BGC0002297 - 1 region(s) - antiSMASH results

Identified secondary metabolite regions using strictness 'relaxed'

BGC0002297 (Phormidium sp. LP904c)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1	NRPS,T1PKS	1	54,162	High	MC-LR/MC-LHty/MC-HphHty/MC-LHph/MC-HphHph	NRPS:Type I+PKS

BGC0002297 - Region 1 - NRPS,T1PKS

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Location: 1 - 54,162 nt. (total: 54,162 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

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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 - 54,163
Label		BGC0002297

Tailoring functions

Oxidoreductases: dehydrogenase

mcyJ: dehydrogenase

smcogs: SMCOG1072: dehydrogenase

Transferases: methyltransferase

mcyI: methyltransferase

smcogs: SMCOG1089: methyltransferase

Ligases: ligase synthase

mcyA: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

mcyB: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

mcyC: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

mcyD: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

mcyE: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

mcyG: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002297.2	1.78	NRPS, PKS	MC-LR, MC-LHty, MC-HphHty, MC-LHph, MC-HphHph	Phormidium sp. LP904c
BGC0001017.5	0.88	NRPS, PKS	microcystin LR	Microcystis aeruginosa PCC 7806
BGC0002135.2	0.87	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.84	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5	0.83	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001132.4	0.82	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001135.5	0.82	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.82	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.81	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5	0.77	NRPS	HC-toxin	Alternaria jesenskae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002297.2	0.98	NRPS, PKS	MC-LR, MC-LHty, MC-HphHty, MC-LHph, MC-HphHph	Phormidium sp. LP904c
BGC0001017.5	0.76	NRPS, PKS	microcystin LR	Microcystis aeruginosa PCC 7806
BGC0001128.4	0.76	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.74	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002075.3	0.73	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

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 - 54162:

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

Polymer prediction:: (ccmal) + (mal - X) + (X - Me-ohmal) + (NMe-Ser - D-Ala) + (Leu - X) + (Arg)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

mcyD: mal

PKS_AT (2645..2929): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 100.0%; inactive: 87.5%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 188.6
inactive: 144.2
Methoxymalonyl-CoA: 65.9
Methylmalonyl-CoA: 64.4
Propionyl-CoA: 33.6
Isobutyryl-CoA: 24.6
Ethylmalonyl-CoA: 21.2
2-Methylbutyryl-CoA: 19.5
Benzoyl-CoA: 17.9
trans-1,2-CPDA: 15.9
CHC-CoA: 13.8
3-Methylbutyryl-CoA: 13.1
Acetyl-CoA: 12.3
fatty_acid: 8.7

mcyE: mal - X

PKS_AT (561..840): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 79.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 162.7
inactive: 114.1
Methoxymalonyl-CoA: 56.0
Methylmalonyl-CoA: 46.6
Propionyl-CoA: 32.6
Isobutyryl-CoA: 29.8
Benzoyl-CoA: 18.6
Acetyl-CoA: 17.6
3-Methylbutyryl-CoA: 14.8
CHC-CoA: 11.4
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Ethylmalonyl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

AMP-binding (2449..2843): X

nrpys: D-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:: glu,gln (Glu, Gln)
Single AA prediction:: glu (Glu)

Stachelhaus prediction details:

Stachelhaus sequence:: DPRHSGVVGK
Nearest Stachelhaus code(s):: D-Glu DPRHSGVVGK (100% 8Å match); Glu or D-Glu DPRHSGVVGK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

mcyG: X - mal

AMP-binding (43..452): X

nrpys: (unknown)

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:: --LWVAASGK
Nearest Stachelhaus code(s):: Cin AILWVAASGK (79% 8Å match)
Stachelhaus code match:: 80% (moderate)

PKS_AT (1224..1517): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 100.0%; inactive: 91.7%; 2-Rhyd-Malonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 169.1
inactive: 115.9
Methoxymalonyl-CoA: 70.6
Methylmalonyl-CoA: 66.7
Propionyl-CoA: 38.3
Ethylmalonyl-CoA: 34.4
Isobutyryl-CoA: 33.8
2-Methylbutyryl-CoA: 33.1
Acetyl-CoA: 29.1
CHC-CoA: 23.0
Benzoyl-CoA: 23.0
fatty_acid: 21.1
trans-1,2-CPDA: 19.3
3-Methylbutyryl-CoA: 14.2

mcyA: Ser - Ala

Search NORINE for peptide: strict or relaxed

AMP-binding (253..653): 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:: DVWHISLIDK
Nearest Stachelhaus code(s):: Ser DVWHISLIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1736..2126): Ala

nrpys: Ala

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:: ala (Ala)

Stachelhaus prediction details:

Stachelhaus sequence:: DLFNNALTYK
Nearest Stachelhaus code(s):: Ala DLFNNALTYK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

mcyB: Leu - X

Search NORINE for peptide: strict or relaxed

AMP-binding (475..872): 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:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

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

AMP-binding (1526..1950): X

nrpys: D-bMe-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:: DARHVGIFVK
Nearest Stachelhaus code(s):: D-bMe-Asp DARHVGIFVK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

mcyC: Arg

Search NORINE for peptide: strict or relaxed

AMP-binding (483..880): Arg

nrpys: Arg

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:: DALFFGLVDK
Nearest Stachelhaus code(s):: Arg DALFFGLVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor