BGC0001056 - 1 region(s) - antiSMASH results

Identified secondary metabolite regions using strictness 'relaxed'

BGC0001056 (Serratia plymuthica RVH1)

Region	Type	From	To	Most similar known cluster		Similarity
Region 1	PUFA,hglE-KS,NRPS,T1PKS	1	55,138	zeamine/zeamine I/zeamine II/prezeamine/prezeamine I	NRPS:Type I+PKS:Type I	100%

BGC0001056 - Region 1 - NRPS,PUFA,T1PKS,hglE-KS

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Location: 1 - 55,138 nt. (total: 55,138 nt) Show pHMM detection rules used

Region on contig edge.

PUFA: PUFA_KS
hglE-KS: (hglE or hglD)
NRPS: cds(Condensation and (AMP-binding or A-OX))
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

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Gene details

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Gene overview

MIBiG

NRPS/PKS domains

MIBiG comparison

KnownClusterBlast

NRPS/PKS modules

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 - 55,139
Label		BGC0001056

Detailed domain annotation

Selected features only

Show module domains

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001056	2.56	NRP, Polyketide	zeamine, zeamine I, zeamine II, prezeamine, prezeamine I	Serratia plymuthica RVH1
BGC0001130	1.24	NRP, Polyketide	fabclavine Ia, fabclavine Ib, fabclavine IIa, fabclavine IIb	Xenorhabdus budapestensis
BGC0001872	1.24	Polyketide	fabclavine-polyamine	Xenorhabdus bovienii SS-2004
BGC0000979	1.16	NRP, Polyketide	cylindrospermopsin	Aphanizomenon sp. 10E9
BGC0000980	1.16	NRP, Polyketide	cylindrospermopsin	Aphanizomenon sp. 22D11
BGC0001133	1.06	NRP	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0000863	1.04	Other	eicosapentaenoic acid	Pseudoalteromonas sp. DS-12
BGC0002071	0.99	NRP	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0002437	0.96	NRP	thermoactinoamide A	Thermoactinomyces sp. AS95
BGC0000284	0.96	Polyketide	phenolic lipids	Azotobacter vinelandii DJ

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001056	1.00	NRP, Polyketide	zeamine, zeamine I, zeamine II, prezeamine, prezeamine I	Serratia plymuthica RVH1
BGC0001130	0.77	NRP, Polyketide	fabclavine Ia, fabclavine Ib, fabclavine IIa, fabclavine IIb	Xenorhabdus budapestensis
BGC0001133	0.73	NRP	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0002071	0.72	NRP	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001872	0.72	Polyketide	fabclavine-polyamine	Xenorhabdus bovienii SS-2004
BGC0000979	0.69	NRP, Polyketide	cylindrospermopsin	Aphanizomenon sp. 10E9
BGC0000980	0.69	NRP, Polyketide	cylindrospermopsin	Aphanizomenon sp. 22D11
BGC0002474	0.69	NRP	agrobactin	Agrobacterium tumefaciens
BGC0001023	0.67	NRP, Polyketide	myxochromide S1	Stigmatella aurantiaca
BGC0001135	0.67	NRP	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Similar known gene clusters from MIBiG 4.0

Module view

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NRPS/PKS products

NRPS/PKS substrates

Predicted core structure(s)

For candidate cluster 1, location 0 - 55138:

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

Polymer prediction:: (mal) + (Asp - His - D-Asn - Asn) + (Thr - Val) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 39527:

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

Polymer prediction:: (mal) + (Asp - His - D-Asn - Asn) + (Thr - Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 0 - 35194:

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

Polymer prediction:: (mal) + (Asp - His - D-Asn - Asn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 5459 - 55138:

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

Polymer prediction:: (mal) + (Asp - His - D-Asn - Asn) + (Thr - Val) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

zmn10

PKS_AT (593..893): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; inactive: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 71.3
Methoxymalonyl-CoA: 37.9
Methylmalonyl-CoA: 36.2
CHC-CoA: 23.2
Isobutyryl-CoA: 19.2
fatty_acid: 18.7
Propionyl-CoA: 17.5
Benzoyl-CoA: 15.3
inactive: 14.1
Ethylmalonyl-CoA: 10.1
trans-1,2-CPDA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

zmn16

Search NORINE for peptide: strict or relaxed

AMP-binding (6..404): Asp

nrpys: Asp

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:: DPRHLALLAK
Nearest Stachelhaus code(s):: Asp DPRHLALLAK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1054..1448): His

nrpys: His

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:: phe (Phe)

Stachelhaus prediction details:

Stachelhaus sequence:: DTWTIASVSK
Nearest Stachelhaus code(s):: His DTWTIASVSK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2091..2493): Asn

nrpys: Asn

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:: DATKVGEVGK
Nearest Stachelhaus code(s):: Asn DATKVGEVGK (100% 8Å match); OH-Asn or Asn DATKVGEVGK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3578..3972): Asn

nrpys: Asn

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:: DATKVGEVGK
Nearest Stachelhaus code(s):: Asn DATKVGEVGK (100% 8Å match); OH-Asn or Asn DATKVGEVGK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

zmn17

Search NORINE for peptide: strict or relaxed

AMP-binding (475..892): 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:: DFWNIGMVHK
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1573..1969): Val

nrpys: Val

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:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DALFIGGTFK
Nearest Stachelhaus code(s):: Val DALFIGGTFK (100% 8Å match); Leu or Ile DALFIGGTFK (74% 8Å match)
Stachelhaus code match:: 100% (strong)

zmn18

PKS_AT (545..830): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 79.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 158.6
inactive: 102.1
Methoxymalonyl-CoA: 51.3
Methylmalonyl-CoA: 44.6
Propionyl-CoA: 33.0
Isobutyryl-CoA: 29.9
Ethylmalonyl-CoA: 19.3
2-Methylbutyryl-CoA: 12.4
CHC-CoA: 9.7
fatty_acid: 9.3
Benzoyl-CoA: 8.9
trans-1,2-CPDA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0