Select genomic region:
Overview
3.1
4.1
6.1
6.2

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

NZ_FNJX01000003.1 (Streptococcus equinus (Streptococcus bovis))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | arylpolyene | 80,646 | 122,838 |

NZ_FNJX01000002.1 (Streptococcus equinus (Streptococcus bovis))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | lanthipeptide-class-ii,terpene-precursor | 59,877 | 93,338 | Medium | streptococcin A-FF22 | ribosomal:RiPP:Lanthipeptide

NZ_FNJX01000001.1 (Streptococcus equinus (Streptococcus bovis))

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 6.1 | RiPP-like | 196,296 | 206,623 |
Region 6.2 | T3PKS | 796,459 | 837,637 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | arylpolyene | 80,646 | 122,838 |
Region 4.1 | lanthipeptide-class-ii,terpene-precursor | 59,877 | 93,338 | Medium | streptococcin A-FF22 | ribosomal:RiPP:Lanthipeptide
Region 6.1 | RiPP-like | 196,296 | 206,623 |
Region 6.2 | T3PKS | 796,459 | 837,637 |

No secondary metabolite regions were found in these records:
  NZ_FNJX01000005.1 (Streptococcus equinus (Streptococcus bovis))
  NZ_FNJX01000004.1 (Streptococcus equinus (Streptococcus bovis))
  NZ_FNJX01000006.1 (Streptococcus equinus (Streptococcus bovis))

Compact view
NZ_FNJX01000003.1 - Region 1 - arylpolyene
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: 80,646 - 122,838 nt. (total: 42,193 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)

#### 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 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
BLR40_RS07325: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: synthase
BLR40_RS07290: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

BLR40_RS07375: pseudouridine synthase

smcogs
  SMCOG1279: pseudouridine synthase

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

Reference | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000107.3 |  | 0.56 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001258.3 |  | 0.56 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001257.3 |  | 0.56 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000888.5 |  | 0.49 | other (other) | bacilysin | Bacillus sp. CS93
BGC0002510.2 |  | 0.47 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0002404.2 |  | 0.45 | other (other) | falcarindiol | Solanum lycopersicum
BGC0001987.2 |  | 0.44 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0001197.5 |  | 0.44 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001184.4 |  | 0.44 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000204.5 |  | 0.43 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000107.3 |  | 0.56 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0001258.3 |  | 0.56 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Glarea lozoyensis
BGC0001257.3 |  | 0.56 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000888.5 |  | 0.49 | other (other) | bacilysin | Bacillus sp. CS93
BGC0002510.2 |  | 0.47 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0002404.2 |  | 0.45 | other (other) | falcarindiol | Solanum lycopersicum
BGC0001987.2 |  | 0.44 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0001197.5 |  | 0.44 | PKS | frankiamicin | Frankia sp. EAN1pec
BGC0001184.4 |  | 0.44 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0000204.5 |  | 0.43 | PKS | benastatin A, benastatin B, BE-43767, TAN1532B | Streptomyces sp. A2991200

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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.06 out of 27.78
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.09 out of 20.97
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.38 out of 26.06
Confidence: medium
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: 23.06 out of 26.06
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
Additional weak hits (4):
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.56 out of 36.53
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.47 out of 28.14
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.51 out of 30.98
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.68 out of 26.85
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
BLR40_RS07330: pk
PKS_AT (72..205): pk
ATSignature: (unknown)
No matches above 50%
minowa: trans-1,2-CPDA

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

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

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MogR | Repressor of flagellar motility genes

NZ_FNJX01000002.1 - Region 1 - lanthipeptide-class-ii,terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 59,877 - 93,338 nt. (total: 33,462 nt) Show pHMM detection rules used
lanthipeptide-class-ii: cds(LANC_like and DUF4135)
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
Lanthipeptides
Terpene
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: carbamoyltransferase
BLR40_RS04980: ornithine carbamoyltransferase

smcogs
  SMCOG1114: ornithine carbamoyltransferase

Lyases: cyclase
BLR40_RS05030: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: synthetase
BLR40_RS05085: 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 | lanthipeptide-class-ii | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000547.5 |  |  | 0.59 | ribosomal | salivaricin 9 | Streptococcus salivarius
BGC0000557.5 |  |  | 0.56 | ribosomal | streptococcin A-FF22 | Streptococcus pyogenes
BGC0000532.3 |  |  | 0.49 | ribosomal | mutacin II | Streptococcus mutans
BGC0000562.3 |  |  | 0.47 | ribosomal | variacin | Kocuria varians
BGC0001788.3 |  |  | 0.47 | ribosomal | suicin 65 | Streptococcus suis
BGC0000521.3 |  |  | 0.47 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0000539.5 |  |  | 0.43 | ribosomal | nukacin ISK-1 | Staphylococcus warneri
BGC0000526.5 |  |  | 0.42 | ribosomal | macedocin | Streptococcus macedonicus
BGC0000527.5 |  |  | 0.35 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000626.3 |  |  | 0.35 | ribosomal | thuricin | Bacillus thuringiensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000532.3 |  | 0.78 | ribosomal | mutacin II | Streptococcus mutans
BGC0000562.3 |  | 0.77 | ribosomal | variacin | Kocuria varians
BGC0000547.5 |  | 0.72 | ribosomal | salivaricin 9 | Streptococcus salivarius
BGC0000557.5 |  | 0.70 | ribosomal | streptococcin A-FF22 | Streptococcus pyogenes
BGC0001788.3 |  | 0.66 | ribosomal | suicin 65 | Streptococcus suis
BGC0000521.3 |  | 0.63 | ribosomal | lacticin 481 | Lactococcus lactis subsp. lactis
BGC0000499.3 |  | 0.61 | ribosomal | butyrivibriocin OR79 | Butyrivibrio fibrisolvens
BGC0000526.5 |  | 0.61 | ribosomal | macedocin | Streptococcus macedonicus
BGC0000539.5 |  | 0.59 | ribosomal | nukacin ISK-1 | Staphylococcus warneri
BGC0000527.5 |  | 0.55 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728

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 BLR40_RS05030

BLR40_RS05025
Leader:
MKNTNIIDIKATEALQELSLEELDTIIGA
Core:
K K G S G V V P T V S H D C H M N S W Q F L F T C C S
Core with dehydrations:
K K G Dha G V V P Dhb V Dha H D Cys H M N Dha W Q F L F Dhb Cys Cys Dha

#### antiSMASH-DB 4.0 matches for BLR40_RS05025

100.0%
NZ_CP046629.1 and 3 others:
NZ_FNJX01000002.1 Lanthipeptides: BLR40_RS05025_lanthipeptide NZ_FNZS01000001.1 Lanthipeptides: BMX70_RS03125_lanthipeptide NZ_FOLK01000002.1 Lanthipeptides: BM262_RS05670_lanthipeptide
Lanthipeptides: GPA00_RS05740_lanthipeptide
1
K K G S G V V P T V S H D C H M N S W Q F L F T C C S
27
K K G S G V V P T V S H D C H M N S W Q F L F T C C S
1
K K G S G V V P T V S H D C H M N S W Q F L F T C C S
27
85.2%
NZ_CP051645.1 and 2 others:
NZ_JAKVFF010000018.1 Lanthipeptides: MKR34_RS11425_lanthipeptide NZ_VDOJ01000018.1 Lanthipeptides: FSV48_RS11975_lanthipeptide
Lanthipeptides: HHJ99_RS13350_lanthipeptide
1
K K G S G V V P T V S H D C H M N S W Q F L F T C C S
27
K K S G V+P T V S H D C H M N S+Q F+F T C C S
1
K K K S G V I P T V S H D C H M N S F Q F V F T C C S
27
81.5%
NZ_CP046304.1:
Lanthipeptides: FOC54_RS00030_lanthipeptide
1
K K G S G V V P T V S H D C H M N S W Q F L F T C C S
27
K K S G V+P T V S H D C H M N++Q F+F T C C S
1
K K K S G V I P T V S H D C H M N T F Q F M F T C C S
27
with 73 more sequence matches
Only the first 10 are displayed here.
74.1%
NZ_CP069183.1:
Lanthipeptides: LLNCDO700_RS13730_lanthipeptide
1
K K G S G V V P T V S H D C H M N S W Q F L F T C C S
27
K G S G V+ T+S H+C+M N S W Q F+F T C C S
1
K G G S G V I H T I S H E C N M N S W Q F V F T C C S
27
70.4%
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
4
S G V V P T V S H D C H M N S W Q F L F T C C S
27
+G V T+S H+C H M N S W Q F L F T C C S
3
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
70.4%
NZ_CP026729.1:
Lanthipeptides: BKKJ1_RS07010_lanthipeptide
3
G S G V V P T V S H D C H M N S W Q F L F T C C
26
G+G V V T+S H+C+M N S W Q F L F T C C
1
G N G V V T T I S H E C N M N S W Q F L F T C C
24
70.4%
NZ_GL882519.1:
Lanthipeptides: HMPREF9056_RS03330_lanthipeptide
3
G S G V V P T V S H D C H M N S W Q F L F T C C S
27
G+G V T+S H+C H M N S W Q F+F T C C S
1
G N G V Y Y T L S H E C H M N S W Q F I F T C C S
25
70.4%
NZ_JH792236.1 and 1 other:
NZ_JH792236.1 Lanthipeptides: IIM_RS26240_lanthipeptide
Lanthipeptides: IIM_RS26245_lanthipeptide
3
G S G V V P T V S H D C H M N S W Q F L F T C C S
27
G S G V+ T+S H+C H M N S W Q +F T C C S
1
G S G V I K T I S H E C H M N S W Q A I F T C C S
25
70.4%
NZ_VDNV01000006.1:
Lanthipeptides: FSV44_RS08765_lanthipeptide
3
G S G V V P T V S H D C H M N S W Q F L F T C C S
27
G G V+ T+S H+C M N S W Q F L F T C C S
1
G G G V I Q T I S H E C R M N S W Q F L F T C C S
25
66.7%
NC_012470.1 and 2 others:
NZ_CABY01000005.1 Lanthipeptides: SZBHS5_RS06490_lanthipeptide NZ_CP078012.1 Lanthipeptides: KV238_RS09840_lanthipeptide
Lanthipeptides: SZO_RS04065_lanthipeptide
4
S G V V P T V S H D C H M N S W Q F L F T C C S
27
+G + T+S H+C H M N S W Q F L F T C C S
3
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
66.7%
NZ_CP023483.1:
Lanthipeptides: CNY62_RS11970_lanthipeptide
3
G S G V V P T V S H D C H M N S W Q F L F T C C S
27
G+G + T+S H+C H M N+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
66.7%
NZ_CP072384.1:
Lanthipeptides: J5A65_RS01395_lanthipeptide
3
G S G V V P T V S H D C H M N S W Q F L F T C C
26
G G V V P T V+H+C H M N S W Q+ F C C
1
G R G V V P T V T H E C H M N S W Q W F F G C C
24
66.7%
NZ_JAEEGA010000010.1:
Lanthipeptides: I6N95_RS15660_lanthipeptide
3
G S G V V P T V S H D C H M N S W Q F L F T C C S
27
G+G V+ T+S H+C H M N S W Q++F T C C S
1
G N G V I K T I S H E C H M N S W Q W I F T C C S
25

#### MIBiG 4.0 matches for BLR40_RS05025

14.8%
BGC0000468.5 (CCM09443.1)and 2 others:
BGC0000469.6 (AFV25481.1) Bottromycin: bottromycin A2 BGC0001157.6 (CBG72694.1) Bottromycin: bottromycin A2
Bottromycin: bottromycin A2
8
P T V S H D C
14
P V D C
2
P V V V F D C
8
14.8%
BGC0000470.6 (AFU90404.1):
Bottromycin: bottromycin D
8
P T V S H D C
14
P V D C
2
P A V V F D C
8
11.1%
BGC0002111.3 (EVG22_32245)and 1 other:
BGC0002111.3 (multiple genes) Lanthipeptide: andalusicin A or andalusicin B
Lanthipeptide: andalusicin A or andalusicin B
9
T V S H D C
14
T+S++C
18
T I S N N C
23

#### Legend:

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP

Genes with terpene domains:
BLR40_RS05085: PT_FPPS_like
Domain 1 (25 - 282): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:
  DMAPP, IPP → 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.79 out of 21.84
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.93 out of 30.25
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.60 out of 30.25
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.60 out of 30.25
Confidence: medium
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
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.99 out of 32.93
Confidence: medium
Additional weak hits (2):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.48 out of 30.25
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.65 out of 30.98
Confidence: weak
Lanthipeptides
Terpene
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

BLR40_RS05025 - Class II
  Cleavage pHMM score: 5.40
  RODEO score: 0
  Monoisotopic mass: 2889.3 Da
  Molecular weight: 2891.3 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2909.3 Da N = 1
    2927.3 Da N = 2
    2945.4 Da N = 3

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
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ColR | Phenol-responsive regulator
LexA variant 3 | Repressor of DNA damage response
MexT | Global virulence regulator
ToxT | Regulator of MSHA biosynthesis

NZ_FNJX01000001.1 - 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: 196,296 - 206,623 nt. (total: 10,328 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
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

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

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000617.5 |  | 0.47 | ribosomal | coagulin | Bacillus coagulans
BGC0002579.2 |  | 0.45 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum
BGC0000624.3 |  | 0.44 | ribosomal | salivaricin CRL1328 α peptide, salivaricin CRL1328 β peptide | Lactobacillus salivarius
BGC0002577.2 |  | 0.41 | ribosomal | lactococcin G | Lactococcus lactis
BGC0000494.5 |  | 0.32 | ribosomal | uberolysin | Streptococcus uberis
BGC0000094.5 |  | 0.29 | PKS, saccharide | methymycin | Streptomyces venezuelae
BGC0000055.5 |  | 0.23 | PKS, saccharide | erythromycin A, erythromycin B, erythromycin C, erythromycin D | Saccharopolyspora erythraea NRRL 2338
BGC0000054.5 |  | 0.20 | PKS | erythromycin | Aeromicrobium erythreum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000617.5 |  | 0.47 | ribosomal | coagulin | Bacillus coagulans
BGC0002579.2 |  | 0.45 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum
BGC0000624.3 |  | 0.44 | ribosomal | salivaricin CRL1328 α peptide, salivaricin CRL1328 β peptide | Lactobacillus salivarius
BGC0002577.2 |  | 0.41 | ribosomal | lactococcin G | Lactococcus lactis
BGC0000494.5 |  | 0.32 | ribosomal | uberolysin | Streptococcus uberis
BGC0000094.5 |  | 0.29 | PKS, saccharide | methymycin | Streptomyces venezuelae
BGC0000055.5 |  | 0.23 | PKS, saccharide | erythromycin A, erythromycin B, erythromycin C, erythromycin D | Saccharopolyspora erythraea NRRL 2338
BGC0000054.5 |  | 0.20 | PKS | erythromycin | Aeromicrobium erythreum

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: 24.91 out of 26.06
Confidence: strong
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.25 out of 25.88
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.08 out of 23.79
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.30 out of 28.19
Confidence: medium
Additional weak hits (2):
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 24.15 out of 35.63
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism
MogR | Repressor of flagellar motility genes
PsrA | Oleic acid responsive regulator
ZuR variant 1 | Zinc-responsive repressor

NZ_FNJX01000001.1 - Region 2 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 796,459 - 837,637 nt. (total: 41,179 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase reductase
BLR40_RS03850: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

BLR40_RS03925: hydroxymethylglutaryl-CoA reductase

smcogs
  SMCOG1187: hydroxymethylglutaryl-CoA reductase

Isomerases: isomerase
BLR40_RS04015: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: synthase
BLR40_RS03930: hydroxymethylglutaryl-CoA synthase

smcogs
  SMCOG1043: hydroxymethylglutaryl-CoA synthase

Translocases: permease
BLR40_RS03955: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002561.3 |  | 0.45 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0000016.4 |  | 0.44 | other (other) | amphotericin B | Streptomyces nodosus
BGC0002707.2 |  | 0.41 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001080.5 |  | 0.41 | other (phenazine) | endophenazine A, endophenazine B | Streptomyces anulatus
BGC0002031.3 |  | 0.41 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000883.5 |  | 0.41 | other (other) | arginomycin | Streptomyces arginensis
BGC0000934.4 |  | 0.41 | other (phenazine) | 5-acetyl-5,10-dihydrophenazine-1-carboxylic acid, 5-(2-hydroxyacetyl)-5,10-dihydrophenazine-1-carboxylic acid, endophenazine A1, endophenazine F, endophenazine G | Kitasatospora sp. HKI 714
BGC0001789.3 |  | 0.41 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000286.3 |  | 0.40 | PKS | viguiepinol | Streptomyces sp. KO-3988

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002561.3 |  | 0.45 | other (other) | phenazine SA, phenazine SB, phenazine SC | Streptomyces sp.
BGC0000016.4 |  | 0.44 | other (other) | amphotericin B | Streptomyces nodosus
BGC0002707.2 |  | 0.41 | terpene | (+)-δ-cadinol | Coniophora puteana RWD-64-598 SS2
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001080.5 |  | 0.41 | other (phenazine) | endophenazine A, endophenazine B | Streptomyces anulatus
BGC0002031.3 |  | 0.41 | other (other) | kitasetaline | Kitasatospora setae KM-6054
BGC0000883.5 |  | 0.41 | other (other) | arginomycin | Streptomyces arginensis
BGC0000934.4 |  | 0.41 | other (phenazine) | 5-acetyl-5,10-dihydrophenazine-1-carboxylic acid, 5-(2-hydroxyacetyl)-5,10-dihydrophenazine-1-carboxylic acid, endophenazine A1, endophenazine F, endophenazine G | Kitasatospora sp. HKI 714
BGC0001789.3 |  | 0.41 | ribosomal | suicin 90-1330 | Streptococcus suis
BGC0000286.3 |  | 0.40 | PKS | viguiepinol | Streptomyces sp. KO-3988

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: 22.69 out of 26.06
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.60 out of 30.25
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.73 out of 26.06
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.98 out of 20.97
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.57 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.58 out of 27.78
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.52 out of 28.19
Confidence: strong
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.18 out of 28.19
Confidence: medium
Additional weak hits (3):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.41 out of 30.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.61 out of 29.38
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 23.74 out of 35.63
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ColR | Phenol-responsive regulator
MogR | Repressor of flagellar motility genes
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor