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Overview
1.1
1.2
1.3
1.4
2.1

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

NZ_CP075970.1 (Clostridium perfringens)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | cyclic-lactone-autoinducer | 1,039,581 | 1,060,144 |
Region 1.2 | cyclic-lactone-autoinducer | 1,981,746 | 2,002,545 |
Region 1.3 | terpene-precursor | 2,255,378 | 2,276,250 |
Region 1.4 | ranthipeptide | 2,384,142 | 2,405,725 |

NZ_CP075971.1 (Clostridium perfringens)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | lanthipeptide-class-i | 43,440 | 69,585 |  |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | cyclic-lactone-autoinducer | 1,039,581 | 1,060,144 |
Region 1.2 | cyclic-lactone-autoinducer | 1,981,746 | 2,002,545 |
Region 1.3 | terpene-precursor | 2,255,378 | 2,276,250 |
Region 1.4 | ranthipeptide | 2,384,142 | 2,405,725 |
Region 2.1 | lanthipeptide-class-i | 43,440 | 69,585 |  |

No secondary metabolite regions were found in these records:
  NZ_CP075972.1 (Clostridium perfringens)

Compact view
NZ_CP075970.1 - Region 1 - cyclic-lactone-autoinducer
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: 1,039,581 - 1,060,144 nt. (total: 20,564 nt) Show pHMM detection rules used
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

#### 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
Hydrolases: peptidase
KLF29_RS04460: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

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 | cyclic-lactone-autoinducer | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001427.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001423.4 |  | 0.29 | NRPS, PKS | myxochromide C | Myxococcus hansupus
BGC0001425.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus DK 1622
BGC0001426.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001421.4 |  | 0.29 | NRPS, PKS | myxochromide B | Myxococcus sp.
BGC0001428.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001424.4 |  | 0.29 | NRPS, PKS | myxochromide C | Myxococcus virescens
BGC0001422.4 |  | 0.27 | NRPS, PKS | myxochromide A | Myxococcus fulvus HW-1
BGC0000897.5 |  | 0.26 | other (other) | dehydrophos | Streptomyces luridus
BGC0002060.3 |  | 0.22 | PKS | secimide | Pseudomonas syringae pv. syringae B728a

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001427.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001423.4 |  | 0.29 | NRPS, PKS | myxochromide C | Myxococcus hansupus
BGC0001425.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus DK 1622
BGC0001426.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001421.4 |  | 0.29 | NRPS, PKS | myxochromide B | Myxococcus sp.
BGC0001428.4 |  | 0.29 | NRPS, PKS | myxochromide A | Myxococcus xanthus
BGC0001424.4 |  | 0.29 | NRPS, PKS | myxochromide C | Myxococcus virescens
BGC0001422.4 |  | 0.27 | NRPS, PKS | myxochromide A | Myxococcus fulvus HW-1
BGC0000897.5 |  | 0.26 | other (other) | dehydrophos | Streptomyces luridus
BGC0002060.3 |  | 0.22 | PKS | secimide | Pseudomonas syringae pv. syringae B728a

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:
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 24.71 out of 29.25
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.87 out of 23.79
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.27 out of 23.79
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.65 out of 28.19
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.20 out of 28.19
Confidence: medium
Additional weak hits (4):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.79 out of 30.25
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.10 out of 36.53
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 15.62 out of 20.47
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
IolR | Regulator of the inositol catabolism
SypG | Regulator of biofilm formation and host colonization
ZuR variant 1 | Zinc-responsive repressor

NZ_CP075970.1 - Region 2 - cyclic-lactone-autoinducer
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: 1,981,746 - 2,002,545 nt. (total: 20,800 nt) Show pHMM detection rules used
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

#### 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
KLF29_RS08630: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: hydrolase
KLF29_RS08685: hydrolase

smcogs
  SMCOG1179: hydrolase

Lyases: cyclase
KLF29_RS08635: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

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 | cyclic-lactone-autoinducer | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000645.3 |  | 0.35 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.34 | terpene | carotenoid | Myxococcus xanthus
BGC0000334.4 |  | 0.29 | NRPS | cyclosporin A | Tolypocladium inflatum NRRL 8044
BGC0002686.2 |  | 0.20 | NRPS | madurastatin D1, madurastatin D2, (-)-Madurastatin C1 | Actinomadura sp. WMMA1423

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000645.3 |  | 0.35 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0000648.3 |  | 0.34 | terpene | carotenoid | Myxococcus xanthus
BGC0000334.4 |  | 0.29 | NRPS | cyclosporin A | Tolypocladium inflatum NRRL 8044
BGC0002686.2 |  | 0.20 | NRPS | madurastatin D1, madurastatin D2, (-)-Madurastatin C1 | Actinomadura sp. WMMA1423

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: 24.36 out of 26.06
Confidence: strong
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.70 out of 29.38
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.07 out of 24.78
Confidence: medium
Additional weak hits (4):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.64 out of 31.73
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 25.19 out of 30.97
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 25.17 out of 33.73
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.02 out of 27.18
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
FuR variant 1 | Ferric Uptake Regulator
LexA variant 2 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes

NZ_CP075970.1 - Region 3 - terpene-precursor
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,255,378 - 2,276,250 nt. (total: 20,873 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
Ligases: synthase synthetase
KLF29_RS09945: 1-deoxy-D-xylulose-5-phosphate synthase

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

KLF29_RS09950: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

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

Reference | terpene-precursor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0002283.2 |  | 0.45 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.45 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000640.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000630.3 |  | 0.36 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000666.5 |  | 0.35 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0002283.2 |  | 0.45 | terpene | sodorifen | Serratia plymuthica
BGC0001361.3 |  | 0.45 | terpene | sodorifen | Serratia plymuthica 4Rx13
BGC0002400.2 |  | 0.44 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000640.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000665.5 |  | 0.37 | other (other), terpene | xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C | Streptomyces sp. HKI0576
BGC0000043.5 |  | 0.36 | PKS | curacin A | Moorea producens 19L
BGC0000630.3 |  | 0.36 | terpene | (2R,3S,3'S)-2-hydroxyastaxanthin | Paracoccus haeundaensis
BGC0000666.5 |  | 0.35 | terpene | xiamycin A | Streptomyces sp. SCSIO 02999

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

No significant matches found.

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

No significant matches found.

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

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

Genes with terpene domains:
KLF29_RS09950: PT_FPPS_like
Domain 1 (28 - 288): 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:
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.37 out of 28.14
Confidence: medium
Additional weak hits (2):
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.66 out of 29.65
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.06 out of 32.93
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
PerR | Peroxide regulator

NZ_CP075970.1 - Region 4 - ranthipeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,384,142 - 2,405,725 nt. (total: 21,584 nt) Show pHMM detection rules used
ranthipeptide: (TIGR03973 or SCIFF or (cds(PF04055 and (TIGR04085 or SPASM)) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]) and not (TIGR01716 or subtilosin or TIGR02111 or TIGR03966 or TIGR04103 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
Hydrolases: esterase hydrolase
KLF29_RS10550: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

KLF29_RS10625: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

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

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 | ranthipeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.47 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002407.3 |  | 0.36 | other (other), saccharide | angustmycin A, angustmycin C | Streptomyces angustmyceticus
BGC0001387.5 |  | 0.35 | other (other) | nucleocidin | Streptomyces calvus
BGC0001591.4 |  | 0.32 | other (other) | fatty acid enol ester, N-tetradecanoyl tyrosine | uncultured bacterium CSLC2
BGC0002621.2 |  | 0.32 | other (other) | angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine | Streptomyces angustmyceticus
BGC0001155.5 |  | 0.31 | ribosomal | GE2270 | Planobispora rosea
BGC0000604.4 |  | 0.30 | ribosomal | GE2270A | Nonomuraea sp. WU8817
BGC0002713.2 |  | 0.30 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0000027.4 |  | 0.30 | PKS | ankaflavin, monascin, rubropunctatine, monascorubrin | Monascus pilosus
BGC0001089.5 |  | 0.26 | NRPS, PKS | bacillaene | Bacillus velezensis FZB42

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.47 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002407.3 |  | 0.36 | other (other), saccharide | angustmycin A, angustmycin C | Streptomyces angustmyceticus
BGC0001387.5 |  | 0.35 | other (other) | nucleocidin | Streptomyces calvus
BGC0001591.4 |  | 0.32 | other (other) | fatty acid enol ester, N-tetradecanoyl tyrosine | uncultured bacterium CSLC2
BGC0002621.2 |  | 0.32 | other (other) | angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine | Streptomyces angustmyceticus
BGC0001155.5 |  | 0.31 | ribosomal | GE2270 | Planobispora rosea
BGC0000604.4 |  | 0.30 | ribosomal | GE2270A | Nonomuraea sp. WU8817
BGC0002713.2 |  | 0.30 | NRPS | mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D | Photorhabdus laumondii subsp. laumondii
BGC0000027.4 |  | 0.30 | PKS | ankaflavin, monascin, rubropunctatine, monascorubrin | Monascus pilosus
BGC0001089.5 |  | 0.26 | NRPS, PKS | bacillaene | Bacillus velezensis FZB42

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:
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.08 out of 21.55
Confidence: medium
Additional weak hits (2):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 18.44 out of 30.11
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

ranthipeptide protocluster (2384141...2405725)
KLF29_RS10585
  RRE type: Ranthipeptide_rSAM_RRE
  Location: 1 - 101
  Score: 89.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ArcA | Repressor of carbon oxidation

NZ_CP075971.1 - Region 1 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 43,440 - 69,585 nt. (total: 26,146 nt) Show pHMM detection rules used
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Lyases: cyclase dehydratase
KLF29_RS14835: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

KLF29_RS14845: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.74 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.57 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000542.3 |  | 0.55 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000506.4 |  | 0.53 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000515.4 |  | 0.52 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000559.4 |  | 0.51 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000560.5 |  | 0.51 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000537.3 |  | 0.51 | ribosomal | nisin U | Streptococcus uberis
BGC0000536.3 |  | 0.51 | ribosomal | nisin Q | Lactococcus lactis
BGC0000535.4 |  | 0.51 | ribosomal | nisin A | Lactococcus lactis subsp. lactis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.74 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001289.5 |  | 0.57 | ribosomal | penisin | Paenibacillus ehimensis
BGC0000542.3 |  | 0.55 | ribosomal | paenicidin B | Paenibacillus terrae
BGC0000506.4 |  | 0.53 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000515.4 |  | 0.52 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000559.4 |  | 0.51 | ribosomal | subtilin | Bacillus subtilis subsp. spizizenii ATCC 6633
BGC0000560.5 |  | 0.51 | ribosomal | subtilomycin | Bacillus subtilis
BGC0000537.3 |  | 0.51 | ribosomal | nisin U | Streptococcus uberis
BGC0000536.3 |  | 0.51 | ribosomal | nisin Q | Lactococcus lactis
BGC0000535.4 |  | 0.51 | ribosomal | nisin A | Lactococcus lactis subsp. lactis

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 KLF29_RS14845

KLF29_RS14850
Leader:
MLKDFDLNLKMETGSSDDKEPR
Core:
ITSVAYCTPGCLTGELCGSSECGLTRSCTNTWLCS
Core with dehydrations:
IDhbDhaVAYCysDhbPGCysLDhbGELCysGDhaDhaECysGLDhbRDhaCysDhbNDhbWLCysDha

#### antiSMASH-DB 4.0 matches for KLF29_RS14850

100.0%
NZ_CP075910.1 and 3 others:
NZ_CP075971.1 Lanthipeptides: KLF29_RS14850_lanthipeptide NZ_CP075982.1 Lanthipeptides: KLF51_RS14900_lanthipeptide NZ_CP075994.1 Lanthipeptides: KLF26_RS16110_lanthipeptide
Lanthipeptides: KLF45_RS14835_lanthipeptide
1
ITSVAYCTPGCLTGELCGSSECGLTRSCTNTWLCS
35
ITSVAYCTPGCLTGELCGSSECGLTRSCTNTWLCS
1
ITSVAYCTPGCLTGELCGSSECGLTRSCTNTWLCS
35
85.7%
NZ_CP029639.1:
Lanthipeptides: DMB88_RS07755_lanthipeptide
1
ITSVAYCTPGCLTGELCGSSECGLTRSCTNTWLCS
35
ITSVAYCTPGC TG CGSSECGLTR CTNTWLC+
1
ITSVAYCTPGCNTGSTCGSSECGLTRQCTNTWLCA
35
82.9%
NZ_QLLI01000019.1:
Lanthipeptides: DET54_RS28075_lanthipeptide
1
ITSVAYCTPGCLTGELCGSSECGLTRSCTNTWLC
34
ITSVAYCTPGC TG CG+SECGLTR+CTNTWLC
1
ITSVAYCTPGCNTGSTCGTSECGLTRNCTNTWLC
34
with 100 more sequence matches
Only the first 10 are displayed here.
80.0%
NZ_CP070896.1 and 2 others:
NZ_CP070896.1 Lanthipeptides: JWH23_RS09310_lanthipeptide NZ_CP070896.1 Lanthipeptides: JWH23_RS09310_lanthipeptide
Lanthipeptides: JWH23_RS09310_lanthipeptide
1
ITSVAYCTPGCLTGELCGSSECGLTRSCTNTWLC
34
I SVAYCTPGCLTG CG+SECG+TR+CTNTWLC
1
IASVAYCTPGCLTGTTCGTSECGMTRNCTNTWLC
34
74.3%
NZ_CABIWO010000014.1:
Lanthipeptides: FY209_RS17155_lanthipeptide
2
TSVAYCTPGCLTGELCGSSECGLTRSCTNTWLCS
35
TSVAYCTPGC+TG+LCGSSECGLTR+CT + C+
1
TSVAYCTPGCVTGQLCGSSECGLTRNCTGSIACA
34
48.6%
NZ_CP073683.1 and 1 other:
NZ_CP092779.1 Lanthipeptides: MJ749_RS08075_lanthipeptide
Lanthipeptides: KAI37_RS08180_lanthipeptide
1
ITSVAYCTPGCLTGELCGSSECG
23
+TSV CTPGC+TG CGSSECG
1
VTSVFACTPGCITGPNCGSSECG
23
48.6%
NZ_CP085954.1:
Lanthipeptides: LK411_RS13585_lanthipeptide
1
ITSVAYCTPGCLTGEL-CGSSECGLTRSCTNT
31
ITS + CTPGC TG L C + C T CT T
1
ITSKSLCTPGCPTGALGCFTQNCDPTNGCTIT
32
45.7%
NZ_CP025696.1 and 1 other:
NZ_LNZF01000001.1 Lanthipeptides: AVK83_RS25720_lanthipeptide
Lanthipeptides: C0638_RS24580_lanthipeptide
1
ITSVAYCTPGCLTGELCGSSECG
23
+TS CT GCLTG CGSSECG
1
VTSWFACTGGCLTGSNCGSSECG
23
42.9%
NZ_AULX01000006.1:
Lanthipeptides: H583_RS0100280_lanthipeptide
1
ITSVAYCTPGCLTGEL-CGSSECGLTRSCTN
30
ITS + CTPGC+TG L C + C ++ SC
1
ITSKSLCTPGCITGVLMCFTKGCEISHSCIK
31
42.9%
NZ_LT732548.1:
Lanthipeptides: CZ379_RS19505_lanthipeptide
1
ITSVAYCTPGCLTGEL-CGSSECGLTRSCTN
30
ITS + CTPGC+TG L C + C ++ SC
1
ITSKSLCTPGCITGVLMCFTKGCEISHSCVK
31
40.0%
NZ_CP034141.1:
Lanthipeptides: EGM68_RS08790_lanthipeptide
2
TSVAYCTPGCLTGELCGSSECG
23
TS +YCT GC+TG C SSEC
2
TSWSYCTTGCITGPNCNSSECA
23
37.1%
NZ_FBTD01000003.1:
Lanthipeptides: PB1E_RS03075_lanthipeptide
1
ITSVAYCTPGCLTGELCG
18
ITSV+ CTPGC TG L G
1
ITSVSLCTPGCKTGALMG
18
37.1%
NZ_JHXK01000032.1 and 1 other:
NZ_JHXK01000032.1 Lanthipeptides: T483_RS30515_lanthipeptide
Lanthipeptides: T483_RS30515_lanthipeptide
1
ITSVAYCTPGCLTGELCGSSECGLTRSC
28
+TS + CTPGC T LTRSC
1
VTSYSACTPGCATSLF----RTCLTRSC
24

#### MIBiG 4.0 matches for KLF29_RS14850

34.3%
BGC0000535.4 (ADJ56352.1):
Lanthipeptide: nisin A
1
ITSVAYCTPGCLTGELCG
18
ITS++ CTPGC TG L G
1
ITSISLCTPGCKTGALMG
18
11.4%
BGC0002110.3 (QKV49893.1):
Lanthipeptide: birimositide
22
CGLTRSC
28
C LT+ C
19
CTLTKEC
25
7.7%
BGC0001229.4 (SBI_06990):
Lanthipeptide: SBI-06990 A1 or SBI-06989 A2
22
CGLTRSC
28
C L++ C
28
CTLSKEC
34

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.05 out of 20.97
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 26.06 out of 26.06
Confidence: strong
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33
Confidence: medium
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 23.46 out of 29.25
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52
Confidence: strong
Additional weak hits (6):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.66 out of 20.01
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 20.27 out of 30.22
Confidence: weak
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 15.12 out of 18.46
Confidence: weak
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 13.73 out of 30.12
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
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.58 out of 19.52
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.

KLF29_RS14850 - Class I
  Cleavage pHMM score: 9.30
  RODEO score: 26
  Monoisotopic mass: 3417.5 Da
  Molecular weight: 3419.9 Da
  Number of bridges: 6
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3437.9 Da N = 1
    3455.9 Da N = 2
    3473.9 Da N = 3
    3492.0 Da N = 4
    3510.0 Da N = 5

RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-i protocluster (43439...69585)
KLF29_RS14845
  RRE type: Lanthipeptide_LanB_RRE
  Location: 168 - 240
  Score: 34.2

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
CcpA | Catabolite control protein A
MogR | Repressor of flagellar motility genes
SypG | Regulator of biofilm formation and host colonization