BGC0002379 - 1 region(s) - antiSMASH results

Identified secondary metabolite regions using strictness 'relaxed'

BGC0002379 (Pseudomonas sp. RtIB026)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1	NRPS	1	150,580	High	MA026	NRPS:Type I

BGC0002379 - Region 1 - NRPS

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Location: 1 - 150,580 nt. (total: 150,580 nt) Show pHMM detection rules used

Region on contig edge.

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 - 150,581
Label		BGC0002379

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase synthase

PRtIB026_34010: riboflavin biosynthesis protein RibD

smcogs: SMCOG1240: riboflavin biosynthesis protein RibD

PRtIB026_34390: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

PRtIB026_34400: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

PRtIB026_34410: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

PRtIB026_34440: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

PRtIB026_34450: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

PRtIB026_34540: riboflavin biosynthesis protein RibD

smcogs: SMCOG1240: riboflavin biosynthesis protein RibD

Transferases: acetyltransferase methyltransferase

PRtIB026_34300: acetyl-CoA acetyltransferase

smcogs: SMCOG1124: acetyl-CoA acetyltransferase

PRtIB026_34530: methyltransferase

smcogs: SMCOG1248: methyltransferase

PRtIB026_34620: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

Hydrolases: synthase

PRtIB026_34010: riboflavin biosynthesis protein RibD

smcogs: SMCOG1240: riboflavin biosynthesis protein RibD

PRtIB026_34540: riboflavin biosynthesis protein RibD

smcogs: SMCOG1240: riboflavin biosynthesis protein RibD

Ligases: ligase

PRtIB026_33940: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

PRtIB026_33950: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

PRtIB026_33960: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

PRtIB026_33970: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

PRtIB026_33980: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

PRtIB026_34290: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

PRtIB026_34640: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

PRtIB026_34650: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

PRtIB026_34660: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Translocases: permease

PRtIB026_34160: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.93	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.89	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.85	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.85	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002379.3	0.85	NRPS	MA026	Pseudomonas sp. RtIB026
BGC0002286.3	0.83	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.83	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002071.2	0.82	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001132.4	0.81	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001641.4	0.81	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002379.3	0.97	NRPS	MA026	Pseudomonas sp. RtIB026
BGC0001758.4	0.78	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.78	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001641.4	0.77	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.77	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002286.3	0.75	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens

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 - 79971:

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

Polymer prediction:: (Gln - Val - Leu) + (Gln - Ser - Val - Leu - Gln) + (Leu) + (Leu) + (Gln - Ile)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 107382 - 150580:

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

Polymer prediction:: (Leu) + (Glu)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

PRtIB026_33940: Leu - Gln - Ile

Search NORINE for peptide: strict or relaxed

AMP-binding (192..580): Leu

nrpys: Leu

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:: leu (Leu)

Stachelhaus prediction details:

Stachelhaus sequence:: DAWFLGNVVK
Nearest Stachelhaus code(s):: Leu DAWFLGNVVK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1233..1632): Gln

nrpys: Gln

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:: DAWQVGVVDK
Nearest Stachelhaus code(s):: Gln DAWQVGVVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2295..2690): 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:: ile (Ile)

Stachelhaus prediction details:

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

PRtIB026_33960: Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (552..940): Leu

nrpys: Leu

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:: leu (Leu)

Stachelhaus prediction details:

Stachelhaus sequence:: DAWFLGNVVK
Nearest Stachelhaus code(s):: Leu DAWFLGNVVK (100% 8Å match); Leu or Ile DAWFLGNVVK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

PRtIB026_33970: Leu - Gln - Ser - Val - Leu - Gln

Search NORINE for peptide: strict or relaxed

AMP-binding (71..451): Leu

nrpys: Leu

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:: leu (Leu)

Stachelhaus prediction details:

Stachelhaus sequence:: DAWFLGNVVK
Nearest Stachelhaus code(s):: Leu DAWFLGNVVK (100% 8Å match); Leu or Ile DAWFLGNVVK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1106..1504): Gln

nrpys: Gln

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:: DAWQVGVVDK
Nearest Stachelhaus code(s):: Gln DAWQVGVVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2162..2558): 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:: DVWHLSLVDK
Nearest Stachelhaus code(s):: Ser DVWHLSLVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3206..3596): 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:: DALWMGGTFK
Nearest Stachelhaus code(s):: Val DALWMGGTFK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4273..4653): Leu

nrpys: Leu

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:: leu (Leu)

Stachelhaus prediction details:

Stachelhaus sequence:: DAWFLGNVVK
Nearest Stachelhaus code(s):: Leu DAWFLGNVVK (100% 8Å match); Leu or Ile DAWFLGNVVK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5312..5710): Gln

nrpys: Gln

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:: DAWQVGVVDK
Nearest Stachelhaus code(s):: Gln DAWQVGVVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

PRtIB026_33980: Gln - Val

Search NORINE for peptide: strict or relaxed

AMP-binding (549..949): Gln

nrpys: Gln

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:: DAWQVGVVDK
Nearest Stachelhaus code(s):: Gln DAWQVGVVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1601..1991): 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:: DALWMGGTFK
Nearest Stachelhaus code(s):: Val DALWMGGTFK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

PRtIB026_34290: X

AMP-binding (7..409): X

nrpys: Asp, Asn, Glu, Gln, Aad

SVM prediction details:

Predicted physicochemical class:: N/A
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:: GAYFVGIMTK
Nearest Stachelhaus code(s):: Hmp GALLVGITVK (41% 8Å match)
Stachelhaus code match:: 60% (weak)

PRtIB026_34640: Glu

Search NORINE for peptide: strict or relaxed

AMP-binding (472..871): Glu

nrpys: Glu

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:: DGWKFGVVDK
Nearest Stachelhaus code(s):: Glu DGWKFGVVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

PRtIB026_34650: Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (121..510): Leu

nrpys: Leu

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:: leu (Leu)

Stachelhaus prediction details:

Stachelhaus sequence:: DAWFLGNVVK
Nearest Stachelhaus code(s):: Leu DAWFLGNVVK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor