Select genomic region:
Overview
1.1
1.2
1.3
1.4
2.1
4.1
5.1
7.1
17.1
19.1
20.1
21.1
24.1

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

NZ_JADEWH010000001.1 (Nodularia sp. LEGE 06071)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | lanthipeptide-class-v,RRE-containing,spliceotide | 1 | 36,845 | Low | PcpA | ribosomal:RiPP
Region 1.2 | microviridin | 106,676 | 127,008 | Low | microviridin 1688/microviridin 1739/microviridin 1748 | ribosomal:RiPP:Microviridin
Region 1.3 | NRPS-like | 374,202 | 416,655 |
Region 1.4 | lanthipeptide-class-v | 474,979 | 517,491 | Low | anacyclamide A10 | ribosomal:RiPP:Cyanobactin

NZ_JADEWH010000002.1 (Nodularia sp. LEGE 06071)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 2.1 | lassopeptide | 176,347 | 203,569 |  |

NZ_JADEWH010000004.1 (Nodularia sp. LEGE 06071)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 4.1 | mycosporine,lanthipeptide-class-ii | 358,687 | 406,940 | Low | hexose-palythine-serine/hexose-shinorine | NRPS:Type I

NZ_JADEWH010000005.1 (Nodularia sp. LEGE 06071)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | terpene | 226,796 | 247,728 |

NZ_JADEWH010000007.1 (Nodularia sp. LEGE 06071)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 7.1 | hglE-KS | 45,128 | 92,123 | Medium | heterocyst glycolipids | other:other

NZ_JADEWH010000017.1 (Nodularia sp. LEGE 06071)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 17.1 | RRE-containing | 73,476 | 93,925 |

NZ_JADEWH010000019.1 (Nodularia sp. LEGE 06071)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 19.1 | NRP-metallophore,NRPS,T1PKS,NRPS-like | 7,815 | 98,582 | High | nocuolin A | other:other

NZ_JADEWH010000020.1 (Nodularia sp. LEGE 06071)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 20.1 | terpene-precursor | 23,351 | 44,280 |

NZ_JADEWH010000021.1 (Nodularia sp. LEGE 06071)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 21.1 | hglE-KS,T1PKS | 20,860 | 72,382 | High | heterocyst glycolipids | other:other

NZ_JADEWH010000024.1 (Nodularia sp. LEGE 06071)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 24.1 | lanthipeptide-class-v | 21,438 | 50,094 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | lanthipeptide-class-v,RRE-containing,spliceotide | 1 | 36,845 | Low | PcpA | ribosomal:RiPP
Region 1.2 | microviridin | 106,676 | 127,008 | Low | microviridin 1688/microviridin 1739/microviridin 1748 | ribosomal:RiPP:Microviridin
Region 1.3 | NRPS-like | 374,202 | 416,655 |
Region 1.4 | lanthipeptide-class-v | 474,979 | 517,491 | Low | anacyclamide A10 | ribosomal:RiPP:Cyanobactin
Region 2.1 | lassopeptide | 176,347 | 203,569 |  |
Region 4.1 | mycosporine,lanthipeptide-class-ii | 358,687 | 406,940 | Low | hexose-palythine-serine/hexose-shinorine | NRPS:Type I
Region 5.1 | terpene | 226,796 | 247,728 |
Region 7.1 | hglE-KS | 45,128 | 92,123 | Medium | heterocyst glycolipids | other:other
Region 17.1 | RRE-containing | 73,476 | 93,925 |
Region 19.1 | NRP-metallophore,NRPS,T1PKS,NRPS-like | 7,815 | 98,582 | High | nocuolin A | other:other
Region 20.1 | terpene-precursor | 23,351 | 44,280 |
Region 21.1 | hglE-KS,T1PKS | 20,860 | 72,382 | High | heterocyst glycolipids | other:other
Region 24.1 | lanthipeptide-class-v | 21,438 | 50,094 |

No secondary metabolite regions were found in these records:
  NZ_JADEWH010000003.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000006.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000008.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000009.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000010.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000011.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000012.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000013.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000014.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000015.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000016.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000018.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000022.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000023.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000025.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000026.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000027.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000028.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000029.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000030.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000031.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000032.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000033.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000034.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000035.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000036.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000037.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000038.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000039.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000040.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000041.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000042.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000043.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000044.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000045.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000046.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000047.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000048.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000049.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000050.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000051.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000052.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000053.1 (Nodularia sp. LEGE 06071)
  NZ_JADEWH010000054.1 (Nodularia sp. LEGE 06071)

Compact view
NZ_JADEWH010000001.1 - Region 1 - RRE-containing,lanthipeptide-class-v,spliceotide
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 - 36,845 nt. (total: 36,845 nt) Show pHMM detection rules used
Region on contig edge.
lanthipeptide-class-v: (APH and HopA1)
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])
spliceotide: (TIGR04103 and TIGR03798)

#### 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
Oxidoreductases: dehydrogenase
IQ233_RS00155: aldehyde oxidase and xanthine dehydrogenase

smcogs
  SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

Ligases: ligase
IQ233_RS00020: cobaltochelatase subunit CobN

smcogs
  SMCOG1263: cobaltochelatase subunit CobN

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-v | RRE-containing | spliceotide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001733.3 |  |  |  | 0.82 | ribosomal | PcpA | Pleurocapsa sp. PCC 7327
BGC0000601.4 |  |  |  | 0.42 | ribosomal | sporulation killing factor | Bacillus subtilis subsp. subtilis str. 168
BGC0002575.2 |  |  |  | 0.35 | ribosomal | cochonodin I | Streptococcus suis
BGC0000188.5 |  |  |  | 0.34 | other (other) | saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2 | Cylindrospermopsis raciborskii T3
BGC0000043.5 |  |  |  | 0.32 | PKS | curacin A | Moorea producens 19L
BGC0000506.4 |  |  |  | 0.32 | ribosomal | entianin | Bacillus subtilis subsp. spizizenii
BGC0000527.5 |  |  |  | 0.31 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0000515.4 |  |  |  | 0.31 | ribosomal | geobacillin I | Geobacillus thermodenitrificans NG80-2
BGC0000556.5 |  |  |  | 0.31 | ribosomal | streptin | Streptococcus pyogenes
BGC0000536.3 |  |  |  | 0.30 | ribosomal | nisin Q | Lactococcus lactis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001733.3 |  | 0.63 | ribosomal | PcpA | Pleurocapsa sp. PCC 7327
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0002005.2 |  | 0.51 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0002306.2 |  | 0.51 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000623.3 |  | 0.48 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0000558.5 |  | 0.48 | ribosomal | sublancin 168 | Bacillus subtilis subsp. subtilis str. 168
BGC0000589.5 |  | 0.45 | ribosomal | microcin M | Escherichia coli Nissle 1917
BGC0000617.5 |  | 0.45 | ribosomal | coagulin | Bacillus coagulans
BGC0000513.3 |  | 0.45 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000587.5 |  | 0.44 | ribosomal | microcin H47 | Escherichia coli

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.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 27.78 out of 27.78
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.48 out of 24.78
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.03 out of 26.06
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
Additional weak hits (3):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.62 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.83 out of 26.12
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.07 out of 33.14
Confidence: weak
Lanthipeptides
RREFinder
TFBS Finder
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists the number of lanthionine bridges, possible molecular weights, and the scores for cleavage site prediction and RODEO.
No core peptides found.
RRE predictions
RREfinder results sidepanel.

lanthipeptide-class-v protocluster (0...36845)
IQ233_RS00090
  RRE type: PlpY_RRE
  Location: 4 - 69
  Score: 77.6
RRE-containing protocluster (7067...27286)
IQ233_RS00090
  RRE type: PlpY_RRE
  Location: 4 - 69
  Score: 77.6
spliceotide protocluster (7290...29336)
IQ233_RS00090
  RRE type: PlpY_RRE
  Location: 4 - 69
  Score: 77.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence

NZ_JADEWH010000001.1 - Region 2 - microviridin
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: 106,676 - 127,008 nt. (total: 20,333 nt) Show pHMM detection rules used
microviridin: (mvd or mvnA)

#### 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
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 | microviridin | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000593.4 |  | 0.72 | ribosomal | microviridin J | Microcystis aeruginosa MRC
BGC0002049.3 |  | 0.58 | ribosomal | microviridin N9, microviridin N8, microviridin N7, microviridin N6, microviridin N5, microviridin N4, microviridin N3 | Nostoc punctiforme PCC 73102
BGC0000592.5 |  | 0.57 | ribosomal | microviridin B | Microcystis aeruginosa NIES-298
BGC0000594.5 |  | 0.43 | ribosomal | microviridin K | Planktothrix agardhii NIVA-CYA 126/8
BGC0000591.5 |  | 0.39 | ribosomal | marinostatin | Alteromonas sp. B-10-31
BGC0002626.2 |  | 0.38 | ribosomal | microviridin 1688, microviridin 1739, microviridin 1748 | Nostoc sp. TH1S01
BGC0002382.3 |  | 0.34 | ribosomal | grimoviridin | Grimontia marina
BGC0000475.5 |  | 0.25 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0001657.4 |  | 0.19 | NRPS | lysocin | Lysobacter sp. RH2180-5
BGC0000636.3 |  | 0.19 | terpene | carotenoid | Brevibacterium linens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000593.4 |  | 0.72 | ribosomal | microviridin J | Microcystis aeruginosa MRC
BGC0002049.3 |  | 0.58 | ribosomal | microviridin N9, microviridin N8, microviridin N7, microviridin N6, microviridin N5, microviridin N4, microviridin N3 | Nostoc punctiforme PCC 73102
BGC0000592.5 |  | 0.57 | ribosomal | microviridin B | Microcystis aeruginosa NIES-298
BGC0000594.5 |  | 0.43 | ribosomal | microviridin K | Planktothrix agardhii NIVA-CYA 126/8
BGC0000591.5 |  | 0.39 | ribosomal | marinostatin | Alteromonas sp. B-10-31
BGC0002626.2 |  | 0.38 | ribosomal | microviridin 1688, microviridin 1739, microviridin 1748 | Nostoc sp. TH1S01
BGC0002382.3 |  | 0.34 | ribosomal | grimoviridin | Grimontia marina
BGC0000475.5 |  | 0.25 | ribosomal | patellamide A, patellamide C | Prochloron didemni
BGC0001657.4 |  | 0.19 | NRPS | lysocin | Lysobacter sp. RH2180-5
BGC0000636.3 |  | 0.19 | terpene | carotenoid | Brevibacterium linens

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.

NZ_JADEWH010000001.1 - Region 3 - NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 374,202 - 416,655 nt. (total: 42,454 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### 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
IQ233_RS01840: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

IQ233_RS01910: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase acyltransferase methyltransferase
IQ233_RS01810: methyltransferase

smcogs
  SMCOG1089: methyltransferase

IQ233_RS01940: acyltransferase

smcogs
  SMCOG1141: acyltransferase

IQ233_RS01955: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

IQ233_RS01995: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Lyases: decarboxylase
IQ233_RS01875: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: ligase synthase
IQ233_RS01885: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IQ233_RS01960: 3-oxoacyl-(acyl carrier protein) synthase III

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

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

Reference | NRPS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001135.5 |  | 0.64 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001160.5 |  | 0.63 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001132.4 |  | 0.63 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002286.3 |  | 0.63 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.62 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  | 0.62 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002135.2 |  | 0.61 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001758.4 |  | 0.60 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454

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

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:
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 24.72 out of 30.25
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 25.38 out of 27.78
Confidence: strong
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.05 out of 20.97
Confidence: strong
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.92 out of 27.78
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.55 out of 27.78
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.47 out of 32.93
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.28 out of 26.06
Confidence: medium
Additional weak hits (9):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.89 out of 32.74
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.07 out of 32.93
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.45 out of 30.25
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.54 out of 21.55
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.40 out of 29.38
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.64 out of 32.93
Confidence: weak
RicR
Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.43 out of 32.93
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.38 out of 29.25
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.82 out of 26.06
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 5, location 374201 - 416655:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
IQ233_RS01885: X
AMP-binding (12..413): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFVDSVWEGILTVSGELNLYGSTEVAGDVTW
  Nearest Stachelhaus code(s):
    bAla VDWVTSLADK (76% 8Å match)
  Stachelhaus code match:
    80% (moderate)

IQ233_RS01955: mal
PKS_AT (6..279): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 81.7
  inactive: 41.2
  Methoxymalonyl-CoA: 35.2
  Propionyl-CoA: 23.7
  Methylmalonyl-CoA: 16.4
  Isobutyryl-CoA: 13.7
  2-Methylbutyryl-CoA: 10.0
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

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

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein
CcpA | Catabolite control protein A
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ColR | Phenol-responsive regulator
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes

NZ_JADEWH010000001.1 - Region 4 - lanthipeptide-class-v
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: 474,979 - 517,491 nt. (total: 42,513 nt) Show pHMM detection rules used
lanthipeptide-class-v: (APH and HopA1)

#### 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
Hydrolases: peptidase
IQ233_RS02385: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

Lyases: dehydratase
IQ233_RS02405: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

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

Reference | lanthipeptide-class-v | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0000623.3 |  | 0.48 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0002382.3 |  | 0.47 | ribosomal | grimoviridin | Grimontia marina
BGC0000554.4 |  | 0.45 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000617.5 |  | 0.45 | ribosomal | coagulin | Bacillus coagulans
BGC0002303.3 |  | 0.44 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0001862.4 |  | 0.44 | ribosomal | pallidocin | Aeribacillus pallidus
BGC0002698.2 |  | 0.44 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001210.5 |  | 0.43 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002579.2 |  | 0.43 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000590.5 |  | 0.51 | ribosomal | microcin N | Escherichia coli
BGC0000623.3 |  | 0.48 | ribosomal | plantaricin W α, plantaricin W β | Lactobacillus plantarum
BGC0002382.3 |  | 0.47 | ribosomal | grimoviridin | Grimontia marina
BGC0000554.4 |  | 0.45 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000617.5 |  | 0.45 | ribosomal | coagulin | Bacillus coagulans
BGC0002303.3 |  | 0.44 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0001862.4 |  | 0.44 | ribosomal | pallidocin | Aeribacillus pallidus
BGC0002698.2 |  | 0.44 | ribosomal | phaeornamide | Pseudophaeobacter arcticus DSM 23566
BGC0001210.5 |  | 0.43 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002579.2 |  | 0.43 | ribosomal | carnobacteriocin XY | Carnobacterium maltaromaticum

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.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.21 out of 23.43
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.75 out of 27.55
Confidence: medium
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.82 out of 27.55
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.87 out of 28.19
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.05 out of 18.16
Confidence: strong
Additional weak hits (4):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.99 out of 25.88
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.79 out of 29.38
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.59 out of 30.97
Confidence: weak
CsoR
Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 20.83 out of 32.38
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.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator
BldD | Development and antibiotic global regulator
GnfM | Regulator of nitrogen-fixation genes
ToxT | Regulator of MSHA biosynthesis
ZuR variant 1 | Zinc-responsive repressor

NZ_JADEWH010000002.1 - Region 1 - lassopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 176,347 - 203,569 nt. (total: 27,223 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
Oxidoreductases: oxygenase
IQ233_RS04490: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: hydrolase
IQ233_RS04515: asparagine synthase (glutamine-hydrolyzing)

smcogs
  SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

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

Reference | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000575.5 |  | 0.52 | ribosomal | lariatin | Rhodococcus jostii
BGC0001634.3 |  | 0.52 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001551.4 |  | 0.50 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0000571.3 |  | 0.49 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0002322.3 |  | 0.49 | ribosomal | citrocin | Citrobacter pasteurii
BGC0002064.2 |  | 0.48 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002103.2 |  | 0.45 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000846.5 |  | 0.43 | other (other) | tabtoxin | Pseudomonas syringae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000575.5 |  | 0.52 | ribosomal | lariatin | Rhodococcus jostii
BGC0001634.3 |  | 0.52 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0001551.4 |  | 0.50 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0000571.3 |  | 0.49 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0002322.3 |  | 0.49 | ribosomal | citrocin | Citrobacter pasteurii
BGC0002064.2 |  | 0.48 | ribosomal | felipeptin A2, felipeptin A1 | Amycolatopsis sp. YIM 10
BGC0002127.3 |  | 0.47 | PKS | flaviolin, 1,3,6,8-tetrahydroxynaphthalene | Streptomyces coelicolor A3(2)
BGC0002103.2 |  | 0.45 | other (other) | pulcherriminic acid | Bacillus subtilis subsp. subtilis str. 168
BGC0002306.2 |  | 0.43 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000846.5 |  | 0.43 | other (other) | tabtoxin | Pseudomonas syringae

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

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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.30 out of 27.78
Confidence: medium
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 27.94 out of 31.73
Confidence: medium
Additional weak hits (1):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.47 out of 30.25
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 (176346...203569)
IQ233_RS04475
  RRE type: Stand_Alone_Lasso_RRE
  Location: 9 - 92
  Score: 79.3

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
HexR | Glucose-responsive regulator

NZ_JADEWH010000004.1 - Region 1 - lanthipeptide-class-ii,mycosporine
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: 358,687 - 406,940 nt. (total: 48,254 nt) Show pHMM detection rules used
Region on contig edge.
mycosporine: (DHQ_synthase and Methyltransf_3 and ATP-grasp_3)
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
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
Transferases: acetyltransferase glycosyltransferase methyltransferase
IQ233_RS09860: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

IQ233_RS09870: Chloramphenicol acetyltransferase

smcogs
  SMCOG1156: Chloramphenicol acetyltransferase

IQ233_RS09890: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

IQ233_RS09900: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

IQ233_RS09905: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

IQ233_RS09910: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Lyases: cyclase dehydratase
IQ233_RS09845: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

IQ233_RS10010: lanthionine synthetase C family protein

smcogs
  SMCOG1070: lanthionine synthetase C family protein

Ligases: synthase
IQ233_RS09970: 3-dehydroquinate synthase

smcogs
  SMCOG1183: 3-dehydroquinate synthase

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

Reference | mycosporine | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000554.4 |  |  | 0.56 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001210.5 |  |  | 0.44 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001555.4 |  |  | 0.38 | ribosomal | colicin V | Escherichia coli chi7122
BGC0000527.5 |  |  | 0.38 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0002005.2 |  |  | 0.37 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0002703.2 |  |  | 0.35 | ribosomal | archalan α | Halorussus salinus
BGC0000588.5 |  |  | 0.34 | ribosomal | microcin L | Escherichia coli
BGC0000525.5 |  |  | 0.34 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0000528.5 |  |  | 0.33 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001311.5 |  |  | 0.32 | ribosomal | flavecins | Ruminococcus flavefaciens FD-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000554.4 |  | 0.62 | ribosomal | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0000427.5 |  | 0.59 | NRPS | shinorine, 4-deoxygadusol, mycosporine glycine | Trichormus variabilis ATCC 29413
BGC0001210.5 |  | 0.57 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001615.3 |  | 0.52 | NRPS | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0000527.5 |  | 0.52 | ribosomal | mersacidin | Bacillus sp. HIL-Y85/54728
BGC0001555.4 |  | 0.51 | ribosomal | colicin V | Escherichia coli chi7122
BGC0002674.2 |  | 0.51 | ribosomal | enterocin F4-9 | Enterococcus faecalis
BGC0000525.5 |  | 0.51 | ribosomal | lichenicidin VK21 A1, lichenicidin VK21 A2 | Bacillus licheniformis
BGC0002005.2 |  | 0.50 | ribosomal | RaxX | Xanthomonas oryzae pv. oryzae
BGC0000732.3 |  | 0.49 | saccharide | capsular polysaccharide | Raoultella planticola

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 IQ233_RS10010

IQ233_RS10005
Leader:
MSNIDIIRAWKDEDYRNSLSEEQRSQLPENPAGLIELPDEESDALSGG
Core:
CSYFTGTCGRVCAVLTPRYGCTICGGGGFTS
Core with dehydrations:
CysDhaYFDhbGDhbCysGRVCysAVLDhbPRYGCysDhbICysGGGGFDhbDha

#### antiSMASH-DB 4.0 matches for IQ233_RS10005

100.0%
NZ_JADEWH010000004.1:
Lanthipeptides: IQ233_RS10005_lanthipeptide
1
CSYFTGTCGRVCAVLTPRYGCTICGGGGFTS
31
CSYFTGTCGRVCAVLTPRYGCTICGGGGFTS
1
CSYFTGTCGRVCAVLTPRYGCTICGGGGFTS
31
22.6%
NZ_FOMZ01000019.1 and 1 other:
NZ_FOMZ01000019.1 Lanthipeptides: BM150_RS22435_lanthipeptide
Lanthipeptides: BM150_RS22435_lanthipeptide
2
SYFTGTCGRVCAVLTPRYGC
21
S CG+ C P+ GC
1
SPTEDNCGQTCESACPQTGC
20
21.1%
NZ_RHQE01000015.1:
Lanthipeptides: allorf_100944_101117_lanthipeptide
7
TCGRVCAVLTPRYGCTICGGGG
28
TC R+ V +PR G + G
3
TCNRLEPVRSPRAGHAVNPSMG
24
with 2 more sequence matches
19.4%
NZ_FNGC01000009.1:
Lanthipeptides: allorf_112052_112270_lanthipeptide
17
PRYGCTICG
25
PRY CT+C
12
PRYDCTLCS
20
16.7%
NZ_BMFU01000012.1 and 7 others:
NZ_BMFU01000012.1 Lanthipeptides: IEW26_RS25375_lanthipeptide NZ_JACHKG010000014.1 Lanthipeptides: allorf_027480_027638_lanthipeptide NZ_JACHKG010000014.1 Lanthipeptides: allorf_027480_027638_lanthipeptide NZ_JAHXMW010000012.1 Lanthipeptides: KZX51_RS23855_lanthipeptide NZ_JAHXMW010000012.1 Lanthipeptides: KZX51_RS23855_lanthipeptide NZ_VDYW01000008.1 Lanthipeptides: FS579_RS24445_lanthipeptide NZ_VDYW01000008.1 Lanthipeptides: FS579_RS24445_lanthipeptide
Lanthipeptides: IEW26_RS25375_lanthipeptide
2
SYFTGTCGRVC
12
SYF G G VC
21
SYFMGNPGHVC
31
allorf_384206_384364
Leader:
MTLKTLNGS
Core:
KRTWLTTLCGECQYHLSLFQSSYYPVFKITALVAPENSGFEYI
Core with dehydrations:
KRDhbWLDhbDhbLCysGECysQYHLDhaLFQDhaDhaYYPVFKIDhbALVAPENDhaGFEYI

#### antiSMASH-DB 4.0 matches for allorf_384206_384364

100.0%
NZ_JADEWH010000004.1:
Lanthipeptides: allorf_384206_384364_lanthipeptide
1
KRTWLTTLCGECQYHLSLFQSSYYPVFKITALVAPENSGFEYI
43
KRTWLTTLCGECQYHLSLFQSSYYPVFKITALVAPENSGFEYI
1
KRTWLTTLCGECQYHLSLFQSSYYPVFKITALVAPENSGFEYI
43
18.2%
NZ_CP016279.1:
Lanthipeptides: AVL59_RS52375_lanthipeptide
4
WLTTLCGECQYHLSLFQSSYYPVFKITALVAPENS
38
W T + ++ + +F ++ P FK+T + N
2
WFTCASTDGKF-VKVFDTTAKPPFKVTVDITGGNG
35
16.3%
NZ_CP060140.1:
Lanthipeptides: allorf_1942151_1942312_lanthipeptide
2
RTWLTTLCGECQYHLSLFQSSYYPVF
27
+ W ++ E Y L ++Q+++ PV+
12
KVWRSSGVREIMYFLHIWQNTWSPVY
37
with 2 more sequence matches
14.0%
NZ_BOSN01000007.1 and 1 other:
NZ_JAHHXV010000040.1 Lanthipeptides: allorf_06582_06767_lanthipeptide
Lanthipeptides: allorf_250666_250851_lanthipeptide
12
CQYHLSLFQSSYY
24
C YH+ ++ SYY
20
CTYHVPSYKCSYY
32
14.0%
NZ_KN125579.1:
Lanthipeptides: allorf_0767429_0767539_lanthipeptide
3
TWLTTLCG
10
+WLT LCG
3
SWLTILCG
10
allorf_393272_393412
Leader:
MSTPVAGIATFLSNLTVA
Core:
LRRLGRRWLAHFRKFPIDQDLRNNCQKS
Core with dehydrations:
LRRLGRRWLAHFRKFPIDQDLRNNCysQKDha

#### antiSMASH-DB 4.0 matches for allorf_393272_393412

100.0%
NZ_JADEWH010000004.1:
Lanthipeptides: allorf_393272_393412_lanthipeptide
1
LRRLGRRWLAHFRKFPIDQDLRNNCQKS
28
LRRLGRRWLAHFRKFPIDQDLRNNCQKS
1
LRRLGRRWLAHFRKFPIDQDLRNNCQKS
28
24.3%
NZ_QNRN01000010.1:
Lanthipeptides: DET63_RS17575_lanthipeptide
11
HFRKFPIDQDLRNNCQKS
28
H +FP D DLR +C K
13
HETQFPGD-DLRKDCPKE
29
21.4%
NZ_LN868937.1:
Lanthipeptides: BN2144_RS20095_lanthipeptide
7
RWLAHFRKFPIDQDLRNNCQK
27
+W F + NNC K
3
KWYTIFTTLIGTSTISNNCGK
23

#### 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:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.06 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.08 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 24.40 out of 27.78
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.11 out of 23.05
Confidence: medium
Additional weak hits (6):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.62 out of 21.55
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.73 out of 30.25
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.16 out of 30.25
Confidence: weak
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.18 out of 29.72
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.73 out of 39.62
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
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.

IQ233_RS10005 - Class II
  Cleavage pHMM score: -1.80
  RODEO score: 0
  Monoisotopic mass: 3010.4 Da
  Molecular weight: 3012.5 Da
  Number of bridges: 5
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3030.5 Da N = 1
    3048.5 Da N = 2
allorf_384206_384364 - Class II
  Cleavage pHMM score: -2.50
  RODEO score: 0
  Monoisotopic mass: 4858.5 Da
  Molecular weight: 4861.5 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4879.5 Da N = 1
    4897.6 Da N = 2
    4915.6 Da N = 3
    4933.6 Da N = 4
    4951.6 Da N = 5
    4969.6 Da N = 6
allorf_393272_393412 - Class II
  Cleavage pHMM score: -7.20
  RODEO score: 0
  Monoisotopic mass: 3504.9 Da
  Molecular weight: 3507.0 Da
  Number of bridges: 1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MogR | Repressor of flagellar motility genes

NZ_JADEWH010000005.1 - Region 1 - terpene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 226,796 - 247,728 nt. (total: 20,933 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 oxidoreductase
IQ233_RS11000: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

IQ233_RS11040: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Transferases: methyltransferase
IQ233_RS11025: methyltransferase

smcogs
  SMCOG1089: methyltransferase

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

Reference | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000645.3 |  | 0.45 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0001864.3 |  | 0.42 | ribosomal | listeriocytocin | Listeria monocytogenes SLCC2540
BGC0000646.5 |  | 0.42 | terpene | β-carotein | uncultured bacterium
BGC0000664.5 |  | 0.40 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000640.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000641.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000642.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000639.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000643.3 |  | 0.40 | terpene | carotenoid | Brevundimonas vesicularis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000656.5 |  | 0.47 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000645.3 |  | 0.45 | terpene | carotenoid | Halobacillus halophilus DSM 2266
BGC0001864.3 |  | 0.42 | ribosomal | listeriocytocin | Listeria monocytogenes SLCC2540
BGC0000646.5 |  | 0.42 | terpene | β-carotein | uncultured bacterium
BGC0000664.5 |  | 0.40 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000640.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000641.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000642.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC413
BGC0000639.3 |  | 0.40 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0000643.3 |  | 0.40 | terpene | carotenoid | Brevundimonas vesicularis

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

No significant matches found.

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
triterpene |  | squalene | C30 | acyclic | none
triterpene | C30 carotenoid | diapophytoene | C30 | acyclic | none
triterpene |  | PSPP | C30 | acyclic | PP
tetraterpene | C40 carotenoid | phytoene | C40 | acyclic | none
triterpene |  | hydroxysqualene | C30 | acyclic | OH

Genes with terpene domains:
IQ233_RS11045: PT_phytoene_like
Domain 1 (18 - 308): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.22 out of 27.78
Confidence: medium
Additional weak hits (1):
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.85 out of 35.63
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
PP | Diphosphate
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ToxT | Regulator of MSHA biosynthesis

NZ_JADEWH010000007.1 - Region 1 - hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 45,128 - 92,123 nt. (total: 46,996 nt) Show pHMM detection rules used
hglE-KS: (hglE or hglD)

#### 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
IQ233_RS12975: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: acylase
IQ233_RS12925: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Ligases: ligase synthase
IQ233_RS12915: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IQ233_RS12920: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IQ233_RS12940: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | hglE-KS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000869.5 |  | 0.62 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002164.2 |  | 0.61 | NRPS | peramine | Epichloe festucae
BGC0001268.4 |  | 0.60 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001244.3 |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001257.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000107.3 |  | 0.59 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002154.2 |  | 0.59 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001276.3 |  | 0.59 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.59 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000869.5 |  | 0.62 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002164.2 |  | 0.61 | NRPS | peramine | Epichloe festucae
BGC0001268.4 |  | 0.60 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0001244.3 |  | 0.60 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001257.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0000107.3 |  | 0.59 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002154.2 |  | 0.59 | PKS | 1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene | Pyricularia oryzae 70-15
BGC0001276.3 |  | 0.59 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.59 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis

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:
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.83 out of 27.78
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 16.22 out of 18.16
Confidence: strong
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.65 out of 18.46
Confidence: strong
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.20 out of 23.79
Confidence: medium
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26
Confidence: medium
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 27.37 out of 30.98
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 23.46 out of 29.25
Confidence: medium
Additional weak hits (3):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.78 out of 30.98
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 45127 - 92123:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
IQ233_RS12915: mal
PKS_AT (625..924): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  inactive: 70.8%
  2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 94.5
  inactive: 44.2
  Methoxymalonyl-CoA: 32.2
  Methylmalonyl-CoA: 20.3
  CHC-CoA: 17.6
  Isobutyryl-CoA: 15.3
  Propionyl-CoA: 14.2
  fatty_acid: 10.2
  trans-1,2-CPDA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

IQ233_RS12920: mxmal
PKS_AT (536..857): mxmal
ATSignature: (unknown)
No matches above 50%
minowa: Methoxymalonyl-CoA

Prediction, score:
  Methoxymalonyl-CoA: 27.2
  Isobutyryl-CoA: 20.3
  inactive: 10.5
  Methylmalonyl-CoA: 10.1
  trans-1,2-CPDA: 0.0
  fatty_acid: 0.0
  Propionyl-CoA: 0.0
  Malonyl-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
--- | ---
AbrC3 | Antibiotic production activator
AfsR | Pleiotropic regulatory for antibiotic production
CRP | Cyclic AMP receptor protein
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
IolR | Regulator of the inositol catabolism
NuR | Nickel-responsive regulator
RpoN | Regulator of nitrogen assimilation and virulence
SypG | Regulator of biofilm formation and host colonization

NZ_JADEWH010000017.1 - Region 1 - RRE-containing
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 73,476 - 93,925 nt. (total: 20,450 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
IQ233_RS21025: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: dehydratase
IQ233_RS21065: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

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

Reference | RRE-containing | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000737.3 |  | 0.53 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000757.3 |  | 0.52 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000756.3 |  | 0.51 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000741.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000744.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000745.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000739.3 |  | 0.47 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000740.3 |  | 0.46 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000746.3 |  | 0.46 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000747.3 |  | 0.46 | saccharide | capsular polysaccharide | Streptococcus agalactiae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000737.3 |  | 0.53 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000757.3 |  | 0.52 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000756.3 |  | 0.51 | saccharide | capsular polysaccharide | Avibacterium paragallinarum
BGC0000741.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000744.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000745.3 |  | 0.47 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000739.3 |  | 0.47 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0000740.3 |  | 0.46 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000746.3 |  | 0.46 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000747.3 |  | 0.46 | saccharide | capsular polysaccharide | Streptococcus agalactiae

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (3):
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.71 out of 28.14
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.83 out of 29.51
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.88 out of 20.01
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (73475...93925)
IQ233_RS21035
  RRE type: Stand_Alone_Lasso_RRE
  Location: 9 - 90
  Score: 57.6

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_JADEWH010000019.1 - Region 1 - NRP-metallophore,NRPS,NRPS-like,T1PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 7,815 - 98,582 nt. (total: 90,768 nt) Show pHMM detection rules used
Region on contig edge.
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
IQ233_RS21865: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

IQ233_RS21890: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: aminotransferase
IQ233_RS21850: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

Lyases: dehydratase
IQ233_RS21710: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Isomerases: isomerase
IQ233_RS21745: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase synthase
IQ233_RS21715: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IQ233_RS21725: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

IQ233_RS21730: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

IQ233_RS21735: 3-oxoacyl-(acyl carrier protein) synthase III

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

IQ233_RS21750: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IQ233_RS21855: 3-oxoacyl-(acyl carrier protein) synthase III

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

IQ233_RS21860: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IQ233_RS21885: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

IQ233_RS21905: Beta-ketoacyl synthase

smcogs
  SMCOG1093: Beta-ketoacyl synthase

IQ233_RS21910: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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

Reference | NRP-metallophore | NRPS | T1PKS | NRPS-like | T1PKS | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
BGC0002597.2 |  |  |  |  |  |  | 2.74 | NRPS, PKS | Nocuolactylate A, Nocuolactylate B, Nocuolactylate C | Nodularia sp. LEGE 06071
BGC0001704.3 |  |  |  |  |  |  | 2.19 | other (other) | nocuolin A | Nodularia sp. HBU26
BGC0001164.3 |  |  |  |  |  |  | 2.15 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001160.5 |  |  |  |  |  |  | 2.15 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001273.3 |  |  |  |  |  |  | 1.83 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  |  |  |  |  | 1.81 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001244.3 |  |  |  |  |  |  | 1.80 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0002191.2 |  |  |  |  |  |  | 1.79 | PKS | prolipyrone B, gibepyrone D | Fusarium graminearum PH-1
BGC0001275.3 |  |  |  |  |  |  | 1.78 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001284.4 |  |  |  |  |  |  | 1.75 | PKS | alternariol | Parastagonospora nodorum SN15

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002597.2 |  | 0.96 | NRPS, PKS | Nocuolactylate A, Nocuolactylate B, Nocuolactylate C | Nodularia sp. LEGE 06071
BGC0001704.3 |  | 0.89 | other (other) | nocuolin A | Nodularia sp. HBU26
BGC0001160.5 |  | 0.74 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001164.3 |  | 0.74 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002135.2 |  | 0.72 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0000342.4 |  | 0.72 | NRPS | enniatin | Fusarium equiseti
BGC0001132.4 |  | 0.70 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001135.5 |  | 0.70 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001128.4 |  | 0.70 | NRPS | gamexpeptide 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:
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.95 out of 27.78
Confidence: strong
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57
Confidence: strong
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.13 out of 27.78
Confidence: medium
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.93 out of 30.25
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.94 out of 27.78
Confidence: medium
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.38 out of 32.93
Confidence: medium
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46
Confidence: medium
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.27 out of 24.78
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.95 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.05 out of 26.06
Confidence: medium
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05
Confidence: medium
Additional weak hits (8):
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.03 out of 26.12
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.12 out of 32.74
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.10 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.88 out of 30.98
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.51 out of 30.98
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.19 out of 29.65
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.69 out of 36.53
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.83 out of 29.25
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 7814 - 98582:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X) + (ohmal) + (Cys) + (NH2) + (mal) + (fatty_acid)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 7814 - 64355:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 46935 - 89029:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2) + (mal) + (fatty_acid)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 58736 - 98582:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (NH2) + (mal) + (fatty_acid)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
IQ233_RS21715: X
AMP-binding (510..918): X
nrpys: (unknown)

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    YAAAFDAAAEEPDLILGGEINTYGPTEATIVTTT
  Nearest Stachelhaus code(s):
    Lys DAEDIGTVVK (74% 8Å match)
  Stachelhaus code match:
    90% (moderate)

IQ233_RS21725: mal
PKS_AT (521..810): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 87.5%
  inactive: 83.3%
  Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 146.1
  inactive: 99.9
  Methoxymalonyl-CoA: 64.8
  Methylmalonyl-CoA: 58.6
  Propionyl-CoA: 49.2
  Ethylmalonyl-CoA: 30.4
  Isobutyryl-CoA: 27.9
  2-Methylbutyryl-CoA: 25.3
  CHC-CoA: 23.2
  trans-1,2-CPDA: 15.4
  Benzoyl-CoA: 15.2
  Acetyl-CoA: 14.0
  3-Methylbutyryl-CoA: 9.0
  fatty_acid: 0.0

IQ233_RS21730: Cys
Search NORINE for peptide: strict or relaxed
AMP-binding (537..938): 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:
    VQTSHDLSVYDGNSILGGDLSIGGPTETTVWNIG
  Nearest Stachelhaus code(s):
    Cys DLYNIGIVWK (88% 8Å match)
  Stachelhaus code match:
    100% (strong)

IQ233_RS21750: X
AMP-binding (23..414): X
nrpys: Val, Leu, Ile, Abu, Ival

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

Stachelhaus prediction details:
  Stachelhaus sequence:
    CQYAFAYGLGSFFGVSAAECEGIGTTEFLHIFLS
  Nearest Stachelhaus code(s):
    pNH2-Bz AYNFIAGSTK (53% 8Å match)
    diOH-Bz AANFVSGAIK (29% 8Å match)
  Stachelhaus code match:
    60% (weak)

IQ233_RS21860: NH2
CAL_domain (178..496): NH2
minowa: NH2

Prediction, score:
  NH2: 153.7
  Acetyl-CoA: 63.6
  fatty_acid: 13.0
  shikimic_acid: 0.0
  AHBA: 0.0

IQ233_RS21885: NH2
CAL_domain (48..506): NH2
minowa: NH2

Prediction, score:
  NH2: 25.5
  AHBA: 17.5
  fatty_acid: 16.9
  shikimic_acid: 8.8
  Acetyl-CoA: 1.6

IQ233_RS21905: mal
PKS_AT (532..764): mal
ATSignature: Malonyl-CoA, inactive

Top 3 matches:
  Malonyl-CoA: 70.8%
  inactive: 70.8%

minowa: inactive

Prediction, score:
  inactive: 99.1
  Malonyl-CoA: 87.5
  Methylmalonyl-CoA: 22.5
  Isobutyryl-CoA: 22.2
  Methoxymalonyl-CoA: 22.1
  Propionyl-CoA: 16.3
  Benzoyl-CoA: 13.1
  Acetyl-CoA: 13.1
  trans-1,2-CPDA: 13.0
  2-Methylbutyryl-CoA: 10.8
  fatty_acid: 0.0
  Ethylmalonyl-CoA: 0.0
  CHC-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0

IQ233_RS21910: fatty_acid
CAL_domain (934..1265): fatty_acid
minowa: fatty_acid

Prediction, score:
  fatty_acid: 33.7
  shikimic_acid: 0.0
  NH2: 0.0
  Acetyl-CoA: 0.0
  AHBA: 0.0

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

Regulator | Description
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
ColR | Phenol-responsive regulator
LexA variant 2 | Repressor of DNA damage response
LexA variant 3 | Repressor of DNA damage response
MogR | Repressor of flagellar motility genes
RpoN | Regulator of nitrogen assimilation and virulence
ToxT | Regulator of MSHA biosynthesis

NZ_JADEWH010000020.1 - 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: 23,351 - 44,280 nt. (total: 20,930 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: synthetase
IQ233_RS22110: 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 |  | 0.48 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.45 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000640.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000641.3 |  | 0.35 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.34 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0001859.4 |  | 0.32 | other (phosphonate) | fosfomycin | Pseudomonas syringae
BGC0001605.3 |  | 0.32 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000678.5 |  | 0.32 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002397.2 |  | 0.48 | terpene | astallatene | Arabidopsis thaliana
BGC0002400.2 |  | 0.45 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0002398.2 |  | 0.39 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000640.3 |  | 0.37 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0002309.2 |  | 0.36 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000641.3 |  | 0.35 | terpene | carotenoid | Enterobacteriaceae bacterium DC416
BGC0000639.3 |  | 0.34 | terpene | carotenoid | Enterobacteriaceae bacterium DC260
BGC0001859.4 |  | 0.32 | other (phosphonate) | fosfomycin | Pseudomonas syringae
BGC0001605.3 |  | 0.32 | terpene | gibberellin | Sinorhizobium fredii NGR234
BGC0000678.5 |  | 0.32 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893

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

No significant matches found.

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

No significant matches found.

Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:
No product predictions
Genes with terpene domains:
IQ233_RS22110: PT_FPPS_like
Domain 1 (44 - 309): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: Farnesyl diphosphate synthase, bacterial or Geranylgeranyl diphosphate synthase or geranylfarnesyl diphosphate synthase, bacterial
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AfsR
Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05
Confidence: medium
Additional weak hits (4):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.15 out of 30.22
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.60 out of 30.97
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.32 out of 31.73
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.53 out of 32.74
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
--- | ---
AfsR | Pleiotropic regulatory for antibiotic production

NZ_JADEWH010000021.1 - Region 1 - T1PKS,hglE-KS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 20,860 - 72,382 nt. (total: 51,523 nt) Show pHMM detection rules used
Region on contig edge.
hglE-KS: (hglE or hglD)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
IQ233_RS22480: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

IQ233_RS22510: oxidoreductase

smcogs
  SMCOG1161: oxidoreductase

Transferases: PPTase acylase glycosyltransferase
IQ233_RS22405: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

IQ233_RS22470: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

IQ233_RS22485: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Lyases: dehydratase
IQ233_RS22430: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
IQ233_RS22455: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

IQ233_RS22465: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

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

Reference | hglE-KS | T1PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000869.5 |  |  | 1.18 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001276.3 |  |  | 0.57 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  | 0.57 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  | 0.57 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001284.4 |  |  | 0.56 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002648.2 |  |  | 0.54 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  |  | 0.54 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0000863.3 |  |  | 0.53 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0002276.2 |  |  | 0.53 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001257.3 |  |  | 0.52 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000869.5 |  | 0.84 | other (other) | heterocyst glycolipids | Nostoc sp. 'Peltigera membranacea cyanobiont'
BGC0001276.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.62 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.62 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001284.4 |  | 0.61 | PKS | alternariol | Parastagonospora nodorum SN15
BGC0002648.2 |  | 0.60 | PKS | eicosapentaenoic acid | Shewanella sp. N2AIL
BGC0000861.5 |  | 0.60 | other (other) | eicosapentaenoic acid | Shewanella sp. BR-2
BGC0000863.3 |  | 0.60 | other (other) | eicosapentaenoic acid | Pseudoalteromonas sp. DS-12
BGC0002276.2 |  | 0.60 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0001257.3 |  | 0.59 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245

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: 24.83 out of 26.06
Confidence: strong
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.15 out of 26.06
Confidence: medium
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.40 out of 26.06
Confidence: medium
Additional weak hits (3):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.98 out of 31.73
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.13 out of 20.01
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.09 out of 32.74
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 20859 - 72382:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (mal)

Direct lookup in NORINE database: strict or relaxed
Link to NORINE database query form
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
IQ233_RS22455: mal
PKS_AT (626..924): mal
ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 100.1
  Methoxymalonyl-CoA: 41.8
  inactive: 36.5
  Methylmalonyl-CoA: 29.8
  Propionyl-CoA: 16.1
  fatty_acid: 14.8
  CHC-CoA: 13.0
  Isobutyryl-CoA: 12.3
  trans-1,2-CPDA: 0.0
  Ethylmalonyl-CoA: 0.0
  Benzoyl-CoA: 0.0
  Acetyl-CoA: 0.0
  3-Methylbutyryl-CoA: 0.0
  2-Methylbutyryl-CoA: 0.0

IQ233_RS22465: pk
PKS_AT (1114..1350): 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
--- | ---
MogR | Repressor of flagellar motility genes

NZ_JADEWH010000024.1 - Region 1 - lanthipeptide-class-v
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: 21,438 - 50,094 nt. (total: 28,657 nt) Show pHMM detection rules used
Region on contig edge.
lanthipeptide-class-v: (APH and HopA1)

#### 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
Transferases: glycosyltransferase
IQ233_RS23185: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: hydrolase
IQ233_RS23190: HAD-superfamily hydrolase, subfamily IA, variant

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

Isomerases: isomerase racemase
IQ233_RS23200: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

IQ233_RS23210: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase
IQ233_RS23215: 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 | lanthipeptide-class-v | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000913.3 |  | 0.39 | other (other) | MK-8 | Enterobacter cloacae
BGC0000649.3 |  | 0.39 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002439.3 |  | 0.38 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0001521.3 |  | 0.38 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0002473.3 |  | 0.38 | NRPS | propanochelin, butanochelin, pentanochelin | Acinetobacter bouvetii DSM 14964 = CIP 107468
BGC0000871.4 |  | 0.38 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
BGC0000352.5 |  | 0.35 | NRPS | fimsbactin A | Acinetobacter sp. ADP1
BGC0000921.5 |  | 0.34 | NRPS, PKS, other (shikimate-derived) | promysalin | Pseudomonas putida
BGC0001185.5 |  | 0.34 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0000309.5 |  | 0.34 | NRPS | bacillibactin | Bacillus subtilis subsp. subtilis str. 168

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000913.3 |  | 0.39 | other (other) | MK-8 | Enterobacter cloacae
BGC0000649.3 |  | 0.39 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0002439.3 |  | 0.38 | other (other) | diastaphenazine, izumiphenazine C | Streptomyces diastaticus
BGC0001521.3 |  | 0.38 | NRPS | auriculamide | Herpetosiphon aurantiacus DSM 785
BGC0002473.3 |  | 0.38 | NRPS | propanochelin, butanochelin, pentanochelin | Acinetobacter bouvetii DSM 14964 = CIP 107468
BGC0000871.4 |  | 0.38 | other (nucleoside) | VEPE, AEPE, TG-1 | Myxococcus xanthus DK 1622
BGC0000352.5 |  | 0.35 | NRPS | fimsbactin A | Acinetobacter sp. ADP1
BGC0000921.5 |  | 0.34 | NRPS, PKS, other (shikimate-derived) | promysalin | Pseudomonas putida
BGC0001185.5 |  | 0.34 | NRPS | bacillibactin | Bacillus velezensis FZB42
BGC0000309.5 |  | 0.34 | NRPS | bacillibactin | Bacillus subtilis subsp. subtilis str. 168

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

No significant matches found.

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

No significant matches found.

Lanthipeptide predictions
Shows the possible core peptides for each biosynthetic enzyme.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
Lanthipeptides - No core peptides found.
Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.37 out of 26.06
Confidence: medium
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.86 out of 27.78
Confidence: medium
Additional weak hits (2):
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 28.31 out of 39.62
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.16 out of 29.38
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.
No core peptides found.
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CodY | Regulator of stationary phase and virulence in Gram-positive bacteria
MogR | Repressor of flagellar motility genes