Select genomic region:
Overview
1.1
1.2
3.1
5.1
8.1
10.1
16.1
18.1
20.1
22.1
23.1
26.1
26.2
30.1
34.1
34.2
34.3
36.1
56.1
56.2
81.1

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

NZ_SWMS01000001.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | NRP-metallophore,NRPS | 632,292 | 688,157 | Low | peucechelin | NRPS:Type I
Region 1.2 | lassopeptide | 770,090 | 796,724 |

NZ_SWMS01000011.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 3.1 | terpene | 25,728 | 49,239 | Low | isorenieratene | terpene

NZ_SWMS01000013.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 5.1 | HR-T2PKS | 114,241 | 156,435 |  |

NZ_SWMS01000016.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 8.1 | thioamitides | 91,965 | 113,832 |

NZ_SWMS01000018.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 10.1 | terpene | 25,412 | 47,628 | High | geosmin | terpene:Sesquiterpene

NZ_SWMS01000023.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 16.1 | triceptide | 39,495 | 63,598 |  |

NZ_SWMS01000025.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 18.1 | arylpolyene | 67,340 | 98,716 |  |

NZ_SWMS01000027.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 20.1 | lanthipeptide-class-i | 1 | 15,974 |  |

NZ_SWMS01000029.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 22.1 | redox-cofactor | 58,933 | 79,922 |  |

NZ_SWMS01000003.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 23.1 | terpene | 1 | 15,412 |  |

NZ_SWMS01000032.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 26.1 | NI-siderophore | 1 | 28,474 | Low | 5-dimethylallylindole-3-acetonitrile | other:other
Region 26.2 | ectoine | 47,283 | 57,675 | High | ectoine | other:ectoine

NZ_SWMS01000036.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 30.1 | t3nrps-iterative,T1PKS,PKS-like | 2,314 | 44,571 | Low | 4-hexadecanoyl-3-hydroxy-2-(hydroxymethyl)-2H-furan-5-one | PKS

NZ_SWMS01000004.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 34.1 | RiPP-like | 30,574 | 42,013 | Low | streptamidine | ribosomal:unmodified
Region 34.2 | terpene | 188,450 | 210,009 |  |
Region 34.3 | ranthipeptide | 221,733 | 243,216 |  |

NZ_SWMS01000041.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 36.1 | NAPAA | 1 | 23,292 | High | ε-Poly-L-lysine | NRPS:Type I

NZ_SWMS01000006.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 56.1 | terpene | 117,910 | 143,869 | Low | hopene | terpene
Region 56.2 | terpene-precursor | 190,261 | 211,295 |  |

NZ_SWMS01000009.1 (Prauserella endophytica)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 81.1 | redox-cofactor | 108,383 | 130,396 | Low | lankacidin C | NRPS:Type I+PKS

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1.1 | NRP-metallophore,NRPS | 632,292 | 688,157 | Low | peucechelin | NRPS:Type I
Region 1.2 | lassopeptide | 770,090 | 796,724 |
Region 3.1 | terpene | 25,728 | 49,239 | Low | isorenieratene | terpene
Region 5.1 | HR-T2PKS | 114,241 | 156,435 |  |
Region 8.1 | thioamitides | 91,965 | 113,832 |
Region 10.1 | terpene | 25,412 | 47,628 | High | geosmin | terpene:Sesquiterpene
Region 16.1 | triceptide | 39,495 | 63,598 |  |
Region 18.1 | arylpolyene | 67,340 | 98,716 |  |
Region 20.1 | lanthipeptide-class-i | 1 | 15,974 |  |
Region 22.1 | redox-cofactor | 58,933 | 79,922 |  |
Region 23.1 | terpene | 1 | 15,412 |  |
Region 26.1 | NI-siderophore | 1 | 28,474 | Low | 5-dimethylallylindole-3-acetonitrile | other:other
Region 26.2 | ectoine | 47,283 | 57,675 | High | ectoine | other:ectoine
Region 30.1 | t3nrps-iterative,T1PKS,PKS-like | 2,314 | 44,571 | Low | 4-hexadecanoyl-3-hydroxy-2-(hydroxymethyl)-2H-furan-5-one | PKS
Region 34.1 | RiPP-like | 30,574 | 42,013 | Low | streptamidine | ribosomal:unmodified
Region 34.2 | terpene | 188,450 | 210,009 |  |
Region 34.3 | ranthipeptide | 221,733 | 243,216 |  |
Region 36.1 | NAPAA | 1 | 23,292 | High | ε-Poly-L-lysine | NRPS:Type I
Region 56.1 | terpene | 117,910 | 143,869 | Low | hopene | terpene
Region 56.2 | terpene-precursor | 190,261 | 211,295 |  |
Region 81.1 | redox-cofactor | 108,383 | 130,396 | Low | lankacidin C | NRPS:Type I+PKS

No secondary metabolite regions were found in these records:
  NZ_SWMS01000010.1 (Prauserella endophytica)
  NZ_SWMS01000012.1 (Prauserella endophytica)
  NZ_SWMS01000014.1 (Prauserella endophytica)
  NZ_SWMS01000015.1 (Prauserella endophytica)
  NZ_SWMS01000017.1 (Prauserella endophytica)
  NZ_SWMS01000019.1 (Prauserella endophytica)
  NZ_SWMS01000002.1 (Prauserella endophytica)
  NZ_SWMS01000020.1 (Prauserella endophytica)
  NZ_SWMS01000021.1 (Prauserella endophytica)
  NZ_SWMS01000022.1 (Prauserella endophytica)
  NZ_SWMS01000024.1 (Prauserella endophytica)
  NZ_SWMS01000026.1 (Prauserella endophytica)
  NZ_SWMS01000028.1 (Prauserella endophytica)
  NZ_SWMS01000030.1 (Prauserella endophytica)
  NZ_SWMS01000031.1 (Prauserella endophytica)
  NZ_SWMS01000033.1 (Prauserella endophytica)
  NZ_SWMS01000034.1 (Prauserella endophytica)
  NZ_SWMS01000035.1 (Prauserella endophytica)
  NZ_SWMS01000037.1 (Prauserella endophytica)
  NZ_SWMS01000038.1 (Prauserella endophytica)
  NZ_SWMS01000039.1 (Prauserella endophytica)
  NZ_SWMS01000040.1 (Prauserella endophytica)
  NZ_SWMS01000042.1 (Prauserella endophytica)
  NZ_SWMS01000043.1 (Prauserella endophytica)
  NZ_SWMS01000044.1 (Prauserella endophytica)
  NZ_SWMS01000045.1 (Prauserella endophytica)
  NZ_SWMS01000046.1 (Prauserella endophytica)
  NZ_SWMS01000047.1 (Prauserella endophytica)
  NZ_SWMS01000048.1 (Prauserella endophytica)
  NZ_SWMS01000049.1 (Prauserella endophytica)
  NZ_SWMS01000005.1 (Prauserella endophytica)
  NZ_SWMS01000050.1 (Prauserella endophytica)
  NZ_SWMS01000051.1 (Prauserella endophytica)
  NZ_SWMS01000052.1 (Prauserella endophytica)
  NZ_SWMS01000053.1 (Prauserella endophytica)
  NZ_SWMS01000054.1 (Prauserella endophytica)
  NZ_SWMS01000055.1 (Prauserella endophytica)
  NZ_SWMS01000056.1 (Prauserella endophytica)
  NZ_SWMS01000057.1 (Prauserella endophytica)
  NZ_SWMS01000058.1 (Prauserella endophytica)
  NZ_SWMS01000059.1 (Prauserella endophytica)
  NZ_SWMS01000060.1 (Prauserella endophytica)
  NZ_SWMS01000061.1 (Prauserella endophytica)
  NZ_SWMS01000062.1 (Prauserella endophytica)
  NZ_SWMS01000063.1 (Prauserella endophytica)
  NZ_SWMS01000064.1 (Prauserella endophytica)
  NZ_SWMS01000065.1 (Prauserella endophytica)
  NZ_SWMS01000066.1 (Prauserella endophytica)
  NZ_SWMS01000067.1 (Prauserella endophytica)
  NZ_SWMS01000068.1 (Prauserella endophytica)
  NZ_SWMS01000069.1 (Prauserella endophytica)
  NZ_SWMS01000007.1 (Prauserella endophytica)
  NZ_SWMS01000070.1 (Prauserella endophytica)
  NZ_SWMS01000071.1 (Prauserella endophytica)
  NZ_SWMS01000072.1 (Prauserella endophytica)
  NZ_SWMS01000073.1 (Prauserella endophytica)
  NZ_SWMS01000074.1 (Prauserella endophytica)
  NZ_SWMS01000075.1 (Prauserella endophytica)
  NZ_SWMS01000076.1 (Prauserella endophytica)
  NZ_SWMS01000077.1 (Prauserella endophytica)
  NZ_SWMS01000078.1 (Prauserella endophytica)
  NZ_SWMS01000079.1 (Prauserella endophytica)
  NZ_SWMS01000008.1 (Prauserella endophytica)
  NZ_SWMS01000080.1 (Prauserella endophytica)
  NZ_SWMS01000081.1 (Prauserella endophytica)

Compact view
NZ_SWMS01000001.1 - Region 1 - NRP-metallophore,NRPS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 632,292 - 688,157 nt. (total: 55,866 nt) Show pHMM detection rules used
NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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 oxygenase
FCN18_RS03355: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs
  SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

FCN18_RS03365: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

FCN18_RS03455: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase aminotransferase formyltransferase glycosyltransferase
FCN18_RS03265: aminotransferase

smcogs
  SMCOG1019: aminotransferase

FCN18_RS03275: aminotransferase

smcogs
  SMCOG1019: aminotransferase

FCN18_RS03360: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

FCN18_RS03415: methionyl-tRNA formyltransferase

smcogs
  SMCOG1228: methionyl-tRNA formyltransferase

FCN18_RS03430: acyltransferase

smcogs
  SMCOG1141: acyltransferase

FCN18_RS03470: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Hydrolases: hydrolase peptidase
FCN18_RS03305: methionine aminopeptidase

smcogs
  SMCOG1172: methionine aminopeptidase

FCN18_RS03465: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Isomerases: racemase
FCN18_RS03300: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase
FCN18_RS03375: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

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

Reference | NRP-metallophore | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0002424.3 |  |  | 0.98 | NRPS | saccharochelin A, saccharochelin B, saccharochelin C, saccharochelin D, saccharochelin E, saccharochelin F, saccharochelin G, saccharochelin H | Saccharothrix sp.
BGC0002135.2 |  |  | 0.87 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  |  | 0.81 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  |  | 0.76 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  |  | 0.76 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000349.5 |  |  | 0.74 | NRPS | erythrochelin | Saccharopolyspora erythraea NRRL 2338
BGC0001261.3 |  |  | 0.73 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  |  | 0.72 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  |  | 0.72 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002424.3 |  | 0.78 | NRPS | saccharochelin A, saccharochelin B, saccharochelin C, saccharochelin D, saccharochelin E, saccharochelin F, saccharochelin G, saccharochelin H | Saccharothrix sp.
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001135.5 |  | 0.72 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.70 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001166.5 |  | 0.70 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000349.5 |  | 0.70 | NRPS | erythrochelin | Saccharopolyspora erythraea NRRL 2338
BGC0001261.3 |  | 0.69 | NRPS | AM-toxin | Alternaria alternata
BGC0001128.4 |  | 0.69 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4 |  | 0.69 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002286.3 |  | 0.69 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.33 out of 26.85
Confidence: strong
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 30.90 out of 36.53
Confidence: medium
Additional weak hits (11):
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.06 out of 31.73
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.09 out of 29.38
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.15 out of 30.25
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.69 out of 20.97
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.39 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.08 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.16 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.73 out of 36.53
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.40 out of 36.53
Confidence: weak
MntR
Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.38 out of 39.62
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.82 out of 27.55
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 632291 - 688157:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Fo-OH-Orn - Ser - OH-Orn - OH-Orn)

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).
FCN18_RS03375: Fo-OH-Orn - Ser - OH-Orn - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (445..820): Fo-OH-Orn
nrpys: Fo-OH-Orn

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTAAFDVAVWDMILVVGTEVAAYGLTEATVNSTL
  Nearest Stachelhaus code(s):
    Fo-OH-Orn DVWIIGAVNK (94% 8Å match)
  Stachelhaus code match:
    90% (moderate)

AMP-binding (1413..1804): Ser
nrpys: Ser

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
  Large clusters prediction:
    Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
  Small clusters prediction:
    ser (Ser)
  Single AA prediction:
    ser (Ser)

Stachelhaus prediction details:
  Stachelhaus sequence:
    RWMTFDVSVWEWHFFSSGEHNLYGPTEAAVDVTW
  Nearest Stachelhaus code(s):
    Ser DVWHFSLVDK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2449..2875): OH-Orn
nrpys: OH-Orn

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Long positively charged side chain (Orn, Lys, Arg)
  Small clusters prediction:
    Orn and hydroxy-Orn specific (Orn, OH-Orn)
  Single AA prediction:
    orn (Orn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    MNHVFDMSWEEWNVLLGGEYNLYGPTEYTINTLG
  Nearest Stachelhaus code(s):
    OH-Orn DMENLGLINK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3512..3901): OH-Orn
nrpys: OH-Orn

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    LTAAFDVFVFEMILLVGTEIAAYGLTEATVNSTL
  Nearest Stachelhaus code(s):
    OH-Orn DVFILGAVNK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
DmdR1 | Iron(II)-dependent repressor
RutR | Regulator of the pyrimidine and purine metabolism

NZ_SWMS01000001.1 - Region 2 - 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: 770,090 - 796,724 nt. (total: 26,635 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
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
Lasso peptides
TFBS Finder
Gene/CDS overview
A brief tabular summary of genes/CDS features within the region.
Filtering the table will also search biosynthetic profiles and gene function data. If enabled, the overview will then zoom to show the area covered by the filtered selection.
Genes selected in the region drawing above will be marked in the table with an indicator to the left of the gene name.
Filter:
Automatically zoom to filtered/selected features

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

No genes match the given filter
Tailoring functions
Tailoring enzymes detected in this region
Transferases: aminotransferase glycosyltransferase transferase
FCN18_RS03890: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs
  SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

FCN18_RS03925: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-III

FCN18_RS04000: glycosyl transferase group 1

smcogs
  SMCOG1045: glycosyl transferase group 1

Lyases: dehydratase
FCN18_RS03900: 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 | lassopeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001552.3 |  | 0.53 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001634.3 |  | 0.52 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0000575.5 |  | 0.52 | ribosomal | lariatin | Rhodococcus jostii
BGC0001549.3 |  | 0.52 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001551.4 |  | 0.50 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001889.2 |  | 0.49 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0002450.2 |  | 0.45 | other (other) | sarasinoside | uncultured bacterium
BGC0000578.3 |  | 0.45 | ribosomal | SRO15-2005 | Streptomyces filamentosus NRRL 15998
BGC0000737.3 |  | 0.44 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0002425.3 |  | 0.43 | ribosomal | stlassin | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001552.3 |  | 0.53 | ribosomal | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001634.3 |  | 0.52 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702
BGC0000575.5 |  | 0.52 | ribosomal | lariatin | Rhodococcus jostii
BGC0001549.3 |  | 0.52 | ribosomal | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001551.4 |  | 0.50 | ribosomal | citrulassin E | Streptomyces glaucescens
BGC0001889.2 |  | 0.49 | ribosomal | fusilassin | Thermobifida fusca YX
BGC0002450.2 |  | 0.45 | other (other) | sarasinoside | uncultured bacterium
BGC0000578.3 |  | 0.45 | ribosomal | SRO15-2005 | Streptomyces filamentosus NRRL 15998
BGC0000737.3 |  | 0.44 | saccharide | capsular polysaccharide | Pasteurella multocida
BGC0002425.3 |  | 0.43 | ribosomal | stlassin | Streptomyces sp.

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.

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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47
Confidence: medium
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52
Confidence: medium
Additional weak hits (7):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.80 out of 28.19
Confidence: weak
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.85 out of 20.01
Confidence: weak
HexR
Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.38 out of 31.73
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.72 out of 36.54
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.44 out of 29.65
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.39 out of 35.63
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 (770089...796724)
FCN18_RS03935
  RRE type: Stand_Alone_Lasso_RRE
  Location: 4 - 83
  Score: 67.8

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production
VqsM | Regulator of quorum-sensing signalling systems

NZ_SWMS01000011.1 - 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: 25,728 - 49,239 nt. (total: 23,512 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 oxidoreductase
FCN18_RS20135: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

FCN18_RS20145: oxidoreductase

smcogs
  SMCOG1083: oxidoreductase

Ligases: synthetase
FCN18_RS20130: 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
--- | --- | --- | --- | --- | ---
BGC0000656.5 |  | 0.63 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000664.5 |  | 0.59 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.58 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.56 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.55 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000649.3 |  | 0.54 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.48 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.46 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000656.5 |  | 0.63 | terpene | zeaxanthin | Xanthobacter autotrophicus Py2
BGC0000664.5 |  | 0.59 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.58 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000633.3 |  | 0.56 | terpene | carotenoid | Streptomyces avermitilis
BGC0001227.3 |  | 0.55 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000649.3 |  | 0.54 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000648.3 |  | 0.48 | terpene | carotenoid | Myxococcus xanthus
BGC0000646.5 |  | 0.47 | terpene | β-carotein | uncultured bacterium
BGC0000640.3 |  | 0.46 | terpene | carotenoid | Enterobacteriaceae bacterium DC404
BGC0000677.5 |  | 0.46 | terpene | cyclooctatin | Streptomyces melanosporofaciens

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

No significant matches found.

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

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

Genes with terpene domains:
FCN18_RS20130: PT_FPPS_like
Domain 1 (45 - 358): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

FCN18_RS20140: PT_phytoene_like
Domain 1 (5 - 289): Prenyltransferase; Phytoene synthase like
Subtype: unknown

Reactions:
  FPP → diapophytoene
  FPP → PSPP
  FPP → squalene
  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:
RpoN
Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46
Confidence: medium
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 27.38 out of 29.65
Confidence: strong
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 24.78 out of 24.78
Confidence: strong
Additional weak hits (10):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.91 out of 26.06
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.95 out of 25.88
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.28 out of 29.25
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.49 out of 28.19
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 21.90 out of 30.11
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.15 out of 30.25
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.09 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.26 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 12.97 out of 26.06
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.15 out of 29.65
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
PSPP | Presqualene diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
LexA variant 1 | Repressor of DNA damage response
LexA variant 2 | Repressor of DNA damage response
RpoN | Regulator of nitrogen assimilation and virulence

NZ_SWMS01000013.1 - Region 1 - HR-T2PKS
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: 114,241 - 156,435 nt. (total: 42,195 nt) Show pHMM detection rules used
HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-synt))

#### 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
FCN18_RS23140: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

Transferases: kinase transferase
FCN18_RS23150: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

FCN18_RS23170: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

Hydrolases: hydrolase protease
FCN18_RS23040: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

FCN18_RS23160: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase
FCN18_RS23115: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

FCN18_RS23175: 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 | HR-T2PKS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.61 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.61 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001240.4 |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000357.5 |  | 0.59 | 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
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001166.5 |  | 0.59 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000595.3 |  | 0.54 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0002510.2 |  | 0.48 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001641.4 |  | 0.61 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4 |  | 0.61 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4 |  | 0.61 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001240.4 |  | 0.60 | NRPS | serinocyclin A, serinocyclin B | Metarhizium robertsii
BGC0000357.5 |  | 0.59 | 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
BGC0001250.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001251.4 |  | 0.59 | NRPS | epichloenin A | Epichloe festucae
BGC0001166.5 |  | 0.59 | NRPS | HC-toxin | Alternaria jesenskae
BGC0000595.3 |  | 0.54 | ribosomal | SCO-2138 | Streptomyces coelicolor A3(2)
BGC0002510.2 |  | 0.48 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.

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: 22.15 out of 29.72
Confidence: medium
Additional weak hits (7):
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.61 out of 26.33
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.06 out of 26.06
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.16 out of 26.06
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.76 out of 21.84
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.75 out of 27.55
Confidence: weak
Detailed domain annotation
Shows NRPS- and PKS-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.
A domain glossary is available here, and an explanation of the visualisation is available here.
Selected features only
Show module domains
NRPS/PKS substrates
TFBS Finder
NRPS/PKS substrate predictions
Shows the predicted substrates for each adenylation domain and acyltransferase within genes. Each gene prediction can be expanded to view detailed predictions of each domain. Each prediction can be expanded to view the predictions by tool (and, for some tools, further expanded for extra details).
FCN18_RS23175: X
AMP-binding (6..384): X
nrpys: (unknown)

SVM prediction details:
  Predicted physicochemical class:
    N/A
  Large clusters prediction:
    N/A
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    TALLHGLILG-GFGVSGSAVERYGMSETLMNTSV
  Nearest Stachelhaus code(s):
    nohBza GLGLVGAIIK (41% 8Å match)
  Stachelhaus code match:
    60% (weak)

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

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

NZ_SWMS01000016.1 - Region 1 - thioamitides
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: 91,965 - 113,832 nt. (total: 21,868 nt) Show pHMM detection rules used
thioamitides: ((YcaO or TIGR03604) and TfuA)

#### 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
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 | thioamitides | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002560.3 |  | 0.45 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0001849.4 |  | 0.45 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0002328.3 |  | 0.40 | ribosomal | Rc-AIP1 | Ruminiclostridium cellulolyticum H10
BGC0001802.5 |  | 0.39 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0001696.5 |  | 0.39 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0000625.5 |  | 0.37 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0002669.2 |  | 0.34 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87
BGC0002120.3 |  | 0.32 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000604.4 |  | 0.27 | ribosomal | GE2270A | Nonomuraea sp. WU8817
BGC0001155.5 |  | 0.27 | ribosomal | GE2270 | Planobispora rosea

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002560.3 |  | 0.45 | ribosomal | thiostreptamide S4 | Streptomyces sp. NRRL S-4
BGC0001849.4 |  | 0.45 | ribosomal | thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D | Streptomyces varsoviensis
BGC0002328.3 |  | 0.40 | ribosomal | Rc-AIP1 | Ruminiclostridium cellulolyticum H10
BGC0001802.5 |  | 0.39 | ribosomal | thioholgamide A, thioholgamide B | Streptomyces malaysiense
BGC0001696.5 |  | 0.39 | ribosomal | neothioviridamide | Streptomyces sp.
BGC0000625.5 |  | 0.37 | ribosomal | thioviridamide | Streptomyces olivoviridis
BGC0002669.2 |  | 0.34 | ribosomal | TVA-YJ-2 | Streptomyces sp. NRRL S-87
BGC0002120.3 |  | 0.32 | ribosomal | nocathioamide A | Nocardia terpenica IFM 0706
BGC0000604.4 |  | 0.27 | ribosomal | GE2270A | Nonomuraea sp. WU8817
BGC0001155.5 |  | 0.27 | ribosomal | GE2270 | Planobispora rosea

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

No significant matches found.

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

No significant matches found.

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
No hits above weak threshold.
Weak hits (6):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.04 out of 32.74
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.33 out of 30.97
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.30 out of 29.65
Confidence: weak
MexT
Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84
Confidence: weak
NuR
Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.40 out of 30.98
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.76 out of 27.04
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_SWMS01000018.1 - 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: 25,412 - 47,628 nt. (total: 22,217 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
Transferases: acyltransferase
FCN18_RS27100: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Hydrolases: hydrolase
FCN18_RS27105: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

Lyases: cyclase
FCN18_RS27120: Terpene synthase/cyclase metal-binding domain protein

smcogs
  SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Isomerases: mutase
FCN18_RS27155: phosphoglycerate mutase

smcogs
  SMCOG1101: phosphoglycerate mutase

Ligases: synthase
FCN18_RS27165: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs
  SMCOG1110: 1-deoxy-D-xylulose-5-phosphate 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 | terpene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.80 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001535.3 |  | 0.53 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0002284.3 |  | 0.40 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0001736.3 |  | 0.39 | NRPS | pepteridine A, pepteridine B | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002582.3 |  | 0.37 | NRPS | guanipiperazine A, guanipiperazine B | Streptomyces chrestomyceticus
BGC0001768.4 |  | 0.36 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4
BGC0001972.4 |  | 0.35 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis
BGC0000111.5 |  | 0.33 | PKS | neocarzilin A, neocarzilin B | Streptomyces carzinostaticus
BGC0001637.3 |  | 0.33 | NRPS | kleboxymycin | Klebsiella oxytoca
BGC0001782.3 |  | 0.32 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001181.4 |  | 0.80 | terpene | geosmin | Streptomyces coelicolor A3(2)
BGC0001535.3 |  | 0.53 | other (other) | branched-chain fatty acids | Streptomyces filamentosus
BGC0002284.3 |  | 0.40 | other (other) | corynecin III, corynecin I, corynecin II | Rhodococcus sp. H-CA8f
BGC0001736.3 |  | 0.39 | NRPS | pepteridine A, pepteridine B | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002582.3 |  | 0.37 | NRPS | guanipiperazine A, guanipiperazine B | Streptomyces chrestomyceticus
BGC0001768.4 |  | 0.36 | NRPS | sansalvamide | [Nectria] haematococca mpVI 77-13-4
BGC0001972.4 |  | 0.35 | other (other) | toxoflavin, fervenulin | Streptomyces hiroshimensis
BGC0000111.5 |  | 0.33 | PKS | neocarzilin A, neocarzilin B | Streptomyces carzinostaticus
BGC0001637.3 |  | 0.33 | NRPS | kleboxymycin | Klebsiella oxytoca
BGC0001782.3 |  | 0.32 | other (other) | spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G | Streptomyces sp. SCSIO 03032

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 |  | germacradienol | C15 | C1-C10 | OH
sesquiterpene |  | geosmin | C12 | C1-C10 | OH

Genes with terpene domains:
FCN18_RS27120: T1TS + T1TS
Domain 1 (1 - 329): Type 1 terpene synthase
Subtype: Geosmin synthase, N terminal domain

Reactions:
  FPP → germacradienol

Domain 2 (338 - 700): Type 1 terpene synthase
Subtype: Geosmin synthase, C terminal domain

Reactions:
  germacradienol → geosmin

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: 18.07 out of 20.47
Confidence: medium
Additional weak hits (3):
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.96 out of 26.06
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.60 out of 35.63
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
FPP | Farnesyl diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_SWMS01000023.1 - Region 1 - triceptide
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: 39,495 - 63,598 nt. (total: 24,104 nt) Show pHMM detection rules used
triceptide: ((cds(PF04055 and (TIGR04085 or SPASM)) and triceptide_precursor) or triceptide_rSAM)

#### 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: aminotransferase
FCN18_RS30140: aminotransferase

smcogs
  SMCOG1019: aminotransferase

Lyases: cyclase
FCN18_RS30205: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Isomerases: racemase
FCN18_RS30145: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

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 | triceptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000600.3 |  | 0.42 | ribosomal | thurincin H | Bacillus thuringiensis
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.41 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000501.3 |  | 0.40 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000496.5 |  | 0.40 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000916.5 |  | 0.40 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0002667.2 |  | 0.40 | ribosomal | estericin A | Clostridium estertheticum
BGC0000772.5 |  | 0.38 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0000340.5 |  | 0.35 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0000932.5 |  | 0.34 | other (other) | tropodithietic acid, hydroxytropodithietic acid | Phaeobacter inhibens DSM 17395

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000600.3 |  | 0.42 | ribosomal | thurincin H | Bacillus thuringiensis
BGC0000513.3 |  | 0.41 | ribosomal | Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3 | Saccharopolyspora erythraea NRRL 2338
BGC0000519.4 |  | 0.41 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0000501.3 |  | 0.40 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0000496.5 |  | 0.40 | ribosomal | AmfS | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000916.5 |  | 0.40 | other (other) | molybdenum cofactor | Staphylococcus carnosus
BGC0002667.2 |  | 0.40 | ribosomal | estericin A | Clostridium estertheticum
BGC0000772.5 |  | 0.38 | saccharide | lipopolysaccharide | Brucella melitensis
BGC0000340.5 |  | 0.35 | NRPS | echoside A, echoside B, echoside C, echoside D, echoside E | Streptomyces sp. LZ35
BGC0000932.5 |  | 0.34 | other (other) | tropodithietic acid, hydroxytropodithietic acid | Phaeobacter inhibens DSM 17395

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:
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.73 out of 27.18
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (3):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.78 out of 21.55
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.41 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.41 out of 30.11
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NrdR | Represses ribonucleotide reductase encoding genes
VqsM | Regulator of quorum-sensing signalling systems

NZ_SWMS01000025.1 - Region 1 - arylpolyene
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 67,340 - 98,716 nt. (total: 31,377 nt) Show pHMM detection rules used
Region on contig edge.
arylpolyene: (APE_KS1 or APE_KS2)

#### 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 electron transfer
FCN18_RS31355: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FCN18_RS31425: flavodoxin

smcogs
  SMCOG1134: flavodoxin

Transferases: kinase
FCN18_RS31365: glycerol kinase

smcogs
  SMCOG1210: glycerol kinase

Lyases: cyclase
FCN18_RS31395: diguanylate cyclase

smcogs
  SMCOG1025: diguanylate cyclase

Isomerases: racemase
FCN18_RS31445: mandelate racemase/muconate lactonizing enzyme

smcogs
  SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: synthase
FCN18_RS31400: 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 | arylpolyene | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001555.4 |  | 0.41 | ribosomal | colicin V | Escherichia coli chi7122
BGC0002704.2 |  | 0.41 | ribosomal | archalan β | Halorussus salinus
BGC0000888.5 |  | 0.41 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000584.5 |  | 0.40 | ribosomal | colicin V | Escherichia coli
BGC0002674.2 |  | 0.40 | ribosomal | enterocin F4-9 | Enterococcus faecalis
BGC0001184.4 |  | 0.40 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002407.3 |  | 0.39 | other (other), saccharide | angustmycin A, angustmycin C | Streptomyces angustmyceticus
BGC0000528.5 |  | 0.39 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002294.3 |  | 0.39 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001555.4 |  | 0.41 | ribosomal | colicin V | Escherichia coli chi7122
BGC0002704.2 |  | 0.41 | ribosomal | archalan β | Halorussus salinus
BGC0000888.5 |  | 0.41 | other (other) | bacilysin | Bacillus sp. CS93
BGC0000584.5 |  | 0.40 | ribosomal | colicin V | Escherichia coli
BGC0002674.2 |  | 0.40 | ribosomal | enterocin F4-9 | Enterococcus faecalis
BGC0001184.4 |  | 0.40 | other (other) | bacilysin | Bacillus velezensis FZB42
BGC0001210.5 |  | 0.40 | ribosomal | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0002407.3 |  | 0.39 | other (other), saccharide | angustmycin A, angustmycin C | Streptomyces angustmyceticus
BGC0000528.5 |  | 0.39 | ribosomal | michiganin A | Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0002294.3 |  | 0.39 | other (other) | streptozotocin | Streptomyces achromogenes subsp. streptozoticus

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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.23 out of 19.52
Confidence: medium
Additional weak hits (6):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.10 out of 25.88
Confidence: weak
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.44 out of 30.25
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 26.62 out of 36.54
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.92 out of 36.54
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.61 out of 23.43
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
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production

NZ_SWMS01000027.1 - Region 1 - lanthipeptide-class-i
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 15,974 nt. (total: 15,974 nt) Show pHMM detection rules used
Region on contig edge.
lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
FCN18_RS31960: aldo/keto reductase family oxidoreductase

smcogs
  SMCOG1039: aldo/keto reductase family oxidoreductase

Lyases: cyclase dehydratase
FCN18_RS31935: Lanthionine synthetase C family protein

smcogs
  SMCOG1140: Lanthionine synthetase C family protein

FCN18_RS31940: Lantibiotic dehydratase domain protein

smcogs
  SMCOG1155: Lantibiotic dehydratase domain protein

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

Reference | lanthipeptide-class-i | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001727.3 |  | 0.45 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0001289.5 |  | 0.44 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002316.2 |  | 0.44 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000544.4 |  | 0.41 | ribosomal | planosporicin | Planomonospora alba
BGC0000514.5 |  | 0.39 | ribosomal | gallidermin | Staphylococcus gallinarum
BGC0001151.5 |  | 0.29 | other (non-nrp beta-lactam) | valclavam, (-)-2-(2-hydroxyethyl)clavam | Streptomyces antibioticus
BGC0001556.5 |  | 0.28 | NRPS, PKS | combamide | Streptomyces sp.
BGC0000796.3 |  | 0.27 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0002081.3 |  | 0.27 | PKS | streptoketide A, streptoketide B, streptoketide C, S2502, S2507, UWM5 | Streptomyces sp. Tue6314

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002576.2 |  | 0.75 | ribosomal | mechercharmycin | Thermoactinomyces sp.
BGC0001727.3 |  | 0.45 | ribosomal | paenilan | Paenibacillus polymyxa E681
BGC0001289.5 |  | 0.44 | ribosomal | penisin | Paenibacillus ehimensis
BGC0002316.2 |  | 0.44 | ribosomal | cebulantin | Saccharopolyspora cebuensis
BGC0000544.4 |  | 0.41 | ribosomal | planosporicin | Planomonospora alba
BGC0000514.5 |  | 0.39 | ribosomal | gallidermin | Staphylococcus gallinarum
BGC0001151.5 |  | 0.29 | other (non-nrp beta-lactam) | valclavam, (-)-2-(2-hydroxyethyl)clavam | Streptomyces antibioticus
BGC0001556.5 |  | 0.28 | NRPS, PKS | combamide | Streptomyces sp.
BGC0000796.3 |  | 0.27 | saccharide | S-layer glycan | Paenibacillus alvei
BGC0002081.3 |  | 0.27 | PKS | streptoketide A, streptoketide B, streptoketide C, S2502, S2507, UWM5 | Streptomyces sp. Tue6314

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:
AfsQ1
Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.33 out of 19.52
Confidence: strong
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-i protocluster (0...15974)
FCN18_RS31940
  RRE type: Lanthipeptide_LanB_RRE
  Location: 147 - 239
  Score: 65.9

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
AfsQ1 | Two-component system AfsQ1-Q2, activator of antibiotic production

NZ_SWMS01000029.1 - Region 1 - redox-cofactor
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: 58,933 - 79,922 nt. (total: 20,990 nt) Show pHMM detection rules used
Region on contig edge.
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### 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
Lyases: hydratase
FCN18_RS33070: enoyl-CoA hydratase

smcogs
  SMCOG1023: enoyl-CoA hydratase

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 | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.49 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002289.2 |  | 0.49 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii
BGC0001496.3 |  | 0.47 | ribosomal | actinokineosin | Actinokineospora spheciospongiae
BGC0000501.3 |  | 0.47 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0001645.3 |  | 0.46 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001779.5 |  | 0.45 | ribosomal | siamycin | Streptomyces nodosus
BGC0001550.3 |  | 0.45 | ribosomal | citrulassin D | Streptomyces katrae
BGC0002575.2 |  | 0.44 | ribosomal | cochonodin I | Streptococcus suis
BGC0001176.4 |  | 0.44 | ribosomal | streptomonomicin | Streptomonospora alba
BGC0001634.3 |  | 0.44 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002306.2 |  | 0.49 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0002289.2 |  | 0.49 | ribosomal | Leepeptin | Streptomyces leeuwenhoekii
BGC0001496.3 |  | 0.47 | ribosomal | actinokineosin | Actinokineospora spheciospongiae
BGC0000501.3 |  | 0.47 | ribosomal | catenulipeptin | Catenulispora acidiphila DSM 44928
BGC0001645.3 |  | 0.46 | ribosomal | lagmysin | Streptomyces sp. NRRL S-118
BGC0001779.5 |  | 0.45 | ribosomal | siamycin | Streptomyces nodosus
BGC0001550.3 |  | 0.45 | ribosomal | citrulassin D | Streptomyces katrae
BGC0002575.2 |  | 0.44 | ribosomal | cochonodin I | Streptococcus suis
BGC0001176.4 |  | 0.44 | ribosomal | streptomonomicin | Streptomonospora alba
BGC0001634.3 |  | 0.44 | ribosomal | keywimysin | Streptomyces sp. NRRL F-5702

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:
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.27 out of 23.79
Confidence: medium
Additional weak hits (9):
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.84 out of 21.55
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.31 out of 27.78
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.51 out of 27.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.03 out of 36.53
Confidence: weak
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.17 out of 29.25
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.19 out of 29.38
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.68 out of 29.38
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.40 out of 33.14
Confidence: weak
HypR
Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (58932...79922)
FCN18_RS33120
  RRE type: PqqD_RRE
  Location: 14 - 99
  Score: 65.0

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
IolR | Regulator of the inositol catabolism

NZ_SWMS01000003.1 - 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: 1 - 15,412 nt. (total: 15,412 nt) Show pHMM detection rules used
Region on contig edge.
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
FCN18_RS07095: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

FCN18_RS07125: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

FCN18_RS07130: 3-hydroxybutyryl-CoA dehydrogenase

smcogs
  SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: methyltransferase
FCN18_RS07100: 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
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.49 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.49 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000649.3 |  | 0.48 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001227.3 |  | 0.47 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000633.3 |  | 0.47 | terpene | carotenoid | Streptomyces avermitilis
BGC0000636.3 |  | 0.47 | terpene | carotenoid | Brevibacterium linens
BGC0000706.3 |  | 0.45 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0002675.2 |  | 0.38 | PKS | prodigiosin | Pseudoalteromonas rubra
BGC0002147.2 |  | 0.37 | NRPS | bohemamine A, bohemamine B, bohemamine C | Streptomyces sp. CB02009
BGC0001485.4 |  | 0.36 | other (other) | chuangxinmycin | Actinoplanes tsinanensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000664.5 |  | 0.49 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3 |  | 0.49 | terpene | isorenieratene | Streptomyces argillaceus
BGC0000649.3 |  | 0.48 | terpene | carotenoid | Streptomyces griseus subsp. griseus NBRC 13350
BGC0001227.3 |  | 0.47 | terpene | isorenieratene | Streptomyces collinus Tu 365
BGC0000633.3 |  | 0.47 | terpene | carotenoid | Streptomyces avermitilis
BGC0000636.3 |  | 0.47 | terpene | carotenoid | Brevibacterium linens
BGC0000706.3 |  | 0.45 | saccharide | kanamycin | Streptomyces kanamyceticus
BGC0002675.2 |  | 0.38 | PKS | prodigiosin | Pseudoalteromonas rubra
BGC0002147.2 |  | 0.37 | NRPS | bohemamine A, bohemamine B, bohemamine C | Streptomyces sp. CB02009
BGC0001485.4 |  | 0.36 | 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.
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:
FCN18_RS07105: Lycopene_cycl
Domain 1 (6 - 97): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

FCN18_RS07110: Lycopene_cycl
Domain 1 (8 - 94): Lycopene cyclase

Reactions:
  C40_carotenoid → C40_carotenoid

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:
ClgR
Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 25.19 out of 30.22
Confidence: medium
Additional weak hits (5):
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.41 out of 30.11
Confidence: weak
CelR
Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 22.04 out of 30.11
Confidence: weak
BldD
Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.45 out of 23.43
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.14 out of 19.26
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.62 out of 32.93
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
--- | ---
ClgR | Caseinolytic protease gene regulator

NZ_SWMS01000032.1 - Region 1 - NI-siderophore
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1 - 28,474 nt. (total: 28,474 nt) Show pHMM detection rules used
Region on contig edge.
NI-siderophore: IucA_IucC

#### 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
Oxidoreductases: dehydrogenase oxygenase
FCN18_RS34055: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

FCN18_RS34075: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FCN18_RS34080: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

Hydrolases: deaminase protease
FCN18_RS33980: alkaline serine protease, subtilase family

smcogs
  SMCOG1075: alkaline serine protease, subtilase family

FCN18_RS34025: ornithine cyclodeaminase

smcogs
  SMCOG1158: ornithine cyclodeaminase

Lyases: decarboxylase
FCN18_RS34005: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
FCN18_RS34030: cysteine synthase

smcogs
  SMCOG1081: cysteine synthase

FCN18_RS34045: 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 | NI-siderophore | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000942.4 |  | 0.59 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0000943.5 |  | 0.57 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002527.2 |  | 0.56 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001499.5 |  | 0.53 | other (other) | aerobactin | Pantoea ananatis
BGC0000946.5 |  | 0.53 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002471.3 |  | 0.53 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0001201.3 |  | 0.52 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0001408.5 |  | 0.49 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002692.2 |  | 0.49 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002128.3 |  | 0.49 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000942.4 |  | 0.59 | other (other) | petrobactin | Bacillus anthracis str. Ames
BGC0000943.5 |  | 0.57 | other (other) | staphyloferrin B | Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002527.2 |  | 0.56 | other (other) | vibrioferrin | Azotobacter vinelandii CA
BGC0001499.5 |  | 0.53 | other (other) | aerobactin | Pantoea ananatis
BGC0000946.5 |  | 0.53 | other (other) | vibrioferrin | Vibrio parahaemolyticus
BGC0002471.3 |  | 0.53 | other (other) | baumannoferrin A, baumannoferrin B | Acinetobacter baumannii AYE
BGC0001201.3 |  | 0.52 | terpene | eremophilene | Sorangium cellulosum So ce56
BGC0001408.5 |  | 0.49 | other (other) | xanthoferrin | Xanthomonas oryzae pv. oryzae KACC 10331
BGC0002692.2 |  | 0.49 | other (other) | speibonoxamine, desoxy-desferrioxamine D1, desferrioxamine D1, desferrioxamine B, didesoxy-desferrioxamine D1, desoxy-desferrioxamine B, didesoxy-desferrioxamine B | Kribbella speibonae
BGC0002128.3 |  | 0.49 | other (other) | 5-dimethylallylindole-3-acetonitrile | Streptomyces coelicolor A3(2)

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:
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 25.40 out of 29.65
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47
Confidence: medium
Additional weak hits (7):
ColR
Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.74 out of 30.25
Confidence: weak
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 17.85 out of 25.88
Confidence: weak
CRP
Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.25 out of 36.53
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.29 out of 24.78
Confidence: weak
DmdR1
Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.57 out of 36.53
Confidence: weak
HgtR
Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.88 out of 36.54
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
LexA variant 1 | Repressor of DNA damage response
VqsM | Regulator of quorum-sensing signalling systems

NZ_SWMS01000032.1 - Region 2 - ectoine
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: 47,283 - 57,675 nt. (total: 10,393 nt) Show pHMM detection rules used
Region on contig edge.
ectoine: ectoine_synt

#### 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: aminotransferase
FCN18_RS34225: aminotransferase class-III

smcogs
  SMCOG1013: aminotransferase class-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 | ectoine | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.82 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.81 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000859.3 |  | 0.72 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000860.3 |  | 0.60 | other (other) | ectoine | Methylarcula marina
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000852.5 |  | 0.57 | other (other) | ectoine | Sporosarcina pasteurii

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000853.3 |  | 0.82 | other (other) | ectoine | Streptomyces anulatus
BGC0002052.3 |  | 0.81 | other (ectoine) | ectoine | Streptomyces sp.
BGC0000859.3 |  | 0.72 | other (other) | ectoine | Methylomicrobium alcaliphilum
BGC0000855.3 |  | 0.66 | other (other) | ectoine | Methylomicrobium kenyense
BGC0000858.3 |  | 0.66 | other (other) | ectoine | Methylobacter marinus
BGC0000856.3 |  | 0.66 | other (other) | ectoine | Methylophaga thalassica
BGC0000860.3 |  | 0.60 | other (other) | ectoine | Methylarcula marina
BGC0000857.3 |  | 0.60 | other (other) | ectoine | Methylophaga alcalica
BGC0000854.3 |  | 0.59 | other (other) | ectoine | Methylomicrobium alcaliphilum 20Z
BGC0000852.5 |  | 0.57 | other (other) | ectoine | Sporosarcina pasteurii

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.
No hits above weak threshold.
Weak hits (3):
PsrA
Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.04 out of 25.88
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.79 out of 29.38
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_SWMS01000036.1 - Region 1 - PKS-like,T1PKS,t3nrps-iterative
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,314 - 44,571 nt. (total: 42,258 nt) Show pHMM detection rules used
Region on contig edge.
t3nrps-iterative: (AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC) and not ATP-grasp)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
PKS-like: (t2pks2 or ksIII)

#### 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 oxygenase
FCN18_RS35125: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

FCN18_RS35130: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FCN18_RS35150: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

FCN18_RS35160: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

FCN18_RS35210: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

FCN18_RS35215: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

Transferases: PPTase kinase
FCN18_RS35120: PfkB domain protein

smcogs
  SMCOG1276: PfkB domain protein

FCN18_RS35175: 4'-phosphopantetheinyl transferase

smcogs
  SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: esterase phosphatase
FCN18_RS35165: thioesterase

smcogs
  SMCOG1004: thioesterase

FCN18_RS35190: FkbH like protein

smcogs
  SMCOG1256: FkbH like protein

Lyases: decarboxylase
FCN18_RS35230: diaminopimelate decarboxylase

smcogs
  SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase
FCN18_RS35195: 3-oxoacyl-(acyl carrier protein) synthase III

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

FCN18_RS35200: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

FCN18_RS35220: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FCN18_RS35235: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FCN18_RS35240: 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 | t3nrps-iterative | T1PKS | PKS-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0001273.3 |  |  |  | 0.97 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  |  |  | 0.97 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  |  |  | 0.96 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  |  |  | 0.95 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001641.4 |  |  |  | 0.91 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 0.91 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  |  |  | 0.91 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0002075.3 |  |  |  | 0.90 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001257.3 |  |  |  | 0.90 | PKS | 1,3,6,8-tetrahydroxynaphthalene | Nodulisporium sp. ATCC74245
BGC0001128.4 |  |  |  | 0.89 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001273.3 |  | 0.67 | PKS | asperlactone | Aspergillus ochraceus
BGC0001276.3 |  | 0.67 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0001275.3 |  | 0.66 | PKS | 6-methylsalicyclic acid | Glarea lozoyensis
BGC0001244.3 |  | 0.66 | PKS | (-)-Mellein | Parastagonospora nodorum
BGC0001254.3 |  | 0.64 | PKS | ACT-Toxin II | Alternaria alternata
BGC0001160.5 |  | 0.64 | PKS | 1-nonadecene, (14Z)-1,14-nonadecadiene | Synechococcus sp. PCC 7002
BGC0001641.4 |  | 0.64 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001164.3 |  | 0.64 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0002286.3 |  | 0.64 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.64 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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:
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.83 out of 20.47
Confidence: medium
Additional weak hits (8):
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.28 out of 32.74
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.87 out of 26.06
Confidence: weak
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.31 out of 27.78
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.94 out of 26.06
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.32 out of 26.33
Confidence: weak
MatP
Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.29 out of 25.75
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.59 out of 33.14
Confidence: weak
LexA variant 1
Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.42 out of 29.65
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 2313 - 44571:
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

For candidate cluster 2, location 17944 - 44571:
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).
FCN18_RS35200: mal
PKS_AT (517..799): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 83.3%
  inactive: 75.0%
  Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 135.5
  inactive: 82.8
  Methoxymalonyl-CoA: 62.1
  Methylmalonyl-CoA: 59.1
  2-Methylbutyryl-CoA: 43.9
  Propionyl-CoA: 39.0
  Ethylmalonyl-CoA: 23.1
  Isobutyryl-CoA: 18.2
  fatty_acid: 14.3
  CHC-CoA: 12.9
  Acetyl-CoA: 12.6
  trans-1,2-CPDA: 7.0
  3-Methylbutyryl-CoA: 3.5
  Benzoyl-CoA: 0.0

FCN18_RS35220: NH2
CAL_domain (26..461): NH2
minowa: NH2

Prediction, score:
  NH2: 120.5
  fatty_acid: 32.8
  AHBA: 9.3
  Acetyl-CoA: 4.6
  shikimic_acid: 0.1

FCN18_RS35235: Asp
Search NORINE for peptide: strict or relaxed
AMP-binding (15..401): Asp
nrpys: Asp

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:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    AAISFDYGLYQLPTTNTGAVSMYGITECKRVTIA
  Nearest Stachelhaus code(s):
    Asp DYYPTTMRVK (85% 8Å match)
  Stachelhaus code match:
    100% (strong)

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

Regulator | Description
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_SWMS01000004.1 - Region 1 - RiPP-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 30,574 - 42,013 nt. (total: 11,440 nt) Show pHMM detection rules used
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
No tailoring functions detected.
Similar gene clusters
Shows areas that are similar to the current region to a reference database.
Mouseover a score cell in the table to get a breakdown of how the score was calculated.The MIBiG database.
Click on an accession to open that entry in the MIBiG database.
Analysis type:

Reference | RiPP-like | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.51 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000519.4 |  | 0.41 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002699.2 |  | 0.40 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0001222.3 |  | 0.39 | ribosomal | acidocin B | Lactobacillus acidophilus
BGC0000491.5 |  | 0.39 | ribosomal | gassericin A | Lactobacillus gasseri
BGC0000571.3 |  | 0.36 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0002322.3 |  | 0.36 | ribosomal | citrocin | Citrobacter pasteurii
BGC0000539.5 |  | 0.36 | ribosomal | nukacin ISK-1 | Staphylococcus warneri

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002115.3 |  | 0.51 | ribosomal | streptamidine | Streptomyces albidoflavus J1074
BGC0002306.2 |  | 0.42 | ribosomal | freyrasin | Paenibacillus polymyxa ATCC 842
BGC0000519.4 |  | 0.41 | ribosomal | labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3 | Actinomadura namibiensis
BGC0002699.2 |  | 0.40 | ribosomal | nostolysamide A, nostolysamide B | Nostoc punctiforme PCC 73102
BGC0001639.3 |  | 0.40 | ribosomal | klebsidin | Klebsiella pneumoniae
BGC0001222.3 |  | 0.39 | ribosomal | acidocin B | Lactobacillus acidophilus
BGC0000491.5 |  | 0.39 | ribosomal | gassericin A | Lactobacillus gasseri
BGC0000571.3 |  | 0.36 | ribosomal | burhizin | Paraburkholderia rhizoxinica HKI 454
BGC0002322.3 |  | 0.36 | ribosomal | citrocin | Citrobacter pasteurii
BGC0000539.5 |  | 0.36 | ribosomal | nukacin ISK-1 | Staphylococcus warneri

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: 22.03 out of 29.72
Confidence: medium
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.65 out of 28.19
Confidence: medium
Additional weak hits (8):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.12 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.01 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.36 out of 32.74
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.74 out of 28.14
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.68 out of 29.38
Confidence: weak
PerR
Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.72 out of 28.14
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.79 out of 20.97
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.55 out of 32.74
Confidence: weak
TFBS Finder
TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
NtrC | Nitrogen regulatory protein C
ZuR variant 1 | Zinc-responsive repressor

NZ_SWMS01000004.1 - Region 2 - 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: 188,450 - 210,009 nt. (total: 21,560 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: oxidase oxygenase
FCN18_RS10125: pyruvate oxidase/decarboxylase

smcogs
  SMCOG1055: pyruvate oxidase/decarboxylase

FCN18_RS10140: cytochrome P450

smcogs
  SMCOG1034: cytochrome P450

Transferases: methyltransferase
FCN18_RS10175: methyltransferase

smcogs
  SMCOG1089: methyltransferase

Hydrolases: hydrolase
FCN18_RS10170: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold protein

Lyases: decarboxylase
FCN18_RS10165: Decarboxylase, pyridoxal-dependent

smcogs
  SMCOG1180: Decarboxylase, pyridoxal-dependent

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
--- | --- | --- | --- | --- | ---
BGC0001453.5 |  | 0.46 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000940.5 |  | 0.46 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0000286.3 |  | 0.43 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0002690.2 |  | 0.43 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0001483.4 |  | 0.43 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001910.4 |  | 0.42 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000495.5 |  | 0.42 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0001478.5 |  | 0.42 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0001572.3 |  | 0.41 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001453.5 |  | 0.46 | other (other) | desferrioxamine | Streptomyces argillaceus
BGC0000940.5 |  | 0.46 | other (other) | desferrioxamin B, desferrioxamine E | Streptomyces coelicolor A3(2)
BGC0000286.3 |  | 0.43 | PKS | viguiepinol | Streptomyces sp. KO-3988
BGC0002690.2 |  | 0.43 | other (other) | FW0622 | Verrucosispora sp. FIM060022
BGC0001483.4 |  | 0.43 | other (other) | 5-isoprenylindole-3-carboxylate β-D-glycosyl ester | Streptomyces sp. RM-5-8
BGC0001910.4 |  | 0.42 | terpene | cyslabdan A, cyslabdan B, cyslabdan C | Streptomyces cyslabdanicus
BGC0000495.5 |  | 0.42 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0001478.5 |  | 0.42 | other (other) | desferrioxamine E | Streptomyces sp. ID38640
BGC0001572.3 |  | 0.41 | other (other) | desferrioxamine E | Pantoea agglomerans
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens

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
--- | --- | --- | --- | --- | ---
diterpene |  |  | C20 | C6-C11 + C10-C15 | PP

Genes with terpene domains:
FCN18_RS10145: T2TS
Domain 1 (12 - 501): Type 2 terpene synthase
Subtype: Diterpene synthase

Reactions:
  GGPP → diterpene_C6-C11/C10-C15_PP

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: 17.92 out of 20.47
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (4):
SypG
Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.96 out of 29.25
Confidence: weak
LuxO
Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.40 out of 26.12
Confidence: weak
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33
Confidence: weak
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 27.04
Confidence: weak
Terpene
TFBS Finder
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
GGPP | Geranylgeranyl diphosphate
PP | Diphosphate

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
VqsM | Regulator of quorum-sensing signalling systems

NZ_SWMS01000004.1 - Region 3 - ranthipeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 221,733 - 243,216 nt. (total: 21,484 nt) Show pHMM detection rules used
ranthipeptide: (TIGR03973 or SCIFF or (cds(PF04055 and (TIGR04085 or SPASM)) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]) and not (TIGR01716 or subtilosin or TIGR02111 or TIGR03966 or TIGR04103 or (YcaO or TIGR03604))))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
Oxidoreductases: dehydrogenase oxidoreductase
FCN18_RS10250: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

FCN18_RS10275: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

FCN18_RS10280: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

FCN18_RS10335: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: halogenase
FCN18_RS10265: halogenase

smcogs
  SMCOG1119: halogenase

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

Reference | ranthipeptide | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001475.4 |  | 0.43 | terpene | aspterric acid | Aspergillus terreus NIH2624
BGC0000906.3 |  | 0.42 | other (other) | heme D1 | Heliophilum fasciatum
BGC0002493.3 |  | 0.41 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0000252.5 |  | 0.40 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0001687.3 |  | 0.40 | other (other) | N-tetradecanoyl tyrosine | uncultured bacterium CSL12
BGC0000880.4 |  | 0.39 | other (nucleoside) | tunicamycin B1 | Streptomyces chartreusis NRRL 3882
BGC0002218.2 |  | 0.39 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0002553.2 |  | 0.39 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0000243.4 |  | 0.38 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0001850.4 |  | 0.37 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001475.4 |  | 0.43 | terpene | aspterric acid | Aspergillus terreus NIH2624
BGC0000906.3 |  | 0.42 | other (other) | heme D1 | Heliophilum fasciatum
BGC0002493.3 |  | 0.41 | NRPS | parabactin | Paracoccus denitrificans PD1222
BGC0000252.5 |  | 0.40 | PKS | nonactin | Streptomyces griseus subsp. griseus
BGC0001687.3 |  | 0.40 | other (other) | N-tetradecanoyl tyrosine | uncultured bacterium CSL12
BGC0000880.4 |  | 0.39 | other (nucleoside) | tunicamycin B1 | Streptomyces chartreusis NRRL 3882
BGC0002218.2 |  | 0.39 | terpene | (-)-Cyatha-3,12-diene | Dentipellis sp. KUC8613
BGC0002553.2 |  | 0.39 | other (other) | tunicamycin | Rathayibacter iranicus
BGC0000243.4 |  | 0.38 | PKS | nonactin, monactin, dinactin, trinactin, tetranactin | Streptomyces griseus subsp. griseus
BGC0001850.4 |  | 0.37 | other (shikimate-derived) | diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G | Streptomyces sp. F001

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.
No hits above weak threshold.
Weak hits (3):
CodY
Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.13 out of 27.78
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.21 out of 35.63
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.26 out of 33.14
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

ranthipeptide protocluster (221732...243216)
FCN18_RS10290
  RRE type: Mycofactocin_RRE
  Location: 8 - 88
  Score: 91.5

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---

NZ_SWMS01000041.1 - 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: 1 - 23,292 nt. (total: 23,292 nt) Show pHMM detection rules used
Region on contig edge.
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
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
Transferases: acyltransferase
FCN18_RS36065: acyltransferase

smcogs
  SMCOG1141: acyltransferase

Ligases: ligase synthase
FCN18_RS36055: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FCN18_RS36120: Pseudouridine synthase

smcogs
  SMCOG1154: Pseudouridine synthase

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

Reference | NAPAA | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.59 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001268.4 |  | 0.55 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002535.2 |  | 0.48 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0001873.3 |  | 0.44 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0002555.3 |  | 0.40 | NRPS, PKS | emerimicin V, emerimicin VI, emerimicin VII, emerimicin VIII, emerimicin IX, emerimicin X | Acremonium sp.
BGC0002660.2 |  | 0.40 | NRPS | pentacitidin A, pentacitidin B | Chitinophaga eiseniae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002174.2 |  | 0.77 | NRPS | ε-Poly-L-lysine | Epichloe festucae
BGC0002135.2 |  | 0.60 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.59 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  | 0.59 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4 |  | 0.59 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001268.4 |  | 0.55 | NRPS, PKS | fusarin C | Fusarium fujikuroi
BGC0002535.2 |  | 0.48 | NRPS | γ-poly-L-2,4-diaminobutyric acid | Streptomyces celluloflavus
BGC0001873.3 |  | 0.44 | NRPS | pyrrolizixenamide A | Xenorhabdus szentirmaii DSM 16338
BGC0002555.3 |  | 0.40 | NRPS, PKS | emerimicin V, emerimicin VI, emerimicin VII, emerimicin VIII, emerimicin IX, emerimicin X | Acremonium sp.
BGC0002660.2 |  | 0.40 | NRPS | pentacitidin A, pentacitidin B | Chitinophaga eiseniae

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.

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
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 0 - 23292:
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).
FCN18_RS36055: X
AMP-binding (37..409): 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
NZ_SWMS01000006.1 - 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: 117,910 - 143,869 nt. (total: 25,960 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
FCN18_RS13470: alcohol dehydrogenase

smcogs
  SMCOG1040: alcohol dehydrogenase

FCN18_RS13495: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

FCN18_RS13520: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: synthetase
FCN18_RS13500: 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
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.60 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002276.2 |  | 0.53 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000644.3 |  | 0.52 | terpene | carotenoid | Dietzia sp. CQ4
BGC0002397.2 |  | 0.52 | terpene | astallatene | Arabidopsis thaliana
BGC0000648.3 |  | 0.51 | terpene | carotenoid | Myxococcus xanthus
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0002400.2 |  | 0.49 | terpene | boleracene | Brassica oleracea var. oleracea

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000663.5 |  | 0.60 | terpene | hopene | Streptomyces coelicolor A3(2)
BGC0000647.3 |  | 0.57 | terpene | carotenoid | Rhodobacter sphaeroides
BGC0002276.2 |  | 0.53 | NRPS | choline | Aspergillus nidulans FGSC A4
BGC0000644.3 |  | 0.52 | terpene | carotenoid | Dietzia sp. CQ4
BGC0002397.2 |  | 0.52 | terpene | astallatene | Arabidopsis thaliana
BGC0000648.3 |  | 0.51 | terpene | carotenoid | Myxococcus xanthus
BGC0002162.3 |  | 0.50 | terpene | sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8 | Aspergillus fischeri NRRL 181
BGC0000646.5 |  | 0.49 | terpene | β-carotein | uncultured bacterium
BGC0002610.3 |  | 0.49 | terpene | stellatic acid | Aspergillus stellatus
BGC0002400.2 |  | 0.49 | terpene | boleracene | Brassica oleracea var. oleracea

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

No significant matches found.

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

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
triterpene | hopanoid |  | C30 | hopanoid skeleton | unknown
triterpene | polypodane |  | C30 | polypodane skeleton | unknown

Genes with terpene domains:
FCN18_RS13485: PT_phytoene_like
Domain 1 (17 - 278): Prenyltransferase; Phytoene synthase like
Subtype: Hydroxysqualene synthase

Reactions:
  PSPP → hydroxysqualene

FCN18_RS13490: PT_phytoene_like
Domain 1 (5 - 282): Prenyltransferase; Phytoene synthase like
Subtype: unknown

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

FCN18_RS13500: PT_FPPS_like
Domain 1 (53 - 329): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

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

FCN18_RS13505: T2TS
Domain 1 (7 - 630): Type 2 terpene synthase
Subtype: Squalene substrate

Reactions:
  squalene → hopanoid
  squalene → polypodane

Transcription Factor Binding Sites
Detailed information for Transcription Factor Binding Site hits, including surrounding genes where applicable.
The strand of the match is shown by an arrow underneath the match.
Detailed documentation is available here.
Binding sites found:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97
Confidence: medium
IolR
Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.58 out of 23.79
Confidence: medium
AbrC3
Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16
Confidence: strong
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47
Confidence: strong
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 25.32 out of 29.51
Confidence: medium
VqsM
Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47
Confidence: medium
Additional weak hits (8):
ArgR
Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.16 out of 20.01
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.83 out of 20.97
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.13 out of 30.97
Confidence: weak
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.32 out of 20.97
Confidence: weak
GnfM
Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.28 out of 27.55
Confidence: weak
LexA variant 3
Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.96 out of 32.93
Confidence: weak
LexA variant 2
Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.46 out of 24.78
Confidence: weak
NrdR
Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.38 out of 27.18
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
--- | ---
AbrC3 | Antibiotic production activator
CcpA | Catabolite control protein A
DosR | Hypoxia stress response regulator
IolR | Regulator of the inositol catabolism
VqsM | Regulator of quorum-sensing signalling systems

NZ_SWMS01000006.1 - 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: 190,261 - 211,295 nt. (total: 21,035 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
Oxidoreductases: dehydrogenase oxygenase
FCN18_RS13845: monooxygenase FAD-binding

smcogs
  SMCOG1050: monooxygenase FAD-binding

FCN18_RS13850: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: synthetase
FCN18_RS13810: 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
--- | --- | --- | --- | --- | ---
BGC0002610.3 |  | 0.50 | terpene | stellatic acid | Aspergillus stellatus
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000657.5 |  | 0.46 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000664.5 |  | 0.37 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000678.5 |  | 0.37 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000516.4 |  | 0.37 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0001911.3 |  | 0.37 | terpene | raimonol | Streptomyces anulatus

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002610.3 |  | 0.50 | terpene | stellatic acid | Aspergillus stellatus
BGC0002397.2 |  | 0.46 | terpene | astallatene | Arabidopsis thaliana
BGC0000657.5 |  | 0.46 | terpene | 2-methylisoborneol | Pseudanabaena sp. dqh15
BGC0002400.2 |  | 0.43 | terpene | boleracene | Brassica oleracea var. oleracea
BGC0000677.5 |  | 0.41 | terpene | cyclooctatin | Streptomyces melanosporofaciens
BGC0002398.2 |  | 0.38 | terpene | (-)-ent-quiannulatene | Arabidopsis thaliana
BGC0000664.5 |  | 0.37 | terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350
BGC0000678.5 |  | 0.37 | terpene | pentalenolactone | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000516.4 |  | 0.37 | ribosomal | geobacillin II | Geobacillus thermodenitrificans
BGC0001911.3 |  | 0.37 | 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
--- | --- | --- | --- | --- | ---
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:
FCN18_RS13810: PT_FPPS_like
Domain 1 (60 - 341): 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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.44 out of 20.97
Confidence: medium
OsdR
Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.07 out of 30.12
Confidence: medium
Additional weak hits (5):
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.30 out of 26.06
Confidence: weak
FuR variant 1
Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.57 out of 29.38
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.02 out of 32.74
Confidence: weak
DosR
Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.65 out of 29.51
Confidence: weak
ZuR variant 1
Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.52 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
--- | ---
CcpA | Catabolite control protein A
OsdR | Development and stress management regulator

NZ_SWMS01000009.1 - Region 1 - redox-cofactor
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: 108,383 - 130,396 nt. (total: 22,014 nt) Show pHMM detection rules used
redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

#### 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
Hydrolases: hydrolase
FCN18_RS17935: metallo-beta-lactamase family protein

smcogs
  SMCOG1170: metallo-beta-lactamase family protein

FCN18_RS18000: alpha/beta hydrolase fold protein

smcogs
  SMCOG1036: alpha/beta hydrolase fold 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 | redox-cofactor | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002667.2 |  | 0.40 | ribosomal | estericin A | Clostridium estertheticum
BGC0001100.5 |  | 0.37 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0000844.5 |  | 0.35 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000495.5 |  | 0.31 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0002362.3 |  | 0.28 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0000270.5 |  | 0.28 | PKS | simocyclinone D8 | Streptomyces antibioticus
BGC0000845.5 |  | 0.27 | other (non-nrp beta-lactam) | clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0001165.5 |  | 0.25 | NRPS, PKS | curacin A | Lyngbya majuscula
BGC0001053.5 |  | 0.25 | NRPS, PKS | tubulysin A | Archangium disciforme
BGC0000986.5 |  | 0.24 | NRPS, PKS | dkxanthene 530, dkxanthene 556, dkxanthene, dkxanthene 504, dkxanthene 508, dkxanthene 518, dkxanthene 520, dkxanthene 534, dkxanthene 544, dkxanthene 548, dkxanthene 560, dkxanthene 574, dkxanthene 586 | Stigmatella aurantiaca DW4/3-1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002667.2 |  | 0.40 | ribosomal | estericin A | Clostridium estertheticum
BGC0001100.5 |  | 0.37 | NRPS, PKS | lankacidin C | Streptomyces rochei
BGC0000844.5 |  | 0.35 | other (other) | clavulanic acid | Streptomyces clavuligerus
BGC0000495.5 |  | 0.31 | ribosomal | actagardine | Actinoplanes garbadinensis
BGC0002362.3 |  | 0.28 | PKS | loseolamycin A1, loseolamycin A2 | Micromonospora endolithica
BGC0000270.5 |  | 0.28 | PKS | simocyclinone D8 | Streptomyces antibioticus
BGC0000845.5 |  | 0.27 | other (non-nrp beta-lactam) | clavulanic acid | Streptomyces clavuligerus ATCC 27064
BGC0001165.5 |  | 0.25 | NRPS, PKS | curacin A | Lyngbya majuscula
BGC0001053.5 |  | 0.25 | NRPS, PKS | tubulysin A | Archangium disciforme
BGC0000986.5 |  | 0.24 | NRPS, PKS | dkxanthene 530, dkxanthene 556, dkxanthene, dkxanthene 504, dkxanthene 508, dkxanthene 518, dkxanthene 520, dkxanthene 534, dkxanthene 544, dkxanthene 548, dkxanthene 560, dkxanthene 574, dkxanthene 586 | Stigmatella aurantiaca DW4/3-1

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:
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.72 out of 20.97
Confidence: medium
CcpA
Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.34 out of 20.97
Confidence: medium
ANR
Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33
Confidence: medium
DasR
Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.33 out of 27.04
Confidence: medium
Additional weak hits (10):
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.95 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.56 out of 21.55
Confidence: weak
MogR
Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.34 out of 26.06
Confidence: weak
ToxT
Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.63 out of 18.57
Confidence: weak
CopR
Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97
Confidence: weak
FuR variant 2
Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.95 out of 32.74
Confidence: weak
RutR
Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.43 out of 26.85
Confidence: weak
ArcA
Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.48 out of 21.55
Confidence: weak
ZuR variant 2
Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.12 out of 33.14
Confidence: weak
NrtR
Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.04 out of 35.63
Confidence: weak
RREFinder
TFBS Finder
RRE predictions
RREfinder results sidepanel.

redox-cofactor protocluster (108382...130396)
FCN18_RS17950
  RRE type: PqqD_RRE
  Location: 1 - 81
  Score: 73.4

TFBS definitions
Shows descriptions for Transcription Factor Binding Site models

Regulator | Description
--- | ---
ANR | Anaerobic transcriptional regulator
CcpA | Catabolite control protein A
DasR | N-acetylglucosamine dependent repressor