Select genomic region:
Overview
4.1
12.1
12.2
29.1
32.1

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

gnlProkkaPCFPDMBM_4 (original name was: gnl|Prokka|PCFPDMBM_4)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 4.1 | arylpolyene | 110 | 40,292 |

gnlProkkaPCFPDMBM_12 (original name was: gnl|Prokka|PCFPDMBM_12)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 12.1 | terpene | 11,162 | 34,731 | carotenoid | Terpene | 100%
Region 12.2 | NRP-metallophore,NRPS | 248,590 | 304,518 | enterobactin | NRP | 100%

gnlProkkaPCFPDMBM_34 (original name was: gnl|Prokka|PCFPDMBM_34)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 29.1 | HR-T2PKS | 1 | 22,441 |

gnlProkkaPCFPDMBM_37 (original name was: gnl|Prokka|PCFPDMBM_37)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 32.1 | thiopeptide | 128,854 | 155,154 | O-antigen | Saccharide | 14%

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 4.1 | arylpolyene | 110 | 40,292 |
Region 12.1 | terpene | 11,162 | 34,731 | carotenoid | Terpene | 100%
Region 12.2 | NRP-metallophore,NRPS | 248,590 | 304,518 | enterobactin | NRP | 100%
Region 29.1 | HR-T2PKS | 1 | 22,441 |
Region 32.1 | thiopeptide | 128,854 | 155,154 | O-antigen | Saccharide | 14%

No secondary metabolite regions were found in these records:
  gnlProkkaPCFPDMBM_1 (original name was: gnl|Prokka|PCFPDMBM_1)
  gnlProkkaPCFPDMBM_2 (original name was: gnl|Prokka|PCFPDMBM_2)
  gnlProkkaPCFPDMBM_3 (original name was: gnl|Prokka|PCFPDMBM_3)
  gnlProkkaPCFPDMBM_5 (original name was: gnl|Prokka|PCFPDMBM_5)
  gnlProkkaPCFPDMBM_6 (original name was: gnl|Prokka|PCFPDMBM_6)
  gnlProkkaPCFPDMBM_7 (original name was: gnl|Prokka|PCFPDMBM_7)
  gnlProkkaPCFPDMBM_8 (original name was: gnl|Prokka|PCFPDMBM_8)
  gnlProkkaPCFPDMBM_9 (original name was: gnl|Prokka|PCFPDMBM_9)
  gnlProkkaPCFPDMBM_10 (original name was: gnl|Prokka|PCFPDMBM_10)
  gnlProkkaPCFPDMBM_11 (original name was: gnl|Prokka|PCFPDMBM_11)
  gnlProkkaPCFPDMBM_13 (original name was: gnl|Prokka|PCFPDMBM_13)
  gnlProkkaPCFPDMBM_14 (original name was: gnl|Prokka|PCFPDMBM_14)
  gnlProkkaPCFPDMBM_15 (original name was: gnl|Prokka|PCFPDMBM_15)
  gnlProkkaPCFPDMBM_16 (original name was: gnl|Prokka|PCFPDMBM_16)
  gnlProkkaPCFPDMBM_17 (original name was: gnl|Prokka|PCFPDMBM_17)
  gnlProkkaPCFPDMBM_18 (original name was: gnl|Prokka|PCFPDMBM_18)
  gnlProkkaPCFPDMBM_19 (original name was: gnl|Prokka|PCFPDMBM_19)
  gnlProkkaPCFPDMBM_20 (original name was: gnl|Prokka|PCFPDMBM_20)
  gnlProkkaPCFPDMBM_21 (original name was: gnl|Prokka|PCFPDMBM_21)
  gnlProkkaPCFPDMBM_22 (original name was: gnl|Prokka|PCFPDMBM_22)
  gnlProkkaPCFPDMBM_23 (original name was: gnl|Prokka|PCFPDMBM_23)
  gnlProkkaPCFPDMBM_24 (original name was: gnl|Prokka|PCFPDMBM_24)
  gnlProkkaPCFPDMBM_25 (original name was: gnl|Prokka|PCFPDMBM_25)
  gnlProkkaPCFPDMBM_26 (original name was: gnl|Prokka|PCFPDMBM_26)
  gnlProkkaPCFPDMBM_27 (original name was: gnl|Prokka|PCFPDMBM_27)
  gnlProkkaPCFPDMBM_33 (original name was: gnl|Prokka|PCFPDMBM_33)
  gnlProkkaPCFPDMBM_35 (original name was: gnl|Prokka|PCFPDMBM_35)
  gnlProkkaPCFPDMBM_36 (original name was: gnl|Prokka|PCFPDMBM_36)
  gnlProkkaPCFPDMBM_38 (original name was: gnl|Prokka|PCFPDMBM_38)

Compact view
gnlProkkaPCFPDMBM_4 - 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: 110 - 40,292 nt. (total: 40,183 nt) Show pHMM detection rules used
arylpolyene: (APE_KS1 or APE_KS2)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
NRPS/PKS domains
KnownClusterBlast
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
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
Similar known gene clusters from MIBiG 3.1
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.
Click on reference genes to show details of similarities to genes within the current region.
Click on an accession to open that entry in the MiBIG database.

No matches found.

gnlProkkaPCFPDMBM_12 - 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: 11,162 - 34,731 nt. (total: 23,570 nt) Show pHMM detection rules used
terpene: (Terpene_synth or Terpene_synth_C or phytoene_synt or Lycopene_cycl or terpene_cyclase or NapT7 or fung_ggpps or fung_ggpps2 or trichodiene_synth or TRI5)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
KnownClusterBlast
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
Similar known gene clusters from MIBiG 3.1
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.
Click on reference genes to show details of similarities to genes within the current region.
Click on an accession to open that entry in the MiBIG database.
gnlProkkaPCFPDMBM_12 - Region 2 - 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: 248,590 - 304,518 nt. (total: 55,929 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))

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
NRPS/PKS domains
KnownClusterBlast
NRPS/PKS modules
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
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
Similar known gene clusters from MIBiG 3.1
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.
Click on reference genes to show details of similarities to genes within the current region.
Click on an accession to open that entry in the MiBIG database.
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
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 2, location 248589 - 304518:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Ser)

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).

ctg12_258: diOH-Bz
  Search NORINE for peptide: strict or relaxed
  AMP-binding (36..433): diOH-Bz
  nrpys: diOH-Bz
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
    Large clusters prediction:
      Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
    Small clusters prediction:
      Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
    Single AA prediction:
      dhb (diOH-Bz)
  Stachelhaus prediction details:
    Stachelhaus sequence:
      AMPSQGVVNK
    Nearest Stachelhaus code(s):
      diOH-Bz TMPSQGVVNK (91% 8Å match)
    Stachelhaus code match:
      90% (moderate)
ctg12_266: Ser
  Search NORINE for peptide: strict or relaxed
  AMP-binding (460..860): 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:
      DVWHFSLVDK
    Nearest Stachelhaus code(s):
      Ser DVWHFSLVDK (100% 8Å match)
    Stachelhaus code match:
      100% (strong)

gnlProkkaPCFPDMBM_34 - 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: 1 - 22,441 nt. (total: 22,441 nt) Show pHMM detection rules used
Region on contig edge.
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
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
NRPS/PKS domains
KnownClusterBlast
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
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
Similar known gene clusters from MIBiG 3.1
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.
Click on reference genes to show details of similarities to genes within the current region.
Click on an accession to open that entry in the MiBIG database.

No matches found.

NRPS/PKS substrates
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).

ctg29_9: pk
  PKS_AT (12..294): pk
  ATSignature: Malonyl-CoA, inactive
  Top 3 matches:
    Malonyl-CoA: 62.5%
    inactive: 62.5%
  minowa: Methoxymalonyl-CoA
  Prediction, score:
    Methoxymalonyl-CoA: 19.7
    Malonyl-CoA: 16.9
    Methylmalonyl-CoA: 12.9
    Acetyl-CoA: 11.3
    inactive: 10.2
    trans-1,2-CPDA: 0.0
    fatty_acid: 0.0
    Propionyl-CoA: 0.0
    Isobutyryl-CoA: 0.0
    Ethylmalonyl-CoA: 0.0
    CHC-CoA: 0.0
    Benzoyl-CoA: 0.0
    3-Methylbutyryl-CoA: 0.0
    2-Methylbutyryl-CoA: 0.0

gnlProkkaPCFPDMBM_37 - Region 1 - thiopeptide
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 128,854 - 155,154 nt. (total: 26,301 nt) Show pHMM detection rules used
thiopeptide: ((YcaO or TIGR03604) and ((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or PF07366 or PF06968 or PF04055) or thiostrepton)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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
KnownClusterBlast
Thiopeptides
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
Similar known gene clusters from MIBiG 3.1
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.
Click on reference genes to show details of similarities to genes within the current region.
Click on an accession to open that entry in the MiBIG database.
Thiopeptide predictions
Lists the possible core peptides for each biosynthetic enzyme. Predicted tail sequences are also shown, if present.
Includes CompaRiPPson results for any available databases, with a detailed explanation here.
No core peptides found.
Thiopeptides
Core peptide predictions
Lists the possible core peptides in the region. Each core peptide lists its possible molecular weights and the scores for cleavage site prediction and RODEO. If relevant, other features, such as macrocycle and amidation, will also be listed.
No core peptides found.