Select genomic region:
Overview
1.1
1.2
3.1
8.1
23.1
34.1
66.1

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

NZ_PSVY01000001.1 (Rathayibacter sp. AY1D1)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | lanthipeptide-class-iii | 20,364 | 42,865 |
Region 1.2 | terpene-precursor | 84,788 | 105,888 |  |

NZ_PSVY01000011.1 (Rathayibacter sp. AY1D1)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | T3PKS | 6,600 | 47,715 |  |

NZ_PSVY01000016.1 (Rathayibacter sp. AY1D1)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 8.1 | lanthipeptide-class-v | 45,390 | 68,218 |

NZ_PSVY01000003.1 (Rathayibacter sp. AY1D1)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 23.1 | NAPAA | 17,116 | 51,054 | High | ε-Poly-L-lysine | NRPS:Type I

NZ_PSVY01000004.1 (Rathayibacter sp. AY1D1)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 34.1 | terpene | 128,856 | 153,063 | Low | carotenoid | terpene

NZ_PSVY01000008.1 (Rathayibacter sp. AY1D1)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 66.1 | RRE-containing | 54,398 | 74,706 |

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | lanthipeptide-class-iii | 20,364 | 42,865 |
Region 1.2 | terpene-precursor | 84,788 | 105,888 |  |
Region 3.1 | T3PKS | 6,600 | 47,715 |  |
Region 8.1 | lanthipeptide-class-v | 45,390 | 68,218 |
Region 23.1 | NAPAA | 17,116 | 51,054 | High | ε-Poly-L-lysine | NRPS:Type I
Region 34.1 | terpene | 128,856 | 153,063 | Low | carotenoid | terpene
Region 66.1 | RRE-containing | 54,398 | 74,706 |

No secondary metabolite regions were found in these records:
  NZ_PSVY01000010.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000012.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000013.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000014.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000015.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000017.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000018.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000019.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000002.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000020.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000021.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000022.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000023.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000024.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000025.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000026.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000027.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000028.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000029.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000030.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000031.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000032.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000033.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000034.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000035.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000036.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000037.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000038.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000039.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000040.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000041.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000042.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000043.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000044.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000045.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000046.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000047.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000048.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000049.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000005.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000050.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000051.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000052.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000053.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000054.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000055.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000056.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000057.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000058.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000059.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000006.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000060.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000061.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000062.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000063.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000064.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000065.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000066.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000067.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000007.1 (Rathayibacter sp. AY1D1)
  NZ_PSVY01000009.1 (Rathayibacter sp. AY1D1)

Compact view
NZ_PSVY01000001.1 - Region 1 - lanthipeptide-class-iii
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 20,364 - 42,865 nt. (total: 22,502 nt) Show pHMM detection rules used
lanthipeptide-class-iii: (micKC and not PKS_KS)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Translocases: permease
C5C56_RS00160: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | lanthipeptide-class-iii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000551.5 |  | 0.49 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.49 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001226.4 |  | 0.49 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000496.5 |  | 0.49 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000519.4 |  | 0.49 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002111.3 |  | 0.48 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000501.3 |  | 0.48 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000553.3 |  | 0.47 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000518.3 |  | 0.45 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002700.2 |  | 0.51 | ribosomal | bacinapeptin | Bacillus nakamurai
BGC0000551.5 |  | 0.49 | ribosomal | SapB | Streptomyces coelicolor A3(2)
BGC0000513.3 |  | 0.49 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0001226.4 |  | 0.49 | ribosomal | streptocollin | Streptomyces collinus Tu 365
BGC0000496.5 |  | 0.49 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000519.4 |  | 0.49 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002111.3 |  | 0.48 | ribosomal | andalusicin A, andalusicin B | Bacillus thuringiensis serovar andalousiensis NRRL B-23139
BGC0000501.3 |  | 0.48 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000553.3 |  | 0.47 | ribosomal | SRO15-2212 | Streptomyces filamentosus NRRL 15998
BGC0000518.3 |  | 0.45 | ribosomal | informatipeptin | Streptomyces viridochromogenes DSM 40736

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

No significant matches found.

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

No significant matches found.

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 C5C56_RS00130

C5C56_RS18210
Leader:
MNRILDFQTLEGEADAHDAAR
Core:
V S T F S V I S P C P G W P S S I T W G N C
Core with dehydrations:
V Dha Dhb F Dha V I Dha P Cys P G W P Dha Dha I Dhb W G N Cys

#### antiSMASH-DB 4.0 matches for C5C56_RS18210

100.0%
NZ_PSTN01000012.1 and 4 others:
NZ_PSVB01000011.1 Lanthipeptides: C5C35_RS17250_lanthipeptide NZ_PSVH01000006.1 Lanthipeptides: C5C41_RS17635_lanthipeptide NZ_PSVQ01000018.1 Lanthipeptides: C5C50_RS17290_lanthipeptide NZ_PSVY01000001.1 Lanthipeptides: C5C56_RS18210_lanthipeptide
Lanthipeptides: C5B92_RS17685_lanthipeptide
1
V S T F S V I S P C P G W P S S I T W G N C
22
V S T F S V I S P C P G W P S S I T W G N C
1
V S T F S V I S P C P G W P S S I T W G N C
22
95.5%
NZ_PSVM01000028.1:
Lanthipeptides: C5C86_RS17755_lanthipeptide
1
V S T F S V I S P C P G W P S S I T W G N C
22
V S T F S V I S P C P W P S S I T W G N C
1
V S T F S V I S P C P D W P S S I T W G N C
22
90.9%
NZ_PSWL01000029.1 and 1 other:
NZ_PSWM01000007.1 Lanthipeptides: C5D44_RS17985_lanthipeptide
Lanthipeptides: C5D08_RS17095_lanthipeptide
1
V S T F S V I S P C P G W P S S I T W G N C
22
V S T F S++S P C P G W P S S I T W G N C
1
V S T F S I V S P C P G W P S S I T W G N C
22
with 4 more sequence matches
77.3%
NZ_CP004350.1 and 1 other:
NZ_CP025330.1 Lanthipeptides: allorf_3183636_3183779_lanthipeptide
Lanthipeptides: allorf_2515666_2515809_lanthipeptide
1
V S T F S V I S P C P G W P S S I T W G N C
22
V S T S V I P C P G W P S++T+G N C
1
V S T V S V I P P C P G W P S A V T F G N C
22
66.7%
NZ_CP007153.1:
Lanthipeptides: allorf_02389419_02389625_lanthipeptide
1
V S T F S V I S P C P G W P S S I T W G N C
22
V S T S+ +P C P G W P S+ T W G N C
3
V S T L S I E A P C P G W P S T F T W G N C
24
59.1%
NZ_RZJP01000001.1 and 2 others:
NZ_RZUG01000019.1 Lanthipeptides: EMO92_RS12090_lanthipeptide NZ_RZUH01000002.1 Lanthipeptides: EMO91_RS13855_lanthipeptide
Lanthipeptides: EMB92_RS11810_lanthipeptide
1
V S T F S V I S P C P G W P S S I T W G N C
22
+S T F S P C P G P S++T+ N C
1
I S T F S F N G P C P G L P S T L T Y S N C
22
31.8%
NZ_MSKU01000037.1:
Lanthipeptides: allorf_43371_43508_lanthipeptide
10
C P G W P S S I T W G N C
22
C G W P S++T C
9
C W G W P S A V T T R Y C
21

#### 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:
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26
Confidence: medium
Additional weak hits (7):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.27 out of 20.01
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.83 out of 36.54
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.69 out of 30.97
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.34 out of 27.78
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.22 out of 20.01
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.35 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 23.04 out of 29.65
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.

C5C56_RS18210 - Class III
  Cleavage pHMM score: 4.60
  RODEO score: 0
  Monoisotopic mass: 2198.1 Da
  Molecular weight: 2199.5 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    2217.5 Da N = 1
    2235.5 Da N = 2
    2253.5 Da N = 3
    2271.6 Da N = 4
    2289.6 Da N = 5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
CRP | Cyclic AMP receptor protein

NZ_PSVY01000001.1 - Region 2 - 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: 84,788 - 105,888 nt. (total: 21,101 nt) Show pHMM detection rules used
terpene-precursor: (PT_FPPS_like and not PT_HPP)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: acyltransferase
C5C56_RS00425: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Hydrolases: deformylase
C5C56_RS00410: peptide deformylase

smcogs
  SMCOG1275: peptide deformylase

Ligases: ligase synthetase
C5C56_RS00415: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

C5C56_RS00445: 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
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000649.3 |  | 0.40 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001456.3 |  | 0.39 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001483.4 |  | 0.38 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus
BGC0000664.5 |  | 0.38 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000678.5 |  | 0.38 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000633.3 |  | 0.37 | terpene | carotenoid | Streptomyces avermitilis
BGC0002348.2 |  | 0.37 | NRPS | aspulvinone E | Aspergillus terreus NIH2624

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000677.5 |  | 0.42 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0000649.3 |  | 0.40 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001910.4 |  | 0.39 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0001456.3 |  | 0.39 | terpene | isorenieratene | Streptomyces argillaceus
BGC0001483.4 |  | 0.38 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001911.3 |  | 0.38 | terpene | raimonol | Streptomyces anulatus
BGC0000664.5 |  | 0.38 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000678.5 |  | 0.38 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000633.3 |  | 0.37 | terpene | carotenoid | Streptomyces avermitilis
BGC0002348.2 |  | 0.37 | NRPS | aspulvinone E | Aspergillus terreus NIH2624

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
C5C56_RS00445: PT_FPPS_like
Domain 1 (45 - 365): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (6):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22
Confidence: weak
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.68 out of 30.22
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.06 out of 24.78
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.66 out of 26.85
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.28 out of 28.19
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.65 out of 28.19
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_PSVY01000011.1 - Region 1 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 6,600 - 47,715 nt. (total: 41,116 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
C5C56_RS09225: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

C5C56_RS09335: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: esterase hydrolase
C5C56_RS09365: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

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

C5C56_RS09420: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: dehydratase
C5C56_RS09350: NAD-dependent epimerase/dehydratase

smcogs
  SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase
C5C56_RS09330: chalcone and stilbene synthase domain protein

smcogs
  SMCOG1024: chalcone and stilbene synthase domain protein

Translocases: permease
C5C56_RS09280: phenylalanine-specific permease

smcogs
  SMCOG1038: phenylalanine-specific permease

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

Reference | T3PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.53 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001962.3 |  | 0.52 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0002332.2 |  | 0.50 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0001928.2 |  | 0.48 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001974.2 |  | 0.46 | other (other) | kainic acid, Kainic acid lactone | Digenea simplex
BGC0002404.2 |  | 0.45 | other (other) | falcarindiol | Solanum lycopersicum
BGC0001831.3 |  | 0.45 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001987.2 |  | 0.43 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000671.3 |  | 0.43 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0002362.3 |  | 0.43 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000282.3 |  | 0.53 | PKS | 2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001962.3 |  | 0.52 | PKS | hierridin B, hierridin C | Cyanobium sp. LEGE 06113
BGC0002332.2 |  | 0.50 | PKS | 4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A | Candidatus Entotheonella sp.
BGC0001928.2 |  | 0.48 | other (other) | (2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid | Streptomyces sp. MA37
BGC0001974.2 |  | 0.46 | other (other) | kainic acid, Kainic acid lactone | Digenea simplex
BGC0002404.2 |  | 0.45 | other (other) | falcarindiol | Solanum lycopersicum
BGC0001831.3 |  | 0.45 | PKS | alkylpyrone-407, alkylpyrone-393 | Myxococcus xanthus DK 1622
BGC0001987.2 |  | 0.43 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0000671.3 |  | 0.43 | terpene | momilactone B | Oryza sativa Japonica Group
BGC0002362.3 |  | 0.43 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica

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:
NtrC
Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.87 out of 29.72
Confidence: medium
Additional weak hits (6):
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.93 out of 19.26
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.41 out of 21.55
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.77 out of 36.54
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.00 out of 31.73
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.52 out of 28.19
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.51 out of 24.78
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C

NZ_PSVY01000016.1 - 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: 45,390 - 68,218 nt. (total: 22,829 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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
Lanthipeptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: oxidoreductase
C5C56_RS11310: FAD dependent oxidoreductase

smcogs
  SMCOG1103: FAD dependent oxidoreductase

Transferases: phosphotransferase
C5C56_RS11335: Glucose-specific phosphotransferase enzyme IIA

smcogs
  SMCOG1145: Glucose-specific phosphotransferase enzyme IIA

Isomerases: mutase
C5C56_RS11350: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

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

Reference | lanthipeptide-class-v | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002303.3 |  | 0.44 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0000590.5 |  | 0.40 | ribosomal | microcin N | Escherichia coli
BGC0000626.3 |  | 0.40 | ribosomal | thuricin | Bacillus thuringiensis
BGC0000541.5 |  | 0.40 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002110.3 |  | 0.39 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908
BGC0000523.3 |  | 0.39 | ribosomal | lactocin S | Lactobacillus sakei
BGC0002323.2 |  | 0.39 | ribosomal | nisin J | Staphylococcus capitis
BGC0000582.4 |  | 0.39 | ribosomal | cypemycin | Streptomyces sp. OH-4156
BGC0000555.3 |  | 0.39 | ribosomal | staphylococcin C55 α, staphylococcin C55 β | Staphylococcus aureus
BGC0001485.4 |  | 0.39 | other (other) | chuangxinmycin | Actinoplanes tsinanensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002303.3 |  | 0.44 | ribosomal | pristinin A3 | Streptomyces pristinaespiralis
BGC0000590.5 |  | 0.40 | ribosomal | microcin N | Escherichia coli
BGC0000626.3 |  | 0.40 | ribosomal | thuricin | Bacillus thuringiensis
BGC0000541.5 |  | 0.40 | ribosomal | paenicidin A | Paenibacillus polymyxa
BGC0002110.3 |  | 0.39 | ribosomal | birimositide | Streptomyces rimosus subsp. rimosus WC-3908
BGC0000523.3 |  | 0.39 | ribosomal | lactocin S | Lactobacillus sakei
BGC0002323.2 |  | 0.39 | ribosomal | nisin J | Staphylococcus capitis
BGC0000582.4 |  | 0.39 | ribosomal | cypemycin | Streptomyces sp. OH-4156
BGC0000555.3 |  | 0.39 | ribosomal | staphylococcin C55 α, staphylococcin C55 β | Staphylococcus aureus
BGC0001485.4 |  | 0.39 | other (other) | chuangxinmycin | Actinoplanes tsinanensis

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.
No hits above weak threshold.
Weak hits (5):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.68 out of 29.25
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.65 out of 29.25
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.55 out of 32.93
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.28 out of 28.19
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
--- | ---

NZ_PSVY01000003.1 - Region 1 - NAPAA
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: 17,116 - 51,054 nt. (total: 33,939 nt) Show pHMM detection rules used
NAPAA: (AMP-binding and TIGR02353)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
C5C56_RS03120: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase aminotransferase
C5C56_RS03130: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

C5C56_RS03150: aminotransferase class V

smcogs
  SMCOG1139: aminotransferase class V

Ligases: ligase
C5C56_RS03140: 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 | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000357.5 |  | 0.60 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001240.4 |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0001135.5 |  | 0.61 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0000307.4 |  | 0.60 | NRPS | AbT1 | Aureobasidium pullulans
BGC0000357.5 |  | 0.60 | NRPS | cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val) | Penicillium rubens Wisconsin 54-1255
BGC0001240.4 |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0001833.4 |  | 0.59 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.59 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
Additional weak hits (8):
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 15.98 out of 29.38
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.49 out of 19.26
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.84 out of 21.55
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.89 out of 33.73
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.95 out of 35.63
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.72 out of 24.78
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.13 out of 28.19
Confidence: weak
Module view
Shows module structures for each candidate cluster in NRPS and PKS regions.
Genes are shown in predicted order, and are only present when containing at least one complete module.
A domain glossary is available here, and an explanation of the visualisation is available here.
Legend
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS products
NRPS/PKS substrates
TFBS Finder
Predicted core structure(s)
Shows estimated product structure and polymer for each candidate cluster in the region. To show the product, click on the expander or the candidate cluster feature drawn in the overview.
For candidate cluster 1, location 17115 - 51054:
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).
C5C56_RS03140: X
AMP-binding (27..417): 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:
    FAELFDASCEELSTIFGGEWNTYGPTEATVVACA
  Nearest Stachelhaus code(s):
    Lys DAEDIGTVVK (71% 8Å match)
    Gln or Tyr DAESVGTVVK (65% 8Å match)
  Stachelhaus code match:
    90% (moderate)

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

Regulator | Description
--- | ---
AbrC3 | Antibiotic production activator

NZ_PSVY01000004.1 - 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: 128,856 - 153,063 nt. (total: 24,208 nt) Show pHMM detection rules used
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

#### Legend:

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

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase
C5C56_RS04660: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

Hydrolases: hydrolase
C5C56_RS04705: beta-lactamase

smcogs
  SMCOG1053: beta-lactamase

Ligases: synthetase
C5C56_RS04665: 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 | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000644.3 |  | 0.65 | terpene | carotenoid | Dietzia sp. CQ4
BGC0000637.3 |  | 0.59 | terpene | carotenoid | Corynebacterium glutamicum
BGC0000664.5 |  | 0.53 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000650.3 |  | 0.51 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000649.3 |  | 0.49 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.49 | terpene | carotenoid | Myxococcus xanthus
BGC0002309.2 |  | 0.46 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000636.3 |  | 0.46 | terpene | carotenoid | Brevibacterium linens
BGC0000677.5 |  | 0.45 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001911.3 |  | 0.43 | terpene | raimonol | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000644.3 |  | 0.65 | terpene | carotenoid | Dietzia sp. CQ4
BGC0000637.3 |  | 0.59 | terpene | carotenoid | Corynebacterium glutamicum
BGC0000664.5 |  | 0.53 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000650.3 |  | 0.51 | terpene | carotenoid | Algoriphagus sp. KK10202C
BGC0000649.3 |  | 0.49 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.49 | terpene | carotenoid | Myxococcus xanthus
BGC0002309.2 |  | 0.46 | terpene | cattleyene | Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000636.3 |  | 0.46 | terpene | carotenoid | Brevibacterium linens
BGC0000677.5 |  | 0.45 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0001911.3 |  | 0.43 | terpene | raimonol | Streptomyces anulatus

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
tetraterpene | C40 carotenoid |  | C40 | unknown | unknown

Genes with terpene domains:
C5C56_RS04650: Lycopene_cycl
Domain 1 (1 - 92): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

C5C56_RS04655: Lycopene_cycl
Domain 1 (4 - 91): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

C5C56_RS04660: PT_phytoene_like
Domain 1 (13 - 289): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

C5C56_RS04665: PT_FPPS_like
Domain 1 (17 - 302): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47
Confidence: strong
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.33 out of 23.79
Confidence: medium
Additional weak hits (3):
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.11 out of 33.73
Confidence: weak
HipB
Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.42 out of 33.73
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.61 out of 32.93
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

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

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

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

NZ_PSVY01000008.1 - 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: 54,398 - 74,706 nt. (total: 20,309 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
TTA codons
binding site
reset view
zoom to selection
Gene details
Shows details of the most recently selected gene, including names, products, location, and other annotations.
Select a gene to view the details available for it
Gene overview
Tailoring
MIBiG comparison
KnownClusterBlast
SubClusterBlast
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: glycosyltransferase
C5C56_RS07910: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

C5C56_RS07915: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

C5C56_RS07940: sugar transferase

smcogs
  SMCOG1146: sugar transferase

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
--- | --- | --- | --- | --- | ---
BGC0000742.3 |  | 0.48 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000743.3 |  | 0.48 | saccharide | capsular polysaccharide | Streptococcus agalactiae
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
BGC0000748.3 |  | 0.46 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000741.3 |  | 0.44 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000744.3 |  | 0.44 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000745.3 |  | 0.44 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0001410.3 |  | 0.44 | saccharide | polysaccharide A | Bacteroides fragilis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000742.3 |  | 0.48 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000743.3 |  | 0.48 | saccharide | capsular polysaccharide | Streptococcus agalactiae
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
BGC0000748.3 |  | 0.46 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000741.3 |  | 0.44 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000744.3 |  | 0.44 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0000745.3 |  | 0.44 | saccharide | capsular polysaccharide | Streptococcus agalactiae
BGC0001410.3 |  | 0.44 | saccharide | polysaccharide A | Bacteroides fragilis

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 (1):
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.85 out of 28.19
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

RRE-containing protocluster (54397...74706)
C5C56_RS17800
  RRE type: Stand_Alone_Lasso_RRE
  Location: 43 - 98
  Score: 35.1

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---