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Overview
1.1
1.2
1.3
1.4
1.5

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

gnlProkkaPHKLFAIJ_1 (original name was: gnl|Prokka|PHKLFAIJ_1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1.1 | T3PKS | 547,822 | 588,991 |
Region 1.2 | NRPS-like,NRPS | 1,833,794 | 1,893,475 |
Region 1.3 | RiPP-like | 2,057,792 | 2,069,051 | salivaricin CRL1328 α peptide/salivaricin CRL1328 β peptide | RiPP | 16%
Region 1.4 | cyclic-lactone-autoinducer | 2,458,740 | 2,479,444 | auriculamide | NRP | 9%
Region 1.5 | terpene | 2,744,842 | 2,765,723 |

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1.1 | T3PKS | 547,822 | 588,991 |
Region 1.2 | NRPS-like,NRPS | 1,833,794 | 1,893,475 |
Region 1.3 | RiPP-like | 2,057,792 | 2,069,051 | salivaricin CRL1328 α peptide/salivaricin CRL1328 β peptide | RiPP | 16%
Region 1.4 | cyclic-lactone-autoinducer | 2,458,740 | 2,479,444 | auriculamide | NRP | 9%
Region 1.5 | terpene | 2,744,842 | 2,765,723 |

No secondary metabolite regions were found in these records:
  gnlProkkaPHKLFAIJ_2 (original name was: gnl|Prokka|PHKLFAIJ_2)
  gnlProkkaPHKLFAIJ_3 (original name was: gnl|Prokka|PHKLFAIJ_3)
  gnlProkkaPHKLFAIJ_4 (original name was: gnl|Prokka|PHKLFAIJ_4)
  gnlProkkaPHKLFAIJ_5 (original name was: gnl|Prokka|PHKLFAIJ_5)
  gnlProkkaPHKLFAIJ_6 (original name was: gnl|Prokka|PHKLFAIJ_6)
  gnlProkkaPHKLFAIJ_7 (original name was: gnl|Prokka|PHKLFAIJ_7)
  gnlProkkaPHKLFAIJ_8 (original name was: gnl|Prokka|PHKLFAIJ_8)
  gnlProkkaPHKLFAIJ_9 (original name was: gnl|Prokka|PHKLFAIJ_9)
  gnlProkkaPHKLFAIJ_10 (original name was: gnl|Prokka|PHKLFAIJ_10)
  gnlProkkaPHKLFAIJ_11 (original name was: gnl|Prokka|PHKLFAIJ_11)
  gnlProkkaPHKLFAIJ_12 (original name was: gnl|Prokka|PHKLFAIJ_12)
  gnlProkkaPHKLFAIJ_13 (original name was: gnl|Prokka|PHKLFAIJ_13)

Compact view
gnlProkkaPHKLFAIJ_1 - Region 1 - T3PKS
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 547,822 - 588,991 nt. (total: 41,170 nt) Show pHMM detection rules used
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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).

gnlProkkaPHKLFAIJ_1 - Region 2 - NRPS,NRPS-like
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,833,794 - 1,893,475 nt. (total: 59,682 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX))
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.

No 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
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 1833793 - 1893475:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X - Ala) + (D-Ser - Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 1833793 - 1875632:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X - Ala) + (D-Ser - Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 1837606 - 1893475:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (X - X - Ala) + (D-Ser - Gly)

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).

ctg1_1912: X
  AMP-binding (11..190): X
ctg1_1915: Ser - Gly
  Search NORINE for peptide: strict or relaxed
  AMP-binding (575..961): 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:
      DVWHFSLIDK
    Nearest Stachelhaus code(s):
      Ser DVWHFSLIDK (94% 8Å match)
    Stachelhaus code match:
      100% (strong)
  AMP-binding (1981..2359): Gly
  nrpys: Gly
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
    Large clusters prediction:
      Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
    Small clusters prediction:
      Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
    Single AA prediction:
      gly (Gly)
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DITQMGIVWK
    Nearest Stachelhaus code(s):
      Gly DILQMGMVWK (62% 8Å match)
    Stachelhaus code match:
      80% (moderate)
ctg1_1916: X - X - Ala
  Search NORINE for peptide: strict or relaxed
  AMP-binding (8..381): X
  nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad
  SVM prediction details:
    Predicted physicochemical class:
      hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
    Large clusters prediction:
      N/A
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      SVTQAAVAGK
    Nearest Stachelhaus code(s):
    Stachelhaus code match:
      0% (weak)
  AMP-binding (1000..1372): 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:
      DSHGYGCVLK
    Nearest Stachelhaus code(s):
    Stachelhaus code match:
      0% (weak)
  AMP-binding (1967..2333): Ala
  nrpys: Ala
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
    Large clusters prediction:
      Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
    Small clusters prediction:
      N/A
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVLIVAAVIK
    Nearest Stachelhaus code(s):
      Ala DVWVVAAVIK (68% 8Å match)
      S-bohPhe or Phe DALIVAAVCK (56% 8Å match)
    Stachelhaus code match:
      80% (moderate)

gnlProkkaPHKLFAIJ_1 - Region 3 - 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: 2,057,792 - 2,069,051 nt. (total: 11,260 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
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.
gnlProkkaPHKLFAIJ_1 - Region 4 - cyclic-lactone-autoinducer
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 2,458,740 - 2,479,444 nt. (total: 20,705 nt) Show pHMM detection rules used
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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.
gnlProkkaPHKLFAIJ_1 - Region 5 - 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: 2,744,842 - 2,765,723 nt. (total: 20,882 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.

No matches found.