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Overview
1.1

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

BGC0002686 (Actinomadura sp. WMMA1423)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | NRP-metallophore,NRPS | 1 | 114,016 | High | madurastatin D1/madurastatin D2/(-)-Madurastatin C1 | NRPS:Type I

BGC0002686 - 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
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Location: 1 - 114,016 nt. (total: 114,016 nt) Show pHMM detection rules used
Region on contig edge.
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
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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
MIBiG
Tailoring
MIBiG comparison
KnownClusterBlast
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
External annotation
This annotation was made externally by 'MIBiG' and not by antiSMASH

Name |  | MIBiG
Version |  | 4.0alpha

Type |  | Subregion
Location |  | 1 - 114,017
Label |  | BGC0002686

Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxygenase
FKD65_RS04195: acyl-CoA dehydrogenase

smcogs
  SMCOG1006: acyl-CoA dehydrogenase

FKD65_RS04320: lysine/ornithine N-monooxygenase

smcogs
  SMCOG1080: lysine/ornithine N-monooxygenase

Transferases: acyltransferase
FKD65_RS04245: acyltransferase 3

smcogs
  SMCOG1088: acyltransferase 3

Isomerases: isomerase
FKD65_RS04335: isochorismate synthase

smcogs
  SMCOG1018: isochorismate synthase

Ligases: ligase
FKD65_RS04210: carboxylate-amine ligase

smcogs
  SMCOG1165: carboxylate-amine ligase

FKD65_RS04300: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FKD65_RS04330: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

FKD65_RS04500: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

FKD65_RS04515: 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 | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0002686.2 |  |  |  | 1.44 | NRPS | madurastatin D1, madurastatin D2, (-)-Madurastatin C1 | Actinomadura sp. WMMA1423
BGC0001261.3 |  |  |  | 1.02 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  |  |  | 1.00 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  |  |  | 0.98 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0000307.4 |  |  |  | 0.97 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001132.4 |  |  |  | 0.96 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  |  |  | 0.95 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0001128.4 |  |  |  | 0.95 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3 |  |  |  | 0.94 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4 |  |  |  | 0.87 | NRPS | kolossin | Photorhabdus laumondii subsp. laumondii TTO1

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0002686.2 |  | 0.98 | NRPS | madurastatin D1, madurastatin D2, (-)-Madurastatin C1 | Actinomadura sp. WMMA1423
BGC0000342.4 |  | 0.73 | NRPS | enniatin | Fusarium equiseti
BGC0002135.2 |  | 0.71 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0001261.3 |  | 0.70 | NRPS | AM-toxin | Alternaria alternata
BGC0001135.5 |  | 0.68 | NRPS | bicornutin A1, bicornutin A2 | Xenorhabdus budapestensis
BGC0001833.4 |  | 0.68 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001132.4 |  | 0.68 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061
BGC0001825.4 |  | 0.67 | NRPS | xenematide | Xenorhabdus nematophila AN6/1
BGC0000307.4 |  | 0.67 | NRPS | AbT1 | Aureobasidium pullulans
BGC0001128.4 |  | 0.67 | NRPS | gamexpeptide 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
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 2843 - 58702:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Gly - X - NMe-OH-Orn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 70653 - 114016:
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).
FKD65_RS04300: X
AMP-binding (16..437): X
nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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:
    HVWSTGGPLK
  Nearest Stachelhaus code(s):
    Ile DFWSTGVILK (29% 8Å match)
  Stachelhaus code match:
    60% (weak)

FKD65_RS04330: Gly - X - OH-Orn
Search NORINE for peptide: strict or relaxed
AMP-binding (499..879): 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:
    DILQLGMIWK
  Nearest Stachelhaus code(s):
    Gly DILQLGMIWK (68% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1512..1867): X
nrpys: me-bAla, bAla

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:
    IDTTISLGDK
  Nearest Stachelhaus code(s):
    me-bAla LDTTVSLGDK (71% 8Å match)
    bAla VDTVISLGDK (53% 8Å match)
  Stachelhaus code match:
    80% (moderate)

AMP-binding (2492..2904): 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:
    DMENLGLINK
  Nearest Stachelhaus code(s):
    OH-Orn DMENLGLINK (97% 8Å match)
  Stachelhaus code match:
    100% (strong)

FKD65_RS04500: X
AMP-binding (30..425): X
nrpys: (unknown)

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:
    ALPAQGVLNK
  Nearest Stachelhaus code(s):
    Sal PLPAQGVLNK (88% 8Å match)
  Stachelhaus code match:
    90% (moderate)

FKD65_RS04515: Ser
Search NORINE for peptide: strict or relaxed
AMP-binding (541..916): 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:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Small clusters prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)
  Single AA prediction:
    Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:
  Stachelhaus sequence:
    DLFNLGLIHK
  Nearest Stachelhaus code(s):
    Ser DLFNLGLIHK (94% 8Å match)
  Stachelhaus code match:
    100% (strong)

Link to PARAS substrate predictor