BGC0002409 - 1 region(s) - antiSMASH results

Identified secondary metabolite regions using strictness 'relaxed'

BGC0002409 (Parafrankia sp. CH37)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1	betalactone,NRPS	1	65,837	High	frankobactin A1/frankobactin A2/frankobactin A3/frankobactin B1/frankobactin B2/frankobactin B3/frankobactin C1	NRPS:Type I

BGC0002409 - Region 1 - NRPS,betalactone

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Location: 1 - 65,837 nt. (total: 65,837 nt) Show pHMM detection rules used

Region on contig edge.

betalactone: (HMGL-like and AMP-binding)
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 - 65,838
Label		BGC0002409

Tailoring functions

Oxidoreductases: dehydrogenase

IHE48_05585: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase

IHE48_05595: alpha/beta hydrolase domain-containing protein

smcogs: SMCOG1066: alpha/beta hydrolase domain-containing protein

Ligases: ligase synthase

IHE48_05520: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

IHE48_05530: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

IHE48_05565: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

IHE48_05570: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002409.3	1.18	NRPS	frankobactin A1, frankobactin A2, frankobactin A3, frankobactin B1, frankobactin B2, frankobactin B3, frankobactin C1	Frankia sp. CH37
BGC0002135.2	0.39	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000351.5	0.38	NRPS	exochelin	Mycolicibacterium smegmatis MC2 155
BGC0001261.3	0.37	NRPS	AM-toxin	Alternaria alternata
BGC0001825.4	0.37	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001833.4	0.36	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001135.5	0.36	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000357.5	0.35	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001166.5	0.35	NRPS	HC-toxin	Alternaria jesenskae
BGC0001132.4	0.35	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002409.3	0.96	NRPS	frankobactin A1, frankobactin A2, frankobactin A3, frankobactin B1, frankobactin B2, frankobactin B3, frankobactin C1	Frankia sp. CH37
BGC0002135.2	0.71	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.70	NRPS	AM-toxin	Alternaria alternata
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001833.4	0.69	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000357.5	0.68	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001166.5	0.68	NRPS	HC-toxin	Alternaria jesenskae
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001050.5	0.68	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis

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 - 65837:

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

Polymer prediction:: (Gly - D-Thr - NMe-OH-Orn - Orn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 6064 - 65837:

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

Polymer prediction:: (Gly - D-Thr - NMe-OH-Orn - Orn)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

IHE48_05520: X

AMP-binding (25..432): X

nrpys: Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad

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:: IGAGCGSVAK
Nearest Stachelhaus code(s):: 6-clTrp DAAMCGGVAK (32% 8Å match)
Stachelhaus code match:: 60% (weak)

IHE48_05565: Gly - Thr - OH-Orn - Orn

Search NORINE for peptide: strict or relaxed

AMP-binding (550..951): 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:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: DPVQLGVVWK
Nearest Stachelhaus code(s):: Gly DILQLGVVWK (74% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1645..2081): 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 (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3277..3735): OH-Orn

nrpys: OH-Orn

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: Orn and hydroxy-Orn specific (Orn, OH-Orn)
Single AA prediction:: orn (Orn)

Stachelhaus prediction details:

Stachelhaus sequence:: DMENMGLINK
Nearest Stachelhaus code(s):: OH-Orn DMENMGLINK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4824..5258): Orn

nrpys: Orn

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: Orn and hydroxy-Orn specific (Orn, OH-Orn)
Single AA prediction:: orn (Orn)

Stachelhaus prediction details:

Stachelhaus sequence:: DGEDMGLVDK
Nearest Stachelhaus code(s):: Orn DGEDAGLVDK (85% 8Å match)
Stachelhaus code match:: 90% (moderate)

IHE48_05570: Fo-OH-Orn

Search NORINE for peptide: strict or relaxed

AMP-binding (62..469): Fo-OH-Orn

nrpys: Fo-OH-Orn

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: Orn and hydroxy-Orn specific (Orn, OH-Orn)
Single AA prediction:: orn (Orn)

Stachelhaus prediction details:

Stachelhaus sequence:: DINYWGGIGK
Nearest Stachelhaus code(s):: Fo-OH-Orn DINYWGGIGK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor