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Overview
1.1
1.2

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

NZ_LR134479.1

Region | Type | From | To | Most similar known cluster | Similarity
--- | --- | --- | --- | --- | ---
Region 1 | lassopeptide,lanthipeptide-class-ii | 246,015 | 287,919 |
Region 2 | NRPS | 1,575,724 | 1,619,980 | steffimycin D | Polyketide:Type II + Saccharide:Hybrid/tailoring | 8%

NZ_LR134479.1 - Region 1 - lanthipeptide-class-ii,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: 246,015 - 287,919 nt. (total: 41,905 nt) Show pHMM detection rules used
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

#### 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
MIBiG comparison
KnownClusterBlast
Lanthipeptides
Lasso peptides
Pfam domains
TIGRFAM domains
Similar gene clusters
Shows careas 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 | lanthipeptide-class-ii | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | ---
BGC0000554.1 |  |  | 0.47 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001311.1 |  |  | 0.45 | RiPP | flavecins | Ruminococcus flavefaciens FD-1
BGC0001550.1 |  |  | 0.45 | RiPP | citrulassin D | Streptomyces katrae
BGC0000575.1 |  |  | 0.45 | RiPP | lariatin | Rhodococcus jostii
BGC0000552.1 |  |  | 0.44 | RiPP | SmbA, SmbB | Streptococcus mutans
BGC0001549.1 |  |  | 0.44 | RiPP | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0000555.1 |  |  | 0.43 | RiPP | staphylococcin C55 α, staphylococcin C55 β | Staphylococcus aureus
BGC0001210.1 |  |  | 0.43 | RiPP | pseudomycoicidin | Bacillus pseudomycoides DSM 12442
BGC0001576.1 |  |  | 0.43 | RiPP | divamide A | Prochloron didemni
BGC0000500.1 |  |  | 0.42 | RiPP | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001550.1 |  | 0.66 | RiPP | citrulassin D | Streptomyces katrae
BGC0000575.1 |  | 0.66 | RiPP | lariatin | Rhodococcus jostii
BGC0000554.1 |  | 0.66 | RiPP | SRO15-3108 | Streptomyces filamentosus NRRL 15998
BGC0001549.1 |  | 0.65 | RiPP | citrulassin B | Streptomyces aurantiacus JA 4570
BGC0001552.1 |  | 0.65 | RiPP | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001655.1 |  | 0.64 | RiPP | LP2006 | Nocardiopsis alba DSM 43377
BGC0001391.1 |  | 0.64 | RiPP | thusin | Bacillus thuringiensis serovar rongseni
BGC0001779.1 |  | 0.63 | RiPP | siamycin | Streptomyces nodosus
BGC0001311.1 |  | 0.63 | RiPP | flavecins | Ruminococcus flavefaciens FD-1
BGC0001889.1 |  | 0.63 | RiPP | fusilassin | Thermobifida fusca YX

Similar known gene clusters
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
Lists the possible core peptides for each biosynthetic enzyme, including the predicted class. Each core peptide shows the leader and core peptide sequences, separated by a dash.

#### Lanthipeptide(s) for ctg1_264 - Putative Class II

ctg1_263 leader / core peptide
  MAKDTMFMEELTDQELEQVNGG - CYDha Dha CGYYGGDhaYGGDhaYGGDhaYGGDha Dha Dha DhaYYGGDhaYDhaGGGYYYAAVGYGYDha C
ctg1_265 leader / core peptide
  MPKDITLLEEISDQELGQVNGG - GDhaHGGGYYDha DhaVGGGDhaYGGGYCGGGCGGYGYGFGFWGGDhaFDha
allorf_0265595_0265780 leader / core peptide
  VTKYCMSHAKYYGA - EDhaQKLMFVIYC DhaPPDhaARGYDhbQNARIMDhaPGVKLWLAGRQPDhaPVAGCPR
allorf_0269996_0270211 leader / core peptide
  LEIMMRTYCILPRWFDTVEGLARVAISLLQGRELIVGVLLRMQRMDSIESFRKLILGS - YCVIGDhbVLHDhaHIDha

#### Lanthipeptide(s) for ctg1_266 - Putative Class II

ctg1_263 leader / core peptide
  MAKDTMFMEELTDQELEQVNGG - CYDha Dha CGYYGGDhaYGGDhaYGGDhaYGGDha Dha Dha DhaYYGGDhaYDhaGGGYYYAAVGYGYDha C
ctg1_265 leader / core peptide
  MPKDITLLEEISDQELGQVNGG - GDhaHGGGYYDha DhaVGGGDhaYGGGYCGGGCGGYGYGFGFWGGDhaFDha
allorf_0265595_0265780 leader / core peptide
  VTKYCMSHAKYYGA - EDhaQKLMFVIYC DhaPPDhaARGYDhbQNARIMDhaPGVKLWLAGRQPDhaPVAGCPR
allorf_0269996_0270211 leader / core peptide
  LEIMMRTYCILPRWFDTVEGLARVAISLLQGRELIVGVLLRMQRMDSIESFRKLILGS - YCVIGDhbVLHDhaHIDha
allorf_0265627_0265695 leader / core peptide
  VYPLADGGEQYM - DhbNINFCDDhaAP
allorf_0265696_0265836 leader / core peptide
  LCRWRIRAVLAS - C DhaLKPDHHLGHPADhbGEGCRPADhaQDhaFDhbPGLIILAF
allorf_0265791_0265895 leader / core peptide
  VFLHPARRLLIGG - GLLGVPDha CAGGAFAPYLLRVP
allorf_0270096_0270281 leader / core peptide
  LLCALIALYYG - HHIDhbKWCDIKWKLRICEDhaVKLFLDhaHNRDhaPIDhaAFGDha DhaQCYPFFADha DhaIEHPQ
allorf_0270410_0270481 leader / core peptide
  VVENRDLASS - DhaPKHDha DhbIKNC DhaRK

#### Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine
Lasso peptide predictions
Lists the possible core peptides for each biosynthetic enzyme, including the predicted class. Each core peptide shows the leader and core peptide sequences, separated by a dash.

#### Lassopeptide(s) for allorf_0255011_0255136 - Putative Class II

allorf_0255011_0255136 leader / core peptide / cleaved tail
  LDNAMYTKATFTKITSFRAATH - G W Y W G N R R DIYGALRYANK

#### Legend:

Red: Putative macrolactam
Purple: Putative cleaved off residues
Detailed Pfam domain annotation
Shows Pfam domains found in each gene within the region. Click on each domain for more information about the domain's accession, location, and description. Domains with a bold border have Gene Ontology information.
Selected features only
Expand to show all names
Detailed TIGRFAM domain annotation
Shows TIGRFAM domains found in each gene within the region. Click on each domain for more information about the domain's accession, location, and description.
Selected features only
Expand to show all names
Lanthipeptides
Lasso peptides
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.

ctg1_263 - Class II
  Cleavage pHMM score: 4.70
  RODEO score: 0
  Monoisotopic mass: 4591.8 Da
  Molecular weight: 4594.7 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4612.7 Da N = 1
    4630.7 Da N = 2
    4648.7 Da N = 3
    4666.7 Da N = 4
    4684.8 Da N = 5
    4702.8 Da N = 6
    4720.8 Da N = 7
    4738.8 Da N = 8
    4756.8 Da N = 9
ctg1_265 - Class II
  Cleavage pHMM score: 3.20
  RODEO score: 0
  Monoisotopic mass: 3620.4 Da
  Molecular weight: 3622.7 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3640.7 Da N = 1
    3658.8 Da N = 2
    3676.8 Da N = 3
    3694.8 Da N = 4
allorf_0265595_0265780 - Class II
  Cleavage pHMM score: -7.00
  RODEO score: 0
  Monoisotopic mass: 5038.6 Da
  Molecular weight: 5041.9 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    5059.9 Da N = 1
    5077.9 Da N = 2
    5095.9 Da N = 3
    5114.0 Da N = 4
allorf_0269996_0270211 - Class II
  Cleavage pHMM score: -4.70
  RODEO score: 0
  Monoisotopic mass: 1373.7 Da
  Molecular weight: 1374.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1392.6 Da N = 1
    1410.6 Da N = 2
ctg1_263 - Class II
  Cleavage pHMM score: 4.70
  RODEO score: 0
  Monoisotopic mass: 4591.8 Da
  Molecular weight: 4594.7 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    4612.7 Da N = 1
    4630.7 Da N = 2
    4648.7 Da N = 3
    4666.7 Da N = 4
    4684.8 Da N = 5
    4702.8 Da N = 6
    4720.8 Da N = 7
    4738.8 Da N = 8
    4756.8 Da N = 9
ctg1_265 - Class II
  Cleavage pHMM score: 3.20
  RODEO score: 0
  Monoisotopic mass: 3620.4 Da
  Molecular weight: 3622.7 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3640.7 Da N = 1
    3658.8 Da N = 2
    3676.8 Da N = 3
    3694.8 Da N = 4
allorf_0265595_0265780 - Class II
  Cleavage pHMM score: -7.00
  RODEO score: 0
  Monoisotopic mass: 5038.6 Da
  Molecular weight: 5041.9 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    5059.9 Da N = 1
    5077.9 Da N = 2
    5095.9 Da N = 3
    5114.0 Da N = 4
allorf_0269996_0270211 - Class II
  Cleavage pHMM score: -4.70
  RODEO score: 0
  Monoisotopic mass: 1373.7 Da
  Molecular weight: 1374.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1392.6 Da N = 1
    1410.6 Da N = 2
allorf_0265627_0265695 - Class II
  Cleavage pHMM score: -7.30
  RODEO score: 0
  Monoisotopic mass: 1044.5 Da
  Molecular weight: 1045.1 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1063.1 Da N = 1
allorf_0265696_0265836 - Class II
  Cleavage pHMM score: -6.10
  RODEO score: 0
  Monoisotopic mass: 3466.8 Da
  Molecular weight: 3468.9 Da
  Number of bridges: 2
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    3487.0 Da N = 1
    3505.0 Da N = 2
    3523.0 Da N = 3
allorf_0265791_0265895 - Class II
  Cleavage pHMM score: -6.00
  RODEO score: 0
  Monoisotopic mass: 2039.1 Da
  Molecular weight: 2040.4 Da
  Number of bridges: 1
allorf_0270096_0270281 - Class II
  Cleavage pHMM score: -6.10
  RODEO score: 0
  Monoisotopic mass: 5695.9 Da
  Molecular weight: 5699.5 Da
  Number of bridges: 3
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    5717.5 Da N = 1
    5735.6 Da N = 2
    5753.6 Da N = 3
    5771.6 Da N = 4
    5789.6 Da N = 5
    5807.6 Da N = 6
allorf_0270410_0270481 - Class II
  Cleavage pHMM score: -6.40
  RODEO score: 0
  Monoisotopic mass: 1412.8 Da
  Molecular weight: 1413.6 Da
  Number of bridges: 1
  Alternative weights
    (assuming N unmodified Ser/Thr residues)
    1431.7 Da N = 1
    1449.7 Da N = 2
    1467.7 Da N = 3

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.

allorf_0255011_0255136 - Class II
  Cleavage pHMM score: -5.50
  RODEO score: 19
  Monoisotopic mass: 2340.2 Da
  Molecular weight: 2341.6 Da
  Number of bridges: 0

NZ_LR134479.1 - Region 2 - 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: 1,575,724 - 1,619,980 nt. (total: 44,257 nt) Show pHMM detection rules used
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
NRPS/PKS domains
MIBiG comparison
KnownClusterBlast
NRPS/PKS modules
Pfam domains
TIGRFAM domains
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 glossary is available here.
Selected features only
Show module domains
Similar gene clusters
Shows careas 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 | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001615.1 |  | 0.33 | NRP | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0001437.1 |  | 0.28 | NRP | obafluorin | Pseudomonas fluorescens
BGC0001710.1 |  | 0.28 | NRP | obafluorin | Pseudomonas fluorescens
BGC0000417.1 |  | 0.26 | NRP | rhodochelin | Rhodococcus jostii RHA1
BGC0001833.1 |  | 0.25 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0000410.1 |  | 0.24 | NRP | pseudomonine | Pseudomonas fluorescens
BGC0001538.1 |  | 0.24 | NRP, Polyketide | caboxamycin | Streptomyces sp. NTK 937
BGC0001825.1 |  | 0.24 | NRP | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.1 |  | 0.24 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000426.1 |  | 0.23 | NRP | sevadicin | Paenibacillus larvae

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0001615.1 |  | 0.67 | NRP | hexose-palythine-serine, hexose-shinorine | Heteroscytonema crispum UCFS10
BGC0001437.1 |  | 0.62 | NRP | obafluorin | Pseudomonas fluorescens
BGC0001710.1 |  | 0.62 | NRP | obafluorin | Pseudomonas fluorescens
BGC0000417.1 |  | 0.60 | NRP | rhodochelin | Rhodococcus jostii RHA1
BGC0001833.1 |  | 0.58 | NRP | icosalide A, icosalide B | Burkholderia gladioli
BGC0000410.1 |  | 0.57 | NRP | pseudomonine | Pseudomonas fluorescens
BGC0001538.1 |  | 0.57 | NRP, Polyketide | caboxamycin | Streptomyces sp. NTK 937
BGC0001825.1 |  | 0.57 | NRP | xenematide | Xenorhabdus nematophila AN6/1
BGC0001132.1 |  | 0.57 | NRP | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0000426.1 |  | 0.56 | NRP | sevadicin | Paenibacillus larvae

Similar known gene clusters
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 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.
Legend
Detailed Pfam domain annotation
Shows Pfam domains found in each gene within the region. Click on each domain for more information about the domain's accession, location, and description. Domains with a bold border have Gene Ontology information.
Selected features only
Expand to show all names
Detailed TIGRFAM domain annotation
Shows TIGRFAM domains found in each gene within the region. Click on each domain for more information about the domain's accession, location, and description.
Selected features only
Expand to show all names
NRPS/PKS products
NRPS/PKS monomers
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 4, location 1575723 - 1619980:
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 monomer predictions
Shows the predicted monomers for each adynelation 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_1361: ser
  Search NORINE for peptide: strict or relaxed
  AMP-binding (515..966): ser
  NRPSPredictor2: ser
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aliphatic
    Large clusters prediction:
      ser, thr, dhpg, hpg
    Small clusters prediction:
      ser
    Single AA prediction:
      ser
  Stachelhaus prediction details:
    Stachelhaus sequence:
      DVWHVSLVDK
    Nearest Stachelhaus code:
      ser
    Stachelhaus code match:
      100% (strong)
ctg1_1363: dhb
  Search NORINE for peptide: strict or relaxed
  AMP-binding (50..465): dhb
  NRPSPredictor2: dhb
  SVM prediction details:
    Predicted physicochemical class:
      hydrophobic-aromatic
    Large clusters prediction:
      dhb, sal
    Small clusters prediction:
      dhb, sal
    Single AA prediction:
      dhb
  Stachelhaus prediction details:
    Stachelhaus sequence:
      TMPaQGVVNK
    Nearest Stachelhaus code:
      dhb
    Stachelhaus code match:
      90% (moderate)