BGC0000429 - 1 region(s) - antiSMASH results

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

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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)

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

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Gene details

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Gene overview

MIBiG

Tailoring

MIBiG comparison

KnownClusterBlast

Terpene

NRPS/PKS modules

NRPS/PKS domains

Gene/CDS overview

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

External annotation

Name		MIBiG
Version		4.0alpha

Type		Subregion
Location		1 - 86,807
Label		BGC0000429

Tailoring functions

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

Analysis type:

Reference	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	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

Detailed terpene predictions

Product predictions:

Class	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

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Detailed domain annotation

Selected features only

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NRPS/PKS products

NRPS/PKS substrates

Terpene

Predicted core structure(s)

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

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

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