Select genomic region:
Overview
1.1

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

BGC0000429 (Streptomyces sp. Acta 2897)

Region | Type | From | To | Similarity Confidence | Most similar known cluster
--- | --- | --- | --- | --- | ---
Region 1 | arylpolyene,terpene-precursor,NRPS | 1 | 86,806 | High | skyllamycin A/skyllamycin B | NRPS:Type I+PKS

BGC0000429 - Region 1 - NRPS,arylpolyene,terpene-precursor
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 - 86,806 nt. (total: 86,806 nt) Show pHMM detection rules used
Region on contig edge.
arylpolyene: (APE_KS1 or APE_KS2)
terpene-precursor: (PT_FPPS_like and not PT_HPP)
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
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
MIBiG
Tailoring
MIBiG comparison
KnownClusterBlast
Terpene
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 - 86,807
Label |  | BGC0000429

Tailoring functions
Tailoring enzymes detected in this region
Oxidoreductases: dehydrogenase oxidoreductase oxygenase
sky26: short-chain dehydrogenase/reductase SDR

smcogs
  SMCOG1001: short-chain dehydrogenase/reductase SDR

sky28: dehydrogenase

smcogs
  SMCOG1222: dehydrogenase

sky32: cytochrome P450

smcogs
  SMCOG1007: cytochrome P450

sky4: NADH:flavin oxidoreductase/NADH oxidase

smcogs
  SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

sky40: flavin reductase domain protein FMN-binding

smcogs
  SMCOG1160: flavin reductase domain protein FMN-binding

Transferases: acylase methyltransferase transferase
sky11: acetyl-CoA carboxylase, carboxyl transferase,

smcogs
  SMCOG1059: acetyl-CoA carboxylase, carboxyl transferase,

sky13: malonyl CoA-acyl carrier protein transacylase

smcogs
  SMCOG1021: malonyl CoA-acyl carrier protein transacylase

sky37: O-methyltransferase

smcogs
  SMCOG1042: O-methyltransferase

Hydrolases: esterase
sky33: thioesterase

smcogs
  SMCOG1004: thioesterase

Ligases: ligase synthase synthetase
AEA30255.1: Polyprenyl synthetase

smcogs
  SMCOG1182: Polyprenyl synthetase

sky17: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

sky18: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

sky19: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

sky22: Beta-ketoacyl synthase

smcogs
  SMCOG1022: Beta-ketoacyl synthase

sky29: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

sky30: AMP-dependent synthetase and ligase

smcogs
  SMCOG1002: AMP-dependent synthetase and ligase

sky31: condensation domain-containing protein

smcogs
  SMCOG1127: condensation domain-containing protein

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 | arylpolyene | terpene-precursor | NRPS | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | --- | --- | ---
BGC0000429.4 |  |  |  | 1.62 | NRPS, PKS | skyllamycin A, skyllamycin B | Streptomyces sp. Acta 2897
BGC0002676.2 |  |  |  | 0.92 | NRPS | skyllamycin D, skyllamycin E | Streptomyces anulatus
BGC0000107.3 |  |  |  | 0.91 | PKS | naphthopyrone | Aspergillus nidulans FGSC A4
BGC0002192.3 |  |  |  | 0.90 | PKS | FR901512 | fungal sp. No.14919
BGC0001164.3 |  |  |  | 0.87 | PKS | 1-heptadecene | Cyanothece sp. PCC 7822
BGC0001276.3 |  |  |  | 0.84 | PKS | 6-methylsalicyclic acid | Aspergillus terreus
BGC0002510.2 |  |  |  | 0.58 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces sp.
BGC0001987.2 |  |  |  | 0.51 | PKS | koreenceine A, koreenceine B, koreenceine C, koreenceine D | Pseudomonas koreensis
BGC0002008.3 |  |  |  | 0.49 | other (other) | aryl polyenes | Xenorhabdus doucetiae
BGC0002547.2 |  |  |  | 0.49 | PKS | youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4 | Streptomyces youssoufiensis

Reference | Aggregated | Similarity score | Type | Compound(s) | Organism
--- | --- | --- | --- | --- | ---
BGC0000429.4 |  | 0.99 | NRPS, PKS | skyllamycin A, skyllamycin B | Streptomyces sp. Acta 2897
BGC0002676.2 |  | 0.80 | NRPS | skyllamycin D, skyllamycin E | Streptomyces anulatus
BGC0001833.4 |  | 0.75 | NRPS | icosalide A, icosalide B | Burkholderia gladioli
BGC0001758.4 |  | 0.75 | NRPS | rhizomide A, rhizomide B, rhizomide C | Paraburkholderia rhizoxinica HKI 454
BGC0002135.2 |  | 0.74 | NRPS | bovienimide A | Xenorhabdus bovienii SS-2004
BGC0002075.3 |  | 0.74 | NRPS | pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E | Pseudomonas fluorescens
BGC0001128.4 |  | 0.73 | NRPS | gamexpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4 |  | 0.73 | NRPS | taxlllaid A | Xenorhabdus bovienii SS-2004
BGC0002286.3 |  | 0.73 | NRPS | ririwpeptide A, ririwpeptide B, ririwpeptide C | Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4 |  | 0.73 | NRPS | xenotetrapeptide | Xenorhabdus nematophila ATCC 19061

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
Detailed terpene predictions
Detailed information for terpene domains. Shows possible products of a terpene cluster and lists the subtype and expected reactions for each terpene-related domain.
Product predictions:

Class | Subclass | Product name | Chain length | Initial cyclisations | Functional groups
--- | --- | --- | --- | --- | ---
sesquiterpene precursor |  | FPP | C15 | acyclic | PP
diterpene precursor |  | GGPP | C20 | acyclic | PP
sesterterpene precursor |  | GFPP | C25 | acyclic | PP
triterpene precursor |  | HPP | C30 | acyclic | PP

Genes with terpene domains:
AEA30255.1: PT_FPPS_like
Domain 1 (55 - 340): Prenyltransferase; Farnesyl diphosphate synthase like
Subtype: unknown

Reactions:
  IPP, DMAPP → FPP
  IPP, DMAPP → GGPP
  IPP, DMAPP → GFPP
  IPP, DMAPP → HPP

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
Terpene
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 0 - 86241:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - Ala - X - D-Gly) + (Phe - Pro - X - D-Trp) + (Gly - D-Leu - Leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 37389:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - Ala - X - D-Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 6088 - 86241:
Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:
  (Thr - Ala - X - D-Gly) + (Phe - Pro - X - D-Trp) + (Gly - D-Leu - Leu)

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).
sky13: mal
PKS_AT (8..292): mal
ATSignature: Malonyl-CoA

Top 3 matches:
  Malonyl-CoA: 75.0%
  Methylmalonyl-CoA: 54.2%
  inactive: 54.2%

minowa: Malonyl-CoA

Prediction, score:
  Malonyl-CoA: 94.0
  Methoxymalonyl-CoA: 44.5
  Methylmalonyl-CoA: 40.2
  inactive: 32.1
  Propionyl-CoA: 14.2
  2-Methylbutyryl-CoA: 10.5
  trans-1,2-CPDA: 8.3
  CHC-CoA: 5.2
  Acetyl-CoA: 4.3
  Ethylmalonyl-CoA: 4.2
  Isobutyryl-CoA: 3.8
  Benzoyl-CoA: 1.2
  3-Methylbutyryl-CoA: 0.0
  fatty_acid: -0.7

sky29: Thr - Ala - X - Gly
Search NORINE for peptide: strict or relaxed
AMP-binding (461..877): Thr
nrpys: Thr

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:
    thr (Thr)
  Single AA prediction:
    thr (Thr)

Stachelhaus prediction details:
  Stachelhaus sequence:
    DFWNVGMVHK
  Nearest Stachelhaus code(s):
    Thr DFWNVGMVHK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1538..1939): 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:
    Tiny, hydrophilic, transition to aliphatic (Gly, Ala)
  Single AA prediction:
    ala (Ala)

Stachelhaus prediction details:
  Stachelhaus sequence:
    DVFSVAFVYK
  Nearest Stachelhaus code(s):
    Ala DVFSVAFVYK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2599..3004): X
nrpys: bMe-Asp, Asp

SVM prediction details:
  Predicted physicochemical class:
    hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
  Large clusters prediction:
    Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
  Small clusters prediction:
    asp,asn (Asp, Asn)
  Single AA prediction:
    asn (Asn)

Stachelhaus prediction details:
  Stachelhaus sequence:
    DLTKMGGVNK
  Nearest Stachelhaus code(s):
    bMe-Asp or Asp DLTKMGGVNK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3664..4060): 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:
    DILQLGMVWK
  Nearest Stachelhaus code(s):
    Gly DILQLGMVWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

sky30: Phe - Pro - X - Trp
Search NORINE for peptide: strict or relaxed
AMP-binding (461..856): Phe
nrpys: Phe

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    Unpolar aromatic ring (Phe, Trp)
  Single AA prediction:
    phe (Phe)

Stachelhaus prediction details:
  Stachelhaus sequence:
    DAWTVAAVCK
  Nearest Stachelhaus code(s):
    Phe DAWTVAAVCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1514..1923): Pro
nrpys: Pro

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:
    Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
  Small clusters prediction:
    pro (Pro)
  Single AA prediction:
    pro (Pro)

Stachelhaus prediction details:
  Stachelhaus sequence:
    DVQYAAHVVK
  Nearest Stachelhaus code(s):
    Pro DVQYAAHVVK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (2582..2976): X
nrpys: omeTyr

SVM prediction details:
  Predicted physicochemical class:
    hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
  Large clusters prediction:
    Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
  Small clusters prediction:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    DAWNIAAVCK
  Nearest Stachelhaus code(s):
    omeTyr DAWNIAAVCK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3639..4036): Trp
nrpys: Trp

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:
    Polar aromatic ring (Tyr, bOH-Tyr)
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    DVGMVGAVAK
  Nearest Stachelhaus code(s):
    Trp DVGMVGAVAK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

sky31: Gly - Leu - Leu
Search NORINE for peptide: strict or relaxed
AMP-binding (462..860): 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:
    DILQLGVVWK
  Nearest Stachelhaus code(s):
    Gly DILQLGVVWK (100% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (1521..1919): Leu
nrpys: 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    DALLVGAVAK
  Nearest Stachelhaus code(s):
    Leu DALLVGAVAK (100% 8Å match)
    3OH-Leu DALLVGAVAK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

AMP-binding (3061..3462): Leu
nrpys: 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:
    N/A
  Single AA prediction:
    N/A

Stachelhaus prediction details:
  Stachelhaus sequence:
    DALLVGAVAK
  Nearest Stachelhaus code(s):
    Leu DALLVGAVAK (100% 8Å match)
    3OH-Leu DALLVGAVAK (79% 8Å match)
  Stachelhaus code match:
    100% (strong)

sky39: X
A-OX (0..351): X
Link to PARAS substrate predictor
Glossary
Glossary showing acronyms and their full names.

Acronym | Full name
--- | ---
DMAPP | Dimethylallyl diphosphate
FPP | Farnesyl diphosphate
GFPP | Geranylfarnesyl diphosphate
GGPP | Geranylgeranyl diphosphate
HPP | Hexaprenyl diphosphate
IPP | Isopentenyl diphosphate
PP | Diphosphate