Select genomic region:
Overview
1.1
2.1
3.1
6.1

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

gnlProkkaNMHGJOML_1 (original name was: gnl|Prokka|NMHGJOML_1)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1.1 | RRE-containing | 1,381,557 | 1,401,910 | polysaccharide C | Saccharide | 16%

gnlProkkaNMHGJOML_2 (original name was: gnl|Prokka|NMHGJOML_2)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 2.1 | phosphonate | 822,119 | 835,678 | polysaccharide B | Saccharide | 13%

gnlProkkaNMHGJOML_3 (original name was: gnl|Prokka|NMHGJOML_3)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 3.1 | lanthipeptide-class-i | 110,163 | 140,368 |

gnlProkkaNMHGJOML_6 (original name was: gnl|Prokka|NMHGJOML_6)

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 6.1 | NRPS-like | 207,479 | 249,908 |

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1.1 | RRE-containing | 1,381,557 | 1,401,910 | polysaccharide C | Saccharide | 16%
Region 2.1 | phosphonate | 822,119 | 835,678 | polysaccharide B | Saccharide | 13%
Region 3.1 | lanthipeptide-class-i | 110,163 | 140,368 |
Region 6.1 | NRPS-like | 207,479 | 249,908 |

No secondary metabolite regions were found in these records:
  gnlProkkaNMHGJOML_4 (original name was: gnl|Prokka|NMHGJOML_4)
  gnlProkkaNMHGJOML_5 (original name was: gnl|Prokka|NMHGJOML_5)
  gnlProkkaNMHGJOML_7 (original name was: gnl|Prokka|NMHGJOML_7)
  gnlProkkaNMHGJOML_8 (original name was: gnl|Prokka|NMHGJOML_8)
  gnlProkkaNMHGJOML_9 (original name was: gnl|Prokka|NMHGJOML_9)
  gnlProkkaNMHGJOML_10 (original name was: gnl|Prokka|NMHGJOML_10)
  gnlProkkaNMHGJOML_11 (original name was: gnl|Prokka|NMHGJOML_11)
  gnlProkkaNMHGJOML_12 (original name was: gnl|Prokka|NMHGJOML_12)
  gnlProkkaNMHGJOML_13 (original name was: gnl|Prokka|NMHGJOML_13)
  gnlProkkaNMHGJOML_14 (original name was: gnl|Prokka|NMHGJOML_14)
  gnlProkkaNMHGJOML_15 (original name was: gnl|Prokka|NMHGJOML_15)
  gnlProkkaNMHGJOML_16 (original name was: gnl|Prokka|NMHGJOML_16)
  gnlProkkaNMHGJOML_17 (original name was: gnl|Prokka|NMHGJOML_17)
  gnlProkkaNMHGJOML_18 (original name was: gnl|Prokka|NMHGJOML_18)
  gnlProkkaNMHGJOML_19 (original name was: gnl|Prokka|NMHGJOML_19)
  gnlProkkaNMHGJOML_20 (original name was: gnl|Prokka|NMHGJOML_20)
  gnlProkkaNMHGJOML_21 (original name was: gnl|Prokka|NMHGJOML_21)
  gnlProkkaNMHGJOML_22 (original name was: gnl|Prokka|NMHGJOML_22)
  gnlProkkaNMHGJOML_23 (original name was: gnl|Prokka|NMHGJOML_23)
  gnlProkkaNMHGJOML_24 (original name was: gnl|Prokka|NMHGJOML_24)
  gnlProkkaNMHGJOML_25 (original name was: gnl|Prokka|NMHGJOML_25)
  gnlProkkaNMHGJOML_26 (original name was: gnl|Prokka|NMHGJOML_26)
  gnlProkkaNMHGJOML_27 (original name was: gnl|Prokka|NMHGJOML_27)
  gnlProkkaNMHGJOML_28 (original name was: gnl|Prokka|NMHGJOML_28)
  gnlProkkaNMHGJOML_29 (original name was: gnl|Prokka|NMHGJOML_29)
  gnlProkkaNMHGJOML_30 (original name was: gnl|Prokka|NMHGJOML_30)
  gnlProkkaNMHGJOML_31 (original name was: gnl|Prokka|NMHGJOML_31)
  gnlProkkaNMHGJOML_32 (original name was: gnl|Prokka|NMHGJOML_32)
  gnlProkkaNMHGJOML_33 (original name was: gnl|Prokka|NMHGJOML_33)
  gnlProkkaNMHGJOML_34 (original name was: gnl|Prokka|NMHGJOML_34)
  gnlProkkaNMHGJOML_35 (original name was: gnl|Prokka|NMHGJOML_35)
  gnlProkkaNMHGJOML_36 (original name was: gnl|Prokka|NMHGJOML_36)
  gnlProkkaNMHGJOML_37 (original name was: gnl|Prokka|NMHGJOML_37)
  gnlProkkaNMHGJOML_38 (original name was: gnl|Prokka|NMHGJOML_38)
  gnlProkkaNMHGJOML_39 (original name was: gnl|Prokka|NMHGJOML_39)
  gnlProkkaNMHGJOML_40 (original name was: gnl|Prokka|NMHGJOML_40)

Compact view
gnlProkkaNMHGJOML_1 - Region 1 - RRE-containing
Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.
More detailed help is available here.
Download region GenBank file
Download region SVG
Location: 1,381,557 - 1,401,910 nt. (total: 20,354 nt) Show pHMM detection rules used
RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

#### Legend:

core biosynthetic genes
additional biosynthetic genes
transport-related genes
regulatory genes
other genes
resistance
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.
gnlProkkaNMHGJOML_2 - Region 1 - phosphonate
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: 822,119 - 835,678 nt. (total: 13,560 nt) Show pHMM detection rules used
phosphonate: (phosphonates and minimum(1, [2-Hacid_dh_C, Aldedh, Aminotran_1_2, Aminotran_5, AurF, CTP_transf_like, DUF4992, Fe-ADH, HMGL-like, Metallophos_2, NTP_transf_3, NTP_transf_5, PALP, PEP_mutase, TPP_enzyme_C, TPP_enzyme_N, phosphonates]) and not (phosphonatesHydrolase or phosphonatesMeIsocitrateLyase))

#### 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.
gnlProkkaNMHGJOML_3 - 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: 110,163 - 140,368 nt. (total: 30,206 nt) Show pHMM detection rules used
lanthipeptide-class-i: ((LANC_like and (Lant_dehydr_N or Lant_dehydr_C)) and not (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
Lanthipeptides
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.

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.
Lanthipeptides
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.
gnlProkkaNMHGJOML_6 - Region 1 - 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: 207,479 - 249,908 nt. (total: 42,430 nt) Show pHMM detection rules used
NRPS-like: cds((PP-binding or NAD_binding_4) 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 1, location 207478 - 249908:
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).

ctg6_184: X
  AMP-binding (12..401): X
  nrpys: Ile, Leu
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
    Large clusters prediction:
      Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
    Small clusters prediction:
      Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
    Single AA prediction:
      N/A
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DALFLGVVLK
    Nearest Stachelhaus code(s):
      Leu or Ile DAIYLGVVLK (59% 8Å match)
      aIle DALVFGVVLK (56% 8Å match)
    Stachelhaus code match:
      80% (moderate)