BGC0001130 - 1 region(s) - antiSMASH results

Identified secondary metabolite regions using strictness 'relaxed'

BGC0001130 (Xenorhabdus budapestensis)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1	T1PKS,hglE-KS,PUFA,NRPS	1	75,863	High	fabclavine Ia/fabclavine Ib/fabclavine IIa/fabclavine IIb	NRPS:Type I+PKS

BGC0001130 - Region 1 - NRPS,PUFA,T1PKS,hglE-KS

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Location: 1 - 75,863 nt. (total: 75,863 nt) Show pHMM detection rules used

Region on contig edge.

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)
PUFA: PUFA_KS
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

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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 - 75,864
Label		BGC0001130

Tailoring functions

Oxidoreductases: dehydrogenase

Xbud_02637: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase

Xbud_02636: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Lyases: dehydratase hydratase

Xbud_02638: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Xbud_02639: Nitrilase/cyanide hydratase and apolipoprotein

smcogs: SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

Ligases: ligase synthase

Xbud_02634: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Xbud_02635: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Xbud_02640: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Xbud_02641: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Xbud_02642: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

Xbud_02643: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001130.5	2.73	NRPS, PKS	fabclavine Ia, fabclavine Ib, fabclavine IIa, fabclavine IIb	Xenorhabdus budapestensis
BGC0001872.3	1.80	PKS	fabclavine-polyamine	Xenorhabdus bovienii SS-2004
BGC0001284.4	1.61	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002191.2	1.51	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001268.4	1.46	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0000107.3	1.45	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002175.3	1.44	PKS	YWA1	Aspergillus oryzae RIB40
BGC0001258.3	1.44	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0001164.3	1.37	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001056.5	1.29	NRPS, PKS	zeamine, zeamine I, zeamine II, prezeamine, prezeamine I	Serratia plymuthica RVH1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001130.5	0.99	NRPS, PKS	fabclavine Ia, fabclavine Ib, fabclavine IIa, fabclavine IIb	Xenorhabdus budapestensis
BGC0001872.3	0.74	PKS	fabclavine-polyamine	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.74	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001056.5	0.74	NRPS, PKS	zeamine, zeamine I, zeamine II, prezeamine, prezeamine I	Serratia plymuthica RVH1
BGC0002135.2	0.73	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.72	NRPS	AM-toxin	Alternaria alternata
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001133.4	0.71	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001023.5	0.70	NRPS, PKS	myxochromide S1	Stigmatella aurantiaca

Similar known clusters from MIBiG 4.0

Module view

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Detailed domain annotation

Selected features only

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NRPS/PKS products

NRPS/PKS substrates

Predicted core structure(s)

For candidate cluster 1, location 0 - 75863:

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

Polymer prediction:: (mal) + (Asp - X - D-Asn - Asn) + (Thr - Pro) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 46072:

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

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

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 6275 - 50751:

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

Polymer prediction:: (mal) + (Asp - X - D-Asn - Asn) + (Thr - Pro)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 16909 - 75863:

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

Polymer prediction:: (mal) + (Asp - X - D-Asn - Asn) + (Thr - Pro) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 36921 - 75863:

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

Polymer prediction:: (Asp - X - D-Asn - Asn) + (Thr - Pro) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

Xbud_02634: mal

PKS_AT (598..903): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 77.2
Methoxymalonyl-CoA: 37.4
Methylmalonyl-CoA: 31.6
Isobutyryl-CoA: 20.7
inactive: 17.8
fatty_acid: 14.4
Benzoyl-CoA: 12.9
Acetyl-CoA: 9.6
CHC-CoA: 9.5
trans-1,2-CPDA: 0.0
Propionyl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

Xbud_02640: Asp - X - Asn - Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (6..418): 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:: DPRHVSLLAK
Nearest Stachelhaus code(s):: Asp DPRHVSLLAK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1093..1484): X

nrpys: Phe, 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:: Unpolar aromatic ring (Phe, Trp)
Single AA prediction:: phe (Phe)

Stachelhaus prediction details:

Stachelhaus sequence:: DTWTLASVGK
Nearest Stachelhaus code(s):: Phe or His DTWTLASVGK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2164..2578): 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 (74% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3698..4129): 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 (79% 8Å match)
Stachelhaus code match:: 100% (strong)

Xbud_02641: Thr - Pro

Search NORINE for peptide: strict or relaxed

AMP-binding (475..899): 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 (1602..2009): 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:: 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:: DAWFIGGTFK
Nearest Stachelhaus code(s):: Pro DAWFIGGTFK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Xbud_02642: mal

PKS_AT (577..873): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 147.8
inactive: 89.0
Methoxymalonyl-CoA: 44.9
Methylmalonyl-CoA: 37.0
Propionyl-CoA: 30.4
Isobutyryl-CoA: 18.9
Ethylmalonyl-CoA: 9.7
2-Methylbutyryl-CoA: 9.0
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor