BGC0000379 - 1 region(s) - antiSMASH results

Identified secondary metabolite regions using strictness 'relaxed'

BGC0000379 (Streptomyces viridochromogenes)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1	NRPS-like,NRPS	1	88,912	High	glycinocin A	NRPS:Type I

BGC0000379 - Region 1 - NRPS,NRPS-like

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Location: 1 - 88,912 nt. (total: 88,912 nt) Show pHMM detection rules used

Region on contig edge.

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
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

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 - 88,913
Label		BGC0000379

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

AEF16019.1: Dioxygenase TauD/TfdA

smcogs: SMCOG1046: Dioxygenase TauD/TfdA

AEG64680.1: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

AEG64681.1: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

AEG64690.1: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: acyltransferase

lpmD: polyketide synthase associated protein papA3

smcogs: SMCOG1209: polyketide synthase associated protein papA3

Hydrolases: deaminase hydrolase

AEF16028.1: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

AEF16030.1: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

Lyases: lyase

dabB: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

dabC: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase

AEF16021.1: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

dabA: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

lpmA: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

lpmB: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

lpmC: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport

AEF16029.1: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000379.5	1.41	NRPS	glycinocin A	Streptomyces viridochromogenes
BGC0001135.5	0.88	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.86	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	0.86	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001261.3	0.85	NRPS	AM-toxin	Alternaria alternata
BGC0001128.4	0.85	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.85	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.81	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.80	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001825.4	0.78	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000379.5	0.99	NRPS	glycinocin A	Streptomyces viridochromogenes
BGC0001135.5	0.77	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.77	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.77	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.77	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.77	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.77	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.77	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	0.76	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001261.3	0.75	NRPS	AM-toxin	Alternaria alternata

Similar known clusters from MIBiG 4.0

Module view

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Predicted core structure(s)

For candidate cluster 1, location 2787 - 88912:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Asp) + (X - D-Hpr) + (Gly - Asp - Gly - Asp - Gly - D-Thr) + (Ile - Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 2787 - 45616:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Asp) + (X - D-Hpr) + (Gly - Asp - Gly - Asp - Gly - D-Thr)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 12711 - 88912:

Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account

Polymer prediction:: (Asp) + (X - D-Hpr) + (Gly - Asp - Gly - Asp - Gly - D-Thr) + (Ile - Pro)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

lpmA: Asp

Search NORINE for peptide: strict or relaxed

AMP-binding (234..639): Asp

nrpys: Asp

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DIWQSTADDK
Nearest Stachelhaus code(s):: Asp DIWQSTADDK (100% 8Å match); dnmeProp or Dab DIWQSTADDK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AEF16021.1: NH2

CAL_domain (53..486): NH2

minowa: NH2

Prediction, score:

NH2: 14.4
AHBA: 13.7
Acetyl-CoA: 10.7
fatty_acid: 0.8
shikimic_acid: 0.0

lpmB: X - Hpr

Search NORINE for peptide: strict or relaxed

AMP-binding (470..844): X

nrpys: Dpr

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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DLTKIGAVNK
Nearest Stachelhaus code(s):: Dpr DLTKIGAVNK (100% 8Å match); Asp DLTKIGAVNK (82% 8Å match); OH-Asp or OMe-Asp DLTKIGAVNK (74% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2050..2467): Hpr

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

Stachelhaus prediction details:

Stachelhaus sequence:: DFQFFGIAAK
Nearest Stachelhaus code(s):: Hpr DFQFFGIAAK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

lpmC: Gly - Asp - Gly - Asp - Gly - Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (434..828): 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:: DILQLGLIWK
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1484..1859): Asp

nrpys: 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:: asp (Asp)

Stachelhaus prediction details:

Stachelhaus sequence:: DLTKIGAVNK
Nearest Stachelhaus code(s):: Asp DLTKIGAVNK (100% 8Å match); Dpr DLTKIGAVNK (97% 8Å match); OH-Asp or OMe-Asp DLTKIGAVNK (76% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2523..2915): 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:: DILQLGLIWK
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3588..3963): Asp

nrpys: 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:: asp (Asp)

Stachelhaus prediction details:

Stachelhaus sequence:: DLTKIGAVNK
Nearest Stachelhaus code(s):: Asp DLTKIGAVNK (100% 8Å match); Dpr DLTKIGAVNK (97% 8Å match); OH-Asp or OMe-Asp DLTKIGAVNK (76% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4629..5021): 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:: DILQLGLIWK
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5687..6078): 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)

lpmD: Ile - Pro

Search NORINE for peptide: strict or relaxed

AMP-binding (473..869): Ile

nrpys: Ile

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:: DAYFWGVCFK
Nearest Stachelhaus code(s):: Ile DAYFWGVCFK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1545..1956): 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:: DVQYIAHVVK
Nearest Stachelhaus code(s):: Pro DVQYIAHVVK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor