BGC0001056 - 1 region(s) - antiSMASH results

Identified secondary metabolite regions using strictness 'relaxed'

BGC0001056 (Serratia plymuthica RVH1)

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

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

Download region GenBank file

Download region SVG

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

Region on contig edge.

PUFA: PUFA_KS
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
hglE-KS: (hglE or hglD)
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

reset view

zoom to selection

Gene details

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

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

zmn13: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase acylase

zmn12: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

zmn5: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1060: 4'-phosphopantetheinyl transferase

Lyases: decarboxylase dehydratase hydratase

zmn14: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

zmn15: Nitrilase/cyanide hydratase and apolipoprotein

smcogs: SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

zmn3: Decarboxylase, pyridoxal-dependent

smcogs: SMCOG1180: Decarboxylase, pyridoxal-dependent

Ligases: ligase synthase

zmn10: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

zmn11: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

zmn16: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

zmn17: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

zmn18: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

zmn19: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001056.5	2.90	NRPS, PKS	zeamine, zeamine I, zeamine II, prezeamine, prezeamine I	Serratia plymuthica RVH1
BGC0001284.4	1.61	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001872.3	1.60	PKS	fabclavine-polyamine	Xenorhabdus bovienii SS-2004
BGC0000107.3	1.46	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002175.3	1.45	PKS	YWA1	Aspergillus oryzae RIB40
BGC0001268.4	1.45	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0001130.5	1.43	NRPS, PKS	fabclavine Ia, fabclavine Ib, fabclavine IIa, fabclavine IIb	Xenorhabdus budapestensis
BGC0001164.3	1.40	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	1.40	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0000863.3	1.30	other (other)	eicosapentaenoic acid	Pseudoalteromonas sp. DS-12

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001056.5	0.99	NRPS, PKS	zeamine, zeamine I, zeamine II, prezeamine, prezeamine I	Serratia plymuthica RVH1
BGC0001130.5	0.77	NRPS, PKS	fabclavine Ia, fabclavine Ib, fabclavine IIa, fabclavine IIb	Xenorhabdus budapestensis
BGC0001135.5	0.74	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.73	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001249.5	0.72	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	0.72	NRPS	AM-toxin	Alternaria alternata
BGC0001872.3	0.72	PKS	fabclavine-polyamine	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.70	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Similar known clusters from MIBiG 4.0

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

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: mal

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: Asp - His - Asn - Asn

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: Thr - Val

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: mal

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

Link to PARAS substrate predictor