Select genomic region:
Overview
4.1
8.1
9.1
15.1
15.2
15.3
17.1
17.2
17.3
17.4

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

NZ_WBPF01000013.1 (Bacillus sp. CH140a_4T)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | terpene-precursor | 464,112 | 485,002 |  |

NZ_WBPF01000002.1 (Bacillus sp. CH140a_4T)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 8.1 | lanthipeptide-class-ii | 24,980 | 48,171 | High | variacin | ribosomal:RiPP:Lanthipeptide

NZ_WBPF01000016.1 (Bacillus sp. CH140a_4T)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 9.1 | azole-containing-RiPP | 450,595 | 474,101 |

NZ_WBPF01000021.1 (Bacillus sp. CH140a_4T)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 15.1 | betalactone | 94,404 | 119,641 | Low | fengycin | NRPS:Type I
Region 15.2 | NRP-metallophore,NRPS | 237,944 | 289,700 | High | bacillibactin | NRPS:Type I
Region 15.3 | NI-siderophore | 592,594 | 624,299 | High | petrobactin | other:other

NZ_WBPF01000005.1 (Bacillus sp. CH140a_4T)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 17.1 | RiPP-like | 77,035 | 87,307 |
Region 17.2 | NRPS | 102,352 | 149,356 |
Region 17.3 | terpene | 881,950 | 903,803 | Low | molybdenum cofactor | other:other
Region 17.4 | lassopeptide | 1,019,103 | 1,043,027 | High | paeninodin | ribosomal:unmodified

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | terpene-precursor | 464,112 | 485,002 |  |
Region 8.1 | lanthipeptide-class-ii | 24,980 | 48,171 | High | variacin | ribosomal:RiPP:Lanthipeptide
Region 9.1 | azole-containing-RiPP | 450,595 | 474,101 |
Region 15.1 | betalactone | 94,404 | 119,641 | Low | fengycin | NRPS:Type I
Region 15.2 | NRP-metallophore,NRPS | 237,944 | 289,700 | High | bacillibactin | NRPS:Type I
Region 15.3 | NI-siderophore | 592,594 | 624,299 | High | petrobactin | other:other
Region 17.1 | RiPP-like | 77,035 | 87,307 |
Region 17.2 | NRPS | 102,352 | 149,356 |
Region 17.3 | terpene | 881,950 | 903,803 | Low | molybdenum cofactor | other:other
Region 17.4 | lassopeptide | 1,019,103 | 1,043,027 | High | paeninodin | ribosomal:unmodified

No secondary metabolite regions were found in these records:
  NZ_WBPF01000010.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000011.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000012.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000014.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000015.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000001.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000017.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000018.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000019.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000020.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000003.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000004.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000022.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000023.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000006.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000007.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000008.1 (Bacillus sp. CH140a_4T)
  NZ_WBPF01000009.1 (Bacillus sp. CH140a_4T)

Compact view
NZ_WBPF01000013.1 - Region 1 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 464,112 - 485,002 nt. (total: 20,891 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
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: carboxylase
F8162_RS11160: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Ligases: synthase synthetase
F8162_RS11125: 1-deoxy-D-xylulose-5-phosphate synthase

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

F8162_RS11130: 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
--- | --- | --- | --- | --- | ---
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0002219.2 |  | 0.39 | terpene | (-)-(R)-nephthenol | Stereum hirsutum FP-91666 SS1
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002284.3 |  | 0.38 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000639.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC413

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002283.2 |  | 0.49 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.49 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002397.2 |  | 0.47 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0002219.2 |  | 0.39 | terpene | (-)-(R)-nephthenol | Stereum hirsutum FP-91666 SS1
BGC0000665.5 |  | 0.38 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0002284.3 |  | 0.38 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000639.3 |  | 0.38 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000642.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC413

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

Genes with terpene domains:
F8162_RS11130: PT_FPPS_like
Domain 1 (32 - 295): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  IPP, DMAPP → FPP

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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.49 out of 27.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.66 out of 26.06
Confidence: medium
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.32 out of 25.88
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 28.19
Confidence: medium
Additional weak hits (1):
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 25.40 out of 33.14
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MogR | Repressor of flagellar motility genes
PsrA | Oleic acid responsive regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_WBPF01000002.1 - 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: 24,980 - 48,171 nt. (total: 23,192 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
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
F8162_RS00200: 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 | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000562.3 |  | 0.70 | ribosomal | variacin | Kocuria varians
BGC0001210.5 |  | 0.62 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000539.5 |  | 0.59 | ribosomal | nukacin ISK-1 | Staphylococcus warneri
BGC0000504.5 |  | 0.57 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000626.3 |  | 0.56 | ribosomal | thuricin | Bacillus thuringiensis
BGC0000554.4 |  | 0.56 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000499.3 |  | 0.54 | ribosomal | butyrivibriocin OR79 | Butyrivibrio fibrisolvens
BGC0000521.3 |  | 0.54 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0000516.4 |  | 0.54 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0000547.5 |  | 0.52 | ribosomal | salivaricin 9 | Streptococcus salivarius

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000562.3 |  | 0.70 | ribosomal | variacin | Kocuria varians
BGC0001210.5 |  | 0.62 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0000539.5 |  | 0.59 | ribosomal | nukacin ISK-1 | Staphylococcus warneri
BGC0000504.5 |  | 0.57 | ribosomal | cytolysin ClyLl, cytolysin ClyLs | Plasmid pAD1
BGC0000626.3 |  | 0.56 | ribosomal | thuricin | Bacillus thuringiensis
BGC0000554.4 |  | 0.56 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000499.3 |  | 0.54 | ribosomal | butyrivibriocin OR79 | Butyrivibrio fibrisolvens
BGC0000521.3 |  | 0.54 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0000516.4 |  | 0.54 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0000547.5 |  | 0.52 | ribosomal | salivaricin 9 | Streptococcus salivarius

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 F8162_RS00200

F8162_RS00195
Leader:
MEKNFELKALEAINDLTDAELENVVGA
Core:
D K G Q F D T I S H E C H W N T W Q F L F T C C S
Core with dehydrations:
D K G Q F D Dhb I Dha H E Cys H W N Dhb W Q F L F Dhb Cys Cys Dha

#### antiSMASH-DB 4.0 matches for F8162_RS00195

100.0%
NZ_WBPF01000002.1:
Lanthipeptides: F8162_RS00195_lanthipeptide
1
D K G Q F D T I S H E C H W N T W Q F L F T C C S
25
D K G Q F D T I S H E C H W N T W Q F L F T C C S
1
D K G Q F D T I S H E C H W N T W Q F L F T C C S
25
76.0%
NZ_CP023483.1:
Lanthipeptides: CNY62_RS11970_lanthipeptide
1
D K G Q F D T I S H E C H W N T W Q F L F T C C S
25
G T I S H E C H N T W Q F L F T C C S
1
G N G A I R T I S H E C H M N T W Q F L F T C C S
25
73.1%
NC_012470.1 and 11 others:
NZ_CABY01000005.1 Lanthipeptides: SZBHS5_RS06485_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_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
1
D K G Q F D T I S H E C H W N T W Q F L F T C C S
25
G F T I S H E C H N+W Q F L F T C C S
2
K N G V F K T I S H E C H M N S W Q F L F T C C S
26
with 68 more sequence matches
Only the first 10 are displayed here.
72.0%
NZ_CP018188.1 and 17 others:
NZ_CP018188.1 Lanthipeptides: BSR19_RS11175_lanthipeptide NZ_CP066093.1 Lanthipeptides: I6I02_RS07300_lanthipeptide NZ_CP066093.1 Lanthipeptides: I6I02_RS07295_lanthipeptide NZ_JALDUD010000010.1 Lanthipeptides: M1G10_RS09705_lanthipeptide NZ_JALDUD010000010.1 Lanthipeptides: M1G10_RS09700_lanthipeptide NZ_JAQDVH010000019.1 Lanthipeptides: PGU04_RS09300_lanthipeptide NZ_JAQDVH010000019.1 Lanthipeptides: PGU04_RS09295_lanthipeptide NZ_JAQDVH010000019.1 Lanthipeptides: PGU04_RS09300_lanthipeptide NZ_JAQDVH010000019.1 Lanthipeptides: PGU04_RS09295_lanthipeptide NZ_JAQMJT010000006.1 Lanthipeptides: PNU26_RS06585_lanthipeptide NZ_JAQMJT010000006.1 Lanthipeptides: PNU26_RS06580_lanthipeptide NZ_JAQMJT010000006.1 Lanthipeptides: PNU26_RS06585_lanthipeptide NZ_JAQMJT010000006.1 Lanthipeptides: PNU26_RS06580_lanthipeptide NZ_KV832031.1 Lanthipeptides: HMPREF2637_RS05120_lanthipeptide NZ_KV832031.1 Lanthipeptides: HMPREF2637_RS05115_lanthipeptide NZ_PKIA01000004.1 Lanthipeptides: CYK22_RS04335_lanthipeptide NZ_PKIA01000004.1 Lanthipeptides: CYK22_RS04330_lanthipeptide
Lanthipeptides: BSR19_RS11180_lanthipeptide
1
D K G Q F D T I S H E C H W N T W Q F L F T C C S
25
G F T I S H E C H N T W F L T C C S
1
G N G V F K T I S H E C H L N T W A F L A T C C S
25
72.0%
NZ_FOZB01000002.1:
Lanthipeptides: BM306_RS07850_lanthipeptide
3
G Q F D T I S H E C H W N T W Q F L F T C C S
25
G F T I S H E C H N T W F+F T C C S
3
G V F R T I S H E C H M N T W M F I F T C C S
25
69.2%
NC_012470.1 and 2 others:
NZ_CABY01000005.1 Lanthipeptides: SZBHS5_RS06490_lanthipeptide NZ_CP078012.1 Lanthipeptides: KV238_RS09840_lanthipeptide
Lanthipeptides: SZO_RS04065_lanthipeptide
1
D K G Q F D T I S H E C H W N T W Q F L F T C C S
25
G T I S H E C H N+W Q F L F T C C S
2
K N G A I K T I S H E C H M N S W Q F L F T C C S
26
69.2%
NZ_ALSD01000046.1 and 49 others:
NZ_CAAHGW010000010.1 Lanthipeptides: E9435_RS08890_lanthipeptide NZ_CAAHHE010000002.1 Lanthipeptides: E9499_RS02935_lanthipeptide NZ_CAAHHF010000009.1 Lanthipeptides: E9478_RS08685_lanthipeptide NZ_CAAHHF010000009.1 Lanthipeptides: E9478_RS08680_lanthipeptide NZ_CAAHHN010000003.1 Lanthipeptides: E9502_RS05700_lanthipeptide NZ_CAAHHU010000009.1 Lanthipeptides: E9510_RS08730_lanthipeptide NZ_CAAHHU010000009.1 Lanthipeptides: E9510_RS08725_lanthipeptide NZ_CAAHHW010000012.1 Lanthipeptides: E9525_RS08980_lanthipeptide NZ_CAAHHW010000012.1 Lanthipeptides: E9525_RS08975_lanthipeptide NZ_CAAHIB010000001.1 Lanthipeptides: E9539_RS01070_lanthipeptide NZ_CAAHIV010000024.1 Lanthipeptides: E9612_RS09265_lanthipeptide NZ_CAAHIV010000024.1 Lanthipeptides: E9612_RS09260_lanthipeptide NZ_CAAHKK010000019.1 Lanthipeptides: E9649_RS08765_lanthipeptide NZ_CAAHKK010000019.1 Lanthipeptides: E9649_RS08760_lanthipeptide NZ_CAAHKP010000014.1 Lanthipeptides: E9652_RS08915_lanthipeptide NZ_CAAHKP010000014.1 Lanthipeptides: E9652_RS08910_lanthipeptide NZ_CAAHKQ010000003.1 Lanthipeptides: E9664_RS02170_lanthipeptide NZ_CAAHKY010000014.1 Lanthipeptides: E9668_RS09655_lanthipeptide NZ_CAAHLP010000002.1 Lanthipeptides: E9684_RS03455_lanthipeptide NZ_CAAHLP010000002.1 Lanthipeptides: E9684_RS03450_lanthipeptide NZ_CAAHQE010000012.1 Lanthipeptides: E9931_RS08825_lanthipeptide NZ_CAAHQE010000012.1 Lanthipeptides: E9931_RS08820_lanthipeptide NZ_CAAHRY010000002.1 Lanthipeptides: E9986_RS03170_lanthipeptide NZ_CAAIES010000002.1 Lanthipeptides: FAH15_RS02470_lanthipeptide NZ_CAAIIA010000012.1 Lanthipeptides: FAH55_RS08470_lanthipeptide NZ_CAAIIA010000012.1 Lanthipeptides: FAH55_RS08465_lanthipeptide NZ_CAAIJM010000015.1 Lanthipeptides: FAI23_RS09580_lanthipeptide NZ_CAAINV010000013.1 Lanthipeptides: FAI86_RS09035_lanthipeptide NZ_CAAINV010000013.1 Lanthipeptides: FAI86_RS09030_lanthipeptide NZ_CAAIRS010000012.1 Lanthipeptides: FAK24_RS08495_lanthipeptide NZ_CAAIRS010000012.1 Lanthipeptides: FAK24_RS08490_lanthipeptide NZ_CAAJFI010000013.1 Lanthipeptides: FAP60_RS08505_lanthipeptide NZ_CAAJFI010000013.1 Lanthipeptides: FAP60_RS08500_lanthipeptide NZ_CAJHJS010000009.1 Lanthipeptides: JMX87_RS06790_lanthipeptide NZ_CAJHJS010000009.1 Lanthipeptides: JMX87_RS06785_lanthipeptide NZ_CM001076.1 Lanthipeptides: SDD27957_RS04310_lanthipeptide NZ_CM001076.1 Lanthipeptides: SDD27957_RS04305_lanthipeptide NZ_CP035426.1 Lanthipeptides: ETT73_RS02595_lanthipeptide NZ_CP035426.1 Lanthipeptides: ETT73_RS02590_lanthipeptide NZ_CP035428.1 Lanthipeptides: ETT71_RS02815_lanthipeptide NZ_CP035437.1 Lanthipeptides: ETT62_RS06680_lanthipeptide NZ_CP035437.1 Lanthipeptides: ETT62_RS06675_lanthipeptide NZ_CP035443.1 Lanthipeptides: ETT56_RS07265_lanthipeptide NZ_GL636070.1 Lanthipeptides: HMPREF9171_RS105315_lanthipeptide NZ_LR793258.1 Lanthipeptides: HV369_RS03145_lanthipeptide NZ_LR793258.1 Lanthipeptides: HV369_RS03140_lanthipeptide NZ_LS483425.1 Lanthipeptides: DQN36_RS06755_lanthipeptide NZ_LS483425.1 Lanthipeptides: DQN36_RS06750_lanthipeptide NZ_LT545678.1 Lanthipeptides: BJR96_RS07040_lanthipeptide
Lanthipeptides: SAG0161_RS120605_lanthipeptide
1
D K G Q F D T I S H E C H W N T W Q F L F T C C S
25
G F T I S H E C H N T W F L T C C S
2
K N G V F K T I S H E C H L N T W A F L A T C C S
26
68.0%
NZ_AP025017.1:
Lanthipeptides: MANAM107_RS05920_lanthipeptide
2
K G Q F D T I S H E C H W N T W Q F L F T C C S
25
G T I S H E C H N T W F F T C C S
1
N G V I T T I S H E C H L N T W A F A F T C C S
24
68.0%
NZ_CP084014.1 and 6 others:
NZ_CP084014.1 Lanthipeptides: LCQ72_RS00100_lanthipeptide NZ_CP084014.1 Lanthipeptides: LCQ72_RS00095_lanthipeptide NZ_CP094679.1 Lanthipeptides: K5I24_RS13105_lanthipeptide NZ_JAQEYW010000015.1 Lanthipeptides: PG422_RS12415_lanthipeptide NZ_JAQEYW010000015.1 Lanthipeptides: PG422_RS12410_lanthipeptide NZ_JAQEYW010000015.1 Lanthipeptides: PG422_RS12405_lanthipeptide
Lanthipeptides: LCQ72_RS00105_lanthipeptide
2
K G Q F D T I S H E C H W N T W Q F L F T C C
24
G T I S H E C+ N T W Q F L F T C C
2
N G V L K T I S H E C N M N T W Q F L F T C C
24
68.0%
NZ_LT732526.1 and 1 other:
NZ_LT732526.1 Lanthipeptides: BQ9856_RS23075_lanthipeptide
Lanthipeptides: BQ9856_RS23080_lanthipeptide
1
D K G Q F D T I S H E C H W N T W Q F L F T C C S
25
G T I S H E C N T W Q F+F T C C S
1
G N G V I K T I S H E C A M N T W Q F I F T C C S
25
68.0%
NZ_QTVL01000002.1 and 5 others:
NZ_QTVL01000002.1 Lanthipeptides: DWZ44_RS04150_lanthipeptide NZ_QTZB01000015.1 Lanthipeptides: DXC15_RS14340_lanthipeptide NZ_QTZB01000015.1 Lanthipeptides: DXC15_RS14335_lanthipeptide NZ_QUKU01000003.1 Lanthipeptides: DXC27_RS02940_lanthipeptide NZ_QUKU01000003.1 Lanthipeptides: DXC27_RS02935_lanthipeptide
Lanthipeptides: DWZ44_RS04155_lanthipeptide
3
G Q F D T I S H E C H W N T W Q F L F T C C
24
G F T I S H E C+ N T W Q F+F T C C
3
G V F R T I S H E C N M N T W Q F I F T C C
24
68.0%
NZ_VDNV01000006.1:
Lanthipeptides: FSV44_RS08765_lanthipeptide
3
G Q F D T I S H E C H W N T W Q F L F T C C S
25
G T I S H E C N+W Q F L F T C C S
3
G V I Q T I S H E C R M N S W Q F L F T C C S
25
65.4%
NZ_CAAHKQ010000003.1:
Lanthipeptides: E9664_RS02165_lanthipeptide
1
D K G Q F D T I S H E C H W N T W Q F L F T C C S
25
G F T I S H E C H N T W F L C C S
2
K N G V F K T I S H E C H L N T W A F L A I C C S
26

#### MIBiG 4.0 matches for F8162_RS00195

17.9%
BGC0000517.4 (BAB04173.1):
Lanthipeptide: haloduracin β or haloduracin α
1
D K G Q F D T I S H E C
12
+K G + T++ E C
12
N K G A Y C T L T V E C
23
12.8%
BGC0001229.4 (SBI_06990):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
7
T I S H E C H W N
15
T+S E C N
29
T L S K E C Q P N
37
allorf_29004_29138
Leader:
MLKGMWLLLCESWRVILKNSAQS
Core:
P F V W I R N E A K W C F E S L D W I E I
Core with dehydrations:
P F V W I R N E A K W Cys F E Dha L D W I E I

#### antiSMASH-DB 4.0 matches for allorf_29004_29138

100.0%
NZ_WBPF01000002.1:
Lanthipeptides: allorf_29004_29138_lanthipeptide
1
P F V W I R N E A K W C F E S L D W I E I
21
P F V W I R N E A K W C F E S L D W I E I
1
P F V W I R N E A K W C F E S L D W I E I
21
28.6%
NC_018750.1 and 1 other:
NZ_CP029196.1 Lanthipeptides: allorf_0617083_0617295_lanthipeptide
Lanthipeptides: allorf_0633794_0634006_lanthipeptide
6
R N E A K W C F E S
15
R N E W C S
10
R N E G S W C P R S
19
13.3%
NZ_CP107567.1 and 3 others:
NZ_CP107567.1 Lanthipeptides: OGH68_RS19760_lanthipeptide NZ_CP107567.1 Lanthipeptides: OGH68_RS19760_lanthipeptide NZ_CP107567.1 Lanthipeptides: OGH68_RS19760_lanthipeptide
Lanthipeptides: OGH68_RS19760_lanthipeptide
4
W I R N E A K W C
12
W+ N+ W C
11
W L G N Q G G W C
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.
No hits above weak threshold.
Weak hits (2):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.55 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.95 out of 36.53
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.

F8162_RS00195 - Class II
  Cleavage pHMM score: 4.50
  RODEO score: 0
  Monoisotopic mass: 2942.3 Da
  Molecular weight: 2944.2 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2962.2 Da N = 1
    2980.3 Da N = 2
allorf_29004_29138 - Class II
  Cleavage pHMM score: -7.00
  RODEO score: 0
  Monoisotopic mass: 2662.3 Da
  Molecular weight: 2664.0 Da
  Number of bridges: 1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_WBPF01000016.1 - Region 1 - azole-containing-RiPP
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 450,595 - 474,101 nt. (total: 23,507 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
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: oxidoreductase
F8162_RS17835: pyridine nucleotide-disulfide oxidoreductase

smcogs
  SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

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

Reference | azole-containing-RiPP | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001146.5 |  | 0.43 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000607.5 |  | 0.43 | ribosomal | micrococcin P1 | Macrococcus caseolyticus
BGC0001535.3 |  | 0.43 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0000569.5 |  | 0.41 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001534.3 |  | 0.41 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001173.5 |  | 0.41 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0001145.5 |  | 0.40 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5 |  | 0.39 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0000606.5 |  | 0.39 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0001640.3 |  | 0.38 | ribosomal | kocurin | Kocuria rosea

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001146.5 |  | 0.43 | ribosomal | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908
BGC0000607.5 |  | 0.43 | ribosomal | micrococcin P1 | Macrococcus caseolyticus
BGC0001535.3 |  | 0.43 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0000569.5 |  | 0.41 | ribosomal | plantazolicin | Bacillus velezensis FZB42
BGC0001534.3 |  | 0.41 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0001173.5 |  | 0.41 | ribosomal | plantazolicin | Bacillus pumilus ATCC 7061
BGC0001145.5 |  | 0.40 | ribosomal | cyclothiazomycin b1 | Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5 |  | 0.39 | ribosomal | cyclothiazomycin | Streptomyces hygroscopicus
BGC0000606.5 |  | 0.39 | ribosomal | lactazole | Streptomyces lactacystinaeus
BGC0001640.3 |  | 0.38 | ribosomal | kocurin | Kocuria rosea

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

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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.81 out of 26.06
Confidence: medium
Additional weak hits (2):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 27.82 out of 39.62
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.60 out of 39.62
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 (450594...474101)
F8162_RS17860
  RRE type: Heterocycloanthracin_C_RRE
  Location: 0 - 100
  Score: 180.5
  RRE type: Thiopeptide_F_RRE
  Location: 10 - 89
  Score: 40.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MogR | Repressor of flagellar motility genes

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_WBPF01000021.1 - Region 1 - 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: 94,404 - 119,641 nt. (total: 25,238 nt) Show pHMM detection rules used
betalactone: (HMGL-like and AMP-binding)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
F8162_RS22410: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: acetyltransferase carboxylase transferase
F8162_RS22370: GCN5-related N-acetyltransferase

smcogs
  SMCOG1111: GCN5-related N-acetyltransferase

F8162_RS22385: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

F8162_RS22405: acetyl-CoA carboxylase biotin carboxylase

smcogs
  SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Hydrolases: dehalogenase
F8162_RS22360: haloalkane dehalogenase

smcogs
  SMCOG1262: haloalkane dehalogenase

Lyases: hydratase
F8162_RS22390: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase
F8162_RS22380: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F8162_RS22395: 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 | betalactone | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002284.3 |  | 0.55 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000131.5 |  | 0.46 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000706.3 |  | 0.46 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000234.5 |  | 0.43 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002034.3 |  | 0.43 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0002000.4 |  | 0.43 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0000623.3 |  | 0.42 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0001464.3 |  | 0.42 | other (other) | tetrabromopyrrole | Pseudoalteromonas sp. PS5
BGC0001463.4 |  | 0.42 | other (other) | 2,3,4,5-tetrabromopyrrole | Pseudoalteromonas piscicida
BGC0001103.5 |  | 0.42 | NRPS, PKS | mycosubtilin | Bacillus subtilis subsp. spizizenii ATCC 6633

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002284.3 |  | 0.55 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0000131.5 |  | 0.46 | PKS | pyrrolomycin | Streptomyces sp. UC 11065
BGC0000706.3 |  | 0.46 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0000234.5 |  | 0.43 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002034.3 |  | 0.43 | other (other) | perquinoline A, perquinoline B, perquinoline C | Streptomyces sp. IB2014 016-6
BGC0002000.4 |  | 0.43 | PKS | setomimycin | Streptomyces aurantiacus JA 4570
BGC0000623.3 |  | 0.42 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0001464.3 |  | 0.42 | other (other) | tetrabromopyrrole | Pseudoalteromonas sp. PS5
BGC0001463.4 |  | 0.42 | other (other) | 2,3,4,5-tetrabromopyrrole | Pseudoalteromonas piscicida
BGC0001103.5 |  | 0.42 | NRPS, PKS | mycosubtilin | Bacillus subtilis subsp. spizizenii ATCC 6633

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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.21 out of 26.06
Confidence: strong
Additional weak hits (2):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.89 out of 32.74
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 25.24 out of 33.14
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
MogR | Repressor of flagellar motility genes

NZ_WBPF01000021.1 - Region 2 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 237,944 - 289,700 nt. (total: 51,757 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
F8162_RS23060: Antibiotic biosynthesis monooxygenase

smcogs
  SMCOG1258: Antibiotic biosynthesis monooxygenase

F8162_RS23140: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F8162_RS23190: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

F8162_RS23195: 3-hydroxyisobutyrate dehydrogenase

smcogs
  SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

F8162_RS23200: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: PPTase
F8162_RS23105: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: hydrolase protease
F8162_RS23080: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

F8162_RS23125: isochorismatase

smcogs
  SMCOG1027: isochorismatase

Lyases: hydratase
F8162_RS23180: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

Isomerases: isomerase
F8162_RS23135: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
F8162_RS23055: Pseudouridine synthase

smcogs
  SMCOG1154: Pseudouridine synthase

F8162_RS23120: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

F8162_RS23130: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0001185.5 |  |  | 1.05 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0000309.5 |  |  | 0.88 | NRPS | bacillibactin | Bacillus subtilis subsp. subtilis str. 168
BGC0000401.5 |  |  | 0.86 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0002075.3 |  |  | 0.86 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000343.5 |  |  | 0.85 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001833.4 |  |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  |  | 0.75 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  | 0.75 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001185.5 |  | 0.80 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0000309.5 |  | 0.75 | NRPS | bacillibactin | Bacillus subtilis subsp. subtilis str. 168
BGC0000401.5 |  | 0.74 | NRPS | paenibactin | Paenibacillus elgii B69
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0000343.5 |  | 0.74 | NRPS | enterobactin | Pseudomonas sp. J465
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.70 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 27.77 out of 29.38
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 29.38 out of 29.38
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 26.61 out of 29.38
Confidence: strong
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.21 out of 30.25
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.93 out of 26.06
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.40 out of 29.38
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.11 out of 29.38
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 24.83 out of 27.78
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.23 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.99 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 24.13 out of 27.78
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.71 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.53 out of 28.19
Confidence: medium
CatR
Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.57 out of 25.31
Confidence: medium
Additional weak hits (8):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.54 out of 30.25
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 20.08 out of 29.72
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.53 out of 30.25
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.67 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.52 out of 32.74
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.92 out of 29.38
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 18.17 out of 30.12
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 2, location 237943 - 289700:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - Thr)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
F8162_RS23120: Gly - Thr
Search NORINE for peptide: strict or relaxed
AMP-binding (464..864): Gly
nrpys: Gly

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    FAMTFDISALELQALVGGETNLYGPTETTIWSTF
  Nearest Stachelhaus code(s):
    Gly DILQLGLIWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1524..1937): 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:
    LATHFDFSVWEGNQVFGGEINMYGITETTVHVSY
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

F8162_RS23130: diOH-Bz
Search NORINE for peptide: strict or relaxed
AMP-binding (31..435): 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:
    SVSLYPMSSPGGALQVGGAQQVFGMAEGLVNYTR
  Nearest Stachelhaus code(s):
    diOH-Bz PMPAQGVVNK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
CatR | H2O2-responsive repressor
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ColR | Phenol-responsive regulator
FuR variant 1 | Ferric Uptake Regulator
MogR | Repressor of flagellar motility genes
ZuR variant 1 | Zinc-responsive repressor

NZ_WBPF01000021.1 - Region 3 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 592,594 - 624,299 nt. (total: 31,706 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
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
F8162_RS24860: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: deacetylase
F8162_RS24925: polysaccharide deacetylase

smcogs
  SMCOG1235: polysaccharide deacetylase

Ligases: ligase synthase
F8162_RS24895: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

F8162_RS24955: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

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

Reference | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000942.4 |  | 0.90 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0002469.2 |  | 0.53 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000295.5 |  | 0.53 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002692.2 |  | 0.50 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002620.2 |  | 0.50 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0001531.5 |  | 0.50 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002471.3 |  | 0.49 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0001498.5 |  | 0.48 | other (other) | aerobactin | Xenorhabdus szentirmaii DSM 16338
BGC0002683.2 |  | 0.47 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000943.5 |  | 0.47 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000942.4 |  | 0.90 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0002469.2 |  | 0.53 | other (other) | woodybactin A, woodybactin B, woodybactin C, woodybactin D | Shewanella woodyi ATCC 51908
BGC0000295.5 |  | 0.53 | NRPS | acinetoferrin | Acinetobacter haemolyticus
BGC0002692.2 |  | 0.50 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002620.2 |  | 0.50 | other (other) | fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4 | Fulvivirga marina
BGC0001531.5 |  | 0.50 | other (other) | bisucaberin B | Tenacibaculum mesophilum
BGC0002471.3 |  | 0.49 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0001498.5 |  | 0.48 | other (other) | aerobactin | Xenorhabdus szentirmaii DSM 16338
BGC0002683.2 |  | 0.47 | NRPS | schizokinen | Nostoc sp. PCC 7120 = FACHB-418
BGC0000943.5 |  | 0.47 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325

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: 21.28 out of 26.33
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.24 out of 18.16
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.20 out of 25.88
Confidence: medium
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.38 out of 29.38
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 24.20 out of 30.25
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.55 out of 19.26
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.85 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.93 out of 28.19
Confidence: medium
Additional weak hits (5):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.60 out of 36.54
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.84 out of 32.74
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.50 out of 32.74
Confidence: weak
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.58 out of 19.52
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AbrC3 | Antibiotic production activator
CRP | Cyclic AMP receptor protein
ColR | Phenol-responsive regulator
FuR variant 1 | Ferric Uptake Regulator
PsrA | Oleic acid responsive regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_WBPF01000005.1 - Region 1 - 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: 77,035 - 87,307 nt. (total: 10,273 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
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase
F8162_RS01345: aminotransferase

smcogs
  SMCOG1019: aminotransferase

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
--- | --- | --- | --- | --- | ---
BGC0002458.3 |  | 0.39 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0001488.3 |  | 0.32 | other (other) | 4-formylaminooxyvinylglycine | Pseudomonas fluorescens WH6
BGC0001964.2 |  | 0.25 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0002536.3 |  | 0.24 | NRPS | alazopeptin | Kitasatospora azatica KCTC 9699
BGC0000381.5 |  | 0.23 | NRPS | lichenysin | Bacillus licheniformis DSM 13 = ATCC 14580
BGC0002440.3 |  | 0.21 | NRPS | longicatenamide B, longicatenamide C, longicatenamide A, longicatenamide D | Streptomyces sp.
BGC0000388.5 |  | 0.21 | NRPS | mannopeptimycin | Streptomyces hygroscopicus
BGC0001814.5 |  | 0.20 | NRPS | ulleungmycin | Streptomyces sp. KCB13F003
BGC0000993.4 |  | 0.19 | NRPS, PKS | FR901228 | Chromobacterium violaceum
BGC0001406.5 |  | 0.19 | NRPS | telomycin | Streptomyces canus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002458.3 |  | 0.39 | NRPS | alazopeptin | Streptacidiphilus griseoplanus
BGC0001488.3 |  | 0.32 | other (other) | 4-formylaminooxyvinylglycine | Pseudomonas fluorescens WH6
BGC0001964.2 |  | 0.25 | PKS | alkylpyrone-407, alkylpyrone-393 | Cystobacterineae bacterium
BGC0002536.3 |  | 0.24 | NRPS | alazopeptin | Kitasatospora azatica KCTC 9699
BGC0000381.5 |  | 0.23 | NRPS | lichenysin | Bacillus licheniformis DSM 13 = ATCC 14580
BGC0002440.3 |  | 0.21 | NRPS | longicatenamide B, longicatenamide C, longicatenamide A, longicatenamide D | Streptomyces sp.
BGC0000388.5 |  | 0.21 | NRPS | mannopeptimycin | Streptomyces hygroscopicus
BGC0001814.5 |  | 0.20 | NRPS | ulleungmycin | Streptomyces sp. KCB13F003
BGC0000993.4 |  | 0.19 | NRPS, PKS | FR901228 | Chromobacterium violaceum
BGC0001406.5 |  | 0.19 | NRPS | telomycin | Streptomyces canus

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

No significant matches found.

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

No significant matches found.

NZ_WBPF01000005.1 - Region 2 - NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 102,352 - 149,356 nt. (total: 47,005 nt) Show pHMM detection rules used
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
F8162_RS01525: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

F8162_RS01680: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase
F8162_RS01675: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Hydrolases: esterase glucanase hydrolase
F8162_RS01550: HAD-superfamily hydrolase, subfamily IA, variant

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

F8162_RS01600: alpha/beta hydrolase domain-containing protein

smcogs
  SMCOG1066: alpha/beta hydrolase domain-containing protein

F8162_RS01625: Pullulanase, type I

smcogs
  SMCOG1297: Pullulanase, type I

F8162_RS01635: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

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

F8162_RS01685: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: decarboxylase
F8162_RS01605: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: ligase
F8162_RS01610: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000357.5 |  | 0.62 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.61 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001261.3 |  | 0.66 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.65 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000307.4 |  | 0.64 | NRPS | AbT1 | Aureobasidium pullulans
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.63 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2 |  | 0.63 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000357.5 |  | 0.62 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001641.4 |  | 0.62 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.61 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.71 out of 26.33
Confidence: medium
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 24.13 out of 29.25
Confidence: medium
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 28.23 out of 31.73
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.81 out of 20.97
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.24 out of 30.25
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 30.31 out of 32.93
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.46 out of 24.78
Confidence: medium
Additional weak hits (3):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.81 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 19.73 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
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 102351 - 149356:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - Cys)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
F8162_RS01610: X - Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (264..654): 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:
    FAMAFDISLLELESLLAGELNIYGPTETTICATV
  Nearest Stachelhaus code(s):
    Ala DILICALICK (47% 8Å match)
  Stachelhaus code match:
    70% (weak)

AMP-binding (1301..1681): Cys
nrpys: Cys

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    TDISFDLSVYDGNTLHSGDVSLGGATEASIWSIY
  Nearest Stachelhaus code(s):
    Cys DLYNLSLIWK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CcpA | Catabolite control protein A
ColR | Phenol-responsive regulator
HexR | Glucose-responsive regulator
LexA variant 2 | Repressor of DNA damage response
LexA variant 3 | Repressor of DNA damage response
SypG | Regulator of biofilm formation and host colonization

NZ_WBPF01000005.1 - Region 3 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 881,950 - 903,803 nt. (total: 21,854 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
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
F8162_RS05560: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

F8162_RS05590: aldehyde dehydrogenase

smcogs
  SMCOG1017: aldehyde dehydrogenase

F8162_RS05595: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: lyase
F8162_RS05565: argininosuccinate lyase/adenylosuccinate lyase

smcogs
  SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000917.3 |  | 0.52 | other (other) | molybdenum cofactor | Rhodobacter capsulatus
BGC0000888.5 |  | 0.48 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001928.2 |  | 0.46 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000916.5 |  | 0.46 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0000812.3 |  | 0.45 | other (other) | huperzine A | Shiraia sp. slf14
BGC0000231.5 |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001197.5 |  | 0.42 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000234.5 |  | 0.41 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002138.2 |  | 0.40 | PKS | fuelimycin A, fuelimicin B, fuelimicin C | Streptomyces albireticuli NRRL B-1670

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000917.3 |  | 0.52 | other (other) | molybdenum cofactor | Rhodobacter capsulatus
BGC0000888.5 |  | 0.48 | other (other) | bacilysin | Bacillus sp. CS93
BGC0001928.2 |  | 0.46 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0000916.5 |  | 0.46 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0000812.3 |  | 0.45 | other (other) | huperzine A | Shiraia sp. slf14
BGC0000231.5 |  | 0.42 | PKS | griseusin A, griseusin B | Streptomyces griseus
BGC0001605.3 |  | 0.42 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0001197.5 |  | 0.42 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0000234.5 |  | 0.41 | PKS | jadomycin | Streptomyces venezuelae ATCC 10712
BGC0002138.2 |  | 0.40 | 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
--- | --- | --- | --- | --- | ---
triterpene | hopanoid |  | C30 | hopanoid skeleton | unknown
triterpene | polypodane |  | C30 | polypodane skeleton | unknown

Genes with terpene domains:
F8162_RS05605: T2TS
Domain 1 (4 - 614): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (1):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.14 out of 39.62
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.
No acronyms to display
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_WBPF01000005.1 - Region 4 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,019,103 - 1,043,027 nt. (total: 23,925 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase glycosyltransferase
F8162_RS06325: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs
  SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

F8162_RS06335: sugar transferase

smcogs
  SMCOG1146: sugar transferase

Hydrolases: esterase hydrolase
F8162_RS06255: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

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

F8162_RS06320: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Ligases: synthase
F8162_RS06360: polyprenol-monophosphomannose synthase ppm1

smcogs
  SMCOG1123: polyprenol-monophosphomannose synthase ppm1

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001356.4 |  | 0.78 | ribosomal | paeninodin | Paenibacillus dendritiformis C454
BGC0000575.5 |  | 0.52 | ribosomal | lariatin | Rhodococcus jostii
BGC0000571.3 |  | 0.51 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001410.3 |  | 0.47 | saccharide | polysaccharide A | Bacteroides fragilis
BGC0000800.5 |  | 0.46 | saccharide | xanthan | Xanthomonas campestris
BGC0000741.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000744.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000745.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000729.3 |  | 0.45 | saccharide | capsular polysaccharide | Klebsiella pneumoniae
BGC0000728.5 |  | 0.45 | saccharide | capsular polysaccharide | Klebsiella pneumoniae subsp. ozaenae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001356.4 |  | 0.78 | ribosomal | paeninodin | Paenibacillus dendritiformis C454
BGC0000575.5 |  | 0.52 | ribosomal | lariatin | Rhodococcus jostii
BGC0000571.3 |  | 0.51 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0001410.3 |  | 0.47 | saccharide | polysaccharide A | Bacteroides fragilis
BGC0000800.5 |  | 0.46 | saccharide | xanthan | Xanthomonas campestris
BGC0000741.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000744.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000745.3 |  | 0.45 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000729.3 |  | 0.45 | saccharide | capsular polysaccharide | Klebsiella pneumoniae
BGC0000728.5 |  | 0.45 | saccharide | capsular polysaccharide | Klebsiella pneumoniae subsp. ozaenae

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

No significant matches found.

Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Each core peptide shows the leader and core peptide sequences.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lassopeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.40 out of 21.55
Confidence: medium
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.33 out of 21.55
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 22.42 out of 24.78
Confidence: strong
Additional weak hits (3):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 24.35 out of 33.73
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 18.92 out of 30.12
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
Lasso peptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of disulfide bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lassopeptide protocluster (1019102...1043027)
F8162_RS06305
  RRE type: Stand_Alone_Lasso_RRE
  Location: 14 - 95
  Score: 87.2
  RRE type: Thurincin_rSAM_RRE
  Location: 13 - 91
  Score: 28.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation
LexA variant 2 | Repressor of DNA damage response