288.2 |  | 0.19 | NRPS | ashimide A, ashimide B | Streptomyces sp. NA03103

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: 26.07 out of 30.12
Confidence: medium
Additional weak hits (5):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.44 out of 30.22
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.29 out of 23.43
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.02 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.23 out of 28.19
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.13 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_AP018365.1 - Region 5 - 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: 726,609 - 749,260 nt. (total: 22,652 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
Transferases: acetyltransferase glycosyltransferase transferase
RVR_RS03145: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

RVR_RS03150: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

RVR_RS03155: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

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 |  | 0.49 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.49 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000519.4 |  | 0.48 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002111.3 |  | 0.48 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000553.3 |  | 0.47 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000518.3 |  | 0.45 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002701.2 |  | 0.44 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0001521.3 |  | 0.40 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0000885.3 |  | 0.39 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000582.4 |  | 0.38 | ribosomal | cypemycin | Streptomyces sp. OH-4156

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000496.5 |  | 0.49 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000551.5 |  | 0.49 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000519.4 |  | 0.48 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002111.3 |  | 0.48 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000553.3 |  | 0.47 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000518.3 |  | 0.45 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736
BGC0002701.2 |  | 0.44 | ribosomal | paenithipeptin | Paenibacillus thiaminolyticus
BGC0001521.3 |  | 0.40 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0000885.3 |  | 0.39 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000582.4 |  | 0.38 | ribosomal | cypemycin | Streptomyces sp. OH-4156

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 RVR_RS03130

RVR_RS03120
Leader:
MADAVDPTNEDTTAETENEVEAHSEALDLQEMGVSGLE
Core:
A P G S T V S L A A C A
Core with dehydrations:
A P G Dha Dhb V Dha L A A Cys A

#### antiSMASH-DB 4.0 matches for RVR_RS03120

100.0%
NZ_AP018365.1:
Lanthipeptides: RVR_RS03120_lanthipeptide
1
A P G S T V S L A A C A
12
A P G S T V S L A A C A
1
A P G S T V S L A A C A
12
30.0%
NZ_CP084585.1:
Lanthipeptides: LFM56_RS02720_lanthipeptide
3
G S T V S L A A C
11
G S T+S+A C
3
G S T I S I A L C
11
25.9%
NZ_CP016076.1:
Lanthipeptides: UA74_RS09535_lanthipeptide
3
G S T V S L A A C
11
G T V S+A A C
7
G I T V S I A A C
15
with 1 more sequence matches
25.8%
NZ_CP048405.1 and 3 others:
NZ_CP048405.1 Lanthipeptides: GXW83_RS22630_lanthipeptide NZ_CP048405.1 Lanthipeptides: GXW83_RS22630_lanthipeptide NZ_CP048405.1 Lanthipeptides: GXW83_RS22630_lanthipeptide
Lanthipeptides: GXW83_RS22630_lanthipeptide
3
G S T V S L A A C A
12
S+V S L A A C A
22
S S S V S L A A C A
31
RVR_RS03125
Leader:
MADPVDPASSAVPDDEQTAPEAADGESEVEAHVANPLDLQEMGVQTSFADNV
Core:
I G S T S A T S L I S C C
Core with dehydrations:
I G Dha Dhb Dha A Dhb Dha L I Dha Cys Cys

#### antiSMASH-DB 4.0 matches for RVR_RS03125

100.0%
NZ_AP018365.1:
Lanthipeptides: RVR_RS03125_lanthipeptide
1
I G S T S A T S L I S C C
13
I G S T S A T S L I S C C
1
I G S T S A T S L I S C C
13

#### 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:
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 (7):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.73 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.11 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.83 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.01 out of 26.06
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.64 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.32 out of 30.25
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.37 out of 18.57
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.

RVR_RS03120 - Class III
  Cleavage pHMM score: 2.10
  RODEO score: 0
  Monoisotopic mass: 992.5 Da
  Molecular weight: 993.1 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1011.1 Da N = 1
    1029.2 Da N = 2
RVR_RS03125 - Class III
  Cleavage pHMM score: 3.70
  RODEO score: 0
  Monoisotopic mass: 1133.6 Da
  Molecular weight: 1134.3 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1152.3 Da N = 1
    1170.3 Da N = 2
    1188.4 Da N = 3
    1206.4 Da N = 4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_AP018365.1 - Region 6 - azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,036,781 - 1,060,759 nt. (total: 23,979 nt) Show pHMM detection rules used
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
RVR_RS04455: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: esterase
RVR_RS04400: putative esterase

smcogs
  SMCOG1104: putative esterase

Lyases: cyclase
RVR_RS04435: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

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

Reference | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002698.2 |  | 0.54 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000565.5 |  | 0.52 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0001555.4 |  | 0.51 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000551.5 |  | 0.51 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.50 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002115.3 |  | 0.47 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0002699.2 |  | 0.46 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0000483.5 |  | 0.45 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0001229.4 |  | 0.45 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000605.5 |  | 0.44 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002698.2 |  | 0.54 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0000565.5 |  | 0.52 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0001555.4 |  | 0.51 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000551.5 |  | 0.51 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.50 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0002115.3 |  | 0.47 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0002699.2 |  | 0.46 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0000483.5 |  | 0.45 | ribosomal | aeruginosamide B, aeruginosamide C | Microcystis aeruginosa PCC 9432
BGC0001229.4 |  | 0.45 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000605.5 |  | 0.44 | ribosomal | GE37468 | Streptomyces sp. ATCC 55365

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

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 (7):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.82 out of 29.38
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.28 out of 31.73
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.66 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.23 out of 21.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.34 out of 26.12
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 26.85
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84
Confidence: weak
(Thi)azol(in)e containing peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
RREFinder
TFBS Finder
Azole RiPPs
RRE predictions
RREfinder results sidepanel.

azole-containing-RiPP protocluster (1036780...1060759)
RVR_RS04430
  RRE type: Goadsporin_CD_RRE
  Location: 7 - 104
  Score: 77.7
  RRE type: NHLP_CD_RRE
  Location: 8 - 101
  Score: 67.2
  RRE type: Cyanobactin_D_RRE
  Location: 8 - 86
  Score: 57.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.
NZ_AP018365.1 - Region 7 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,159,768 - 1,200,952 nt. (total: 41,185 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
RVR_RS04890: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

RVR_RS04895: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

RVR_RS04940: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

RVR_RS04985: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

RVR_RS05035: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

RVR_RS05050: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

RVR_RS05055: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Hydrolases: deacetylase
RVR_RS04925: acetylornithine deacetylase

smcogs
  SMCOG1247: acetylornithine deacetylase

Ligases: synthase
RVR_RS04990: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.85 | other (other) | germicidin | Streptomyces argillaceus
BGC0000244.4 |  | 0.46 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0001905.4 |  | 0.45 | PKS | violapyrone B | Streptomyces somaliensis
BGC0000908.3 |  | 0.40 | other (other) | melanin | Streptomyces avermitilis
BGC0001441.5 |  | 0.39 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0000252.5 |  | 0.39 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0002282.2 |  | 0.39 | other (other) | formycin A | Streptomyces kaniharaensis
BGC0001927.4 |  | 0.39 | other (other) | A-94964 | Streptomyces sp.
BGC0000916.5 |  | 0.38 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0001940.3 |  | 0.38 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.85 | other (other) | germicidin | Streptomyces argillaceus
BGC0000244.4 |  | 0.46 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0001905.4 |  | 0.45 | PKS | violapyrone B | Streptomyces somaliensis
BGC0000908.3 |  | 0.40 | other (other) | melanin | Streptomyces avermitilis
BGC0001441.5 |  | 0.39 | other (other) | belactosin A, belactosin C | Streptomyces sp.
BGC0000252.5 |  | 0.39 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0002282.2 |  | 0.39 | other (other) | formycin A | Streptomyces kaniharaensis
BGC0001927.4 |  | 0.39 | other (other) | A-94964 | Streptomyces sp.
BGC0000916.5 |  | 0.38 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0001940.3 |  | 0.38 | PKS | pyxidicycline A, pyxidicycline B | Pyxidicoccus fallax

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
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.78 out of 25.88
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 17.98 out of 23.79
Confidence: medium
Additional weak hits (6):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.16 out of 26.06
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.99 out of 25.31
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.52 out of 32.74
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.73 out of 30.98
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
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
PsrA | Oleic acid responsive regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP018365.1 - Region 8 - 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: 1,216,732 - 1,237,760 nt. (total: 21,029 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
RVR_RS05145: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase
RVR_RS05180: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase
RVR_RS05175: Terpene synthase/cyclase metal-binding domain protein

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

Isomerases: racemase
RVR_RS05135: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

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 |  | 0.64 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000894.4 |  | 0.46 | other (other) | citrinin | Monascus aurantiacus
BGC0002493.3 |  | 0.41 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001928.2 |  | 0.40 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001219.3 |  | 0.40 | PKS | shanorellin | Chaetomium globosum CBS 148.51
BGC0000678.5 |  | 0.40 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001605.3 |  | 0.39 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002138.2 |  | 0.38 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670

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 |  | 0.64 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0000894.4 |  | 0.46 | other (other) | citrinin | Monascus aurantiacus
BGC0002493.3 |  | 0.41 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001928.2 |  | 0.40 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001219.3 |  | 0.40 | PKS | shanorellin | Chaetomium globosum CBS 148.51
BGC0000678.5 |  | 0.40 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001605.3 |  | 0.39 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002138.2 |  | 0.38 | 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:
RVR_RS05175: T1TS
Domain 1 (12 - 336): 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
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
Additional weak hits (3):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.87 out of 32.74
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.85 out of 30.97
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40
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_AP018365.1 - Region 9 - T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,352,155 - 1,424,634 nt. (total: 72,480 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
RVR_RS05785: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS05800: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS05820: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS05825: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS05860: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS05890: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS05900: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS05905: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: methyltransferase sulfotransferase
RVR_RS05810: Sulfotransferase domain

extras
  Sulfotransfer_4: Sulfotransferase domain

RVR_RS05970: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: amidase back translocase dehalogenase hydrolase
RVR_RS05775: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

RVR_RS05840: GTP-binding protein LepA

smcogs
  SMCOG1190: GTP-binding protein LepA

RVR_RS05940: amidase

smcogs
  SMCOG1105: amidase

RVR_RS05985: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: cyclase lyase
RVR_RS05870: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

RVR_RS05895: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

RVR_RS05950: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

RVR_RS05975: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

RVR_RS05990: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: synthase
RVR_RS05875: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS05880: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: transport
RVR_RS05745: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.83 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.77 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.76 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002458.3 |  | 0.66 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0002047.2 |  | 0.64 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000272.3 |  | 0.61 | PKS | spore pigment | Streptomyces collinus
BGC0000253.4 |  | 0.60 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000235.5 |  | 0.59 | PKS | kiamycin | Streptomyces sp. W007
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002504.2 |  | 0.57 | PKS | nocardiopsistin A, nocardiopsistin B, nocardiopsistin C | Nocardiopsis sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.83 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.77 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001723.5 |  | 0.76 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002458.3 |  | 0.66 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0002047.2 |  | 0.64 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000272.3 |  | 0.61 | PKS | spore pigment | Streptomyces collinus
BGC0000253.4 |  | 0.60 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000235.5 |  | 0.59 | PKS | kiamycin | Streptomyces sp. W007
BGC0002276.2 |  | 0.58 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002504.2 |  | 0.57 | PKS | nocardiopsistin A, nocardiopsistin B, nocardiopsistin C | Nocardiopsis 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.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 17.91 out of 23.79
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.90 out of 28.19
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
Additional weak hits (9):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.79 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.82 out of 27.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.60 out of 25.88
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.49 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.82 out of 28.19
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.63 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.19 out of 33.14
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  1352154 to 1424634
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:
  8|9 (Score: 694.9; E-value: 6.4e-212)
Product class(es):
  angucycline
Product molecular weight(s):
  acetyl-CoA_8: 446 Da
  acetyl-CoA_9: 488 Da

RVR_RS05780
  DIMER (Score: 340.1; E-value: 2.3e-104)
RVR_RS05785
  OXY (Score: 315.4; E-value: 1.7e-96)
RVR_RS05800
  KR (Score: 143.0; E-value: 3e-44)
RVR_RS05820
  OXY (Score: 468.1; E-value: 8.3e-143)
RVR_RS05825
  OXY (Score: 495.9; E-value: 3.1e-151)
RVR_RS05860
  OXY (Score: 532.2; E-value: 2.9e-162)
RVR_RS05870
  CYC C4-C17/C2-C19 (Score: 197.9; E-value: 3.7e-61)
RVR_RS05875
  KS (Score: 770.9; E-value: 6.5e-235)
RVR_RS05880
  CLF 8|9 (Score: 694.9; E-value: 6.4e-212)
RVR_RS05885
  ACP (Score: 122.2; E-value: 1.6e-38)
RVR_RS05890
  KR C9 (Score: 465.0; E-value: 1.5e-142)
RVR_RS05895
  CYC C7-C12 (Score: 471.0; E-value: 3.1e-144)
RVR_RS05900
  OXY (Score: 561.4; E-value: 4.1e-171)
RVR_RS05905
  OXY (Score: 565.1; E-value: 3.2e-172)
RVR_RS05970
  MET (Score: 289.3; E-value: 8.9e-89)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_AP018365.1 - Region 10 - 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: 1,429,832 - 1,474,994 nt. (total: 45,163 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
RVR_RS06205: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

RVR_RS06210: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

RVR_RS06225: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase transferase
RVR_RS06175: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

RVR_RS06235: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: esterase
RVR_RS06160: putative esterase

smcogs
  SMCOG1104: putative esterase

Isomerases: racemase
RVR_RS06195: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase synthase
RVR_RS06065: 1-deoxy-D-xylulose-5-phosphate synthase

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

RVR_RS06165: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS06170: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS06220: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001535.3 |  | 0.68 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001275.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.60 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002276.2 |  | 0.59 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001161.5 |  | 0.53 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0001162.3 |  | 0.53 | PKS | 1-heptadecene | Moorea producens JHB

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001535.3 |  | 0.68 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001275.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001276.3 |  | 0.60 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.60 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002276.2 |  | 0.59 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001161.5 |  | 0.53 | PKS | 1-heptadecene | Moorea bouillonii PNG
BGC0001162.3 |  | 0.53 | PKS | 1-heptadecene | Moorea producens JHB

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
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
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.73 out of 23.79
Confidence: medium
Additional weak hits (13):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.56 out of 28.14
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.91 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.60 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.83 out of 30.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.56 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.91 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.90 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.08 out of 32.93
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.51 out of 26.85
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.73 out of 35.63
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 12, location 1429831 - 1474994:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (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).
RVR_RS06165: mmal
PKS_AT (775..1068): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 66.7%
  Ethylmalonyl-CoA: 62.5%
  Methoxymalonyl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 111.1
  Methoxymalonyl-CoA: 100.8
  Ethylmalonyl-CoA: 93.6
  Malonyl-CoA: 69.4
  Propionyl-CoA: 61.7
  trans-1,2-CPDA: 54.0
  2-Methylbutyryl-CoA: 43.5
  Acetyl-CoA: 42.8
  fatty_acid: 41.5
  Isobutyryl-CoA: 41.4
  CHC-CoA: 32.6
  inactive: 25.9
  3-Methylbutyryl-CoA: 14.3
  Benzoyl-CoA: 13.1

RVR_RS06170: AHBA
CAL_domain (46..520): AHBA
minowa: AHBA

Prediction, score:
  AHBA: 18.0
  fatty_acid: 17.0
  NH2: 14.8
  Acetyl-CoA: 1.5
  shikimic_acid: 0.0

RVR_RS06220: X
AMP-binding (32..483): 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:
    NRQLITGMVCQAVGASGGAANGYGLTECTAPCAS
  Nearest Stachelhaus code(s):
    Ac or MalAc TTIMAGGGPK (32% 8Å match)
  Stachelhaus code match:
    60% (weak)

Link to PARAS substrate predictor
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_AP018365.1 - Region 11 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,482,777 - 1,503,805 nt. (total: 21,029 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
RVR_RS06320: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
RVR_RS06330: 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
--- | --- | --- | --- | --- | ---
BGC0002007.2 |  | 0.39 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000646.5 |  | 0.38 | terpene | β-carotein | uncultured bacterium
BGC0000641.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000642.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000639.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000638.3 |  | 0.37 | terpene | carotenoid | Pantoea ananatis
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000640.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000635.3 |  | 0.36 | terpene | carotenoid | Paracoccus sp. N81106
BGC0001456.3 |  | 0.36 | terpene | isorenieratene | Streptomyces argillaceus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002007.2 |  | 0.39 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0000646.5 |  | 0.38 | terpene | β-carotein | uncultured bacterium
BGC0000641.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000642.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000639.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000638.3 |  | 0.37 | terpene | carotenoid | Pantoea ananatis
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000640.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000635.3 |  | 0.36 | terpene | carotenoid | Paracoccus sp. N81106
BGC0001456.3 |  | 0.36 | terpene | isorenieratene | Streptomyces argillaceus

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:
RVR_RS06330: PT_FPPS_like
Domain 1 (46 - 341): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 17.99 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84
Confidence: medium
Additional weak hits (17):
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.36 out of 21.84
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.54 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.07 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.60 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.54 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.32 out of 18.57
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.82 out of 27.55
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.41 out of 18.57
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.19 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.95 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.00 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.16 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.97 out of 24.78
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
MexT | Global virulence regulator

NZ_AP018365.1 - Region 12 - HR-T2PKS,thioamide-NRP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,747,500 - 1,803,059 nt. (total: 55,560 nt) Show pHMM detection rules used
thioamide-NRP: (ATP-grasp and AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC))
HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-synt))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS 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
RVR_RS07345: flavodoxin

smcogs
  SMCOG1134: flavodoxin

RVR_RS07425: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: halogenase methyltransferase
RVR_RS07325: methyltransferase

smcogs
  SMCOG1089: methyltransferase

RVR_RS07365: halogenase

smcogs
  SMCOG1119: halogenase

Hydrolases: esterase
RVR_RS07350: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

RVR_RS07535: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

smcogs
  SMCOG1283: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

Lyases: decarboxylase
RVR_RS07450: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
RVR_RS07375: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS07380: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS07385: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS07435: 3-oxoacyl-(acyl carrier protein) synthase III

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

RVR_RS07460: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | thioamide-NRP | HR-T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001250.4 |  |  | 0.54 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  |  | 0.54 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  |  | 0.53 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  |  | 0.53 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001166.5 |  |  | 0.52 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001261.3 |  |  | 0.52 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  |  | 0.51 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  |  | 0.51 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  |  | 0.51 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002164.2 |  |  | 0.50 | NRPS | peramine | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001250.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.60 | NRPS | epichloenin A | Epichloe festucae
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001166.5 |  | 0.60 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001261.3 |  | 0.60 | NRPS | AM-toxin | Alternaria alternata
BGC0001249.5 |  | 0.59 | NRPS | dimethylcoprogen | Alternaria alternata
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002164.2 |  | 0.58 | 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.56 out of 23.79
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.87 out of 29.72
Confidence: medium
Additional weak hits (11):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.34 out of 26.85
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.67 out of 29.72
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.03 out of 30.97
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.42 out of 29.38
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.81 out of 29.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.70 out of 21.55
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.43 out of 29.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.43 out of 21.55
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
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.33 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.48 out of 29.65
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
RVR_RS07375: X
AMP-binding (22..423): 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:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    ala (Ala)

Stachelhaus prediction details:
  Stachelhaus sequence:
    YHVFFDLAMFDCFSLFCGEENLYGPTELTISCSA
  Nearest Stachelhaus code(s):
    Gly DLFFLCLLSK (82% 8Å match)
    foGly DLFFLCLIAK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP018365.1 - Region 13 - 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: 1,887,695 - 1,909,971 nt. (total: 22,277 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 oxidoreductase
RVR_RS07910: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

RVR_RS07940: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

RVR_RS07945: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: phosphorylase
RVR_RS07930: thiamine-phosphate pyrophosphorylase

smcogs
  SMCOG1280: thiamine-phosphate pyrophosphorylase

Lyases: cyclase
RVR_RS07915: 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
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.75 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0002345.2 |  | 0.40 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0001521.3 |  | 0.38 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001782.3 |  | 0.36 | 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
BGC0002294.3 |  | 0.35 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000934.4 |  | 0.34 | other (phenazine) | 5-acetyl-5,10-dihydrophenazine-1-carboxylic acid, 5-(2-hydroxyacetyl)-5,10-dihydrophenazine-1-carboxylic acid, endophenazine A1, endophenazine F, endophenazine G | Kitasatospora sp. HKI 714
BGC0002578.2 |  | 0.34 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000648.3 |  | 0.34 | terpene | carotenoid | Myxococcus xanthus
BGC0001302.5 |  | 0.34 | other (other) | lomofungin | Streptomyces lomondensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.81 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001746.3 |  | 0.75 | terpene | pristinol | Streptomyces pristinaespiralis ATCC 25486
BGC0002345.2 |  | 0.40 | other (other) | hydrogen cyanide | Pseudomonas fluorescens
BGC0001521.3 |  | 0.38 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0001782.3 |  | 0.36 | 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
BGC0002294.3 |  | 0.35 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus
BGC0000934.4 |  | 0.34 | other (phenazine) | 5-acetyl-5,10-dihydrophenazine-1-carboxylic acid, 5-(2-hydroxyacetyl)-5,10-dihydrophenazine-1-carboxylic acid, endophenazine A1, endophenazine F, endophenazine G | Kitasatospora sp. HKI 714
BGC0002578.2 |  | 0.34 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0000648.3 |  | 0.34 | terpene | carotenoid | Myxococcus xanthus
BGC0001302.5 |  | 0.34 | 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.

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:
RVR_RS07915: T1TS + T1TS
Domain 1 (2 - 326): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (328 - 706): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.68 out of 20.47
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.53 out of 23.79
Confidence: medium
Additional weak hits (2):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.24 out of 35.63
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP018365.1 - Region 14 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,998,428 - 2,024,872 nt. (total: 26,445 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
RVR_RS08445: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

RVR_RS08450: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.54 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0002298.2 |  | 0.41 | ribosomal | lassomycin-like peptide | Sanguibacter keddieii DSM 10542
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000565.5 |  | 0.40 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000285.5 |  | 0.39 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0002289.2 |  | 0.38 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii
BGC0002116.3 |  | 0.38 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0002668.2 |  | 0.37 | ribosomal | cesin A | Clostridium estertheticum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.54 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0002298.2 |  | 0.41 | ribosomal | lassomycin-like peptide | Sanguibacter keddieii DSM 10542
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000565.5 |  | 0.40 | ribosomal | goadsporin | Streptomyces sp. TP-A0584
BGC0000285.5 |  | 0.39 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0002289.2 |  | 0.38 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii
BGC0002116.3 |  | 0.38 | ribosomal | darobactin A | Photorhabdus khanii HGB 1456
BGC0002668.2 |  | 0.37 | ribosomal | cesin A | Clostridium estertheticum

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 RVR_RS08445

RVR_RS08440
Leader:
MTQKVSTSITRTEEQPPSDGFDLNVSLLEVSDAASL
Core:
T S L T D D N C G S T C G A C T T N V A
Core with dehydrations:
Dhb Dha L Dhb D D N Cys G Dha Dhb Cys G A Cys Dhb Dhb N V A

#### antiSMASH-DB 4.0 matches for RVR_RS08440

100.0%
NZ_AP018365.1:
Lanthipeptides: RVR_RS08440_lanthipeptide
1
T S L T D D N C G S T C G A C T T N V A
20
T S L T D D N C G S T C G A C T T N V A
1
T S L T D D N C G S T C G A C T T N V A
20
90.0%
NC_021177.1 and 1 other:
NZ_BMUG01000006.1 Lanthipeptides: IE264_RS18330_lanthipeptide
Lanthipeptides: SFUL_RS28885_lanthipeptide
3
L T D D N C G S T C G A C T T N V A
20
L T D D N C G S T C G A C T T N V A
1
L T D D N C G S T C G A C T T N V A
18
85.0%
NZ_BMSI01000021.1 and 1 other:
NZ_JAPTYM010000001.1 Lanthipeptides: O1M07_RS07535_lanthipeptide
Lanthipeptides: IE189_RS36010_lanthipeptide
3
L T D D N C G S T C G A C T T N V A
20
L T D D C G S T C G A C T T N V A
1
L T D D G C G S T C G A C T T N V A
18
with 139 more sequence matches
Only the first 10 are displayed here.
81.8%
NZ_AQRK01000088.1 and 27 others:
NZ_BMVQ01000014.1 Lanthipeptides: IE283_RS30975_lanthipeptide NZ_CP019724.1 Lanthipeptides: B1H29_RS19645_lanthipeptide NZ_CP019724.1 Lanthipeptides: B1H29_RS08000_lanthipeptide NZ_CP022438.1 Lanthipeptides: CGZ69_RS15030_lanthipeptide NZ_CP022438.1 Lanthipeptides: CGZ69_RS15030_lanthipeptide NZ_CP023202.1 Lanthipeptides: SXIN_RS04650_lanthipeptide NZ_CP023700.1 Lanthipeptides: CP969_RS17265_lanthipeptide NZ_CP023702.1 Lanthipeptides: CP967_RS19640_lanthipeptide NZ_CP033073.1 Lanthipeptides: D9753_RS20300_lanthipeptide NZ_CP063808.1 Lanthipeptides: IOD14_RS42650_lanthipeptide NZ_CP071872.1 Lanthipeptides: J4032_RS33705_lanthipeptide NZ_CP071872.1 Lanthipeptides: J4032_RS33705_lanthipeptide NZ_CP075691.1 Lanthipeptides: KKZ08_RS16460_lanthipeptide NZ_CP082362.1 Lanthipeptides: K4G22_RS18080_lanthipeptide NZ_CP094676.1 Lanthipeptides: L6J92_RS33095_lanthipeptide NZ_CP101138.1 Lanthipeptides: M6G08_RS35600_lanthipeptide NZ_CP117709.1 Lanthipeptides: PSQ21_RS13565_lanthipeptide NZ_CP117866.1 Lanthipeptides: PBV52_RS22590_lanthipeptide NZ_JAFIQY010000056.1 Lanthipeptides: JXZ78_RS36930_lanthipeptide NZ_JAJDST010000050.1 Lanthipeptides: LJC81_RS33260_lanthipeptide NZ_JAJDST010000050.1 Lanthipeptides: LJC81_RS33260_lanthipeptide NZ_JH993790.1 Lanthipeptides: STRVIR_RS0119395_lanthipeptide NZ_KB890926.1 Lanthipeptides: B053_RS0114140_lanthipeptide NZ_KB891987.1 Lanthipeptides: B079_RS0100320_lanthipeptide NZ_KB912961.1 Lanthipeptides: B065_RS0117615_lanthipeptide NZ_KQ947985.1 Lanthipeptides: AQI70_RS05650_lanthipeptide NZ_LIPF01000016.1 Lanthipeptides: AMK11_RS35705_lanthipeptide
Lanthipeptides: YUW_RS13695_lanthipeptide
2
S L T D D N C G S T C G A C T T N V A
20
+L T D D N C G S T C G A C T T N V A
4
N L T D D N C G S T C G A C T T N V A
22
80.0%
NZ_BBVA01000002.1 and 7 others:
NZ_CP030865.1 Lanthipeptides: MicB006_RS27820_lanthipeptide NZ_FMCS01000017.1 Lanthipeptides: GA0070214_RS30700_lanthipeptide NZ_JAGPXW010000015.1 Lanthipeptides: KBX71_RS18490_lanthipeptide NZ_JALJRJ010000030.1 Lanthipeptides: OC439_RS27920_lanthipeptide NZ_LT594324.1 Lanthipeptides: GA0070621_RS04875_lanthipeptide NZ_LT607410.1 Lanthipeptides: GA0074696_RS20405_lanthipeptide NZ_LT607753.1 Lanthipeptides: GA0070614_RS02740_lanthipeptide
Lanthipeptides: A4R25_RS30565_lanthipeptide
2
S L T D D N C G S T C G A C T T N V A
20
+L T D D C G S T C A C T T N V A
1
N L T D D G C G S T C T A C T T N V A
19
80.0%
NZ_CP018870.1 and 1 other:
NZ_CP030862.1 Lanthipeptides: C0216_RS09890_lanthipeptide
Lanthipeptides: BSL84_RS27525_lanthipeptide
2
S L T D D N C G S T C G A C T T N V
19
+L T D D N C G S T C G A C T T V
2
T L T D D N C G S T C G A C T T G V
19
77.3%
NZ_BCMN01000021.1:
Lanthipeptides: AV140_RS32375_lanthipeptide
2
S L T D D N C G S T C G A C T T N V A
20
+L T D D C G S T C G A C T T N V A
4
N L T D D G C G S T C G A C T T N V A
22
77.3%
NZ_CP028834.1 and 1 other:
NZ_CP074380.1 Lanthipeptides: KGS77_RS25025_lanthipeptide
Lanthipeptides: DBP13_RS26755_lanthipeptide
2
S L T D D N C G S T C G A C T T N V A
20
S L T D D C G T C G A C T T N V A
4
S L T D D G C G E T C G A C T T N V A
22
77.3%
NZ_CP070379.1 and 1 other:
NZ_LFBV01000012.1 Lanthipeptides: AB852_RS38205_lanthipeptide
Lanthipeptides: JVE63_RS15825_lanthipeptide
2
S L T D D N C G S T C G A C T T N V A
20
+L T D D N C G+T C G A C T T N V A
4
N L T D D N C G T T C G A C T T N V A
22
75.0%
NZ_CP023701.1:
Lanthipeptides: CP968_RS31915_lanthipeptide
2
S L T D D N C G S T C G A C T T N V
19
+L T D D C G S T C G A C T T V
1
N L T D D G C G S T C G A C T T G V
18
75.0%
NZ_CP026498.1 and 1 other:
NZ_KK853997.1 Lanthipeptides: KCH_RS39425_lanthipeptide
Lanthipeptides: C2142_RS04990_lanthipeptide
3
L T D D N C G S T C G A C T T N V
19
L T D D C G S T C G A C T T V
2
L T D D G C G S T C G A C T T G V
18
75.0%
NZ_FZOF01000021.1:
Lanthipeptides: CHF15_RS30750_lanthipeptide
3
L T D D N C G S T C G A C T T N V A
20
L T D D C G S T C G A C T T A
1
L T D D G C G S T C G A C T T G A A
18
75.0%
NZ_JAINUL010000001.1:
Lanthipeptides: K7B10_RS07615_lanthipeptide
2
S L T D D N C G S T C G A C T T N V
19
+L T D D C G S T C G A C T T V
2
T L T D D G C G S T C G A C T T G V
19

#### 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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.52 out of 23.79
Confidence: medium
Additional weak hits (3):
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.74 out of 29.72
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.68 out of 23.43
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
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

RVR_RS08440 - Class I
  Cleavage pHMM score: -7.70
  RODEO score: 20
  Monoisotopic mass: 1806.7 Da
  Molecular weight: 1807.9 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1825.9 Da N = 1
    1843.9 Da N = 2
    1862.0 Da N = 3
    1880.0 Da N = 4

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (1998427...2024872)
RVR_RS08445
  RRE type: Lanthipeptide_LanB_RRE
  Location: 161 - 253
  Score: 63.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_AP018365.1 - Region 15 - T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,275,676 - 2,383,532 nt. (total: 107,857 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 oxidoreductase oxygenase
RVR_RS09375: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

RVR_RS09415: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

RVR_RS09440: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

RVR_RS09485: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

RVR_RS09645: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

RVR_RS09725: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: glycosyltransferase
RVR_RS09390: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: dehalogenase esterase hydrolase
RVR_RS09425: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

RVR_RS09550: thioesterase superfamily protein

smcogs
  SMCOG1144: thioesterase superfamily protein

RVR_RS09555: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: decarboxylase
RVR_RS09450: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: ligase synthase
RVR_RS09455: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS09560: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS09640: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS09660: 3-oxoacyl-(acyl carrier protein) synthase III

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

RVR_RS09665: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS37450: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001276.3 |  |  | 0.57 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001164.3 |  |  | 0.53 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001268.4 |  |  | 0.50 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002171.2 |  |  | 0.36 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger ATCC 1015
BGC0002275.2 |  |  | 0.36 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger CBS 101883
BGC0001163.3 |  |  | 0.35 | PKS | 1-heptadecene | Moorea producens 3L
BGC0002434.2 |  |  | 0.31 | NRPS, PKS | clifednamide D, clifednamide E, clifednamide F, clifednamide G, clifednamide H, clifednamide I, clifednamide J | Kitasatospora sp.
BGC0002240.3 |  |  | 0.30 | PKS | BAB, BAA | Metarhizium anisopliae
BGC0001556.5 |  |  | 0.30 | NRPS, PKS | combamide | Streptomyces sp.
BGC0001298.4 |  |  | 0.30 | PKS | 4-Z-annimycin, 4-E-annimycin | Streptomyces calvus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.76 | PKS | asperlactone | Aspergillus ochraceus
BGC0001275.3 |  | 0.76 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.75 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001160.5 |  | 0.65 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.65 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001268.4 |  | 0.62 | NRPS, PKS | fusarin C | Fusarium fujikuroi

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.73 out of 23.79
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 24.14 out of 29.65
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.89 out of 26.85
Confidence: medium
Additional weak hits (48):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.83 out of 31.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.26 out of 20.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.86 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.43 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.66 out of 21.55
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 15.66 out of 31.73
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.14 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.02 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
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.72 out of 31.73
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.15 out of 18.57
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.06 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.45 out of 26.06
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 15.90 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.68 out of 27.78
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.82 out of 28.14
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.92 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.67 out of 29.38
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.58 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
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.21 out of 30.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.01 out of 21.55
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.13 out of 18.57
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.68 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.67 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.45 out of 26.06
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.49 out of 20.97
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.68 out of 36.54
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.65 out of 26.12
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.49 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.81 out of 32.74
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.88 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.60 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.80 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.10 out of 27.04
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.94 out of 27.55
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.96 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.62 out of 29.65
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 14.91 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.03 out of 28.19
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.46 out of 23.43
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.22 out of 27.04
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.88 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.40 out of 33.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.68 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 17, location 2275675 - 2383532:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-redmal) + (ccmal - Me-ccmal - redmal - redmal)
Non-colinear ordering:
  RVR_RS09640 + RVR_RS37450

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 19, location 2309704 - 2383532:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-redmal) + (ccmal - Me-ccmal - redmal - redmal)
Non-colinear ordering:
  RVR_RS09640 + RVR_RS37450

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).
RVR_RS09455: mal
PKS_AT (547..856): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 110.6
  Methoxymalonyl-CoA: 58.8
  inactive: 50.9
  Methylmalonyl-CoA: 49.0
  Propionyl-CoA: 33.7
  CHC-CoA: 29.6
  2-Methylbutyryl-CoA: 21.5
  trans-1,2-CPDA: 12.3
  Acetyl-CoA: 12.2
  fatty_acid: 11.3
  Isobutyryl-CoA: 9.0
  3-Methylbutyryl-CoA: 1.0
  Ethylmalonyl-CoA: 0.2
  Benzoyl-CoA: 0.0

RVR_RS09560: X
AMP-binding (8..410): 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:
    TGTPLAGFAFWGLLAYGASLQVYGMTELSPSTTL
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

RVR_RS37450: mal - mmal - mal - mal
PKS_AT (573..876): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 87.5%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 181.5
  inactive: 105.3
  Methoxymalonyl-CoA: 59.9
  Methylmalonyl-CoA: 53.3
  Benzoyl-CoA: 43.2
  Isobutyryl-CoA: 33.7
  Ethylmalonyl-CoA: 25.4
  fatty_acid: 19.7
  CHC-CoA: 19.0
  Acetyl-CoA: 15.3
  Propionyl-CoA: 13.7
  trans-1,2-CPDA: 9.0
  2-Methylbutyryl-CoA: 7.0
  3-Methylbutyryl-CoA: 5.5

PKS_AT (2362..2662): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 196.3
  Ethylmalonyl-CoA: 192.4
  Methoxymalonyl-CoA: 152.3
  trans-1,2-CPDA: 119.4
  2-Methylbutyryl-CoA: 112.7
  Propionyl-CoA: 102.3
  Malonyl-CoA: 88.3
  CHC-CoA: 63.5
  Isobutyryl-CoA: 63.3
  Benzoyl-CoA: 61.5
  Acetyl-CoA: 46.8
  fatty_acid: 45.8
  inactive: 38.9
  3-Methylbutyryl-CoA: 19.9

PKS_AT (4121..4424): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 177.3
  inactive: 101.1
  Methoxymalonyl-CoA: 60.3
  Methylmalonyl-CoA: 52.0
  Benzoyl-CoA: 37.6
  Isobutyryl-CoA: 36.0
  Ethylmalonyl-CoA: 32.1
  CHC-CoA: 25.1
  Propionyl-CoA: 19.3
  fatty_acid: 17.7
  Acetyl-CoA: 16.4
  trans-1,2-CPDA: 11.3
  3-Methylbutyryl-CoA: 8.1
  2-Methylbutyryl-CoA: 4.0

PKS_AT (6245..6548): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 91.7%
  inactive: 87.5%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 186.4
  inactive: 108.1
  Methoxymalonyl-CoA: 60.4
  Methylmalonyl-CoA: 53.2
  Benzoyl-CoA: 40.5
  Isobutyryl-CoA: 36.1
  Ethylmalonyl-CoA: 32.6
  CHC-CoA: 23.1
  fatty_acid: 19.0
  Propionyl-CoA: 18.0
  Acetyl-CoA: 15.2
  trans-1,2-CPDA: 9.1
  2-Methylbutyryl-CoA: 4.4
  3-Methylbutyryl-CoA: 0.0

RVR_RS09640: mmal - mmal
PKS_AT (553..851): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 208.9
  Ethylmalonyl-CoA: 202.8
  Methoxymalonyl-CoA: 162.7
  2-Methylbutyryl-CoA: 132.3
  trans-1,2-CPDA: 111.4
  Malonyl-CoA: 104.1
  Propionyl-CoA: 96.6
  CHC-CoA: 84.7
  Isobutyryl-CoA: 74.4
  Benzoyl-CoA: 60.3
  3-Methylbutyryl-CoA: 47.2
  Acetyl-CoA: 28.4
  inactive: 27.0
  fatty_acid: 20.1

PKS_AT (1575..1875): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 196.1
  Ethylmalonyl-CoA: 186.6
  Methoxymalonyl-CoA: 152.6
  2-Methylbutyryl-CoA: 114.6
  trans-1,2-CPDA: 112.8
  Propionyl-CoA: 104.1
  Malonyl-CoA: 90.2
  CHC-CoA: 69.6
  Isobutyryl-CoA: 67.4
  Benzoyl-CoA: 56.4
  Acetyl-CoA: 45.3
  fatty_acid: 44.6
  inactive: 39.2
  3-Methylbutyryl-CoA: 22.0

RVR_RS09665: X
AMP-binding (22..440): 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:
    NVLLHDMGLLAMAGIVGGEHPAYGLAENTSAVTA
  Nearest Stachelhaus code(s):
    Leu DALLIGAIAK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
LexA variant 1 | Repressor of DNA damage response
RutR | Regulator of the pyrimidine and purine metabolism

NZ_AP018365.1 - Region 16 - T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,483,008 - 2,555,514 nt. (total: 72,507 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase
RVR_RS10230: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS10280: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS10315: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

RVR_RS10375: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS10385: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS10390: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS10410: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

RVR_RS10425: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

RVR_RS10430: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS10445: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

RVR_RS10475: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

Transferases: aminotransferase glycosyltransferase methyltransferase transferase
RVR_RS10400: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

RVR_RS10435: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

RVR_RS10440: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

RVR_RS10450: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

RVR_RS10465: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Lyases: cyclase dehydratase
RVR_RS10355: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

RVR_RS10380: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

RVR_RS10455: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

RVR_RS10460: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

RVR_RS10495: L-carnitine dehydratase/bile acid-inducible

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

Ligases: synthase
RVR_RS10360: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS10365: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: transporter
RVR_RS10240: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

RVR_RS10310: 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 | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002383.3 |  | 1.00 | PKS | kinanthraquinone B, kinanthraquinone | Streptomyces sp. SN-593
BGC0000231.5 |  | 0.84 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.78 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000278.3 |  | 0.72 | PKS | urdamycin | Streptomyces fradiae
BGC0001723.5 |  | 0.66 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002047.2 |  | 0.66 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000235.5 |  | 0.64 | PKS | kiamycin | Streptomyces sp. W007
BGC0002276.2 |  | 0.63 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002477.3 |  | 0.61 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0001895.4 |  | 0.60 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002383.3 |  | 1.00 | PKS | kinanthraquinone B, kinanthraquinone | Streptomyces sp. SN-593
BGC0000231.5 |  | 0.84 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0000234.5 |  | 0.78 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0000278.3 |  | 0.72 | PKS | urdamycin | Streptomyces fradiae
BGC0001723.5 |  | 0.66 | PKS | oviedomycin | Streptomyces antibioticus
BGC0002047.2 |  | 0.66 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000235.5 |  | 0.64 | PKS | kiamycin | Streptomyces sp. W007
BGC0002276.2 |  | 0.63 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0002477.3 |  | 0.61 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0001895.4 |  | 0.60 | PKS | huanglongmycin A, huanglongmycin B, huanglongmycin C | Streptomyces sp. CB09001

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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.12 out of 29.72
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.98 out of 27.55
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
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: 18.46 out of 23.05
Confidence: medium
Additional weak hits (25):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.92 out of 30.22
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.98 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.31 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.96 out of 27.78
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.82 out of 27.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.14 out of 26.12
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.39 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.73 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: 13.17 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.57 out of 36.54
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.70 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.02 out of 18.57
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.37 out of 19.26
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.83 out of 25.88
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.53 out of 31.73
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.04 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.08 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.08 out of 21.55
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.09 out of 28.19
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.67 out of 32.93
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.91 out of 32.93
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 27.04
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  2483007 to 2555514
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:
  8|9 (Score: 713.4; E-value: 1.6e-217)
Product class(es):
  angucycline
Product molecular weight(s):
  acetyl-CoA_8: 595 Da
  acetyl-CoA_9: 637 Da

RVR_RS10230
  KR (Score: 179.2; E-value: 2.9e-55)
RVR_RS10280
  KR (Score: 164.5; E-value: 8.4e-51)
RVR_RS10355
  CYC C4-C17/C2-C19 (Score: 199.4; E-value: 1.2e-61)
RVR_RS10360
  KS (Score: 791.8; E-value: 3.1e-241)
RVR_RS10365
  CLF 8|9 (Score: 713.4; E-value: 1.6e-217)
RVR_RS10370
  ACP (Score: 139.4; E-value: 6.7e-44)
RVR_RS10375
  KR C9 (Score: 493.3; E-value: 3.4e-151)
RVR_RS10380
  CYC C7-C12 (Score: 502.1; E-value: 1.1e-153)
RVR_RS10385
  OXY (Score: 574.1; E-value: 5.8e-175)
RVR_RS10390
  OXY (Score: 593.7; E-value: 6.3e-181)
RVR_RS10400
  GT (Score: 399.9; E-value: 3.7e-122)
RVR_RS10430
  OXY (Score: 479.4; E-value: 3.1e-146)
RVR_RS10435
  MET (Score: 282.0; E-value: 1.5e-86)
RVR_RS10440
  MET (Score: 273.3; E-value: 6.3e-84)

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
GnfM | Regulator of nitrogen-fixation genes
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator

NZ_AP018365.1 - Region 17 - T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,872,734 - 2,945,294 nt. (total: 72,561 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
RVR_RS11790: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

RVR_RS11815: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

RVR_RS11915: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

Transferases: carboxylase methyltransferase transferase
RVR_RS11800: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

RVR_RS11805: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

RVR_RS11955: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Lyases: cyclase
RVR_RS11945: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

RVR_RS11950: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

RVR_RS12060: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Isomerases: mutase
RVR_RS11990: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: synthase
RVR_RS11810: 2-isopropylmalate synthase

smcogs
  SMCOG1271: 2-isopropylmalate synthase

RVR_RS11930: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS11935: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: transporter
RVR_RS11875: 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 | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000271.5 |  | 0.74 | PKS | spore pigment | Streptomyces avermitilis
BGC0000272.3 |  | 0.73 | PKS | spore pigment | Streptomyces collinus
BGC0000215.5 |  | 0.65 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.61 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002284.3 |  | 0.60 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001273.3 |  | 0.56 | PKS | asperlactone | Aspergillus ochraceus
BGC0001513.3 |  | 0.55 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000275.4 |  | 0.55 | PKS | tetracenomycin C | Streptomyces glaucescens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000271.5 |  | 0.74 | PKS | spore pigment | Streptomyces avermitilis
BGC0000272.3 |  | 0.73 | PKS | spore pigment | Streptomyces collinus
BGC0000215.5 |  | 0.65 | PKS | curamycin | Streptomyces cyaneus
BGC0000231.5 |  | 0.61 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002284.3 |  | 0.60 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000234.5 |  | 0.58 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0001197.5 |  | 0.57 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001273.3 |  | 0.56 | PKS | asperlactone | Aspergillus ochraceus
BGC0001513.3 |  | 0.55 | PKS | anthrabenzoxocinone | Actinobacteria bacterium
BGC0000275.4 |  | 0.55 | PKS | tetracenomycin C | Streptomyces glaucescens

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:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.91 out of 26.85
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.15 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 28.65 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.19 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 25.19 out of 30.11
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 26.65 out of 30.11
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.04 out of 23.79
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 27.04
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.18 out of 27.04
Confidence: medium
Additional weak hits (21):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.09 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.03 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.51 out of 27.78
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.84 out of 25.75
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.10 out of 21.55
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.14 out of 20.97
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.01 out of 21.55
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.17 out of 21.55
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.62 out of 23.43
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.57 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 30.11
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.21 out of 36.53
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.29 out of 31.73
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.93 out of 33.14
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.23 out of 20.01
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 30.11
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.81 out of 27.78
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.45 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.09 out of 28.19
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.30 out of 36.53
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  2872733 to 2945294
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Product class(es):
  pentangular polyphenol
  tetracenomycin

RVR_RS11915
  OXY (Score: 298.8; E-value: 1.9e-91)
RVR_RS11925
  CYC C5-C18 (Score: 213.3; E-value: 2.1e-66)
RVR_RS11930
  KS (Score: 712.0; E-value: 5e-217)
RVR_RS11935
  CLF (Score: 530.9; E-value: 4.5e-162)
RVR_RS11940
  ACP (Score: 64.7; E-value: 1.4e-20)
RVR_RS11945
  CYC C9-C14 (Score: 251.2; E-value: 6.5e-78)
RVR_RS11950
  CYC C4-C21/C2-C23|C2-C19 (Score: 140.9; E-value: 3e-44)
RVR_RS11955
  MET C6|C8 (Score: 506.2; E-value: 8e-155)
RVR_RS12020
  OXY (Score: 59.3; E-value: 8e-19)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CelR | Cellobiose uptake repressor
DasR | N-acetylglucosamine dependent repressor
IolR | Regulator of the inositol catabolism
RutR | Regulator of the pyrimidine and purine metabolism

NZ_AP018365.1 - Region 18 - 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: 3,425,894 - 3,436,811 nt. (total: 10,918 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
Hydrolases: hydrolase
RVR_RS14105: 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 | butyrolactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.57 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.54 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.44 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002571.2 |  | 0.31 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0001458.4 |  | 0.30 | 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
BGC0000914.5 |  | 0.29 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0002657.2 |  | 0.26 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0001457.4 |  | 0.26 | NRPS | jomthonic acid A, jomthonic acid B, jomthonic acid C | Streptomyces caniferus
BGC0001771.4 |  | 0.25 | NRPS | scleric acid | Streptomyces sclerotialus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000848.5 |  | 0.76 | other (other) | A-factor | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000849.4 |  | 0.57 | other (butyrolactone) | SCB1, SCB2, SCB3 | Streptomyces coelicolor A3(2)
BGC0000850.5 |  | 0.54 | other (other) | γ-butyrolactone | Streptomyces acidiscabies
BGC0002578.2 |  | 0.44 | other (other) | gaburedin A, gaburedin B, gaburedin C, gaburedin D, gaburedin E, gaburedin F | Streptomyces venezuelae ATCC 10712
BGC0002571.2 |  | 0.31 | NRPS | pyoverdine DC3000 | Pseudomonas syringae pv. tomato str. DC3000
BGC0001458.4 |  | 0.30 | 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
BGC0000914.5 |  | 0.29 | other (other) | methylenomycin A | Streptomyces coelicolor A3(2)
BGC0002657.2 |  | 0.26 | NRPS, PKS | deoxyhangtaimycin | Streptomyces spectabilis
BGC0001457.4 |  | 0.26 | NRPS | jomthonic acid A, jomthonic acid B, jomthonic acid C | Streptomyces caniferus
BGC0001771.4 |  | 0.25 | NRPS | scleric acid | Streptomyces sclerotialus

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:
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.49 out of 27.04
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47
Confidence: medium
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.92 out of 30.22
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 12.12 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.99 out of 29.38
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.63 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 16.61 out of 36.54
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 18.65 out of 27.55
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.11 out of 30.22
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_AP018365.1 - Region 19 - T3PKS,other,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: 3,541,570 - 3,597,532 nt. (total: 55,963 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
terpene-precursor: (PT_FPPS_like and not PT_HPP)
other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
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: Oxidation oxygenase
RVR_RS14720: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

RVR_RS14750: Oxidation

MITE
  MITE0000084Oxidation (identity: 70.30%)

Transferases: aminotransferase methyltransferase
RVR_RS14655: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

RVR_RS14730: Methylation

MITE
  MITE0000085Methylation (identity: 71.30%)
smcogs
  SMCOG1042: O-methyltransferase

RVR_RS14740: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

RVR_RS14745: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

RVR_RS14835: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Lyases: dehydratase lyase
RVR_RS14615: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

RVR_RS14675: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

RVR_RS14775: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase synthetase
RVR_RS14665: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

RVR_RS14685: 3-oxoacyl-(acyl carrier protein) synthase III

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

RVR_RS14690: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

RVR_RS14735: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS14755: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | terpene-precursor | other | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001078.5 |  |  |  | 1.49 | PKS, terpene | furaquinocin B | Streptomyces sp. KO-3988
BGC0002458.3 |  |  |  | 1.12 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000286.3 |  |  |  | 0.82 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0001080.5 |  |  |  | 0.73 | other (phenazine) | endophenazine A, endophenazine B | Streptomyces anulatus
BGC0002561.3 |  |  |  | 0.66 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0000673.3 |  |  |  | 0.64 | terpene | pimara-8(14),15-diene | Aspergillus nidulans FGSC A4
BGC0002127.3 |  |  |  | 0.60 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001310.5 |  |  |  | 0.57 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0000902.4 |  |  |  | 0.56 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0000679.5 |  |  |  | 0.56 | terpene | diazepinomicin | Micromonospora sp. M42

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001078.5 |  | 0.85 | PKS, terpene | furaquinocin B | Streptomyces sp. KO-3988
BGC0002458.3 |  | 0.72 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0000286.3 |  | 0.65 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0002127.3 |  | 0.63 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001310.5 |  | 0.62 | PKS | naringenin | Streptomyces clavuligerus ATCC 27064
BGC0000902.4 |  | 0.62 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001080.5 |  | 0.61 | other (phenazine) | endophenazine A, endophenazine B | Streptomyces anulatus
BGC0000285.5 |  | 0.57 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0002561.3 |  | 0.56 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0000673.3 |  | 0.54 | terpene | pimara-8(14),15-diene | 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.
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:
RVR_RS14665: PT_FPPS_like
Domain 1 (58 - 332): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.12 out of 30.25
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.02 out of 23.79
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.72 out of 20.47
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
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
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 (10):
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.26 out of 20.97
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.09 out of 29.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.94 out of 30.25
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.05 out of 27.55
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: 19.81 out of 29.65
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.24 out of 32.93
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.77 out of 35.63
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.98 out of 29.65
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).
RVR_RS14735: X
AMP-binding (44..432): 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:
    RPQIHSRNVAALEASSTFDFQIYGQSEVGPAVGR
  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
CRP | Cyclic AMP receptor protein
ColR | Phenol-responsive regulator
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP018365.1 - Region 20 - indole
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 3,680,693 - 3,701,850 nt. (total: 21,158 nt) Show pHMM detection rules used
indole: (indsynth or dmat or indole_PTase)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxygenase
RVR_RS15190: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

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

Reference | indole | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001294.5 |  | 0.62 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002128.3 |  | 0.45 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001483.4 |  | 0.44 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000902.4 |  | 0.41 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001911.3 |  | 0.35 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.34 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002805.2 |  | 0.33 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0002643.2 |  | 0.33 | other (other) | aetokthonotoxin | Aetokthonos hydrillicola Thurmond2011
BGC0000285.5 |  | 0.33 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001840.2 |  | 0.32 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001294.5 |  | 0.62 | other (other) | 7-prenylisatin | Streptomyces sp. MBT28
BGC0002128.3 |  | 0.45 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)
BGC0001483.4 |  | 0.44 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0000902.4 |  | 0.41 | PKS | flaviolin | Saccharopolyspora erythraea NRRL 2338
BGC0001911.3 |  | 0.35 | terpene | raimonol | Streptomyces anulatus
BGC0001910.4 |  | 0.34 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0002805.2 |  | 0.33 | other (other) | Azodyrecin A, Azodyrecin B, Azodyrecin C | Streptomyces mirabilis strain P8-A
BGC0002643.2 |  | 0.33 | other (other) | aetokthonotoxin | Aetokthonos hydrillicola Thurmond2011
BGC0000285.5 |  | 0.33 | PKS, saccharide | flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin | Saccharopolyspora erythraea
BGC0001840.2 |  | 0.32 | NRPS, PKS | detoxin S1 | Streptomyces sp. NRRL S-325

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (6):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.31 out of 36.54
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.73 out of 27.18
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.66 out of 29.65
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.00 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.18 out of 24.78
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_AP018365.1 - Region 21 - 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: 4,108,974 - 4,119,402 nt. (total: 10,429 nt) Show pHMM detection rules used
melanin: melC

#### Legend:

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

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

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

Reference | melanin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.79 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.64 | other (other) | melanin | Streptomyces avermitilis
BGC0000911.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000912.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.47 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.32 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000662.5 |  | 0.31 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000889.5 |  | 0.31 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.31 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.24 | other (other) | iso-A82775C | Pestalotiopsis fici

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000910.3 |  | 0.79 | other (other) | melanin | Streptomyces coelicolor A3(2)
BGC0000909.3 |  | 0.64 | other (other) | melanin | Streptomyces avermitilis
BGC0000911.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000912.3 |  | 0.60 | other (other) | melanin | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000908.3 |  | 0.47 | other (other) | melanin | Streptomyces avermitilis
BGC0000885.3 |  | 0.32 | other (other) | 4-hydroxy-3-nitrosobenzamide | Streptomyces murayamaensis
BGC0000662.5 |  | 0.31 | terpene | grixazone A | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000889.5 |  | 0.31 | other (other) | bagremycin A, bagremycin B | Streptomyces sp. WK-5344
BGC0001592.5 |  | 0.31 | other (other) | ferroverdin, bagremycin | Streptomyces lunaelactis
BGC0001624.3 |  | 0.24 | other (other) | iso-A82775C | Pestalotiopsis fici

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
Additional weak hits (6):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.67 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 13.84 out of 21.55
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.92 out of 20.01
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.61 out of 27.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.81 out of 21.84
Confidence: weak
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 17.61 out of 25.31
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_AP018365.1 - Region 22 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 4,670,936 - 4,696,228 nt. (total: 25,293 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
RVR_RS19630: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

RVR_RS19635: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000544.4 |  | 0.41 | ribosomal | planosporicin | Planomonospora alba
BGC0000514.5 |  | 0.39 | ribosomal | gallidermin | Staphylococcus gallinarum
BGC0002120.3 |  | 0.37 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000529.5 |  | 0.35 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000453.5 |  | 0.29 | NRPS | valinomycin | Streptomyces tsusimaensis
BGC0000796.3 |  | 0.26 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0001812.3 |  | 0.24 | PKS | tylactone | Micromonospora chalcea subsp. izumensis
BGC0000001.5 |  | 0.22 | PKS | abyssomicin C, atrop-abyssomicin C | Verrucosispora maris AB-18-032
BGC0002552.2 |  | 0.21 | PKS | ansacarbamitocin | Amycolatopsis sp. CP2808

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002635.2 |  | 0.44 | ribosomal | daspyromycin A, daspyromycin B | Actinokineospora diospyrosa
BGC0000544.4 |  | 0.41 | ribosomal | planosporicin | Planomonospora alba
BGC0000514.5 |  | 0.39 | ribosomal | gallidermin | Staphylococcus gallinarum
BGC0002120.3 |  | 0.37 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000529.5 |  | 0.35 | ribosomal | microbisporicin A2 | Microbispora corallina
BGC0000453.5 |  | 0.29 | NRPS | valinomycin | Streptomyces tsusimaensis
BGC0000796.3 |  | 0.26 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0001812.3 |  | 0.24 | PKS | tylactone | Micromonospora chalcea subsp. izumensis
BGC0000001.5 |  | 0.22 | PKS | abyssomicin C, atrop-abyssomicin C | Verrucosispora maris AB-18-032
BGC0002552.2 |  | 0.21 | PKS | ansacarbamitocin | Amycolatopsis sp. CP2808

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

No significant matches found.

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.50 out of 20.47
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (5):
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.70 out of 25.88
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.35 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: 18.73 out of 24.78
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (4670935...4696228)
RVR_RS19635
  RRE type: Lanthipeptide_LanB_RRE
  Location: 156 - 246
  Score: 61.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP018365.1 - Region 23 - linaridin
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,109,216 - 5,129,791 nt. (total: 20,576 nt) Show pHMM detection rules used
linaridin: (cypemycin or cypI)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: methyltransferase
RVR_RS21630: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Ligases: synthetase
RVR_RS21650: 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 | linaridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001735.5 |  | 0.42 | other (other) | pentostatine, vidarabine | Streptomyces antibioticus
BGC0001075.5 |  | 0.36 | PKS, terpene | aurachin RE | Rhodococcus erythropolis
BGC0000906.3 |  | 0.35 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000905.5 |  | 0.35 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000643.3 |  | 0.35 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.3 |  | 0.35 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000678.5 |  | 0.34 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000648.3 |  | 0.34 | terpene | carotenoid | Myxococcus xanthus
BGC0000665.5 |  | 0.33 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002591.2 |  | 0.30 | PKS, terpene | aurachin C, aurachin D, aurachin SS | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001735.5 |  | 0.42 | other (other) | pentostatine, vidarabine | Streptomyces antibioticus
BGC0001075.5 |  | 0.36 | PKS, terpene | aurachin RE | Rhodococcus erythropolis
BGC0000906.3 |  | 0.35 | other (other) | heme D1 | Heliophilum fasciatum
BGC0000905.5 |  | 0.35 | other (other) | heme D1 | Heliobacillus mobilis
BGC0000643.3 |  | 0.35 | terpene | carotenoid | Brevundimonas vesicularis
BGC0000634.3 |  | 0.35 | terpene | carotenoid | Brevundimonas sp. SD212
BGC0000678.5 |  | 0.34 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000648.3 |  | 0.34 | terpene | carotenoid | Myxococcus xanthus
BGC0000665.5 |  | 0.33 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002591.2 |  | 0.30 | PKS, terpene | aurachin C, aurachin D, aurachin SS | 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.

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.85 out of 29.51
Confidence: medium
Additional weak hits (7):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.32 out of 28.14
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.93 out of 27.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.71 out of 26.06
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.47 out of 28.14
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.05 out of 30.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.07 out of 33.14
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
--- | ---
DosR | Hypoxia stress response regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP018365.1 - Region 24 - benzoxazole,hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 5,858,552 - 5,927,828 nt. (total: 69,277 nt) Show pHMM detection rules used
benzoxazole: (ksIII and AMP-binding and PP-binding and Amidohydro_1)
hglE-KS: (hglE or hglD)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
RVR_RS25050: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

RVR_RS25055: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

RVR_RS25120: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS25175: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

RVR_RS25180: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: PPTase acylase aminotransferase
RVR_RS25070: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

RVR_RS25170: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

RVR_RS25185: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: hydrolase
RVR_RS25125: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Isomerases: isomerase
RVR_RS25130: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
RVR_RS25095: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS25100: 3-oxoacyl-(acyl carrier protein) synthase III

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

RVR_RS25105: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS25160: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS25165: 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 | benzoxazole | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001444.5 |  |  | 0.76 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0001292.5 |  |  | 0.74 | other (other) | A33853 | Streptomyces sp. NRRL 12068
BGC0002493.3 |  |  | 0.54 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0002474.2 |  |  | 0.52 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0000343.5 |  |  | 0.46 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001850.4 |  |  | 0.41 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001
BGC0002826.2 |  |  | 0.39 | other (other) | closoxazole A, closoxazole B | Clostridium cavendishii DSM 21758
BGC0000451.5 |  |  | 0.38 | NRPS | turnerbactin | Teredinibacter turnerae T7901
BGC0002476.2 |  |  | 0.38 | NRPS | enterobactin | Escherichia coli str. K-12 substr. MG1655
BGC0000936.5 |  |  | 0.37 | other (other) | pyocyanine | Pseudomonas aeruginosa PAO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001292.5 |  | 0.79 | other (other) | A33853 | Streptomyces sp. NRRL 12068
BGC0001444.5 |  | 0.70 | other (shikimate-derived) | caboxamycin | Streptomyces sp. NTK 937
BGC0001276.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.65 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.65 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002493.3 |  | 0.60 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0001160.5 |  | 0.60 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002474.2 |  | 0.60 | NRPS | agrobactin | Agrobacterium tumefaciens
BGC0001164.3 |  | 0.59 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0000861.5 |  | 0.58 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.17 out of 23.79
Confidence: medium
Additional weak hits (15):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.33 out of 26.85
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.32 out of 31.73
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.43 out of 21.55
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.91 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.51 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.49 out of 30.22
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.24 out of 27.55
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.16 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
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.95 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.48 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.91 out of 20.01
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 19.79 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 29, location 5858551 - 5927828:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 30, location 5858551 - 5895324:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 31, location 5872872 - 5927828:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
RVR_RS25095: X
AMP-binding (63..246): 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:
    LRYTITGHLAHAWSFVGGEVEEYGSTETGTLAGQ
  Nearest Stachelhaus code(s):
    nohBza or oh-nitroBza AGAWYAEPLK (62% 8Å match)
  Stachelhaus code match:
    60% (weak)

RVR_RS25105: Hpr
Search NORINE for peptide: strict or relaxed
AMP-binding (32..451): Hpr
nrpys: 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:
    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:
    QAALFTWGCPGGSVQIGSAQQVFGMAEGLCTFTR
  Nearest Stachelhaus code(s):
    Hpa TWPSQGVLCK (91% 8Å match)
  Stachelhaus code match:
    80% (moderate)

RVR_RS25160: mal
PKS_AT (570..868): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 82.7
  Methoxymalonyl-CoA: 39.2
  Methylmalonyl-CoA: 32.0
  inactive: 26.0
  CHC-CoA: 18.1
  fatty_acid: 11.4
  2-Methylbutyryl-CoA: 11.1
  Ethylmalonyl-CoA: 9.9
  Isobutyryl-CoA: 9.8
  Propionyl-CoA: 9.7
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

RVR_RS25165: pk
PKS_AT (1209..1361): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

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

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

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

NZ_AP018365.1 - Region 25 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,500,719 - 6,533,241 nt. (total: 32,523 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
RVR_RS27975: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

Transferases: aminotransferase
RVR_RS27930: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Isomerases: mutase
RVR_RS27980: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002692.2 |  | 0.55 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0001713.5 |  | 0.53 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0000941.3 |  | 0.52 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002683.2 |  | 0.52 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002633.2 |  | 0.51 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0001531.5 |  | 0.51 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002470.2 |  | 0.51 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0001572.3 |  | 0.50 | other (other) | desferrioxamine E | Pantoea agglomerans

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 |  | 0.53 | other (other) | ochrobactin | Ochrobactrum anthropi
BGC0000941.3 |  | 0.52 | other (other) | desferrioxamin B | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002683.2 |  | 0.52 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0002469.2 |  | 0.51 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000295.5 |  | 0.51 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002633.2 |  | 0.51 | other (other) | schizokinen | Leptolyngbya sp. PCC 7376
BGC0001531.5 |  | 0.51 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002470.2 |  | 0.51 | other (other) | synechobactin C9, synechobactin C11, synechobactin 13, synechobactin 14, synechobactin 16, synechobactin A, synechobactin B, synechobactin C | Synechococcus sp. PCC 7002
BGC0001572.3 |  | 0.50 | other (other) | desferrioxamine E | Pantoea agglomerans

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.54 out of 23.79
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.95 out of 29.65
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.44 out of 27.18
Confidence: medium
Additional weak hits (10):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.46 out of 25.75
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.56 out of 29.38
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.86 out of 26.33
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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.79 out of 19.52
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.84 out of 21.55
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
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.32 out of 27.18
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
IolR | Regulator of the inositol catabolism
LexA variant 1 | Repressor of DNA damage response
LexA variant 2 | Repressor of DNA damage response
NrdR | Represses ribonucleotide reductase encoding genes

NZ_AP018365.1 - Region 26 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,083,210 - 7,110,057 nt. (total: 26,848 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
RVR_RS30680: dehydrogenase

smcogs
  SMCOG1181: dehydrogenase

Transferases: aminotransferase transferase
RVR_RS30675: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

RVR_RS30745: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Ligases: synthase synthetase
RVR_RS30720: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

RVR_RS30740: 1-deoxy-D-xylulose-5-phosphate synthase

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

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.70 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.51 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.50 | terpene | stellatic acid | Aspergillus stellatus
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
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.70 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0000656.5 |  | 0.51 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0002610.3 |  | 0.50 | terpene | stellatic acid | Aspergillus stellatus
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
BGC0000640.3 |  | 0.48 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002173.2 |  | 0.48 | saccharide, terpene | fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol | Aspergillus fumigatus A1163

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
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:
RVR_RS30705: PT_phytoene_like
Domain 1 (14 - 281): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

RVR_RS30710: PT_phytoene_like
Domain 1 (17 - 308): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

RVR_RS30720: PT_FPPS_like
Domain 1 (62 - 347): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

RVR_RS30725: T2TS
Domain 1 (20 - 655): 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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84
Confidence: medium
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.44 out of 27.18
Confidence: medium
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.22 out of 23.43
Confidence: medium
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.04 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.75 out of 29.38
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.82 out of 36.54
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.21 out of 18.57
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.91 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.89 out of 27.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.40 out of 36.53
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
BldD | Development and antibiotic global regulator
MexT | Global virulence regulator
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP018365.1 - Region 27 - 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: 7,145,500 - 7,279,965 nt. (total: 134,466 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))
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
RVR_RS30930: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

RVR_RS30985: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

RVR_RS31000: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

RVR_RS31005: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

RVR_RS31010: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS31020: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

RVR_RS31040: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

RVR_RS31085: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

RVR_RS31090: dehydrogenase

smcogs
  SMCOG1072: dehydrogenase

RVR_RS31115: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS31130: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

RVR_RS31155: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS31165: dioxygenase, TauD/TfdA

smcogs
  SMCOG1121: dioxygenase, TauD/TfdA

RVR_RS31170: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase aminotransferase glycosyltransferase methyltransferase sulfotransferase
RVR_RS31030: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

RVR_RS31120: Sulfotransferase domain

extras
  Sulfotransfer_4: Sulfotransferase domain

RVR_RS31125: glycosyltransferase, MGT family

smcogs
  SMCOG1062: glycosyltransferase, MGT family

RVR_RS31135: aminotransferase

smcogs
  SMCOG1019: aminotransferase

RVR_RS31160: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: hydrolase peptidase
RVR_RS31045: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

RVR_RS31080: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Ligases: ligase synthase synthetase
RVR_RS30975: 3-oxoacyl-(acyl carrier protein) synthase III

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

RVR_RS30980: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS30990: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

RVR_RS30995: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS31050: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS31140: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

RVR_RS38750: 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000135.5 |  |  | 1.00 | PKS | reveromycin A | Streptomyces sp. SN-593
BGC0002084.4 |  |  | 0.48 | ribosomal | biarylitide YYH | Planomonospora sp. ID82291
BGC0002631.2 |  |  | 0.42 | ribosomal | Myxarylin | Pyxidicoccus fallax
BGC0000844.5 |  |  | 0.35 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0002007.2 |  |  | 0.34 | terpene | atolypene A, atolypene B | Amycolatopsis tolypomycina
BGC0001529.5 |  |  | 0.34 | other (other) | benzastatin J, 7-hydroxyl benzastatin B, 7-hydroxyl O-demethylbenzastatin A, JBIR-67, 7-hydroxyl benzastatin F, 7-hydroxyl O-demethylbenzastatin D, O-demethylvirantmycin, 7-hydroxyl benzastatin D, virantmycin, benzastatin K, methylbenzastatin K | Streptomyces sp. RI18
BGC0000058.5 |  |  | 0.33 | PKS | FD-891 | Streptomyces graminofaciens
BGC0001012.3 |  |  | 0.32 | NRPS, PKS | meridamycin | Streptomyces violaceusniger
BGC0001605.3 |  |  | 0.32 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0002193.2 |  |  | 0.31 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000135.5 |  | 0.98 | PKS | reveromycin A | Streptomyces sp. SN-593
BGC0002193.2 |  | 0.65 | other (other) | phenguignardic acid | Aspergillus terreus NIH2624
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.63 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  | 0.63 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001833.4 |  | 0.63 | NRPS | icosalide A, icosalide B | Burkholderia gladioli

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
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:
RVR_RS31140: PT_FPPS_like
Domain 1 (41 - 329): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

RVR_RS31150: T2TS
Domain 1 (281 - 558): 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: 20.53 out of 23.79
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.62 out of 23.79
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
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (32):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.52 out of 21.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.32 out of 26.85
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.78 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.77 out of 21.55
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.25 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.64 out of 27.78
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.85 out of 39.62
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.68 out of 26.06
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.84 out of 36.54
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.16 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.63 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.53 out of 21.55
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.69 out of 26.85
Confidence: weak
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: 18.65 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.96 out of 29.38
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.42 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.43 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.03 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.76 out of 27.78
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.03 out of 19.26
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.27 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.43 out of 35.63
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.08 out of 35.63
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.48 out of 28.19
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.78 out of 30.98
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.69 out of 27.18
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.93 out of 28.19
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.90 out of 27.04
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 30.11
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 34, location 7145499 - 7279965:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - ccmal - Me-ccmal - ccmal) + (Me-ohmal - redmal - ohmal) + (Me-redmal - ohmal) + (Me-ccmal - ccmal - Me-ohmal - ccmal)
Non-colinear ordering:
  RVR_RS31050 + RVR_RS30990 + RVR_RS30995 + RVR_RS38750

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 35, location 7145499 - 7264988:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - ccmal - Me-ccmal - ccmal) + (Me-ohmal - redmal - ohmal) + (Me-redmal - ohmal) + (Me-ccmal - ccmal - Me-ohmal - ccmal)
Non-colinear ordering:
  RVR_RS31050 + RVR_RS30990 + RVR_RS30995 + RVR_RS38750

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).
RVR_RS30980: fatty_acid
CAL_domain (43..477): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 14.9
  NH2: 11.2
  Acetyl-CoA: 1.0
  shikimic_acid: 0.0
  AHBA: -0.5

RVR_RS30990: mmal - mal - mal
PKS_AT (563..863): mmal
ATSignature: Methylmalonyl-CoA, Ethylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 79.2%
  Ethylmalonyl-CoA: 79.2%
  Malonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 174.6
  Ethylmalonyl-CoA: 163.3
  Methoxymalonyl-CoA: 147.8
  2-Methylbutyryl-CoA: 100.9
  CHC-CoA: 96.8
  trans-1,2-CPDA: 95.4
  Isobutyryl-CoA: 78.4
  Propionyl-CoA: 75.3
  Malonyl-CoA: 71.4
  Benzoyl-CoA: 71.1
  3-Methylbutyryl-CoA: 36.9
  fatty_acid: 36.2
  Acetyl-CoA: 22.5
  inactive: 17.2

PKS_AT (2105..2379): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 211.6
  inactive: 96.4
  Methoxymalonyl-CoA: 59.7
  Methylmalonyl-CoA: 50.3
  Propionyl-CoA: 28.3
  Isobutyryl-CoA: 25.3
  Acetyl-CoA: 24.9
  Benzoyl-CoA: 20.9
  Ethylmalonyl-CoA: 19.9
  fatty_acid: 14.9
  2-Methylbutyryl-CoA: 14.1
  CHC-CoA: 12.0
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4165..4444): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 201.4
  inactive: 90.5
  Methoxymalonyl-CoA: 59.1
  Methylmalonyl-CoA: 44.6
  Isobutyryl-CoA: 27.0
  Acetyl-CoA: 26.1
  Propionyl-CoA: 24.7
  Ethylmalonyl-CoA: 20.2
  Benzoyl-CoA: 19.5
  fatty_acid: 13.4
  2-Methylbutyryl-CoA: 13.1
  CHC-CoA: 9.8
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

RVR_RS30995: mmal - mal
PKS_AT (602..894): 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: 213.5
  Ethylmalonyl-CoA: 208.8
  Methoxymalonyl-CoA: 165.5
  2-Methylbutyryl-CoA: 133.3
  Propionyl-CoA: 123.4
  trans-1,2-CPDA: 122.6
  Malonyl-CoA: 118.6
  CHC-CoA: 106.1
  Isobutyryl-CoA: 81.2
  Acetyl-CoA: 71.5
  Benzoyl-CoA: 65.6
  inactive: 45.6
  3-Methylbutyryl-CoA: 36.1
  fatty_acid: 25.6

PKS_AT (2704..2982): 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: 218.1
  inactive: 97.9
  Methoxymalonyl-CoA: 69.7
  Methylmalonyl-CoA: 53.8
  Propionyl-CoA: 35.0
  Isobutyryl-CoA: 28.2
  Acetyl-CoA: 23.7
  Benzoyl-CoA: 22.7
  fatty_acid: 22.0
  CHC-CoA: 20.6
  Ethylmalonyl-CoA: 19.8
  trans-1,2-CPDA: 17.7
  2-Methylbutyryl-CoA: 9.5
  3-Methylbutyryl-CoA: 0.0

RVR_RS31030: pk
PKS_AT (11..275): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

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

RVR_RS31035: X
AMP-binding (91..307): 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:
    HFHTIGLGVQESNTRVSGTVGSYG---NTFGTSA
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

RVR_RS31050: mmal - mal - mmal - mal
PKS_AT (546..858): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 210.6
  Ethylmalonyl-CoA: 206.6
  Methoxymalonyl-CoA: 163.5
  2-Methylbutyryl-CoA: 150.5
  Malonyl-CoA: 116.7
  CHC-CoA: 115.3
  trans-1,2-CPDA: 107.9
  Propionyl-CoA: 107.2
  Isobutyryl-CoA: 84.3
  Benzoyl-CoA: 63.3
  3-Methylbutyryl-CoA: 46.5
  Acetyl-CoA: 45.6
  fatty_acid: 40.1
  inactive: 30.0

PKS_AT (1587..1866): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 201.7
  inactive: 86.5
  Methoxymalonyl-CoA: 60.0
  Methylmalonyl-CoA: 44.6
  Isobutyryl-CoA: 27.1
  Acetyl-CoA: 26.0
  Propionyl-CoA: 24.8
  Benzoyl-CoA: 20.2
  Ethylmalonyl-CoA: 18.6
  fatty_acid: 13.7
  2-Methylbutyryl-CoA: 13.6
  CHC-CoA: 11.5
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3338..3628): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 213.5
  Ethylmalonyl-CoA: 206.9
  Methoxymalonyl-CoA: 171.9
  2-Methylbutyryl-CoA: 148.3
  trans-1,2-CPDA: 127.7
  Propionyl-CoA: 113.3
  CHC-CoA: 111.3
  Malonyl-CoA: 98.5
  Isobutyryl-CoA: 76.6
  Benzoyl-CoA: 70.9
  Acetyl-CoA: 54.3
  fatty_acid: 52.7
  3-Methylbutyryl-CoA: 33.3
  inactive: 29.7

PKS_AT (5034..5313): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 202.5
  inactive: 86.8
  Methoxymalonyl-CoA: 61.4
  Methylmalonyl-CoA: 46.9
  Isobutyryl-CoA: 29.5
  Acetyl-CoA: 26.5
  Propionyl-CoA: 26.2
  Ethylmalonyl-CoA: 23.2
  Benzoyl-CoA: 19.7
  2-Methylbutyryl-CoA: 15.4
  fatty_acid: 13.5
  CHC-CoA: 12.2
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

RVR_RS38750: mmal - mal - mmal - mal
PKS_AT (577..867): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 214.1
  Ethylmalonyl-CoA: 208.8
  Methoxymalonyl-CoA: 171.7
  2-Methylbutyryl-CoA: 148.2
  trans-1,2-CPDA: 131.0
  Propionyl-CoA: 114.2
  CHC-CoA: 110.1
  Malonyl-CoA: 100.2
  Isobutyryl-CoA: 77.9
  Benzoyl-CoA: 70.5
  Acetyl-CoA: 54.0
  fatty_acid: 52.7
  3-Methylbutyryl-CoA: 32.7
  inactive: 29.5

PKS_AT (2328..2605): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 207.8
  inactive: 91.4
  Methoxymalonyl-CoA: 58.9
  Methylmalonyl-CoA: 48.5
  Propionyl-CoA: 27.5
  Acetyl-CoA: 25.9
  Isobutyryl-CoA: 25.4
  Benzoyl-CoA: 20.9
  Ethylmalonyl-CoA: 19.8
  2-Methylbutyryl-CoA: 14.9
  fatty_acid: 14.0
  CHC-CoA: 12.6
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4055..4345): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 100.0%
  Methoxymalonyl-CoA: 91.7%
  Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 213.0
  Ethylmalonyl-CoA: 205.5
  Methoxymalonyl-CoA: 172.1
  2-Methylbutyryl-CoA: 144.1
  trans-1,2-CPDA: 130.6
  Propionyl-CoA: 115.5
  CHC-CoA: 108.2
  Malonyl-CoA: 99.9
  Isobutyryl-CoA: 72.9
  Benzoyl-CoA: 68.4
  Acetyl-CoA: 56.8
  fatty_acid: 50.4
  3-Methylbutyryl-CoA: 36.6
  inactive: 32.5

PKS_AT (5564..5843): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 95.8%
  inactive: 70.8%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 199.9
  inactive: 88.6
  Methoxymalonyl-CoA: 59.1
  Methylmalonyl-CoA: 44.6
  Isobutyryl-CoA: 29.0
  Acetyl-CoA: 26.0
  Propionyl-CoA: 23.6
  Benzoyl-CoA: 19.3
  Ethylmalonyl-CoA: 18.6
  2-Methylbutyryl-CoA: 14.9
  fatty_acid: 13.4
  CHC-CoA: 12.3
  trans-1,2-CPDA: 0.0
  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
--- | ---
AbrC3 | Antibiotic production activator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
IolR | Regulator of the inositol catabolism

NZ_AP018365.1 - Region 28 - 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: 7,316,223 - 7,443,763 nt. (total: 127,541 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
RVR_RS31435: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

RVR_RS31450: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

RVR_RS31470: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

RVR_RS31480: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

RVR_RS31485: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

RVR_RS38755: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Hydrolases: esterase hydrolase
RVR_RS31400: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

RVR_RS31430: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase hydratase
RVR_RS31405: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

RVR_RS31420: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: synthase
RVR_RS31445: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

RVR_RS31495: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS38080: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter
RVR_RS31580: sugar-binding lipoprotein

smcogs
  SMCOG1143: sugar-binding lipoprotein

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

Reference | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001258.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001276.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001273.3 |  | 0.74 | PKS | asperlactone | Aspergillus ochraceus
BGC0001244.3 |  | 0.74 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001275.3 |  | 0.74 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001164.3 |  | 0.63 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002154.2 |  | 0.63 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001258.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001257.3 |  | 0.63 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002191.2 |  | 0.63 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.54 out of 23.79
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 30.11 out of 30.11
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
Additional weak hits (9):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.58 out of 26.12
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.07 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.27 out of 29.38
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
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.76 out of 29.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.93 out of 25.88
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.41 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 37, location 7316222 - 7443763:
Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:
  (mal - Me-redmal - Me-redmal - Me-ccmal) + (redmal - Me-redmal - Me-redmal - redmal) + (redmal - redmal - Me-ccmal - Me-redmal) + (pk)
Non-colinear ordering:
  RVR_RS38755 + RVR_RS31495 + RVR_RS38080 + RVR_RS31445

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).
RVR_RS31445: pk
PKS_AT (567..846): pk
ATSignature: Ethylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 181.3
  Ethylmalonyl-CoA: 180.2
  Methoxymalonyl-CoA: 154.4
  2-Methylbutyryl-CoA: 117.7
  trans-1,2-CPDA: 107.5
  Propionyl-CoA: 101.3
  CHC-CoA: 99.6
  Malonyl-CoA: 96.4
  Isobutyryl-CoA: 67.2
  Acetyl-CoA: 56.6
  Benzoyl-CoA: 51.5
  fatty_acid: 31.7
  inactive: 24.8
  3-Methylbutyryl-CoA: 12.0

RVR_RS38755: mal - mmal - mmal - mmal
PKS_AT (569..838): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 162.9
  Methoxymalonyl-CoA: 51.7
  inactive: 50.5
  Methylmalonyl-CoA: 43.2
  Acetyl-CoA: 24.0
  Propionyl-CoA: 16.0
  Isobutyryl-CoA: 15.7
  fatty_acid: 13.5
  Ethylmalonyl-CoA: 6.6
  CHC-CoA: 5.3
  2-Methylbutyryl-CoA: 1.0
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (1985..2264): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 189.2
  Ethylmalonyl-CoA: 165.8
  Methoxymalonyl-CoA: 147.7
  2-Methylbutyryl-CoA: 116.9
  trans-1,2-CPDA: 108.3
  Propionyl-CoA: 98.3
  CHC-CoA: 95.7
  Malonyl-CoA: 85.5
  Isobutyryl-CoA: 72.9
  Benzoyl-CoA: 50.2
  Acetyl-CoA: 46.4
  fatty_acid: 29.4
  inactive: 22.0
  3-Methylbutyryl-CoA: 13.1

PKS_AT (4035..4322): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 190.4
  Ethylmalonyl-CoA: 165.8
  Methoxymalonyl-CoA: 145.4
  2-Methylbutyryl-CoA: 115.5
  trans-1,2-CPDA: 110.7
  Propionyl-CoA: 101.8
  Malonyl-CoA: 99.4
  CHC-CoA: 98.7
  Isobutyryl-CoA: 77.5
  Benzoyl-CoA: 51.7
  Acetyl-CoA: 44.7
  fatty_acid: 30.0
  inactive: 29.9
  3-Methylbutyryl-CoA: 12.9

PKS_AT (6081..6360): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 193.2
  Ethylmalonyl-CoA: 167.2
  Methoxymalonyl-CoA: 147.1
  2-Methylbutyryl-CoA: 118.0
  trans-1,2-CPDA: 112.1
  Propionyl-CoA: 100.3
  Malonyl-CoA: 99.2
  CHC-CoA: 97.2
  Isobutyryl-CoA: 79.0
  Benzoyl-CoA: 55.4
  Acetyl-CoA: 50.1
  fatty_acid: 35.8
  inactive: 24.4
  3-Methylbutyryl-CoA: 20.1

RVR_RS31495: mal - mmal - mmal - mal
PKS_AT (600..869): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 162.9
  Methoxymalonyl-CoA: 51.7
  inactive: 50.5
  Methylmalonyl-CoA: 43.2
  Acetyl-CoA: 24.0
  Propionyl-CoA: 16.0
  Isobutyryl-CoA: 15.7
  fatty_acid: 13.5
  Ethylmalonyl-CoA: 6.6
  CHC-CoA: 5.3
  2-Methylbutyryl-CoA: 1.0
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2657..2936): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 189.8
  Ethylmalonyl-CoA: 165.1
  Methoxymalonyl-CoA: 149.3
  2-Methylbutyryl-CoA: 116.0
  trans-1,2-CPDA: 106.8
  CHC-CoA: 96.7
  Propionyl-CoA: 96.5
  Malonyl-CoA: 86.2
  Isobutyryl-CoA: 68.3
  Benzoyl-CoA: 49.7
  Acetyl-CoA: 44.7
  fatty_acid: 28.2
  inactive: 23.1
  3-Methylbutyryl-CoA: 9.5

PKS_AT (4710..4989): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 192.0
  Ethylmalonyl-CoA: 168.4
  Methoxymalonyl-CoA: 150.0
  2-Methylbutyryl-CoA: 117.7
  trans-1,2-CPDA: 111.5
  Propionyl-CoA: 98.0
  CHC-CoA: 97.9
  Malonyl-CoA: 91.4
  Isobutyryl-CoA: 69.3
  Benzoyl-CoA: 51.2
  Acetyl-CoA: 46.8
  fatty_acid: 30.2
  inactive: 23.5
  3-Methylbutyryl-CoA: 11.1

PKS_AT (6780..7049): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 162.9
  Methoxymalonyl-CoA: 51.7
  inactive: 50.5
  Methylmalonyl-CoA: 43.2
  Acetyl-CoA: 24.0
  Propionyl-CoA: 16.0
  Isobutyryl-CoA: 15.7
  fatty_acid: 13.5
  Ethylmalonyl-CoA: 6.6
  CHC-CoA: 5.3
  2-Methylbutyryl-CoA: 1.0
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

RVR_RS38080: mal - mal - mmal - mmal
PKS_AT (602..871): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 162.9
  Methoxymalonyl-CoA: 51.7
  inactive: 50.5
  Methylmalonyl-CoA: 43.2
  Acetyl-CoA: 24.0
  Propionyl-CoA: 16.0
  Isobutyryl-CoA: 15.7
  fatty_acid: 13.5
  Ethylmalonyl-CoA: 6.6
  CHC-CoA: 5.3
  2-Methylbutyryl-CoA: 1.0
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (2649..2918): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 162.9
  Methoxymalonyl-CoA: 51.7
  inactive: 50.5
  Methylmalonyl-CoA: 43.2
  Acetyl-CoA: 24.0
  Propionyl-CoA: 16.0
  Isobutyryl-CoA: 15.7
  fatty_acid: 13.5
  Ethylmalonyl-CoA: 6.6
  CHC-CoA: 5.3
  2-Methylbutyryl-CoA: 1.0
  trans-1,2-CPDA: 0.0
  Benzoyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (4694..4973): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 189.5
  Ethylmalonyl-CoA: 163.6
  Methoxymalonyl-CoA: 147.6
  2-Methylbutyryl-CoA: 114.7
  trans-1,2-CPDA: 105.9
  CHC-CoA: 98.9
  Propionyl-CoA: 95.9
  Malonyl-CoA: 86.2
  Isobutyryl-CoA: 71.3
  Benzoyl-CoA: 48.5
  Acetyl-CoA: 45.6
  fatty_acid: 30.9
  inactive: 26.4
  3-Methylbutyryl-CoA: 14.9

PKS_AT (6441..6726): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 187.9
  Ethylmalonyl-CoA: 164.7
  Methoxymalonyl-CoA: 145.0
  2-Methylbutyryl-CoA: 114.9
  trans-1,2-CPDA: 109.1
  Propionyl-CoA: 99.8
  CHC-CoA: 95.2
  Malonyl-CoA: 94.7
  Isobutyryl-CoA: 73.0
  Benzoyl-CoA: 53.5
  Acetyl-CoA: 46.2
  inactive: 27.6
  fatty_acid: 26.9
  3-Methylbutyryl-CoA: 11.0

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
CelR | Cellobiose uptake repressor
IolR | Regulator of the inositol catabolism
OsdR | Development and stress management regulator
RpoN | Regulator of nitrogen assimilation and virulence
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP018365.1 - Region 29 - T2PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,450,327 - 7,522,815 nt. (total: 72,489 nt) Show pHMM detection rules used
T2PKS: (t2ks and t2clf)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
RVR_RS31720: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

RVR_RS31785: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

RVR_RS31810: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

RVR_RS31830: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS31840: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS31865: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS31880: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

RVR_RS31885: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

RVR_RS31890: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS31895: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

RVR_RS31940: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Transferases: methyltransferase
RVR_RS31725: methyltransferase

smcogs
  SMCOG1089: methyltransferase

RVR_RS31820: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: peptidase
RVR_RS31930: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: cyclase
RVR_RS31835: cyclase/dehydrase

smcogs
  SMCOG1128: cyclase/dehydrase

RVR_RS31860: Polyketide synthesis cyclase

smcogs
  SMCOG1225: Polyketide synthesis cyclase

Ligases: synthase
RVR_RS31850: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

RVR_RS31855: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS31985: 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 | T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.83 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002712.2 |  | 0.82 | PKS | WS-5995 D, WS-5995 B, WS-5995 C, SEK 43 | Streptomyces yanglinensis
BGC0001723.5 |  | 0.78 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000234.5 |  | 0.77 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002477.3 |  | 0.65 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0002000.4 |  | 0.64 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0000235.5 |  | 0.64 | PKS | kiamycin | Streptomyces sp. W007
BGC0002047.2 |  | 0.60 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000272.3 |  | 0.60 | PKS | spore pigment | Streptomyces collinus
BGC0002672.2 |  | 0.59 | PKS | saccharothrixin D, saccharothrixin E, saccharothrixin F, saccharothrixin G, saccharothrixin H, saccharothrixin I, saccharothrixin J, saccharothrixin K, saccharothrixin L, saccharothrixin M | Saccharothrix sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000231.5 |  | 0.83 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0002712.2 |  | 0.82 | PKS | WS-5995 D, WS-5995 B, WS-5995 C, SEK 43 | Streptomyces yanglinensis
BGC0001723.5 |  | 0.78 | PKS | oviedomycin | Streptomyces antibioticus
BGC0000234.5 |  | 0.77 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002477.3 |  | 0.65 | PKS | thioangucycline A, thioangucycline B | Streptomyces sp. CB00072
BGC0002000.4 |  | 0.64 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0000235.5 |  | 0.64 | PKS | kiamycin | Streptomyces sp. W007
BGC0002047.2 |  | 0.60 | PKS | brasiliquinone A, brasiliquinone B | Nocardia brasiliensis
BGC0000272.3 |  | 0.60 | PKS | spore pigment | Streptomyces collinus
BGC0002672.2 |  | 0.59 | PKS | saccharothrixin D, saccharothrixin E, saccharothrixin F, saccharothrixin G, saccharothrixin H, saccharothrixin I, saccharothrixin J, saccharothrixin K, saccharothrixin L, saccharothrixin M | Saccharothrix sp.

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.98 out of 20.97
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 24.00 out of 29.65
Confidence: medium
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 24.46 out of 30.11
Confidence: medium
Additional weak hits (11):
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.99 out of 26.33
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.84 out of 29.38
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.84 out of 27.78
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.80 out of 31.73
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.58 out of 26.12
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.48 out of 29.25
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.40 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.16 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
Type II PKS
TFBS Finder
Type II PKS gene cluster prediction details
Predictions of starter units, elongations, product classes, and potential molecular weights for type II PKS clusters.
More detailed information is available here.

Cluster section:
  7450326 to 7522815
Starter unit(s):
  acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:
  8|9 (Score: 682.5; E-value: 3.8e-208)
Product class(es):
  angucycline
Product molecular weight(s):
  acetyl-CoA_8: 398 Da
  acetyl-CoA_9: 440 Da

RVR_RS31820
  MET (Score: 294.7; E-value: 2e-90)
RVR_RS31830
  OXY (Score: 537.1; E-value: 9.5e-164)
RVR_RS31835
  CYC C7-C12 (Score: 478.7; E-value: 1.4e-146)
RVR_RS31840
  KR C9 (Score: 464.4; E-value: 2.2e-142)
RVR_RS31845
  ACP (Score: 122.0; E-value: 1.9e-38)
RVR_RS31850
  CLF 8|9 (Score: 682.5; E-value: 3.8e-208)
RVR_RS31855
  KS (Score: 788.4; E-value: 3.2e-240)
RVR_RS31860
  CYC C4-C17/C2-C19 (Score: 196.1; E-value: 1.2e-60)
RVR_RS31865
  OXY (Score: 580.5; E-value: 6.4e-177)
RVR_RS31890
  KR (Score: 173.5; E-value: 1.5e-53)
RVR_RS31895
  OXY (Score: 383.9; E-value: 2.9e-117)

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
CelR | Cellobiose uptake repressor
LexA variant 1 | Repressor of DNA damage response

NZ_AP018365.1 - Region 30 - lanthipeptide-class-ii,lanthipeptide-class-iv
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,986,833 - 8,018,583 nt. (total: 31,751 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)
lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
RVR_RS33995: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: aminotransferase
RVR_RS34015: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Lyases: cyclase
RVR_RS33960: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: synthase
RVR_RS33930: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | lanthipeptide-class-ii | lanthipeptide-class-iv | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001226.4 |  |  | 0.35 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0001229.4 |  |  | 0.32 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000528.5 |  |  | 0.31 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000517.4 |  |  | 0.30 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0000519.4 |  |  | 0.27 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0001454.5 |  |  | 0.27 | other (other) | germicidin | Streptomyces argillaceus
BGC0002110.3 |  |  | 0.27 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908
BGC0002699.2 |  |  | 0.24 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0002663.2 |  |  | 0.23 | ribosomal | amyloliquecidin GF610 | Bacillus amyloliquefaciens UMAF6639
BGC0000527.5 |  |  | 0.23 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.60 | other (other) | germicidin | Streptomyces argillaceus
BGC0001226.4 |  | 0.51 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000528.5 |  | 0.48 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001229.4 |  | 0.47 | ribosomal | SBI-06990 A1, SBI-06989 A2 | Streptomyces bingchenggensis BCW-1
BGC0000517.4 |  | 0.46 | ribosomal | haloduracin β, haloduracin α | Bacillus halodurans C-125
BGC0000519.4 |  | 0.45 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002110.3 |  | 0.43 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908
BGC0002127.3 |  | 0.42 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0001485.4 |  | 0.42 | other (other) | chuangxinmycin | Actinoplanes tsinanensis
BGC0001896.4 |  | 0.41 | other (other) | carbazomycin B | Streptomyces luteoverticillatus

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

No significant matches found.

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

No significant matches found.

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

#### Lanthipeptide(s) for RVR_RS33960

allorf_8002653_8002877
Leader:
MRRHETLLPRRGHAARAVRAVGPLPRRRGARRVPGA
allorf_8002653_8002877
Leader:
MRRHETLLPRRGHAARAVRAVGPLPRRRGARRVPGA
Shared core:
P R R D R T G A T G S T G A T R A T R A P C A T G T D D V S G P R P G H G C
Core with dehydrations:
P R R D R Dhb G A Dhb G Dha Dhb G A Dhb R A Dhb R A P Cys A Dhb G Dhb D D V Dha G P R P G H G Cys

#### antiSMASH-DB 4.0 matches for allorf_8002653_8002877

100.0%
NZ_AP018365.1 and 3 others:
NZ_AP018365.1 Lanthipeptides: allorf_8002653_8002877_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8002653_8002877_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8002653_8002877_lanthipeptide
Lanthipeptides: allorf_8002653_8002877_lanthipeptide
1
P R R D R T G A T G S T G A T R A T R A P C A T G T D D V S G P R P G H G C
38
P R R D R T G A T G S T G A T R A T R A P C A T G T D D V S G P R P G H G C
1
P R R D R T G A T G S T G A T R A T R A P C A T G T D D V S G P R P G H G C
38
34.2%
NZ_CP033923.1:
Lanthipeptides: EG343_RS10035_lanthipeptide
7
G A T G S T G A T R A T R A P C A T G T D D V S G P R P
34
G A T G S+ A T A C T + P R P
4
G A T G S S S G C D A T-A V C G C V T Q T I R I P R P
30
18.4%
NZ_KB976165.1 and 1 other:
NZ_MOOT01000054.1 Lanthipeptides: BK765_RS17675_lanthipeptide
Lanthipeptides: ICC_RS37095_lanthipeptide
12
T G A T R A T R A P C A T G T
26
T + +R A P C +G T
3
T S I L K V S R A P C K S G T
17
with 1 more sequence matches
13.6%
NZ_CP046514.1 and 9 others:
NZ_CP069278.1 Lanthipeptides: allorf_1033752_1033973_lanthipeptide NZ_GL622638.1 Lanthipeptides: allorf_31875_32096_lanthipeptide NZ_JADMSA010000006.1 Lanthipeptides: allorf_049253_049474_lanthipeptide NZ_JADMUN010000007.1 Lanthipeptides: allorf_076793_077014_lanthipeptide NZ_JADNBL010000011.1 Lanthipeptides: allorf_61109_61330_lanthipeptide NZ_JADPBZ010000019.1 Lanthipeptides: allorf_14831_15052_lanthipeptide NZ_JADPCP010000015.1 Lanthipeptides: allorf_17792_18013_lanthipeptide NZ_JAHTKJ010000004.1 Lanthipeptides: allorf_025782_026003_lanthipeptide NZ_NJNX01000015.1 Lanthipeptides: allorf_53588_53809_lanthipeptide
Lanthipeptides: allorf_1935663_1935884_lanthipeptide
16
R A T R A P C A T G T D D V S G P R P
34
R A T+ P C A R P
4
R A T K K P C A Q A E Q Y N L A K R P
22
allorf_8005631_8005744
Leader:
MSQVLNLQEMEIPAPEQEQEVEGS
allorf_8005631_8005744
Leader:
MSQVLNLQEMEIPAPEQEQEVEGS
Shared core:
Y F I C S D A S W F L C A
Core with dehydrations:
Y F I Cys Dha D A Dha W F L Cys A

#### antiSMASH-DB 4.0 matches for allorf_8005631_8005744

100.0%
NZ_AP018365.1 and 8 others:
NZ_AP018365.1 Lanthipeptides: allorf_8005631_8005744_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8005631_8005744_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8005631_8005744_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide
Lanthipeptides: allorf_8005631_8005744_lanthipeptide
1
Y F I C S D A S W F L C A
13
Y F I C S D A S W F L C A
1
Y F I C S D A S W F L C A
13
35.0%
NZ_BMUN01000002.1 and 14 others:
NZ_BMUN01000002.1 Lanthipeptides: IE238_RS37930_lanthipeptide NZ_CP027297.1 Lanthipeptides: C1N79_RS19645_lanthipeptide NZ_CP027297.1 Lanthipeptides: C1N79_RS36515_lanthipeptide NZ_CP039123.1 Lanthipeptides: E5N77_RS19350_lanthipeptide NZ_CP039123.1 Lanthipeptides: E5N77_RS37620_lanthipeptide NZ_CP058693.1 Lanthipeptides: HYQ63_RS44930_lanthipeptide NZ_CP058693.1 Lanthipeptides: HYQ63_RS44925_lanthipeptide NZ_CP104697.1 Lanthipeptides: N6Q81_RS18965_lanthipeptide NZ_CP104697.1 Lanthipeptides: N6Q81_RS18960_lanthipeptide NZ_CP117709.1 Lanthipeptides: PSQ21_RS19060_lanthipeptide NZ_CP117709.1 Lanthipeptides: PSQ21_RS19055_lanthipeptide NZ_JACWAA010000005.1 Lanthipeptides: ICA23_RS27195_lanthipeptide NZ_JACWAA010000005.1 Lanthipeptides: ICA23_RS34925_lanthipeptide NZ_KZ819185.1 Lanthipeptides: DBP22_RS30620_lanthipeptide
Lanthipeptides: IE238_RS05610_lanthipeptide
4
C S D A S W F L C
12
C S D A S W C
12
C S D A S W V F C
20
31.6%
NZ_CP024036.1:
Lanthipeptides: CR091_RS27895_lanthipeptide
5
S D A S W F L C
12
S+ S W F L C
12
S N T S W F L C
19
with 3 more sequence matches
31.6%
NZ_CP084585.1:
Lanthipeptides: allorf_0614669_0614794_lanthipeptide
5
S D A S W F L C
12
S S W F L C
12
S T T S W F L C
19
27.8%
NZ_BNBY01000001.1 and 2 others:
NZ_BNBY01000001.1 Lanthipeptides: IE332_RS00510_lanthipeptide NZ_BNBY01000001.1 Lanthipeptides: IE332_RS00505_lanthipeptide
Lanthipeptides: IE332_RS00515_lanthipeptide
4
C S D A S W F L C
12
C S++S W C
9
C S N S S W L W C
17
15.4%
NZ_CP061368.1:
Lanthipeptides: IC757_RS01025_lanthipeptide
3
I C S D A S W F L C A
13
+C D +W+ C
16
L C P D G T W Y Q C P
26
allorf_8005707_8005826
Leader:
MRPRAGGEVGPRAGG
allorf_8005707_8005826
Leader:
MRPRAGGEVGPRAGG
Shared core:
A T R G T D A S P R R C L R R R G T S W R R C R
Core with dehydrations:
A Dhb R G Dhb D A Dha P R R Cys L R R R G Dhb Dha W R R Cys R

#### antiSMASH-DB 4.0 matches for allorf_8005707_8005826

100.0%
NZ_AP018365.1 and 3 others:
NZ_AP018365.1 Lanthipeptides: allorf_8005707_8005826_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8005707_8005826_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8005707_8005826_lanthipeptide
Lanthipeptides: allorf_8005707_8005826_lanthipeptide
1
A T R G T D A S P R R C L R R R G T S W R R C R
24
A T R G T D A S P R R C L R R R G T S W R R C R
1
A T R G T D A S P R R C L R R R G T S W R R C R
24
24.4%
NZ_JALGRP010000007.1 and 1 other:
NZ_JALGRP010000007.1 Lanthipeptides: allorf_190248_190481_lanthipeptide
Lanthipeptides: allorf_190248_190481_lanthipeptide
5
T D A S P R R C L R R R G T S W R R
22
T D + R R C R R G W+R
24
T D V A D R R C-R R C G P Q W K R
40
23.1%
NZ_BKZV01000001.1:
Lanthipeptides: allorf_0684420_0684575_lanthipeptide
12
C L R R R G T S W R
21
C R R S W R
6
C F R Y R P I S W R
15
with 3 more sequence matches
18.6%
NZ_ML123085.1 and 3 others:
NZ_ML123085.1 Lanthipeptides: allorf_0381774_0381971_lanthipeptide NZ_RDBM01000037.1 Lanthipeptides: allorf_1275501_1275698_lanthipeptide NZ_RDBM01000037.1 Lanthipeptides: allorf_1275501_1275698_lanthipeptide
Lanthipeptides: allorf_0381774_0381971_lanthipeptide
1
A T R G T D A S P R R C
12
A R G+ A S P R C
2
A R R G S G A S P G R C
13
16.7%
NZ_LMGS01000001.1 and 2 others:
NZ_LMJF01000001.1 Lanthipeptides: allorf_1222404_1222598_lanthipeptide NZ_LMJO01000001.1 Lanthipeptides: allorf_0602455_0602649_lanthipeptide
Lanthipeptides: allorf_1210898_1211092_lanthipeptide
9
P R R C L R R R G T S W R R C R
24
P R R C R R R R C+
34
P R R C A A R R R D G I R R C K
49
13.7%
NZ_LN850107.1:
Lanthipeptides: BN1701_RS10695_lanthipeptide
2
T R G T D A S P R R C L R R R G T S W R R C R
24
G T+ + C L G W R
14
A E G T E G P K Q H C L D H I G L V W T D M R
36
allorf_8008609_8008725
Leader:
MRTIVHQSWRSDGLNGRVHPLSIGANLAAS
allorf_8008609_8008725
Leader:
MRTIVHQSWRSDGLNGRVHPLSIGANLAAS
Shared core:
R P R C Y V P T
Core with dehydrations:
R P R Cys Y V P Dhb

#### antiSMASH-DB 4.0 matches for allorf_8008609_8008725

100.0%
NZ_AP018365.1 and 3 others:
NZ_AP018365.1 Lanthipeptides: allorf_8008609_8008725_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8008609_8008725_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8008609_8008725_lanthipeptide
Lanthipeptides: allorf_8008609_8008725_lanthipeptide
1
R P R C Y V P T
8
R P R C Y V P T
1
R P R C Y V P T
8

#### Lanthipeptide(s) for RVR_RS33980

allorf_8002653_8002877
Leader:
MRRHETLLPRRGHAARAVRAVGPLPRRRGARRVPGA
allorf_8002653_8002877
Leader:
MRRHETLLPRRGHAARAVRAVGPLPRRRGARRVPGA
Shared core:
P R R D R T G A T G S T G A T R A T R A P C A T G T D D V S G P R P G H G C
Core with dehydrations:
P R R D R Dhb G A Dhb G Dha Dhb G A Dhb R A Dhb R A P Cys A Dhb G Dhb D D V Dha G P R P G H G Cys

#### antiSMASH-DB 4.0 matches for allorf_8002653_8002877

100.0%
NZ_AP018365.1 and 3 others:
NZ_AP018365.1 Lanthipeptides: allorf_8002653_8002877_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8002653_8002877_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8002653_8002877_lanthipeptide
Lanthipeptides: allorf_8002653_8002877_lanthipeptide
1
P R R D R T G A T G S T G A T R A T R A P C A T G T D D V S G P R P G H G C
38
P R R D R T G A T G S T G A T R A T R A P C A T G T D D V S G P R P G H G C
1
P R R D R T G A T G S T G A T R A T R A P C A T G T D D V S G P R P G H G C
38
34.2%
NZ_CP033923.1:
Lanthipeptides: EG343_RS10035_lanthipeptide
7
G A T G S T G A T R A T R A P C A T G T D D V S G P R P
34
G A T G S+ A T A C T + P R P
4
G A T G S S S G C D A T-A V C G C V T Q T I R I P R P
30
18.4%
NZ_KB976165.1 and 1 other:
NZ_MOOT01000054.1 Lanthipeptides: BK765_RS17675_lanthipeptide
Lanthipeptides: ICC_RS37095_lanthipeptide
12
T G A T R A T R A P C A T G T
26
T + +R A P C +G T
3
T S I L K V S R A P C K S G T
17
with 1 more sequence matches
13.6%
NZ_CP046514.1 and 9 others:
NZ_CP069278.1 Lanthipeptides: allorf_1033752_1033973_lanthipeptide NZ_GL622638.1 Lanthipeptides: allorf_31875_32096_lanthipeptide NZ_JADMSA010000006.1 Lanthipeptides: allorf_049253_049474_lanthipeptide NZ_JADMUN010000007.1 Lanthipeptides: allorf_076793_077014_lanthipeptide NZ_JADNBL010000011.1 Lanthipeptides: allorf_61109_61330_lanthipeptide NZ_JADPBZ010000019.1 Lanthipeptides: allorf_14831_15052_lanthipeptide NZ_JADPCP010000015.1 Lanthipeptides: allorf_17792_18013_lanthipeptide NZ_JAHTKJ010000004.1 Lanthipeptides: allorf_025782_026003_lanthipeptide NZ_NJNX01000015.1 Lanthipeptides: allorf_53588_53809_lanthipeptide
Lanthipeptides: allorf_1935663_1935884_lanthipeptide
16
R A T R A P C A T G T D D V S G P R P
34
R A T+ P C A R P
4
R A T K K P C A Q A E Q Y N L A K R P
22
allorf_8005631_8005744
Leader:
MSQVLNLQEMEIPAPEQEQEVEGS
allorf_8005631_8005744
Leader:
MSQVLNLQEMEIPAPEQEQEVEGS
Shared core:
Y F I C S D A S W F L C A
Core with dehydrations:
Y F I Cys Dha D A Dha W F L Cys A

#### antiSMASH-DB 4.0 matches for allorf_8005631_8005744

100.0%
NZ_AP018365.1 and 8 others:
NZ_AP018365.1 Lanthipeptides: allorf_8005631_8005744_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8005631_8005744_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8005631_8005744_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide NZ_FONG01000023.1 Lanthipeptides: allorf_109527_109640_lanthipeptide
Lanthipeptides: allorf_8005631_8005744_lanthipeptide
1
Y F I C S D A S W F L C A
13
Y F I C S D A S W F L C A
1
Y F I C S D A S W F L C A
13
35.0%
NZ_BMUN01000002.1 and 14 others:
NZ_BMUN01000002.1 Lanthipeptides: IE238_RS37930_lanthipeptide NZ_CP027297.1 Lanthipeptides: C1N79_RS19645_lanthipeptide NZ_CP027297.1 Lanthipeptides: C1N79_RS36515_lanthipeptide NZ_CP039123.1 Lanthipeptides: E5N77_RS19350_lanthipeptide NZ_CP039123.1 Lanthipeptides: E5N77_RS37620_lanthipeptide NZ_CP058693.1 Lanthipeptides: HYQ63_RS44930_lanthipeptide NZ_CP058693.1 Lanthipeptides: HYQ63_RS44925_lanthipeptide NZ_CP104697.1 Lanthipeptides: N6Q81_RS18965_lanthipeptide NZ_CP104697.1 Lanthipeptides: N6Q81_RS18960_lanthipeptide NZ_CP117709.1 Lanthipeptides: PSQ21_RS19060_lanthipeptide NZ_CP117709.1 Lanthipeptides: PSQ21_RS19055_lanthipeptide NZ_JACWAA010000005.1 Lanthipeptides: ICA23_RS27195_lanthipeptide NZ_JACWAA010000005.1 Lanthipeptides: ICA23_RS34925_lanthipeptide NZ_KZ819185.1 Lanthipeptides: DBP22_RS30620_lanthipeptide
Lanthipeptides: IE238_RS05610_lanthipeptide
4
C S D A S W F L C
12
C S D A S W C
12
C S D A S W V F C
20
31.6%
NZ_CP024036.1:
Lanthipeptides: CR091_RS27895_lanthipeptide
5
S D A S W F L C
12
S+ S W F L C
12
S N T S W F L C
19
with 3 more sequence matches
31.6%
NZ_CP084585.1:
Lanthipeptides: allorf_0614669_0614794_lanthipeptide
5
S D A S W F L C
12
S S W F L C
12
S T T S W F L C
19
27.8%
NZ_BNBY01000001.1 and 2 others:
NZ_BNBY01000001.1 Lanthipeptides: IE332_RS00510_lanthipeptide NZ_BNBY01000001.1 Lanthipeptides: IE332_RS00505_lanthipeptide
Lanthipeptides: IE332_RS00515_lanthipeptide
4
C S D A S W F L C
12
C S++S W C
9
C S N S S W L W C
17
15.4%
NZ_CP061368.1:
Lanthipeptides: IC757_RS01025_lanthipeptide
3
I C S D A S W F L C A
13
+C D +W+ C
16
L C P D G T W Y Q C P
26
allorf_8005707_8005826
Leader:
MRPRAGGEVGPRAGG
allorf_8005707_8005826
Leader:
MRPRAGGEVGPRAGG
Shared core:
A T R G T D A S P R R C L R R R G T S W R R C R
Core with dehydrations:
A Dhb R G Dhb D A Dha P R R Cys L R R R G Dhb Dha W R R Cys R

#### antiSMASH-DB 4.0 matches for allorf_8005707_8005826

100.0%
NZ_AP018365.1 and 3 others:
NZ_AP018365.1 Lanthipeptides: allorf_8005707_8005826_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8005707_8005826_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8005707_8005826_lanthipeptide
Lanthipeptides: allorf_8005707_8005826_lanthipeptide
1
A T R G T D A S P R R C L R R R G T S W R R C R
24
A T R G T D A S P R R C L R R R G T S W R R C R
1
A T R G T D A S P R R C L R R R G T S W R R C R
24
24.4%
NZ_JALGRP010000007.1 and 1 other:
NZ_JALGRP010000007.1 Lanthipeptides: allorf_190248_190481_lanthipeptide
Lanthipeptides: allorf_190248_190481_lanthipeptide
5
T D A S P R R C L R R R G T S W R R
22
T D + R R C R R G W+R
24
T D V A D R R C-R R C G P Q W K R
40
23.1%
NZ_BKZV01000001.1:
Lanthipeptides: allorf_0684420_0684575_lanthipeptide
12
C L R R R G T S W R
21
C R R S W R
6
C F R Y R P I S W R
15
with 3 more sequence matches
18.6%
NZ_ML123085.1 and 3 others:
NZ_ML123085.1 Lanthipeptides: allorf_0381774_0381971_lanthipeptide NZ_RDBM01000037.1 Lanthipeptides: allorf_1275501_1275698_lanthipeptide NZ_RDBM01000037.1 Lanthipeptides: allorf_1275501_1275698_lanthipeptide
Lanthipeptides: allorf_0381774_0381971_lanthipeptide
1
A T R G T D A S P R R C
12
A R G+ A S P R C
2
A R R G S G A S P G R C
13
16.7%
NZ_LMGS01000001.1 and 2 others:
NZ_LMJF01000001.1 Lanthipeptides: allorf_1222404_1222598_lanthipeptide NZ_LMJO01000001.1 Lanthipeptides: allorf_0602455_0602649_lanthipeptide
Lanthipeptides: allorf_1210898_1211092_lanthipeptide
9
P R R C L R R R G T S W R R C R
24
P R R C R R R R C+
34
P R R C A A R R R D G I R R C K
49
13.7%
NZ_LN850107.1:
Lanthipeptides: BN1701_RS10695_lanthipeptide
2
T R G T D A S P R R C L R R R G T S W R R C R
24
G T+ + C L G W R
14
A E G T E G P K Q H C L D H I G L V W T D M R
36
allorf_8008609_8008725
Leader:
MRTIVHQSWRSDGLNGRVHPLSIGANLAAS
allorf_8008609_8008725
Leader:
MRTIVHQSWRSDGLNGRVHPLSIGANLAAS
Shared core:
R P R C Y V P T
Core with dehydrations:
R P R Cys Y V P Dhb

#### antiSMASH-DB 4.0 matches for allorf_8008609_8008725

100.0%
NZ_AP018365.1 and 3 others:
NZ_AP018365.1 Lanthipeptides: allorf_8008609_8008725_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8008609_8008725_lanthipeptide NZ_AP018365.1 Lanthipeptides: allorf_8008609_8008725_lanthipeptide
Lanthipeptides: allorf_8008609_8008725_lanthipeptide
1
R P R C Y V P T
8
R P R C Y V P T
1
R P R C Y V P T
8

#### 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:
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 27.49 out of 30.12
Confidence: strong
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.09 out of 30.12
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.72 out of 20.47
Confidence: medium
Additional weak hits (10):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.17 out of 26.12
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 21.84
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.49 out of 30.22
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.63 out of 26.33
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.80 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 11.39 out of 26.06
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.34 out of 26.12
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 15.47 out of 28.19
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 14.65 out of 33.14
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.16 out of 27.18
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.

allorf_8002653_8002877 - Class II
  Cleavage pHMM score: -1.70
  RODEO score: 0
  Monoisotopic mass: 3603.8 Da
  Molecular weight: 3605.9 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3623.9 Da N = 1
    3641.9 Da N = 2
    3659.9 Da N = 3
    3677.9 Da N = 4
    3696.0 Da N = 5
    3714.0 Da N = 6
    3732.0 Da N = 7
allorf_8005631_8005744 - Class II
  Cleavage pHMM score: -4.50
  RODEO score: 0
  Monoisotopic mass: 1488.6 Da
  Molecular weight: 1489.7 Da
  Number of bridges: 2
allorf_8005707_8005826 - Class II
  Cleavage pHMM score: -7.10
  RODEO score: 0
  Monoisotopic mass: 2783.5 Da
  Molecular weight: 2785.2 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2803.2 Da N = 1
    2821.2 Da N = 2
    2839.2 Da N = 3
allorf_8008609_8008725 - Class II
  Cleavage pHMM score: -4.80
  RODEO score: 0
  Monoisotopic mass: 972.5 Da
  Molecular weight: 973.1 Da
  Number of bridges: 1
allorf_8002653_8002877 - Class II
  Cleavage pHMM score: -1.70
  RODEO score: 0
  Monoisotopic mass: 3603.8 Da
  Molecular weight: 3605.9 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3623.9 Da N = 1
    3641.9 Da N = 2
    3659.9 Da N = 3
    3677.9 Da N = 4
    3696.0 Da N = 5
    3714.0 Da N = 6
    3732.0 Da N = 7
allorf_8005631_8005744 - Class II
  Cleavage pHMM score: -4.50
  RODEO score: 0
  Monoisotopic mass: 1488.6 Da
  Molecular weight: 1489.7 Da
  Number of bridges: 2
allorf_8005707_8005826 - Class II
  Cleavage pHMM score: -7.10
  RODEO score: 0
  Monoisotopic mass: 2783.5 Da
  Molecular weight: 2785.2 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2803.2 Da N = 1
    2821.2 Da N = 2
    2839.2 Da N = 3
allorf_8008609_8008725 - Class II
  Cleavage pHMM score: -4.80
  RODEO score: 0
  Monoisotopic mass: 972.5 Da
  Molecular weight: 973.1 Da
  Number of bridges: 1
allorf_8002653_8002877 - Class II
  Cleavage pHMM score: -1.70
  RODEO score: 0
  Monoisotopic mass: 3603.8 Da
  Molecular weight: 3605.9 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3623.9 Da N = 1
    3641.9 Da N = 2
    3659.9 Da N = 3
    3677.9 Da N = 4
    3696.0 Da N = 5
    3714.0 Da N = 6
    3732.0 Da N = 7
allorf_8005631_8005744 - Class II
  Cleavage pHMM score: -4.50
  RODEO score: 0
  Monoisotopic mass: 1488.6 Da
  Molecular weight: 1489.7 Da
  Number of bridges: 2
allorf_8005707_8005826 - Class II
  Cleavage pHMM score: -7.10
  RODEO score: 0
  Monoisotopic mass: 2783.5 Da
  Molecular weight: 2785.2 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2803.2 Da N = 1
    2821.2 Da N = 2
    2839.2 Da N = 3
allorf_8008609_8008725 - Class II
  Cleavage pHMM score: -4.80
  RODEO score: 0
  Monoisotopic mass: 972.5 Da
  Molecular weight: 973.1 Da
  Number of bridges: 1
allorf_8002653_8002877 - Class II
  Cleavage pHMM score: -1.70
  RODEO score: 0
  Monoisotopic mass: 3603.8 Da
  Molecular weight: 3605.9 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3623.9 Da N = 1
    3641.9 Da N = 2
    3659.9 Da N = 3
    3677.9 Da N = 4
    3696.0 Da N = 5
    3714.0 Da N = 6
    3732.0 Da N = 7
allorf_8005631_8005744 - Class II
  Cleavage pHMM score: -4.50
  RODEO score: 0
  Monoisotopic mass: 1488.6 Da
  Molecular weight: 1489.7 Da
  Number of bridges: 2
allorf_8005707_8005826 - Class II
  Cleavage pHMM score: -7.10
  RODEO score: 0
  Monoisotopic mass: 2783.5 Da
  Molecular weight: 2785.2 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2803.2 Da N = 1
    2821.2 Da N = 2
    2839.2 Da N = 3
allorf_8008609_8008725 - Class II
  Cleavage pHMM score: -4.80
  RODEO score: 0
  Monoisotopic mass: 972.5 Da
  Molecular weight: 973.1 Da
  Number of bridges: 1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
OsdR | Development and stress management regulator
VqsM | Regulator of quorum-sensing signalling systems

NZ_AP018365.1 - Region 31 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,044,760 - 8,100,439 nt. (total: 55,680 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
RVR_RS34155: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

RVR_RS34160: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS34195: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

RVR_RS34240: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acetyltransferase
RVR_RS34185: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: esterase hydrolase
RVR_RS34220: thioesterase

smcogs
  SMCOG1004: thioesterase

RVR_RS34235: HAD-superfamily hydrolase, subfamily IA, variant

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

Lyases: dehydratase hydratase
RVR_RS34135: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

RVR_RS34165: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase synthetase
RVR_RS34170: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS34205: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS34210: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

RVR_RS34215: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS34225: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

RVR_RS38770: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.76 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  |  | 0.74 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.74 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  |  | 0.73 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  | 0.71 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.70 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5 |  |  | 0.69 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000342.4 |  |  | 0.69 | NRPS | enniatin | Fusarium equiseti

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.70 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001833.4 |  | 0.69 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.69 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
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 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  | 0.68 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0000342.4 |  | 0.68 | NRPS | enniatin | Fusarium equiseti

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

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:
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 26.61 out of 30.22
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12
Confidence: medium
Additional weak hits (10):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.95 out of 26.85
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.37 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.08 out of 20.97
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 17.70 out of 26.33
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.17 out of 27.55
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.46 out of 32.93
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.67 out of 25.88
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.44 out of 29.65
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.78 out of 27.18
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.21 out of 29.65
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 42, location 8044759 - 8100439:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Pro) + (redmal) + (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).
RVR_RS34170: X
AMP-binding (15..418): 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:
    YARLHGAGEGQRSTGVGGAHEAYGATEVGTITSM
  Nearest Stachelhaus code(s):
    2S-Hic GANLIGATIK (29% 8Å match)
  Stachelhaus code match:
    70% (weak)

RVR_RS34205: X - Pro
Search NORINE for peptide: strict or relaxed
AMP-binding (223..637): 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:
    LTTHFDASVWEGALVLCAECNMYGITETTVHSTH
  Nearest Stachelhaus code(s):
    Thr DFWSVGMVHK (76% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1337..1732): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LWQAFDVSVQETFLLTAGEVNQYGPTETHVAVAH
  Nearest Stachelhaus code(s):
    Pro DVQFMAQVVK (79% 8Å match)
    4Me-Pro DVQFIAHVAK (71% 8Å match)
  Stachelhaus code match:
    80% (moderate)

RVR_RS34210: mal
PKS_AT (540..824): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 133.3
  Methoxymalonyl-CoA: 70.4
  Methylmalonyl-CoA: 59.6
  inactive: 53.1
  Propionyl-CoA: 47.4
  Ethylmalonyl-CoA: 43.0
  Isobutyryl-CoA: 38.4
  fatty_acid: 27.8
  2-Methylbutyryl-CoA: 23.8
  Acetyl-CoA: 21.1
  CHC-CoA: 16.2
  Benzoyl-CoA: 15.4
  trans-1,2-CPDA: 7.1
  3-Methylbutyryl-CoA: 2.3

RVR_RS34215: X
AMP-binding (572..921): 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:
    RAFPYDPGMRDTAVRCCGEHNDYGPSEATMVSVS
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

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

Regulator | Description
--- | ---
ClgR | Caseinolytic protease gene regulator
OsdR | Development and stress management regulator

NZ_AP018365.1 - Region 32 - NRPS,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,126,442 - 8,210,090 nt. (total: 83,649 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase
RVR_RS34450: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

RVR_RS34480: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: kinase
RVR_RS34460: acetylglutamate kinase

smcogs
  SMCOG1174: acetylglutamate kinase

Hydrolases: esterase hydrolase
RVR_RS34425: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

RVR_RS34510: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase
RVR_RS34465: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

RVR_RS34490: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

RVR_RS34495: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

RVR_RS34505: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

RVR_RS34515: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS34520: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS34525: 1-deoxy-D-xylulose-5-phosphate synthase

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

RVR_RS34535: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS34540: 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 | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002135.2 |  |  | 0.94 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.89 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001758.4 |  |  | 0.88 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001833.4 |  |  | 0.87 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  | 0.85 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  |  | 0.83 | NRPS | HC-toxin | Alternaria jesenskae
BGC0002286.3 |  |  | 0.82 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  | 0.81 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001261.3 |  |  | 0.79 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  |  | 0.79 | NRPS | xenematide | Xenorhabdus nematophila AN6/1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002135.2 |  | 0.77 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001758.4 |  | 0.76 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.75 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002071.2 |  | 0.74 | NRPS | virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D | Pseudomonas sp. QS1027
BGC0001128.4 |  | 0.74 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5 |  | 0.73 | NRPS | HC-toxin | Alternaria jesenskae
BGC0001133.4 |  | 0.73 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.72 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.11 out of 28.19
Confidence: medium
Additional weak hits (18):
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.35 out of 36.54
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.44 out of 30.25
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 19.26
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.10 out of 29.25
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
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.82 out of 18.57
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.47 out of 26.33
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.78 out of 20.97
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.01 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.27 out of 27.78
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 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.98 out of 29.65
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.28 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.67 out of 26.06
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.70 out of 30.98
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.42 out of 27.04
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 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 43, location 8126441 - 8210090:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ile - Gln - Ile - D-Gln) + (X - Phe) + (NH2 - X) + (ohmal) + (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
RVR_RS34490: X
AMP-binding (10..419): X
nrpys: Orn, Lys, Arg

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YWVTSDACLQQAHCFLGGDANVYGPTEATVQVTG
  Nearest Stachelhaus code(s):
    Arg DPLDFGVVQK (56% 8Å match)
    Gln DAWQFGVVDK (53% 8Å match)
    Ile DAQDLGVVDK (50% 8Å match)
    aIle DALVFGVVLK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

RVR_RS34515: mal
PKS_AT (536..822): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 66.7%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 149.1
  inactive: 74.0
  Methoxymalonyl-CoA: 61.5
  Methylmalonyl-CoA: 50.4
  Propionyl-CoA: 41.4
  CHC-CoA: 18.4
  Ethylmalonyl-CoA: 16.0
  Benzoyl-CoA: 14.1
  2-Methylbutyryl-CoA: 12.9
  Isobutyryl-CoA: 11.2
  fatty_acid: 10.8
  trans-1,2-CPDA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

RVR_RS34520: NH2 - X
CAL_domain (43..468): NH2
minowa: NH2

Prediction, score:
  NH2: 100.4
  fatty_acid: 14.8
  AHBA: 6.1
  Acetyl-CoA: -2.1
  shikimic_acid: -7.0

AMP-binding (1170..1567): 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:
    LWQLFDFGLQETYLVLGGEVNGYGPTEASINCSM
  Nearest Stachelhaus code(s):
    Gln DVQIVGGIHK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

RVR_RS34535: X - Phe
Search NORINE for peptide: strict or relaxed
AMP-binding (472..872): 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:
    LDSSFDASTFETFVASGGEHNAYGPTETTTFATL
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (76% 8Å match)
    Val DAFFVGGTFK (74% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (1535..1931): 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:
    MTQAFDAAFWEMTLVLAGEVNAYGPTETTVCATM
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (91% 8Å match)
  Stachelhaus code match:
    100% (strong)

RVR_RS34540: Ile - Gln - Ile - Gln
Search NORINE for peptide: strict or relaxed
AMP-binding (501..901): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDSSFDATTFEAFLGAGGELHVYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (79% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1605..2005): 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:
    gln (Gln)

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

AMP-binding (2715..3128): Ile
nrpys: Ile

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    LDSSFDASTFETFLCAGGELHVYGPTETTTFATR
  Nearest Stachelhaus code(s):
    Ile DAFFLGVTFK (85% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (3789..4216): 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:
    HWMTFDASVWELQFLCGGEHNLYGPTEATVDATA
  Nearest Stachelhaus code(s):
    Gln DAWQFGLVDK (71% 8Å match)
  Stachelhaus code match:
    90% (moderate)

Link to PARAS substrate predictor
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
ZuR variant 1 | Zinc-responsive repressor

NZ_AP018365.1 - Region 33 - NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 8,439,228 - 8,740,152 nt. (total: 300,925 nt) Show pHMM detection rules used
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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
RVR_RS35600: oxidoreductase

smcogs
  SMCOG1079: oxidoreductase

RVR_RS35640: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

RVR_RS35845: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

RVR_RS35855: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

RVR_RS35990: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS36030: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS36035: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

RVR_RS36075: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

RVR_RS36125: FAD linked oxidase domain protein

smcogs
  SMCOG1138: FAD linked oxidase domain protein

Transferases: PPTase acetyltransferase acylase
RVR_RS35695: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

RVR_RS35765: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

RVR_RS35945: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1060: 4'-phosphopantetheinyl transferase

RVR_RS38280: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

RVR_RS38805: acetyl-CoA acetyltransferase

smcogs
  SMCOG1124: acetyl-CoA acetyltransferase

RVR_RS38810: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase phosphatase
RVR_RS35860: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

RVR_RS35950: thioesterase

smcogs
  SMCOG1004: thioesterase

RVR_RS36080: thioesterase

smcogs
  SMCOG1004: thioesterase

Lyases: dehydratase
RVR_RS35605: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase
RVR_RS35660: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS36020: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

RVR_RS36065: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS36070: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS36120: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS38790: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS38795: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

RVR_RS38800: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

RVR_RS38815: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

Translocases: transport
RVR_RS35650: MMPL domain-containing transport protein

smcogs
  SMCOG1035: MMPL domain-containing transport protein

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

Reference | T1PKS | NRPS | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001833.4 |  |  |  | 0.94 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000041.3 |  |  |  | 0.91 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001641.4 |  |  |  | 0.90 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001276.3 |  |  |  | 0.90 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002191.2 |  |  |  | 0.90 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0002192.3 |  |  |  | 0.89 | PKS | FR901512 | fungal sp. No.14919
BGC0002171.2 |  |  |  | 0.72 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger ATCC 1015
BGC0002275.2 |  |  |  | 0.72 | NRPS, PKS | pyrophen, campyrone B | Aspergillus niger CBS 101883
BGC0001132.4 |  |  |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001012.3 |  |  |  | 0.66 | NRPS, PKS | meridamycin | Streptomyces violaceusniger

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001132.4 |  | 0.69 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
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
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0002164.2 |  | 0.66 | NRPS | peramine | Epichloe festucae
BGC0000041.3 |  | 0.65 | PKS | oronofacic acid | Pseudomonas syringae
BGC0001240.4 |  | 0.65 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001641.4 |  | 0.65 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001257.3 |  | 0.64 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0002192.3 |  | 0.64 | PKS | FR901512 | fungal sp. No.14919

Similar known clusters from MIBiG 4.0
Shows clusters from the MIBiG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Click on an accession to open that entry in the MIBiG database.
Location:
Identifier
Identity
Coverage
Similar subclusters
Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.
Detailed help and explanations are available here.
Click on reference genes to show details of similarities to genes within the current region.
Double click on a reference drawing to reverse the display of the genes.
Location:
Identifier
Identity
Coverage
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.94 out of 26.85
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.66 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 17.89 out of 23.79
Confidence: medium
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.77 out of 29.51
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.95 out of 23.79
Confidence: medium
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.52 out of 29.72
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.07 out of 30.12
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05
Confidence: medium
Additional weak hits (27):
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.11 out of 25.75
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.14 out of 26.12
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.58 out of 26.12
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.10 out of 29.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.31 out of 32.74
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.82 out of 21.55
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 16.76 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.75 out of 27.78
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.23 out of 29.38
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.90 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.22 out of 27.78
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 39.62
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 30.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.19 out of 28.19
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.72 out of 29.65
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.97 out of 24.78
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.53 out of 21.84
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.35 out of 29.65
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 19.72 out of 27.18
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.80 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.46 out of 25.88
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.68 out of 24.78
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.83 out of 25.88
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.14 out of 26.12
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 44, location 8439227 - 8740152:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 45, location 8439227 - 8728915:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 46, location 8698343 - 8740152:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Me-mal - Me-redmal) + (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).
RVR_RS35660: mmal - mal - mmal
PKS_AT (589..891): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 70.8%
  Malonyl-CoA: 66.7%
  Methoxymalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 150.6
  Methoxymalonyl-CoA: 132.8
  Ethylmalonyl-CoA: 114.0
  2-Methylbutyryl-CoA: 94.3
  trans-1,2-CPDA: 78.2
  Propionyl-CoA: 74.3
  CHC-CoA: 73.2
  Malonyl-CoA: 67.6
  Isobutyryl-CoA: 66.6
  Benzoyl-CoA: 48.1
  Acetyl-CoA: 33.0
  inactive: 32.3
  3-Methylbutyryl-CoA: 28.5
  fatty_acid: 16.6

PKS_AT (2104..2386): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 155.1
  inactive: 66.8
  Methoxymalonyl-CoA: 65.2
  Methylmalonyl-CoA: 47.3
  Isobutyryl-CoA: 29.3
  fatty_acid: 26.9
  Ethylmalonyl-CoA: 20.2
  Benzoyl-CoA: 16.8
  Propionyl-CoA: 15.5
  Acetyl-CoA: 15.3
  trans-1,2-CPDA: 7.5
  3-Methylbutyryl-CoA: 4.5
  CHC-CoA: 1.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (3668..3966): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 75.0%
  Malonyl-CoA: 70.8%
  Methoxymalonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 158.9
  Methoxymalonyl-CoA: 140.9
  Ethylmalonyl-CoA: 129.5
  2-Methylbutyryl-CoA: 90.3
  trans-1,2-CPDA: 84.7
  Malonyl-CoA: 78.2
  Isobutyryl-CoA: 76.5
  Propionyl-CoA: 71.1
  CHC-CoA: 67.5
  Benzoyl-CoA: 46.3
  Acetyl-CoA: 36.6
  inactive: 32.9
  3-Methylbutyryl-CoA: 32.9
  fatty_acid: 17.7

RVR_RS38280: mmal - mmal
PKS_AT (620..908): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 83.3%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 166.8
  Ethylmalonyl-CoA: 156.3
  Methoxymalonyl-CoA: 149.9
  2-Methylbutyryl-CoA: 115.7
  Propionyl-CoA: 93.6
  trans-1,2-CPDA: 93.4
  Malonyl-CoA: 80.1
  CHC-CoA: 68.7
  Isobutyryl-CoA: 67.8
  3-Methylbutyryl-CoA: 60.3
  Benzoyl-CoA: 58.0
  Acetyl-CoA: 46.5
  inactive: 32.1
  fatty_acid: 19.4

PKS_AT (2221..2518): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 195.7
  Ethylmalonyl-CoA: 177.0
  Methoxymalonyl-CoA: 157.8
  2-Methylbutyryl-CoA: 131.7
  Propionyl-CoA: 98.7
  trans-1,2-CPDA: 93.0
  CHC-CoA: 87.8
  Malonyl-CoA: 86.6
  Isobutyryl-CoA: 63.1
  Benzoyl-CoA: 50.0
  inactive: 41.2
  3-Methylbutyryl-CoA: 32.6
  fatty_acid: 24.5
  Acetyl-CoA: 20.6

RVR_RS35695: mal - mmal - mmal - mal
PKS_AT (576..858): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 154.9
  Methoxymalonyl-CoA: 64.4
  inactive: 60.7
  Methylmalonyl-CoA: 48.8
  Isobutyryl-CoA: 29.2
  fatty_acid: 24.5
  Acetyl-CoA: 18.0
  Propionyl-CoA: 16.6
  Benzoyl-CoA: 16.4
  Ethylmalonyl-CoA: 15.5
  trans-1,2-CPDA: 12.6
  CHC-CoA: 10.9
  3-Methylbutyryl-CoA: 8.0
  2-Methylbutyryl-CoA: 5.9

PKS_AT (2118..2413): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 75.0%
  Malonyl-CoA: 70.8%
  Methoxymalonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 155.9
  Methoxymalonyl-CoA: 141.9
  Ethylmalonyl-CoA: 125.2
  trans-1,2-CPDA: 88.1
  2-Methylbutyryl-CoA: 87.8
  Malonyl-CoA: 73.6
  Isobutyryl-CoA: 71.6
  Propionyl-CoA: 70.3
  CHC-CoA: 60.2
  Benzoyl-CoA: 51.7
  Acetyl-CoA: 38.8
  3-Methylbutyryl-CoA: 34.0
  inactive: 33.3
  fatty_acid: 18.6

PKS_AT (3672..3964): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 70.8%
  Malonyl-CoA: 66.7%
  Methoxymalonyl-CoA: 62.5%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 148.0
  Methoxymalonyl-CoA: 128.4
  Ethylmalonyl-CoA: 112.5
  2-Methylbutyryl-CoA: 90.9
  Isobutyryl-CoA: 75.4
  CHC-CoA: 73.6
  Propionyl-CoA: 73.4
  trans-1,2-CPDA: 71.4
  Malonyl-CoA: 58.8
  Benzoyl-CoA: 47.1
  Acetyl-CoA: 31.3
  3-Methylbutyryl-CoA: 28.3
  inactive: 28.1
  fatty_acid: 16.8

PKS_AT (5239..5523): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 154.9
  inactive: 73.3
  Methoxymalonyl-CoA: 64.3
  Methylmalonyl-CoA: 46.4
  Isobutyryl-CoA: 27.2
  fatty_acid: 20.6
  Propionyl-CoA: 17.4
  Acetyl-CoA: 16.6
  Ethylmalonyl-CoA: 15.6
  Benzoyl-CoA: 13.6
  trans-1,2-CPDA: 8.3
  CHC-CoA: 7.5
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

RVR_RS38790: mmal - mmal - mal
PKS_AT (590..892): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 75.0%
  Malonyl-CoA: 70.8%
  Methoxymalonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 158.3
  Methoxymalonyl-CoA: 140.5
  Ethylmalonyl-CoA: 126.9
  2-Methylbutyryl-CoA: 89.0
  trans-1,2-CPDA: 82.8
  Isobutyryl-CoA: 74.9
  Malonyl-CoA: 74.1
  Propionyl-CoA: 71.5
  CHC-CoA: 67.7
  Benzoyl-CoA: 49.8
  Acetyl-CoA: 40.0
  3-Methylbutyryl-CoA: 35.4
  inactive: 33.1
  fatty_acid: 18.6

PKS_AT (2139..2430): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 83.3%
  Ethylmalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 167.3
  Ethylmalonyl-CoA: 160.2
  Methoxymalonyl-CoA: 149.3
  2-Methylbutyryl-CoA: 111.2
  trans-1,2-CPDA: 94.6
  Malonyl-CoA: 90.4
  Propionyl-CoA: 86.5
  CHC-CoA: 73.1
  Isobutyryl-CoA: 60.5
  Acetyl-CoA: 55.2
  Benzoyl-CoA: 54.3
  3-Methylbutyryl-CoA: 48.8
  inactive: 36.8
  fatty_acid: 21.3

PKS_AT (3703..3987): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 163.8
  inactive: 73.1
  Methoxymalonyl-CoA: 72.0
  Methylmalonyl-CoA: 56.5
  Isobutyryl-CoA: 35.2
  fatty_acid: 28.9
  Ethylmalonyl-CoA: 20.9
  Acetyl-CoA: 17.3
  Propionyl-CoA: 16.6
  trans-1,2-CPDA: 13.8
  Benzoyl-CoA: 13.7
  CHC-CoA: 13.5
  2-Methylbutyryl-CoA: 6.1
  3-Methylbutyryl-CoA: 4.3

RVR_RS35765: mal - mmal
PKS_AT (582..865): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 154.0
  inactive: 69.8
  Methoxymalonyl-CoA: 68.9
  Methylmalonyl-CoA: 51.1
  Isobutyryl-CoA: 28.9
  fatty_acid: 23.8
  Propionyl-CoA: 17.6
  Acetyl-CoA: 16.9
  Ethylmalonyl-CoA: 16.6
  Benzoyl-CoA: 14.0
  trans-1,2-CPDA: 11.1
  CHC-CoA: 10.6
  2-Methylbutyryl-CoA: 3.3
  3-Methylbutyryl-CoA: 1.0

PKS_AT (2653..2950): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 194.3
  Ethylmalonyl-CoA: 173.7
  Methoxymalonyl-CoA: 154.9
  2-Methylbutyryl-CoA: 126.1
  CHC-CoA: 93.8
  trans-1,2-CPDA: 93.5
  Propionyl-CoA: 93.2
  Malonyl-CoA: 84.8
  Benzoyl-CoA: 62.5
  Isobutyryl-CoA: 56.1
  inactive: 44.2
  3-Methylbutyryl-CoA: 36.4
  fatty_acid: 30.6
  Acetyl-CoA: 22.4

RVR_RS38795: mal - mmal - mmal
PKS_AT (570..853): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 154.4
  Methoxymalonyl-CoA: 64.6
  inactive: 60.2
  Methylmalonyl-CoA: 50.6
  Isobutyryl-CoA: 32.6
  fatty_acid: 23.4
  Acetyl-CoA: 18.0
  Benzoyl-CoA: 16.4
  Ethylmalonyl-CoA: 15.0
  Propionyl-CoA: 14.9
  trans-1,2-CPDA: 12.9
  CHC-CoA: 10.2
  3-Methylbutyryl-CoA: 8.3
  2-Methylbutyryl-CoA: 6.3

PKS_AT (2662..2971): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 197.4
  Ethylmalonyl-CoA: 179.9
  Methoxymalonyl-CoA: 156.6
  2-Methylbutyryl-CoA: 113.9
  Propionyl-CoA: 91.2
  trans-1,2-CPDA: 90.2
  CHC-CoA: 87.6
  Malonyl-CoA: 87.5
  Isobutyryl-CoA: 64.9
  Benzoyl-CoA: 54.3
  inactive: 36.3
  3-Methylbutyryl-CoA: 33.0
  fatty_acid: 23.5
  Acetyl-CoA: 19.3

PKS_AT (4803..5102): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 75.0%
  Methoxymalonyl-CoA: 75.0%
  Ethylmalonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 153.3
  Methoxymalonyl-CoA: 143.9
  Ethylmalonyl-CoA: 139.7
  2-Methylbutyryl-CoA: 90.8
  Malonyl-CoA: 86.8
  Propionyl-CoA: 86.4
  trans-1,2-CPDA: 84.0
  Isobutyryl-CoA: 70.3
  CHC-CoA: 56.8
  Benzoyl-CoA: 44.7
  3-Methylbutyryl-CoA: 37.3
  inactive: 35.7
  Acetyl-CoA: 34.8
  fatty_acid: 13.1

RVR_RS38800: mal - mal - mmal - mmal
PKS_AT (534..816): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 161.3
  inactive: 69.4
  Methoxymalonyl-CoA: 66.0
  Methylmalonyl-CoA: 48.6
  fatty_acid: 27.9
  Isobutyryl-CoA: 27.3
  Ethylmalonyl-CoA: 18.4
  Propionyl-CoA: 18.3
  Acetyl-CoA: 16.9
  Benzoyl-CoA: 14.6
  trans-1,2-CPDA: 11.1
  CHC-CoA: 10.7
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

PKS_AT (1559..1850): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 199.2
  inactive: 87.3
  Methoxymalonyl-CoA: 53.8
  Methylmalonyl-CoA: 47.5
  Propionyl-CoA: 22.1
  Isobutyryl-CoA: 19.8
  Acetyl-CoA: 17.9
  Ethylmalonyl-CoA: 17.6
  fatty_acid: 16.2
  Benzoyl-CoA: 9.0
  CHC-CoA: 5.7
  2-Methylbutyryl-CoA: 1.7
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0

PKS_AT (3737..4035): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 83.3%
  Ethylmalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 187.8
  Ethylmalonyl-CoA: 168.9
  Methoxymalonyl-CoA: 158.7
  2-Methylbutyryl-CoA: 116.8
  Propionyl-CoA: 100.1
  trans-1,2-CPDA: 95.6
  CHC-CoA: 92.4
  Malonyl-CoA: 91.7
  Benzoyl-CoA: 69.0
  Isobutyryl-CoA: 57.7
  inactive: 38.3
  3-Methylbutyryl-CoA: 33.1
  Acetyl-CoA: 23.4
  fatty_acid: 22.2

PKS_AT (5815..6112): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 196.2
  Ethylmalonyl-CoA: 178.9
  Methoxymalonyl-CoA: 157.5
  2-Methylbutyryl-CoA: 131.3
  Propionyl-CoA: 98.3
  trans-1,2-CPDA: 92.2
  CHC-CoA: 88.0
  Malonyl-CoA: 87.8
  Isobutyryl-CoA: 62.5
  Benzoyl-CoA: 50.0
  inactive: 39.0
  3-Methylbutyryl-CoA: 32.7
  fatty_acid: 24.6
  Acetyl-CoA: 20.8

RVR_RS36020: mmal - mmal - mmal
PKS_AT (578..876): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 168.5
  Ethylmalonyl-CoA: 154.2
  Methoxymalonyl-CoA: 151.2
  2-Methylbutyryl-CoA: 108.6
  CHC-CoA: 93.3
  trans-1,2-CPDA: 92.8
  Propionyl-CoA: 84.7
  Malonyl-CoA: 70.7
  Isobutyryl-CoA: 64.6
  Acetyl-CoA: 57.1
  Benzoyl-CoA: 40.5
  3-Methylbutyryl-CoA: 36.4
  inactive: 20.9
  fatty_acid: 17.6

PKS_AT (2176..2474): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 173.9
  Ethylmalonyl-CoA: 168.9
  Methoxymalonyl-CoA: 157.6
  2-Methylbutyryl-CoA: 107.9
  CHC-CoA: 101.1
  trans-1,2-CPDA: 98.0
  Propionyl-CoA: 93.0
  Malonyl-CoA: 85.8
  Isobutyryl-CoA: 67.7
  Acetyl-CoA: 51.1
  Benzoyl-CoA: 46.2
  3-Methylbutyryl-CoA: 30.2
  fatty_acid: 21.8
  inactive: 21.1

PKS_AT (3784..4083): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 169.9
  Ethylmalonyl-CoA: 161.0
  Methoxymalonyl-CoA: 155.9
  2-Methylbutyryl-CoA: 98.2
  trans-1,2-CPDA: 96.5
  CHC-CoA: 87.7
  Malonyl-CoA: 81.5
  Propionyl-CoA: 79.7
  Isobutyryl-CoA: 76.3
  Acetyl-CoA: 57.0
  Benzoyl-CoA: 47.4
  3-Methylbutyryl-CoA: 32.4
  inactive: 32.0
  fatty_acid: 15.0

RVR_RS38805: mmal - mmal - mmal - mmal
PKS_AT (609..910): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 174.4
  Ethylmalonyl-CoA: 168.9
  Methoxymalonyl-CoA: 157.2
  2-Methylbutyryl-CoA: 106.3
  CHC-CoA: 101.1
  trans-1,2-CPDA: 97.5
  Propionyl-CoA: 92.7
  Malonyl-CoA: 87.8
  Isobutyryl-CoA: 73.3
  Acetyl-CoA: 48.3
  Benzoyl-CoA: 44.3
  3-Methylbutyryl-CoA: 30.1
  inactive: 20.9
  fatty_acid: 17.5

PKS_AT (2205..2503): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 162.2
  Methoxymalonyl-CoA: 151.4
  Ethylmalonyl-CoA: 150.1
  2-Methylbutyryl-CoA: 100.7
  trans-1,2-CPDA: 91.9
  CHC-CoA: 87.9
  Propionyl-CoA: 82.0
  Malonyl-CoA: 64.9
  Isobutyryl-CoA: 57.3
  Acetyl-CoA: 53.9
  Benzoyl-CoA: 40.3
  3-Methylbutyryl-CoA: 27.3
  inactive: 18.7
  fatty_acid: 14.1

PKS_AT (3786..4074): mmal
ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 87.5%
  Methoxymalonyl-CoA: 87.5%
  Ethylmalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 173.7
  Ethylmalonyl-CoA: 168.4
  Methoxymalonyl-CoA: 158.3
  2-Methylbutyryl-CoA: 107.1
  CHC-CoA: 100.8
  trans-1,2-CPDA: 98.0
  Propionyl-CoA: 92.0
  Malonyl-CoA: 85.0
  Isobutyryl-CoA: 64.0
  Acetyl-CoA: 50.9
  Benzoyl-CoA: 46.5
  3-Methylbutyryl-CoA: 30.7
  fatty_acid: 21.9
  inactive: 21.5

PKS_AT (5385..5691): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 91.7%
  Methoxymalonyl-CoA: 83.3%
  Malonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 183.2
  Methoxymalonyl-CoA: 154.6
  Ethylmalonyl-CoA: 149.1
  2-Methylbutyryl-CoA: 123.1
  Propionyl-CoA: 114.5
  Malonyl-CoA: 103.4
  CHC-CoA: 100.7
  trans-1,2-CPDA: 83.1
  Isobutyryl-CoA: 74.2
  Benzoyl-CoA: 50.2
  inactive: 41.1
  3-Methylbutyryl-CoA: 38.8
  Acetyl-CoA: 36.5
  fatty_acid: 26.8

RVR_RS36030: mmal - mmal
PKS_AT (616..922): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 184.3
  Ethylmalonyl-CoA: 155.7
  Methoxymalonyl-CoA: 155.1
  2-Methylbutyryl-CoA: 118.5
  Propionyl-CoA: 107.7
  Malonyl-CoA: 106.1
  CHC-CoA: 103.3
  trans-1,2-CPDA: 85.5
  Isobutyryl-CoA: 65.2
  Benzoyl-CoA: 45.9
  inactive: 44.1
  Acetyl-CoA: 39.2
  3-Methylbutyryl-CoA: 36.6
  fatty_acid: 25.1

PKS_AT (2176..2472): mmal
ATSignature: Methylmalonyl-CoA

Top 3 matches:
  Methylmalonyl-CoA: 83.3%
  Methoxymalonyl-CoA: 79.2%
  Malonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 160.1
  Methoxymalonyl-CoA: 140.0
  Ethylmalonyl-CoA: 129.6
  Malonyl-CoA: 92.4
  2-Methylbutyryl-CoA: 87.8
  Propionyl-CoA: 86.6
  CHC-CoA: 79.4
  trans-1,2-CPDA: 77.3
  Isobutyryl-CoA: 42.8
  Acetyl-CoA: 36.2
  Benzoyl-CoA: 35.9
  inactive: 33.4
  3-Methylbutyryl-CoA: 33.0
  fatty_acid: 14.7

RVR_RS36035: mmal - mmal - mmal - mmal
PKS_AT (577..879): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 191.4
  Ethylmalonyl-CoA: 169.2
  Methoxymalonyl-CoA: 162.2
  2-Methylbutyryl-CoA: 131.1
  Propionyl-CoA: 119.0
  Malonyl-CoA: 114.1
  CHC-CoA: 100.0
  trans-1,2-CPDA: 90.4
  Isobutyryl-CoA: 74.9
  Benzoyl-CoA: 55.7
  inactive: 46.4
  Acetyl-CoA: 39.9
  3-Methylbutyryl-CoA: 39.7
  fatty_acid: 25.5

PKS_AT (2199..2499): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 183.9
  Methoxymalonyl-CoA: 155.2
  Ethylmalonyl-CoA: 152.0
  2-Methylbutyryl-CoA: 125.0
  Propionyl-CoA: 106.6
  Malonyl-CoA: 100.9
  CHC-CoA: 95.3
  trans-1,2-CPDA: 82.9
  Isobutyryl-CoA: 63.8
  inactive: 43.2
  Benzoyl-CoA: 42.3
  3-Methylbutyryl-CoA: 36.7
  Acetyl-CoA: 34.5
  fatty_acid: 23.5

PKS_AT (3768..4069): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 190.2
  Ethylmalonyl-CoA: 161.1
  Methoxymalonyl-CoA: 159.7
  2-Methylbutyryl-CoA: 128.6
  Propionyl-CoA: 113.8
  Malonyl-CoA: 111.9
  CHC-CoA: 100.5
  trans-1,2-CPDA: 91.3
  Isobutyryl-CoA: 68.4
  Benzoyl-CoA: 45.4
  inactive: 43.8
  3-Methylbutyryl-CoA: 38.0
  Acetyl-CoA: 30.9
  fatty_acid: 28.1

PKS_AT (5395..5700): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 193.4
  Ethylmalonyl-CoA: 170.9
  Methoxymalonyl-CoA: 161.7
  2-Methylbutyryl-CoA: 136.4
  Propionyl-CoA: 108.1
  CHC-CoA: 103.9
  Malonyl-CoA: 100.6
  trans-1,2-CPDA: 91.6
  Isobutyryl-CoA: 71.9
  Benzoyl-CoA: 56.0
  inactive: 49.4
  Acetyl-CoA: 40.4
  3-Methylbutyryl-CoA: 31.6
  fatty_acid: 25.4

RVR_RS38810: mmal - mmal - mmal - mmal
PKS_AT (589..896): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 182.5
  Methoxymalonyl-CoA: 158.0
  Ethylmalonyl-CoA: 153.9
  2-Methylbutyryl-CoA: 118.0
  Propionyl-CoA: 108.2
  Malonyl-CoA: 106.1
  CHC-CoA: 97.1
  trans-1,2-CPDA: 86.7
  Isobutyryl-CoA: 66.7
  Benzoyl-CoA: 53.9
  inactive: 45.6
  Acetyl-CoA: 34.4
  3-Methylbutyryl-CoA: 31.8
  fatty_acid: 26.8

PKS_AT (2212..2517): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 184.0
  Methoxymalonyl-CoA: 157.7
  Ethylmalonyl-CoA: 154.3
  2-Methylbutyryl-CoA: 122.4
  Propionyl-CoA: 105.2
  Malonyl-CoA: 97.3
  CHC-CoA: 97.3
  trans-1,2-CPDA: 85.2
  Isobutyryl-CoA: 65.3
  inactive: 45.9
  Benzoyl-CoA: 43.2
  3-Methylbutyryl-CoA: 38.6
  Acetyl-CoA: 35.5
  fatty_acid: 22.8

PKS_AT (3793..4095): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 185.8
  Methoxymalonyl-CoA: 157.9
  Ethylmalonyl-CoA: 153.9
  2-Methylbutyryl-CoA: 131.3
  Propionyl-CoA: 113.0
  Malonyl-CoA: 101.9
  CHC-CoA: 99.5
  trans-1,2-CPDA: 86.4
  Isobutyryl-CoA: 62.0
  Benzoyl-CoA: 44.4
  inactive: 41.4
  3-Methylbutyryl-CoA: 34.8
  Acetyl-CoA: 30.9
  fatty_acid: 26.8

PKS_AT (5393..5693): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 189.6
  Methoxymalonyl-CoA: 162.2
  Ethylmalonyl-CoA: 161.9
  2-Methylbutyryl-CoA: 129.0
  Propionyl-CoA: 110.8
  Malonyl-CoA: 109.8
  CHC-CoA: 102.5
  trans-1,2-CPDA: 86.8
  Isobutyryl-CoA: 61.2
  Benzoyl-CoA: 42.8
  inactive: 41.9
  3-Methylbutyryl-CoA: 37.0
  Acetyl-CoA: 35.2
  fatty_acid: 25.0

RVR_RS38815: mmal
PKS_AT (589..890): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 190.3
  Ethylmalonyl-CoA: 164.2
  Methoxymalonyl-CoA: 159.7
  2-Methylbutyryl-CoA: 126.9
  Propionyl-CoA: 116.0
  Malonyl-CoA: 105.1
  CHC-CoA: 103.3
  trans-1,2-CPDA: 101.2
  Isobutyryl-CoA: 66.6
  Benzoyl-CoA: 53.5
  Acetyl-CoA: 42.8
  inactive: 42.4
  3-Methylbutyryl-CoA: 37.3
  fatty_acid: 32.3

RVR_RS36065: Ala
Search NORINE for peptide: strict or relaxed
AMP-binding (515..879): 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:
    AHVRFQALVE-LPVAVHGEYSVYAAPGVGSWALS
  Nearest Stachelhaus code(s):
  Stachelhaus code match:
    0% (weak)

RVR_RS36070: mal
PKS_AT (795..1106): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 75.0%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 185.2
  inactive: 86.7
  Methoxymalonyl-CoA: 53.6
  Methylmalonyl-CoA: 46.4
  Propionyl-CoA: 24.4
  Acetyl-CoA: 16.2
  Benzoyl-CoA: 15.9
  Isobutyryl-CoA: 15.6
  Ethylmalonyl-CoA: 7.6
  fatty_acid: 6.4
  2-Methylbutyryl-CoA: 1.1
  trans-1,2-CPDA: 0.0
  3-Methylbutyryl-CoA: 0.0
  CHC-CoA: -3.9

RVR_RS36075: mmal - mmal
PKS_AT (589..887): 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: 212.2
  Ethylmalonyl-CoA: 209.5
  Methoxymalonyl-CoA: 173.0
  2-Methylbutyryl-CoA: 148.8
  trans-1,2-CPDA: 144.6
  Propionyl-CoA: 113.4
  CHC-CoA: 110.7
  Malonyl-CoA: 91.7
  Isobutyryl-CoA: 83.8
  Benzoyl-CoA: 57.5
  Acetyl-CoA: 40.9
  fatty_acid: 34.9
  3-Methylbutyryl-CoA: 33.6
  inactive: 23.4

PKS_AT (1671..1976): mmal
ATSignature: Methylmalonyl-CoA

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

minowa: Methylmalonyl-CoA

Prediction, score:
  Methylmalonyl-CoA: 186.3
  Methoxymalonyl-CoA: 160.7
  Ethylmalonyl-CoA: 158.4
  2-Methylbutyryl-CoA: 122.8
  Propionyl-CoA: 110.0
  Malonyl-CoA: 106.0
  CHC-CoA: 98.0
  trans-1,2-CPDA: 87.6
  Isobutyryl-CoA: 57.6
  Benzoyl-CoA: 46.6
  inactive: 39.2
  3-Methylbutyryl-CoA: 34.6
  Acetyl-CoA: 24.2
  fatty_acid: 21.1

RVR_RS36120: X
AMP-binding (25..418): 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:
    IDWLWDAFGLDGFLGTGGEHNMYGPVESTIASTD
  Nearest Stachelhaus code(s):
    Leu DALLVGAIAK (44% 8Å match)
    Val DALFVGLVAK (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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
NtrC | Nitrogen regulatory protein C
OsdR | Development and stress management regulator
RutR | Regulator of the pyrimidine and purine metabolism

NZ_AP018365.1 - Region 34 - NRP-metallophore,NRPS,T1PKS,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: 8,753,029 - 8,819,825 nt. (total: 66,797 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
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
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Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
NRPS/PKS modules
NRPS/PKS domains
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Hydrolases: esterase
RVR_RS36280: thioesterase

smcogs
  SMCOG1004: thioesterase

Isomerases: isomerase
RVR_RS36290: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
RVR_RS36255: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

RVR_RS36260: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

RVR_RS36265: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS36270: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS36275: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

RVR_RS36295: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

RVR_RS36335: 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 | NRP-metallophore | NRPS | T1PKS | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0000342.4 |  |  |  |  | 1.44 | NRPS | enniatin | Fusarium equiseti
BGC0001050.5 |  |  |  |  | 1.40 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0002135.2 |  |  |  |  | 1.40 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  |  |  |  | 1.37 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  |  |  |  | 1.36 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  |  |  |  | 1.35 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  |  |  |  | 1.33 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  |  |  |  | 1.33 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  |  |  |  | 1.32 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  |  |  |  | 1.32 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000342.4 |  | 0.69 | NRPS | enniatin | Fusarium equiseti
BGC0001050.5 |  | 0.68 | NRPS, PKS | thalassospiramide A | Tistrella bauzanensis
BGC0002135.2 |  | 0.68 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001132.4 |  | 0.67 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001833.4 |  | 0.67 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001825.4 |  | 0.66 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001758.4 |  | 0.66 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0001135.5 |  | 0.66 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 34.36 out of 36.53
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.31 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.71 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.73 out of 36.53
Confidence: medium
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 29.03 out of 36.53
Confidence: medium
Additional weak hits (15):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.22 out of 26.85
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.63 out of 30.22
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 13.96 out of 27.78
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.20 out of 30.22
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.20 out of 39.62
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.11 out of 21.55
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.01 out of 29.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.03 out of 27.78
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.78 out of 21.55
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.73 out of 36.53
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 14.88 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.05 out of 35.63
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.15 out of 33.14
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 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 47, location 8753028 - 8819825:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Fo-OH-Orn) + (Cys) + (Me-mal) + (fatty_acid)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 48, location 8753028 - 8817892:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Fo-OH-Orn) + (Cys) + (Me-mal) + (fatty_acid)

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).
RVR_RS36255: fatty_acid
CAL_domain (782..1196): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 15.4
  Acetyl-CoA: 8.7
  AHBA: 6.1
  shikimic_acid: 0.0
  NH2: -3.5

RVR_RS36260: mal
PKS_AT (1069..1339): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 101.9
  Methoxymalonyl-CoA: 53.9
  inactive: 52.7
  Methylmalonyl-CoA: 37.7
  Ethylmalonyl-CoA: 19.6
  fatty_acid: 18.8
  Propionyl-CoA: 11.2
  Isobutyryl-CoA: 10.3
  trans-1,2-CPDA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

RVR_RS36265: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (472..912): 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:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

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

RVR_RS36270: Fo-OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (506..906): Fo-OH-Orn
nrpys: Fo-OH-Orn

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWQAFDISINELYIWCGGEYHGYGPAETTIGVSC
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DINYWGGIGK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

RVR_RS36295: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (31..441): 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:
    NAALFALACPGGALQVGGAQQVFGMAEGLLCLTR
  Nearest Stachelhaus code(s):
    diOH-Bz PLPAQGVLCK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AbrC3 | Antibiotic production activator
DmdR1 | Iron(II)-dependent repressor

NZ_AP018367.1 - Region 1 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 32,347 nt. (total: 32,347 nt) Show pHMM detection rules used
Region on contig edge.
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
TTA codons
binding site
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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
Ligases: synthase
RVR_RS37045: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.77 | other (other) | germicidin | Streptomyces argillaceus
BGC0000518.3 |  | 0.28 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001454.5 |  | 0.77 | other (other) | germicidin | Streptomyces argillaceus
BGC0000518.3 |  | 0.28 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736

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

No significant matches found.

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

No significant matches found.

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: 17.94 out of 20.97
Confidence: medium
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.16 out of 20.01
Confidence: medium
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.95 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.09 out of 28.14
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.73 out of 27.78
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.23 out of 32.74
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.05 out of 20.97
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.09 out of 30.98
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.47 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArgR | Regulator of arginine biosynthesis genes
CcpA | Catabolite control protein A