BGC0001033 - 1 region(s) - antiSMASH results

Identified secondary metabolite regions using strictness 'relaxed'

BGC0001033 (Paenibacillus larvae subsp. larvae DSM 25430)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1	NRPS,T1PKS	1	98,753	High	paenilamicin/paenilamicin A2/paenilamicin B1/paenilamicin B2	NRPS:Type I+PKS

BGC0001033 - Region 1 - NRPS,T1PKS

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Location: 1 - 98,753 nt. (total: 98,753 nt) Show pHMM detection rules used

Region on contig edge.

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
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

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 - 98,754
Label		BGC0001033

Tailoring functions

Oxidoreductases: dehydrogenase

ERIC2_c18140: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

Transferases: methyltransferase

ERIC2_c18060: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: hydrolase

ERIC2_c18130: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase synthase

ERIC2_c18040: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

ERIC2_c18050: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

ERIC2_c18070: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

ERIC2_c18080: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

ERIC2_c18090: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

ERIC2_c18100: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

ERIC2_c18110: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

ERIC2_c18170: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001033.5	1.83	NRPS, PKS	paenilamicin, paenilamicin A2, paenilamicin B1, paenilamicin B2	Paenibacillus larvae subsp. larvae DSM 25430
BGC0002135.2	0.87	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.81	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.77	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.76	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.74	NRPS	AM-toxin	Alternaria alternata
BGC0002286.3	0.74	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.72	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001240.4	0.72	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001033.5	0.99	NRPS, PKS	paenilamicin, paenilamicin A2, paenilamicin B1, paenilamicin B2	Paenibacillus larvae subsp. larvae DSM 25430
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001261.3	0.70	NRPS	AM-toxin	Alternaria alternata
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001240.4	0.69	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

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 - 98753:

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

Polymer prediction:: (X - ohmal) + (ohmal - D-Ala) + (D-Lys) + (Ser) + (ohmal) + (Gly) + (D-Asn)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

ERIC2_c18040: X - mal

AMP-binding (470..858): X

nrpys: Lys, Arg

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:: DPEDIGGVEK
Nearest Stachelhaus code(s):: Lys or Arg DPEDIGGVEK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

PKS_AT (1575..1866): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 79.2%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 151.8
inactive: 91.5
Methoxymalonyl-CoA: 62.7
Methylmalonyl-CoA: 48.8
Propionyl-CoA: 28.8
fatty_acid: 25.1
2-Methylbutyryl-CoA: 24.2
CHC-CoA: 21.3
Benzoyl-CoA: 18.9
Isobutyryl-CoA: 16.7
Acetyl-CoA: 16.3
Ethylmalonyl-CoA: 13.0
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

ERIC2_c18050: mal - D-Ala

Search NORINE for peptide: strict or relaxed

PKS_AT (529..816): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; 2-Rhyd-Malonyl-CoA: 62.5%; inactive: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 136.6
Methoxymalonyl-CoA: 75.6
inactive: 67.7
Methylmalonyl-CoA: 56.3
Propionyl-CoA: 38.9
Ethylmalonyl-CoA: 30.8
Isobutyryl-CoA: 24.9
2-Methylbutyryl-CoA: 20.2
CHC-CoA: 17.2
3-Methylbutyryl-CoA: 11.0
trans-1,2-CPDA: 9.7
Acetyl-CoA: 9.7
fatty_acid: 0.0
Benzoyl-CoA: 0.0

AMP-binding (1971..2365): D-Ala

nrpys: D-Ala

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: N/A
Small clusters prediction:: asp,asn (Asp, Asn)
Single AA prediction:: asn (Asn)

Stachelhaus prediction details:

Stachelhaus sequence:: DLTKVNEVGK
Nearest Stachelhaus code(s):: D-Ala DLTKVNEVGK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

ERIC2_c18060: X

AMP-binding (845..1135): X

nrpys: Dpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DIWEVTADDK
Nearest Stachelhaus code(s):: Dpr DIWEVTADDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

ERIC2_c18070: Lys

Search NORINE for peptide: strict or relaxed

AMP-binding (276..683): Lys

nrpys: Lys

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:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DMEDVGSVDK
Nearest Stachelhaus code(s):: Lys DMEDVGSVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

ERIC2_c18080: Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (482..889): Ser

nrpys: Ser

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:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: DVWHFSLVDK
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

ERIC2_c18090: mal

PKS_AT (533..828): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 83.3%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 141.9
inactive: 110.5
Methoxymalonyl-CoA: 71.8
Methylmalonyl-CoA: 54.8
Propionyl-CoA: 32.4
Ethylmalonyl-CoA: 28.0
trans-1,2-CPDA: 22.5
Acetyl-CoA: 22.4
fatty_acid: 19.6
Isobutyryl-CoA: 17.1
CHC-CoA: 12.9
2-Methylbutyryl-CoA: 11.0
Benzoyl-CoA: 10.9
3-Methylbutyryl-CoA: 0.0

ERIC2_c18110: X - X - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (280..545): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: IPVLVL-VSK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

AMP-binding (840..1130): X

nrpys: Dpr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DIWEVTADDK
Nearest Stachelhaus code(s):: Dpr DIWEVTADDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1778..2204): 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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DIFHMGMIWK
Nearest Stachelhaus code(s):: Gly DIFHMGMIWK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

ERIC2_c18170: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (461..858): 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:: DLTKIGEVGK
Nearest Stachelhaus code(s):: Asn DLTKIGEVGK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor