Kutzneria_NPDC052558 - 59 region(s)

Identified secondary metabolite regions using strictness 'relaxed'

NPDC052558.ctg-0001 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1.1	T1PKS,NRPS-like	300,411	370,228	Low	piericidin A1	PKS
Region 1.2	NRPS,NAPAA	390,826	491,912
Region 1.3	NRPS-like	507,845	549,497	Low	tyrobetaine	NRPS:Type I
Region 1.4	lanthipeptide-class-i	567,326	591,578
Region 1.5	terpene	662,222	683,103	High	(-)-δ-cadinene	terpene

NPDC052558.ctg-0002 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 2.1	terpene	343,631	369,306

NPDC052558.ctg-0003 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 3.1	hydrogen-cyanide	288,459	300,976

NPDC052558.ctg-0004 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 4.1	terpene	167,269	193,186	Low	hopene	terpene
Region 4.2	NRPS-like,terpene	255,535	298,954
Region 4.3	RRE-containing	415,701	438,187

NPDC052558.ctg-0005 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 5.1	terpene,lassopeptide	34,316	76,240	Low	anantin C	ribosomal:RiPP
Region 5.2	NRPS-like	152,152	195,493
Region 5.3	NAPAA,T1PKS,hglE-KS	244,171	302,010
Region 5.4	NRPS,HR-T2PKS,terpene,T1PKS	352,834	437,737	Low	coprisamide C/coprisamide D	NRPS:Type I

NPDC052558.ctg-0006 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 6.1	RRE-containing	26,588	47,685
Region 6.2	oligosaccharide,T1PKS	97,190	231,151	High	epemicin B/epemicin A	PKS:Type I
Region 6.3	terpene	343,580	364,443

NPDC052558.ctg-0007 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 7.1	terpene	177,663	198,721
Region 7.2	NRP-metallophore,NRPS	275,791	338,376	Medium	scabichelin	NRPS:Type I

NPDC052558.ctg-0008 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 8.1	hglE-KS,T1PKS	146,302	197,169

NPDC052558.ctg-0009 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 9.1	CDPS	191,202	211,918
Region 9.2	NRPS-like,T1PKS	269,967	316,110	Low	aculeximycin	PKS

NPDC052558.ctg-0010 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 10.1	T1PKS	53,530	148,640
Region 10.2	T1PKS,arylpolyene	182,258	329,639	Medium	pladienolide B	PKS

NPDC052558.ctg-0011 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 11.1	terpene-precursor,RiPP-like	237,893	258,933

NPDC052558.ctg-0012 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 12.1	terpene	33,759	56,979

NPDC052558.ctg-0013 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 13.1	oligosaccharide	40,546	64,047

NPDC052558.ctg-0014 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 14.1	HR-T2PKS	45,976	87,094

NPDC052558.ctg-0016 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 16.1	T1PKS	1	43,987	Low	midecamycin	PKS
Region 16.2	butyrolactone	100,164	111,135
Region 16.3	RiPP-like	179,577	190,716

NPDC052558.ctg-0020 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 20.1	T1PKS	94,472	140,615

NPDC052558.ctg-0021 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 21.1	terpene	37,409	58,278

NPDC052558.ctg-0022 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 22.1	NRPS-like	86,865	130,941

NPDC052558.ctg-0024 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 24.1	redox-cofactor	121,206	143,212	Low	lankacidin C	NRPS:Type I+PKS

NPDC052558.ctg-0026 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 26.1	indole	25,172	48,312	High	BE-54017	other:other
Region 26.2	T2PKS	62,032	134,493	Low	mutaxanthene A/mutaxanthene B/mutaxanthene D	PKS

NPDC052558.ctg-0027 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 27.1	NRPS,betalactone	13,991	106,274	Low	rimosamide	NRPS:Type I

NPDC052558.ctg-0029 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 29.1	terpene	111,367	130,048

NPDC052558.ctg-0030 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 30.1	NRPS-like,NRPS,T1PKS	1	127,449	Low	fluvirucin B2	PKS

NPDC052558.ctg-0031 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 31.1	thioamitides	19,994	42,422
Region 31.2	oligosaccharide	73,051	97,797

NPDC052558.ctg-0032 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 32.1	T3PKS	2,772	43,788

NPDC052558.ctg-0033 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 33.1	NRPS,T1PKS,NRPS-like,PKS-like,butyrolactone	1	64,145

NPDC052558.ctg-0034 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 34.1	NRPS	1	48,962	Low	omnipeptin	NRPS:Type I

NPDC052558.ctg-0035 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 35.1	thioamide-NRP,NRPS	1	49,908

NPDC052558.ctg-0036 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 36.1	T1PKS,NRPS-like,T3PKS	6,709	71,403	Low	kendomycin B	PKS

NPDC052558.ctg-0039 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 39.1	NRPS	41,541	86,322

NPDC052558.ctg-0042 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 42.1	lanthipeptide-class-ii	5,876	28,959

NPDC052558.ctg-0044 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 44.1	T1PKS	45,732	71,995

NPDC052558.ctg-0045 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 45.1	other,NRPS,NRPS-like	6,208	64,790	High	branched-chain fatty acids	other:other

NPDC052558.ctg-0046 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 46.1	T2PKS,oligosaccharide	1	68,177	Low	lysolipin I	PKS

NPDC052558.ctg-0048 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 48.1	lanthipeptide-class-i,NRPS	10,871	62,898

NPDC052558.ctg-0051 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 51.1	terpene-precursor	35,514	56,662	Low	isorenieratene	terpene

NPDC052558.ctg-0052 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 52.1	NRPS-like,NRPS,HR-T2PKS	1	44,563	Low	WS9326A/WS9326C/WS9326D	NRPS:Type I

NPDC052558.ctg-0054 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 54.1	NRPS	1	52,097

NPDC052558.ctg-0055 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 55.1	RiPP-like	35,830	46,645

NPDC052558.ctg-0060 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 60.1	PKS-like,T1PKS,amglyccycl	1	28,309

NPDC052558.ctg-0063 (Kutzneria spp)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 63.1	RRE-containing	1	20,201

No secondary metabolite regions were found in these records:: NPDC052558.ctg-0015 (Kutzneria spp); NPDC052558.ctg-0017 (Kutzneria spp); NPDC052558.ctg-0018 (Kutzneria spp); NPDC052558.ctg-0019 (Kutzneria spp); NPDC052558.ctg-0023 (Kutzneria spp); NPDC052558.ctg-0025 (Kutzneria spp); NPDC052558.ctg-0028 (Kutzneria spp); NPDC052558.ctg-0037 (Kutzneria spp); NPDC052558.ctg-0038 (Kutzneria spp); NPDC052558.ctg-0040 (Kutzneria spp); NPDC052558.ctg-0041 (Kutzneria spp); NPDC052558.ctg-0043 (Kutzneria spp); NPDC052558.ctg-0047 (Kutzneria spp); NPDC052558.ctg-0049 (Kutzneria spp); NPDC052558.ctg-0050 (Kutzneria spp); NPDC052558.ctg-0053 (Kutzneria spp); NPDC052558.ctg-0056 (Kutzneria spp); NPDC052558.ctg-0057 (Kutzneria spp); NPDC052558.ctg-0058 (Kutzneria spp); NPDC052558.ctg-0059 (Kutzneria spp); NPDC052558.ctg-0061 (Kutzneria spp); NPDC052558.ctg-0062 (Kutzneria spp); NPDC052558.ctg-0064 (Kutzneria spp); NPDC052558.ctg-0065 (Kutzneria spp); NPDC052558.ctg-0066 (Kutzneria spp); NPDC052558.ctg-0067 (Kutzneria spp); NPDC052558.ctg-0068 (Kutzneria spp); NPDC052558.ctg-0069 (Kutzneria spp); NPDC052558.ctg-0070 (Kutzneria spp); NPDC052558.ctg-0071 (Kutzneria spp); NPDC052558.ctg-0072 (Kutzneria spp); NPDC052558.ctg-0073 (Kutzneria spp); NPDC052558.ctg-0074 (Kutzneria spp); NPDC052558.ctg-0075 (Kutzneria spp); NPDC052558.ctg-0076 (Kutzneria spp); NPDC052558.ctg-0077 (Kutzneria spp); NPDC052558.ctg-0078 (Kutzneria spp); NPDC052558.ctg-0079 (Kutzneria spp); NPDC052558.ctg-0080 (Kutzneria spp); NPDC052558.ctg-0081 (Kutzneria spp); NPDC052558.ctg-0082 (Kutzneria spp); NPDC052558.ctg-0083 (Kutzneria spp); NPDC052558.ctg-0084 (Kutzneria spp); NPDC052558.ctg-0085 (Kutzneria spp); NPDC052558.ctg-0086 (Kutzneria spp); NPDC052558.ctg-0087 (Kutzneria spp); NPDC052558.ctg-0088 (Kutzneria spp)

Compact view

NPDC052558.ctg-0001 - Region 1 - NRPS-like,T1PKS

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Location: 300,411 - 370,228 nt. (total: 69,818 nt) Show pHMM detection rules used

T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) 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

binding site

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Gene details

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Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

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Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidase oxidoreductase oxygenase

CDS_00313: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00314: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

CDS_00315: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_00325: pyruvate oxidase/decarboxylase

smcogs: SMCOG1055: pyruvate oxidase/decarboxylase

CDS_00326: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

Transferases: glycosyltransferase

CDS_00303: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: esterase

CDS_00308: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase synthase

CDS_00304: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_00305: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_00306: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_00307: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_00310: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00311: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.95	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.94	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.94	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000041.3	0.81	PKS	oronofacic acid	Pseudomonas syringae
BGC0001276.3	0.68	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002164.2	0.67	NRPS	peramine	Epichloe festucae
BGC0002286.3	0.67	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.78	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.77	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.77	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000041.3	0.73	PKS	oronofacic acid	Pseudomonas syringae
BGC0001276.3	0.68	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002164.2	0.67	NRPS	peramine	Epichloe festucae
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.66	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.28 out of 19.52

Confidence: medium

Additional weak hits (15):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.35 out of 26.33

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.38 out of 29.38

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.44 out of 20.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.82 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.93 out of 29.38

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.03 out of 30.22

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.62 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.22 out of 30.25

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 21.55

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.42 out of 30.25

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.84 out of 33.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.62 out of 29.65

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.28 out of 26.85

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 300410 - 370228:

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

Polymer prediction:: (X) + (mal) + (Me-mal - Me-redmal) + (Me-ccmal) + (ccmal - ccmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00305: mal - mal

PKS_AT (551..832): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 83.3%; inactive: 70.8%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 162.8
inactive: 83.0
Methoxymalonyl-CoA: 54.2
Methylmalonyl-CoA: 44.0
Acetyl-CoA: 20.2
Isobutyryl-CoA: 17.7
Propionyl-CoA: 15.8
Benzoyl-CoA: 13.0
CHC-CoA: 9.5
fatty_acid: 7.6
trans-1,2-CPDA: 0.0
Ethylmalonyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

PKS_AT (2219..2494): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 190.5
inactive: 102.5
Methoxymalonyl-CoA: 60.9
Methylmalonyl-CoA: 42.8
Propionyl-CoA: 22.3
Acetyl-CoA: 21.2
Isobutyryl-CoA: 17.4
Benzoyl-CoA: 17.1
Ethylmalonyl-CoA: 15.2
fatty_acid: 14.5
CHC-CoA: 9.1
2-Methylbutyryl-CoA: 9.0
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_00306: mmal

PKS_AT (553..843): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Methoxymalonyl-CoA: 91.7%; Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 211.5
Ethylmalonyl-CoA: 204.0
Methoxymalonyl-CoA: 169.1
2-Methylbutyryl-CoA: 145.5
trans-1,2-CPDA: 129.6
Propionyl-CoA: 115.3
CHC-CoA: 108.0
Malonyl-CoA: 95.8
Isobutyryl-CoA: 81.8
Benzoyl-CoA: 71.6
fatty_acid: 47.8
Acetyl-CoA: 47.2
inactive: 40.7
3-Methylbutyryl-CoA: 39.9

CDS_00307: mmal - mmal

PKS_AT (515..804): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Methoxymalonyl-CoA: 91.7%; Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 203.9
Ethylmalonyl-CoA: 196.2
Methoxymalonyl-CoA: 162.0
2-Methylbutyryl-CoA: 131.3
trans-1,2-CPDA: 115.1
Propionyl-CoA: 110.0
CHC-CoA: 107.5
Isobutyryl-CoA: 86.9
Malonyl-CoA: 78.5
Benzoyl-CoA: 60.2
Acetyl-CoA: 43.7
fatty_acid: 41.5
3-Methylbutyryl-CoA: 32.1
inactive: 32.0

PKS_AT (1525..1817): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Methoxymalonyl-CoA: 95.8%; Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 216.5
Ethylmalonyl-CoA: 212.3
Methoxymalonyl-CoA: 174.1
2-Methylbutyryl-CoA: 142.5
trans-1,2-CPDA: 114.8
Propionyl-CoA: 114.4
Malonyl-CoA: 106.2
CHC-CoA: 100.9
Isobutyryl-CoA: 86.4
Benzoyl-CoA: 62.3
Acetyl-CoA: 46.8
fatty_acid: 43.6
inactive: 38.6
3-Methylbutyryl-CoA: 32.3

CDS_00309: mal

PKS_AT (326..607): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 66.7%; Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 188.7
inactive: 81.8
Methoxymalonyl-CoA: 65.8
Methylmalonyl-CoA: 61.9
Isobutyryl-CoA: 36.3
Propionyl-CoA: 34.3
Acetyl-CoA: 28.2
Ethylmalonyl-CoA: 23.4
Benzoyl-CoA: 12.5
fatty_acid: 12.0
2-Methylbutyryl-CoA: 11.0
CHC-CoA: 7.4
trans-1,2-CPDA: 6.2
3-Methylbutyryl-CoA: 0.0

CDS_00310: X

AMP-binding (13..405): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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:: DALFGGMIAK
Nearest Stachelhaus code(s):: Leu DALLVGAIAK (47% 8Å match); Val DALFVGLVAK (44% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production

NPDC052558.ctg-0001 - Region 2 - NAPAA,NRPS

Download region GenBank file

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Location: 390,826 - 491,912 nt. (total: 101,087 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NAPAA: (AMP-binding and TIGR02353)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

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Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_00353: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_00356: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_00368: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00381: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00382: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00392: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_00401: NADH:flavin oxidoreductase/NADH oxidase

smcogs: SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

CDS_00408: aldehyde oxidase and xanthine dehydrogenase

smcogs: SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

Transferases: acetyltransferase glycosyltransferase

CDS_00352: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_00367: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: dehalogenase hydrolase

CDS_00371: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_00384: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_00386: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Isomerases: racemase

CDS_00389: mandelate racemase/muconate lactonizing enzyme

smcogs: SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase

CDS_00370: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00373: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_00380: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00397: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.72	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.71	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000342.4	0.65	NRPS	enniatin	Fusarium equiseti
BGC0001240.4	0.64	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0000307.4	0.64	NRPS	AbT1	Aureobasidium pullulans

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002174.2	0.80	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0002135.2	0.76	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.75	NRPS	AM-toxin	Alternaria alternata
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.75	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.74	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.73	NRPS	HC-toxin	Alternaria jesenskae
BGC0001758.4	0.71	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 26.01 out of 29.65

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.15 out of 29.72

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

Additional weak hits (14):

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.39 out of 24.78

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.91 out of 20.01

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.41 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.95 out of 28.14

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.81 out of 18.57

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.38 out of 23.43

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.90 out of 25.88

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.86 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.05 out of 27.78

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.77 out of 26.85

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.45 out of 31.73

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.85 out of 30.22

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.02 out of 27.04

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 390825 - 491912:

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

Polymer prediction:: (X) + (Leu - D-Ala - D-Val - D-Val - X) + (D-Orn - Thr - D-Arg - Val - D-X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 390825 - 468139:

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

Polymer prediction:: (Leu - D-Ala - D-Val - D-Val - X) + (D-Orn - Thr - D-Arg - Val - D-X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 458078 - 491912:

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

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00370: Orn - Thr - Arg - Val - X

Search NORINE for peptide: strict or relaxed

AMP-binding (484..870): Orn

nrpys: Orn

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:: DTEDMGFVDK
Nearest Stachelhaus code(s):: Orn DTEDMGFVDK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1897..2265): 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 (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2870..3225): Arg

nrpys: 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:: DAENVGLVDK
Nearest Stachelhaus code(s):: Arg DADDVGLVDK (59% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (4199..4566): 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:: DAYFWGGTFK
Nearest Stachelhaus code(s):: Ile DAYFWGVTFK (94% 8Å match); Val DAYWWGGTFK (91% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (5162..5553): X

nrpys: Leu, 3OH-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:: DALLIGAVVK
Nearest Stachelhaus code(s):: Leu or 3OH-Leu DALLIGAVVK (79% 8Å match); Leu DALLIGAVVK (65% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_00373: Leu - Ala - Val - Val - X

Search NORINE for peptide: strict or relaxed

AMP-binding (23..408): 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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DALLIGSVVK
Nearest Stachelhaus code(s):: Leu or 3OH-Leu DALLIGAVVK (82% 8Å match); Leu DALLIGAVVK (62% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1038..1410): 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:: DVFGVAIVYK
Nearest Stachelhaus code(s):: Ala DVFSVAIVYK (91% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2414..2792): 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:: DAYWWGGTFK
Nearest Stachelhaus code(s):: Val DAYWWGGTFK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3824..4183): 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:: DAYWWGGTFK
Nearest Stachelhaus code(s):: Val DAYWWGGTFK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5207..5585): X

nrpys: Leu, 3OH-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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DALLIGAVVK
Nearest Stachelhaus code(s):: Leu or 3OH-Leu DALLIGAVVK (79% 8Å match); Leu DALLIGAVVK (59% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_00380: NH2

CAL_domain (155..488): NH2

minowa: NH2

Prediction, score:

NH2: 83.2
Acetyl-CoA: 42.6
AHBA: 16.7
shikimic_acid: 0.0
fatty_acid: 0.0

CDS_00397: X

AMP-binding (22..389): 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:: DAESIGTVVK
Nearest Stachelhaus code(s):: Lys DAEDIGTVVK (71% 8Å match); Gln or Tyr DAESVGTVVK (65% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
LexA variant 1	Repressor of DNA damage response
NtrC	Nitrogen regulatory protein C
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0001 - Region 3 - NRPS-like

Download region GenBank file

Download region SVG

Location: 507,845 - 549,497 nt. (total: 41,653 nt) Show pHMM detection rules used

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidase

CDS_00439: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_00441: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_00456: FAD linked oxidase domain protein

smcogs: SMCOG1138: FAD linked oxidase domain protein

Transferases: carboxylase

CDS_00451: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Ligases: ligase synthase

CDS_00434: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00442: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_00443: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00444: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_00446: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_00447: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_00450: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.69	NRPS	peramine	Epichloe festucae
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.66	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.65	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.64	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002164.2	0.69	NRPS	peramine	Epichloe festucae
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.66	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.65	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.64	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47

Confidence: medium

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.75 out of 25.75

Confidence: strong

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26

Confidence: medium

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.35 out of 18.57

Confidence: medium

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.02 out of 21.84

Confidence: medium

Additional weak hits (6):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.06 out of 29.25

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.62 out of 32.93

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.66 out of 30.25

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.04 out of 31.73

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.22 out of 29.51

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.54 out of 33.14

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 5, location 507844 - 549497:

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

Polymer prediction:: (Val)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_00434: X

AMP-binding (44..441): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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:: AHSCGVGIGK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_00443: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (16..381): 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:: DAFFVGGTFK
Nearest Stachelhaus code(s):: Val DAFFVGGTFK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_00447: Ala

Search NORINE for peptide: strict or relaxed

AMP-binding (7..393): 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:: DPFFVITVAK
Nearest Stachelhaus code(s):: Ala DVFFVGLVAK (56% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
MatP	Cell cycle regulator
MexT	Global virulence regulator
ToxT	Regulator of MSHA biosynthesis
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0001 - Region 4 - lanthipeptide-class-i

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Location: 567,326 - 591,578 nt. (total: 24,253 nt) Show pHMM detection rules used

lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))

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core biosynthetic genes

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transport-related genes

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Pfam domains

TIGRFAM domains

Gene/CDS overview

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Hydrolases: deacetylase

CDS_00472: acetylornithine deacetylase

smcogs: SMCOG1247: acetylornithine deacetylase

Lyases: cyclase dehydratase

CDS_00475: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_00479: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

CDS_00480: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

Isomerases: racemase

CDS_00471: mandelate racemase/muconate lactonizing enzyme

smcogs: SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0001289.5	0.59	ribosomal	penisin	Paenibacillus ehimensis
BGC0000541.5	0.58	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000542.3	0.58	ribosomal	paenicidin B	Paenibacillus terrae
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0002635.2	0.56	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000544.4	0.53	ribosomal	planosporicin	Planomonospora alba
BGC0000560.5	0.52	ribosomal	subtilomycin	Bacillus subtilis
BGC0000515.4	0.52	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2
BGC0000551.5	0.52	ribosomal	SapB	Streptomyces coelicolor A3(2)

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0001289.5	0.59	ribosomal	penisin	Paenibacillus ehimensis
BGC0000541.5	0.58	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000542.3	0.58	ribosomal	paenicidin B	Paenibacillus terrae
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0002635.2	0.56	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000544.4	0.53	ribosomal	planosporicin	Planomonospora alba
BGC0000560.5	0.52	ribosomal	subtilomycin	Bacillus subtilis
BGC0000515.4	0.52	ribosomal	geobacillin I	Geobacillus thermodenitrificans NG80-2
BGC0000551.5	0.52	ribosomal	SapB	Streptomyces coelicolor A3(2)

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26

Confidence: medium

Additional weak hits (7):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.70 out of 30.25

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.51 out of 21.84

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.92 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.12 out of 28.14

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.85 out of 35.63

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.42 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Lanthipeptides

RREFinder

TFBS Finder

Core peptide predictions

No core peptides found.

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 133 - 224; Score: 52.2

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0001 - Region 5 - terpene

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Location: 662,222 - 683,103 nt. (total: 20,882 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

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Pfam domains

Gene/CDS overview

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_00556: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_00559: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

Transferases: methyltransferase

CDS_00561: methyltransferase

smcogs: SMCOG1089: methyltransferase

Lyases: cyclase

CDS_00560: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000674.5	0.76	terpene	(-)-δ-cadinene	Streptomyces clavuligerus ATCC 27064
BGC0002708.2	0.74	terpene	(+)-δ-cadinol	Coniophora puteana RWD-64-598 SS2
BGC0000675.5	0.48	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0002707.2	0.47	terpene	(+)-δ-cadinol	Coniophora puteana RWD-64-598 SS2
BGC0001262.3	0.45	PKS	AK-toxin I	Alternaria alternata
BGC0000677.5	0.45	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000812.3	0.45	other (other)	huperzine A	Shiraia sp. slf14
BGC0001317.3	0.43	terpene	lupeol	Lotus japonicus
BGC0002406.2	0.41	other (other)	hydroxycinnamoyltyramine	Oryza sativa Japonica Group
BGC0001911.3	0.41	terpene	raimonol	Streptomyces anulatus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000674.5	0.76	terpene	(-)-δ-cadinene	Streptomyces clavuligerus ATCC 27064
BGC0002708.2	0.74	terpene	(+)-δ-cadinol	Coniophora puteana RWD-64-598 SS2
BGC0000675.5	0.48	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0002707.2	0.47	terpene	(+)-δ-cadinol	Coniophora puteana RWD-64-598 SS2
BGC0001262.3	0.45	PKS	AK-toxin I	Alternaria alternata
BGC0000677.5	0.45	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000812.3	0.45	other (other)	huperzine A	Shiraia sp. slf14
BGC0001317.3	0.43	terpene	lupeol	Lotus japonicus
BGC0002406.2	0.41	other (other)	hydroxycinnamoyltyramine	Oryza sativa Japonica Group
BGC0001911.3	0.41	terpene	raimonol	Streptomyces anulatus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_00560: T1TS

Domain 1 (7 - 284): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.37 out of 20.47

Confidence: strong

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 24.85 out of 30.12

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.08 out of 26.85

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16

Confidence: strong

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46

Confidence: strong

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.07 out of 18.16

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.37 out of 20.47

Confidence: strong

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.13 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47

Confidence: medium

Additional weak hits (5):

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.57 out of 29.51

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.20 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.76 out of 29.38

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.27 out of 26.85

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
IolR	Regulator of the inositol catabolism
OsdR	Development and stress management regulator
RpoN	Regulator of nitrogen assimilation and virulence
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0002 - Region 1 - terpene

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Location: 343,631 - 369,306 nt. (total: 25,676 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Terpene

TFBS Finder

Pfam domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_00916: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_00917: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_00923: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_00924: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Hydrolases: hydrolase

CDS_00933: HAD-superfamily hydrolase, subfamily IA, variant

smcogs: SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

Isomerases: racemase

CDS_00935: mandelate racemase/muconate lactonizing enzyme

smcogs: SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase synthetase

CDS_00925: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

CDS_00927: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002631.2	0.53	ribosomal	Myxarylin	Pyxidicoccus fallax
BGC0000286.3	0.51	PKS	viguiepinol	Streptomyces sp. KO-3988
BGC0000677.5	0.51	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001911.3	0.50	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.50	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0002309.2	0.50	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001605.3	0.46	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0000601.4	0.45	ribosomal	sporulation killing factor	Bacillus subtilis subsp. subtilis str. 168
BGC0000902.4	0.45	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002631.2	0.53	ribosomal	Myxarylin	Pyxidicoccus fallax
BGC0000286.3	0.51	PKS	viguiepinol	Streptomyces sp. KO-3988
BGC0000677.5	0.51	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001911.3	0.50	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.50	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0002309.2	0.50	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001605.3	0.46	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0000601.4	0.45	ribosomal	sporulation killing factor	Bacillus subtilis subsp. subtilis str. 168
BGC0000902.4	0.45	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
diterpene			C20	C6-C11 + C10-C15	PP

Genes with terpene domains:

CDS_00922: T1TS

Domain 1 (27 - 253): Type 1 terpene synthase

Subtype: unknown

CDS_00925: PT_FPPS_like

Domain 1 (51 - 326): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

CDS_00926: T2TS

Domain 1 (12 - 480): Type 2 terpene synthase

Subtype: Diterpene synthase

Reactions:: GGPP → diterpene_C6-C11/C10-C15_PP

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.16 out of 20.97

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 25.31

Confidence: medium

Additional weak hits (4):

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.33 out of 30.97

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.48 out of 21.55

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.43 out of 33.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.44 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
CcpA	Catabolite control protein A

NPDC052558.ctg-0003 - Region 1 - hydrogen-cyanide

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Location: 288,459 - 300,976 nt. (total: 12,518 nt) Show pHMM detection rules used

hydrogen-cyanide: (Fer2_4 and cds(Pyr_redox_2 and Fer2_BFD) and DAO)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

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TFBS Finder

Pfam domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxidoreductase reductase

CDS_01564: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

CDS_01566: alkyl hydroperoxide reductase subunit

smcogs: SMCOG1176: alkyl hydroperoxide reductase subunit

Hydrolases: peptidase

CDS_01569: methionine aminopeptidase

smcogs: SMCOG1172: methionine aminopeptidase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002345.2	0.54	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0002436.2	0.37	other (other)	coformycin	Streptomyces citricolor
BGC0001386.5	0.30	PKS	JBIR-76, JBIR-77	Streptomyces sp. RI-77
BGC0001007.5	0.25	NRPS, PKS	lymphostin, neolymphostinol B, lymphostinol, neolymphostin b	Salinispora arenicola CNS-205
BGC0002285.2	0.24	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0001006.5	0.23	NRPS, PKS	lymphostin, neolymphostinol B, lymphostinol, neolymphostin B	Salinispora tropica CNB-440
BGC0000903.3	0.23	other (other)	fluorometabolite	Streptomyces cattleya
BGC0001114.5	0.22	NRPS, PKS	thailanstatin A	Burkholderia thailandensis
BGC0000883.5	0.20	other (other)	arginomycin	Streptomyces arginensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002345.2	0.54	other (other)	hydrogen cyanide	Pseudomonas fluorescens
BGC0002436.2	0.37	other (other)	coformycin	Streptomyces citricolor
BGC0001386.5	0.30	PKS	JBIR-76, JBIR-77	Streptomyces sp. RI-77
BGC0001007.5	0.25	NRPS, PKS	lymphostin, neolymphostinol B, lymphostinol, neolymphostin b	Salinispora arenicola CNS-205
BGC0002285.2	0.24	ribosomal	aborycin	Streptomyces sp. ZS0098
BGC0001006.5	0.23	NRPS, PKS	lymphostin, neolymphostinol B, lymphostinol, neolymphostin B	Salinispora tropica CNB-440
BGC0000903.3	0.23	other (other)	fluorometabolite	Streptomyces cattleya
BGC0001114.5	0.22	NRPS, PKS	thailanstatin A	Burkholderia thailandensis
BGC0000883.5	0.20	other (other)	arginomycin	Streptomyces arginensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.76 out of 25.31

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

Additional weak hits (4):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.16 out of 30.22

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.96 out of 29.65

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.38 out of 21.84

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.54 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0004 - Region 1 - terpene

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Location: 167,269 - 193,186 nt. (total: 25,918 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_01925: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

Hydrolases: hydrolase

CDS_01928: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: synthetase

CDS_01924: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000663.5	0.62	terpene	hopene	Streptomyces coelicolor A3(2)
BGC0000647.3	0.57	terpene	carotenoid	Rhodobacter sphaeroides
BGC0000644.3	0.52	terpene	carotenoid	Dietzia sp. CQ4
BGC0002320.3	0.50	terpene	conidiogenone	Penicillium rubens Wisconsin 54-1255
BGC0000646.5	0.49	terpene	β-carotein	uncultured bacterium
BGC0000630.3	0.49	terpene	(2R,3S,3'S)-2-hydroxyastaxanthin	Paracoccus haeundaensis
BGC0002173.2	0.48	saccharide, terpene	fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol	Aspergillus fumigatus A1163
BGC0000640.3	0.48	terpene	carotenoid	Enterobacteriaceae bacterium DC404
BGC0000641.3	0.47	terpene	carotenoid	Enterobacteriaceae bacterium DC416
BGC0000638.3	0.47	terpene	carotenoid	Pantoea ananatis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000663.5	0.62	terpene	hopene	Streptomyces coelicolor A3(2)
BGC0000647.3	0.57	terpene	carotenoid	Rhodobacter sphaeroides
BGC0000644.3	0.52	terpene	carotenoid	Dietzia sp. CQ4
BGC0002320.3	0.50	terpene	conidiogenone	Penicillium rubens Wisconsin 54-1255
BGC0000646.5	0.49	terpene	β-carotein	uncultured bacterium
BGC0000630.3	0.49	terpene	(2R,3S,3'S)-2-hydroxyastaxanthin	Paracoccus haeundaensis
BGC0002173.2	0.48	saccharide, terpene	fumihopaside A, compound 3, 21-β-H-hopane-3beta, 22-diol	Aspergillus fumigatus A1163
BGC0000640.3	0.48	terpene	carotenoid	Enterobacteriaceae bacterium DC404
BGC0000641.3	0.47	terpene	carotenoid	Enterobacteriaceae bacterium DC416
BGC0000638.3	0.47	terpene	carotenoid	Pantoea ananatis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
triterpene	hopanoid		C30	hopanoid skeleton	unknown
triterpene	polypodane		C30	polypodane skeleton	unknown

Genes with terpene domains:

CDS_01923: T2TS

Domain 1 (7 - 610): Type 2 terpene synthase

Subtype: Squalene substrate

Reactions:: squalene → hopanoid; squalene → polypodane

CDS_01924: PT_FPPS_like

Domain 1 (46 - 329): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

CDS_01926: PT_phytoene_like

Domain 1 (9 - 286): Prenyltransferase; Phytoene synthase like

Subtype: unknown

Reactions:: FPP → diapophytoene; FPP → squalene; FPP → PSPP; GGPP → phytoene; PSPP → hydroxysqualene

CDS_01927: PT_phytoene_like

Domain 1 (30 - 288): Prenyltransferase; Phytoene synthase like

Subtype: Hydroxysqualene synthase

Reactions:: PSPP → hydroxysqualene

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.08 out of 23.79

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26

Confidence: strong

Additional weak hits (13):

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.16 out of 30.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.81 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.64 out of 31.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.20 out of 31.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.38 out of 26.06

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.29 out of 25.75

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.40 out of 26.12

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.70 out of 26.12

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.73 out of 35.63

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.46 out of 35.63

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.16 out of 20.01

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PSPP	Presqualene diphosphate

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
IolR	Regulator of the inositol catabolism

NPDC052558.ctg-0004 - Region 2 - NRPS-like,terpene

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Location: 255,535 - 298,954 nt. (total: 43,420 nt) Show pHMM detection rules used

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_01997: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02015: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02016: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02019: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_02022: aldehyde oxidase and xanthine dehydrogenase

smcogs: SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

Transferases: aminotransferase methyltransferase

CDS_02002: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_02026: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Lyases: cyclase

CDS_02012: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: ligase

CDS_02013: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease

CDS_02025: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.51	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.49	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.49	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.49	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.49	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.48	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000528.5	0.32	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0000866.5	0.31	other (other)	polyhydroxyalkanoate	Burkholderia sp. DSM 9242
BGC0001197.5	0.30	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0002518.3	0.30	NRPS	syringafactin A, syringafactin C	Pseudomonas sp. SZ57

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.59	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.58	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.58	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.58	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.58	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.58	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001201.3	0.56	terpene	eremophilene	Sorangium cellulosum So ce56
BGC0001475.4	0.48	terpene	aspterric acid	Aspergillus terreus NIH2624
BGC0000844.5	0.48	other (other)	clavulanic acid	Streptomyces clavuligerus
BGC0002000.4	0.48	PKS	setomimycin	Streptomyces aurantiacus JA 4570

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_02012: T1TS

Domain 1 (17 - 326): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47

Confidence: strong

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.52 out of 19.26

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 26.07 out of 30.12

Confidence: medium

Additional weak hits (7):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 18.11 out of 31.73

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.38 out of 26.85

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 35.63

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.91 out of 24.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.83 out of 28.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.86 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Terpene

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 255534 - 298954:

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

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_02013: X

AMP-binding (90..496): 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:: VLLVYGGPIK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
OsdR	Development and stress management regulator
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0004 - Region 3 - RRE-containing

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Location: 415,701 - 438,187 nt. (total: 22,487 nt) Show pHMM detection rules used

RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_02154: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_02156: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_02158: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: methyltransferase

CDS_02145: methyltransferase

smcogs: SMCOG1089: methyltransferase

Lyases: cyclase dehydratase hydratase

CDS_02144: Nitrilase/cyanide hydratase and apolipoprotein

smcogs: SMCOG1294: Nitrilase/cyanide hydratase and apolipoprotein

CDS_02152: diguanylate cyclase

smcogs: SMCOG1025: diguanylate cyclase

CDS_02155: L-carnitine dehydratase/bile acid-inducible

smcogs: SMCOG1189: L-carnitine dehydratase/bile acid-inducible

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000131.5	0.43	PKS	pyrrolomycin	Streptomyces sp. UC 11065
BGC0000902.4	0.41	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0000207.5	0.41	PKS	chartreusin	Streptomyces chartreusis
BGC0000003.3	0.39	PKS	AF-toxin	Alternaria alternata
BGC0001850.4	0.39	other (shikimate-derived)	diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G	Streptomyces sp. F001
BGC0001687.3	0.39	other (other)	N-tetradecanoyl tyrosine	uncultured bacterium CSL12
BGC0001483.4	0.38	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0001782.3	0.38	other (other)	spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G	Streptomyces sp. SCSIO 03032
BGC0001625.5	0.38	PKS	Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F	Streptomyces sp. CB01883
BGC0002387.2	0.37	PKS	yangpumicin A	Micromonospora yangpuensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000131.5	0.43	PKS	pyrrolomycin	Streptomyces sp. UC 11065
BGC0000902.4	0.41	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0000207.5	0.41	PKS	chartreusin	Streptomyces chartreusis
BGC0000003.3	0.39	PKS	AF-toxin	Alternaria alternata
BGC0001850.4	0.39	other (shikimate-derived)	diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G	Streptomyces sp. F001
BGC0001687.3	0.39	other (other)	N-tetradecanoyl tyrosine	uncultured bacterium CSL12
BGC0001483.4	0.38	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0001782.3	0.38	other (other)	spiroindimicin A, spiroindimicin B, spiroindimicin C, spiroindimicin D, indimicin A, indimicin B, indimicin C, indimicin D, indimicin E, lynamicin A, lynamicin D, lynamicin F, lynamicin G	Streptomyces sp. SCSIO 03032
BGC0001625.5	0.38	PKS	Isofuranonaphthoquinone A, Isofuranonaphthoquinone B, Isofuranonaphthoquinone C, Isofuranonaphthoquinone D, Isofuranonaphthoquinone E, Isofuranonaphthoquinone F	Streptomyces sp. CB01883
BGC0002387.2	0.37	PKS	yangpumicin A	Micromonospora yangpuensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.17 out of 25.31

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.79 out of 25.31

Confidence: medium

Additional weak hits (3):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.16 out of 31.73

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.38 out of 29.65

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.52 out of 33.14

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

RREFinder

TFBS Finder

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 273 - 335; Score: 26.5

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0005 - Region 1 - lassopeptide,terpene

Download region GenBank file

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Location: 34,316 - 76,240 nt. (total: 41,925 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lasso peptides

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidase

CDS_02210: pyruvate oxidase/decarboxylase

smcogs: SMCOG1055: pyruvate oxidase/decarboxylase

CDS_02222: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_02230: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02231: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Transferases: aminotransferase methyltransferase

CDS_02213: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_02232: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

CDS_02233: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Hydrolases: hydrolase

CDS_02235: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: cyclase

CDS_02214: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: synthase

CDS_02208: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs: SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

CDS_02211: polyprenol-monophosphomannose synthase ppm1

smcogs: SMCOG1123: polyprenol-monophosphomannose synthase ppm1

CDS_02217: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001539.4	0.41	ribosomal	cattlecin	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002053.3	0.40	ribosomal	ulleungdin	Streptomyces sp.
BGC0001507.3	0.38	ribosomal	anantin C	Streptomyces olindensis
BGC0001493.5	0.36	ribosomal	achromosin	Streptomyces achromogenes subsp. achromogenes
BGC0000659.3	0.28	terpene	2-methylisoborneol	Saccharopolyspora erythraea NRRL 2338
BGC0000658.3	0.28	terpene	2-methylisoborneol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002289.2	0.27	ribosomal	Leepeptin	Streptomyces leeuwenhoekii
BGC0001551.4	0.27	ribosomal	citrulassin E	Streptomyces glaucescens
BGC0002318.2	0.27	ribosomal	canucin A, canucin B	Streptomyces canus
BGC0001548.4	0.26	ribosomal	citrulassin A	Streptomyces albulus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001539.4	0.72	ribosomal	cattlecin	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0002053.3	0.72	ribosomal	ulleungdin	Streptomyces sp.
BGC0001507.3	0.70	ribosomal	anantin C	Streptomyces olindensis
BGC0001493.5	0.69	ribosomal	achromosin	Streptomyces achromogenes subsp. achromogenes
BGC0001551.4	0.63	ribosomal	citrulassin E	Streptomyces glaucescens
BGC0002289.2	0.63	ribosomal	Leepeptin	Streptomyces leeuwenhoekii
BGC0001549.3	0.62	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0002318.2	0.62	ribosomal	canucin A, canucin B	Streptomyces canus
BGC0001889.2	0.62	ribosomal	fusilassin	Thermobifida fusca YX
BGC0000659.3	0.62	terpene	2-methylisoborneol	Saccharopolyspora erythraea NRRL 2338

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lasso peptide predictions

Lassopeptides - No core peptides found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
monoterpene		2-methylisoborneol	C11	C1-C6	OH
monoterpene		2-methylenebornane	C11	C1-C6	none

Genes with terpene domains:

CDS_02214: T1TS

Domain 1 (60 - 405): Type 1 terpene synthase

Subtype: 2-Methylisoborneol synthase type

Reactions:: 2-MeGPP → 2-methylisoborneol; 2-MeGPP → 2-methylenebornane

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 22.37 out of 23.79

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.51 out of 25.31

Confidence: medium

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 23.82 out of 27.18

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.95 out of 26.85

Confidence: medium

Additional weak hits (8):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.79 out of 36.54

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.89 out of 21.55

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 18.61 out of 30.97

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.54 out of 27.04

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.87 out of 35.63

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.24 out of 28.19

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.72 out of 30.98

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.67 out of 23.43

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lasso peptides

RREFinder

Terpene

TFBS Finder

Core peptide predictions

No core peptides found.

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 1 - 83; Score: 71.9; RRE type: Lasso_Fused_RRE; Location: 1 - 58; Score: 25.8

Glossary

Acronym	Full name
2-MeGPP	2-methylgeranyl diphosphate

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
IolR	Regulator of the inositol catabolism
NrdR	Represses ribonucleotide reductase encoding genes
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0005 - Region 2 - NRPS-like

Download region GenBank file

Download region SVG

Location: 152,152 - 195,493 nt. (total: 43,342 nt) Show pHMM detection rules used

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxidoreductase

CDS_02332: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Hydrolases: amidase dehalogenase

CDS_02331: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

CDS_02333: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

CDS_02341: amidase

smcogs: SMCOG1105: amidase

Isomerases: racemase

CDS_02326: mandelate racemase/muconate lactonizing enzyme

smcogs: SMCOG1268: mandelate racemase/muconate lactonizing enzyme

Ligases: ligase

CDS_02330: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease transporter

CDS_02325: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

CDS_02334: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.59	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.58	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.58	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.58	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.58	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002518.3	0.45	NRPS	syringafactin A, syringafactin C	Pseudomonas sp. SZ57
BGC0001168.5	0.44	NRPS	Livipeptin	Streptomyces lividans 1326
BGC0000595.3	0.42	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0000597.4	0.41	ribosomal	SWA-2138	Streptomyces sp. e14
BGC0002034.3	0.41	other (other)	perquinoline A, perquinoline B, perquinoline C	Streptomyces sp. IB2014 016-6

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.59	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.58	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.58	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.58	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.58	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002518.3	0.45	NRPS	syringafactin A, syringafactin C	Pseudomonas sp. SZ57
BGC0001168.5	0.44	NRPS	Livipeptin	Streptomyces lividans 1326
BGC0000595.3	0.42	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0000597.4	0.41	ribosomal	SWA-2138	Streptomyces sp. e14
BGC0002034.3	0.41	other (other)	perquinoline A, perquinoline B, perquinoline C	Streptomyces sp. IB2014 016-6

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 18.25 out of 18.46

Confidence: strong

Additional weak hits (9):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.53 out of 29.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.37 out of 26.06

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.88 out of 29.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.63 out of 28.19

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.94 out of 23.43

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.04 out of 32.74

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.22 out of 30.22

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 4, location 152151 - 195493:

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

Polymer prediction:: (Val)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_02330: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (57..469): Val

nrpys: Val

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:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: AAAMFGGAIK
Nearest Stachelhaus code(s):: 6-clTrp DAAMCGGVAK (32% 8Å match); diOH-Bz AANFVSGAIK (29% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
RpoN	Regulator of nitrogen assimilation and virulence

NPDC052558.ctg-0005 - Region 3 - NAPAA,T1PKS,hglE-KS

Download region GenBank file

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Location: 244,171 - 302,010 nt. (total: 57,840 nt) Show pHMM detection rules used

NAPAA: (AMP-binding and TIGR02353)
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)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_02406: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02420: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02421: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_02424: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase

CDS_02416: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_02426: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_02432: alpha/beta hydrolase domain-containing protein

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

CDS_02433: alpha/beta hydrolase domain-containing protein

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

Ligases: ligase synthase

CDS_02409: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02418: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_02419: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002174.2	1.47	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001273.3	0.86	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.86	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.86	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001128.4	0.86	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.86	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.85	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.85	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002075.3	0.85	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002286.3	0.84	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002174.2	0.78	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001273.3	0.62	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.62	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.62	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0000037.4	0.62	PKS	cichorine	Aspergillus nidulans FGSC A4
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.62	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.62	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.62	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002075.3	0.62	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.59 out of 23.43

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.82 out of 18.46

Confidence: medium

Additional weak hits (10):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.22 out of 20.97

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.68 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.80 out of 30.25

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.49 out of 20.97

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.18 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.44 out of 29.65

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 20.32 out of 30.98

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.98 out of 29.65

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.95 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 5, location 244170 - 302010:

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

Polymer prediction:: (mxmal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 6, location 244170 - 277983:

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

Polymer prediction:: (mxmal) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 251826 - 302010:

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

Polymer prediction:: (mxmal) + (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_02409: X

AMP-binding (39..406): 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:: DAESIGTVVK
Nearest Stachelhaus code(s):: Lys DAEDIGTVVK (71% 8Å match); Gln or Tyr DAESVGTVVK (62% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_02418: mxmal

PKS_AT (597..813): mxmal

ATSignature: (unknown)

No matches above 50%

minowa: Methoxymalonyl-CoA

Prediction, score:

Methoxymalonyl-CoA: 9.8
Malonyl-CoA: 6.7
inactive: 0.9
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Methylmalonyl-CoA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

CDS_02419: mal

PKS_AT (1086..1371): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; inactive: 70.8%; Propionyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 92.3
inactive: 35.9
Methoxymalonyl-CoA: 34.2
Methylmalonyl-CoA: 33.6
Propionyl-CoA: 33.1
2-Methylbutyryl-CoA: 14.5
CHC-CoA: 11.3
Ethylmalonyl-CoA: 7.5
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Isobutyryl-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
BldD	Development and antibiotic global regulator
CcpA	Catabolite control protein A
RpoN	Regulator of nitrogen assimilation and virulence

NPDC052558.ctg-0005 - Region 4 - HR-T2PKS,NRPS,T1PKS,terpene

Download region GenBank file

Download region SVG

Location: 352,834 - 437,737 nt. (total: 84,904 nt) Show pHMM detection rules used

Region on contig edge.

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-synt))
terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_02488: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02505: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_02506: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

CDS_02515: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_02517: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_02525: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: acyltransferase aminotransferase formyltransferase methyltransferase sulfhydrylase

CDS_02492: O-succinylhomoserine sulfhydrylase

smcogs: SMCOG1168: O-succinylhomoserine sulfhydrylase

CDS_02507: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_02510: polyketide synthase associated protein papA3

smcogs: SMCOG1209: polyketide synthase associated protein papA3

CDS_02523: methionyl-tRNA formyltransferase

smcogs: SMCOG1228: methionyl-tRNA formyltransferase

CDS_02527: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Hydrolases: deaminase hydrolase

CDS_02496: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

CDS_02521: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

Ligases: ligase synthase

CDS_02497: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

CDS_02498: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_02501: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_02502: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_02526: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_02528: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	1.12	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001132.4	1.10	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	1.10	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	1.08	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001128.4	1.07	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	1.05	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	1.02	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001261.3	1.02	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	1.01	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000342.4	1.00	NRPS	enniatin	Fusarium equiseti

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.73	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.71	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.70	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.69	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

No product predictions

Genes with terpene domains:

CDS_02518: T1TS

Domain 1 (105 - 321): Type 1 terpene synthase

Subtype: unknown

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 24.84 out of 29.72

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.32 out of 26.85

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.09 out of 26.85

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.90 out of 28.19

Confidence: medium

Additional weak hits (12):

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.44 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.82 out of 27.78

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.95 out of 27.04

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.99 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.28 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.27 out of 29.38

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 19.16 out of 36.54

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.13 out of 26.06

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.87 out of 26.06

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.79 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

Terpene

TFBS Finder

Predicted core structure(s)

For candidate cluster 8, location 352833 - 437737:

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

Polymer prediction:: (X - D-Phe) + (X - Gly) + (X) + (mal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_02498: X - Phe

Search NORINE for peptide: strict or relaxed

AMP-binding (461..857): 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 (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1510..1906): Phe

nrpys: Phe

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:: DAWVIAAVCK
Nearest Stachelhaus code(s):: omeTyr DAWNIAAVCK (74% 8Å match); Phe DAWTIAAVCK (65% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_02510: X - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (451..847): 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 (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1499..1884): 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:: DILQLGVIWK
Nearest Stachelhaus code(s):: Gly DILQLGVIWK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_02527: X

AMP-binding (1359..1703): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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:: DYASNGIVAK
Nearest Stachelhaus code(s):: dclTrp DVCSAGIAAK (50% 8Å match); Thr DYWSVGMVHK (47% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_02528: mal

PKS_AT (530..797): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; inactive: 58.3%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 85.7
Methylmalonyl-CoA: 57.5
Propionyl-CoA: 46.6
inactive: 44.9
Methoxymalonyl-CoA: 44.5
2-Methylbutyryl-CoA: 25.9
Ethylmalonyl-CoA: 25.2
fatty_acid: 23.8
Acetyl-CoA: 21.8
CHC-CoA: 19.1
trans-1,2-CPDA: 17.6
Isobutyryl-CoA: 15.3
Benzoyl-CoA: 11.7
3-Methylbutyryl-CoA: 6.3

Link to PARAS substrate predictor

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
NtrC	Nitrogen regulatory protein C
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems
ZuR variant 1	Zinc-responsive repressor

NPDC052558.ctg-0006 - Region 1 - RRE-containing

Download region GenBank file

Download region SVG

Location: 26,588 - 47,685 nt. (total: 21,098 nt) Show pHMM detection rules used

RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002317.2	0.45	ribosomal	herbicolin O, mcceh252, pantocin A	Pantoea agglomerans
BGC0000585.5	0.40	ribosomal	microcin C7	Escherichia coli
BGC0002064.2	0.26	ribosomal	felipeptin A2, felipeptin A1	Amycolatopsis sp. YIM 10
BGC0001647.3	0.26	PKS	lagunapyrone A, lagunapyrone B, lagunapyrone C	Streptomyces sp. MP131-18
BGC0000821.5	0.25	other (other)	rebeccamycin	Lechevalieria aerocolonigenes
BGC0000877.5	0.24	other (other)	polyoxin A, polyoxin H	Streptomyces cacaoi subsp. asoensis
BGC0000204.5	0.24	PKS	benastatin A, benastatin B, BE-43767, TAN1532B	Streptomyces sp. A2991200
BGC0000197.5	0.24	PKS, saccharide	aranciamycin	Streptomyces echinatus
BGC0000632.5	0.23	saccharide, terpene	brasilicardin A	Nocardia terpenica
BGC0002443.3	0.23	PKS	mycemycin C, mycemycin A, mycemycin B	Streptomyces olivaceus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002317.2	0.45	ribosomal	herbicolin O, mcceh252, pantocin A	Pantoea agglomerans
BGC0000585.5	0.40	ribosomal	microcin C7	Escherichia coli
BGC0002064.2	0.26	ribosomal	felipeptin A2, felipeptin A1	Amycolatopsis sp. YIM 10
BGC0001647.3	0.26	PKS	lagunapyrone A, lagunapyrone B, lagunapyrone C	Streptomyces sp. MP131-18
BGC0000821.5	0.25	other (other)	rebeccamycin	Lechevalieria aerocolonigenes
BGC0000877.5	0.24	other (other)	polyoxin A, polyoxin H	Streptomyces cacaoi subsp. asoensis
BGC0000204.5	0.24	PKS	benastatin A, benastatin B, BE-43767, TAN1532B	Streptomyces sp. A2991200
BGC0000197.5	0.24	PKS, saccharide	aranciamycin	Streptomyces echinatus
BGC0000632.5	0.23	saccharide, terpene	brasilicardin A	Nocardia terpenica
BGC0002443.3	0.23	PKS	mycemycin C, mycemycin A, mycemycin B	Streptomyces olivaceus

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (4):

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.13 out of 25.75

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.81 out of 24.78

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.85 out of 36.53

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.81 out of 25.88

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

RREFinder

TFBS Finder

RRE predictions

: RRE type: Pantocin_Microcin_RRE; Location: 0 - 93; Score: 59.5

TFBS definitions

Regulator	Description

NPDC052558.ctg-0006 - Region 2 - T1PKS,oligosaccharide

Download region GenBank file

Download region SVG

Location: 97,190 - 231,151 nt. (total: 133,962 nt) Show pHMM detection rules used

oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_02631: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_02638: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_02639: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_02649: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: aminotransferase glycosyltransferase transferase

CDS_02625: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_02626: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs: SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CDS_02627: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_02630: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_02650: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_02651: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_02652: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs: SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

Hydrolases: esterase

CDS_02663: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: dehydratase

CDS_02624: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_02636: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_02654: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase

CDS_02621: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_02637: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_02643: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_02644: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_02645: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_02648: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002349.3	0.80	PKS	epemicin B, epemicin A	Kutzneria sp. CA-103260
BGC0001275.3	0.71	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001817.5	0.61	other (other)	vancosamine	Streptomyces sp. WAC2288
BGC0001258.3	0.60	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0001160.5	0.58	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.58	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001254.3	0.56	PKS	ACT-Toxin II	Alternaria alternata
BGC0000898.5	0.50	saccharide	desosamine, pikromycin, neomethymycin, narbomycin	Streptomyces venezuelae
BGC0001268.4	0.49	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0000019.5	0.48	PKS	angolamycin	Streptomyces eurythermus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002349.3	0.80	PKS	epemicin B, epemicin A	Kutzneria sp. CA-103260
BGC0001275.3	0.74	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001276.3	0.74	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.73	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001160.5	0.64	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.64	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001257.3	0.64	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0000107.3	0.64	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002175.3	0.64	PKS	YWA1	Aspergillus oryzae RIB40

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.82 out of 23.79

Confidence: medium

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 28.31 out of 30.12

Confidence: strong

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.10 out of 23.43

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.96 out of 23.79

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.15 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.28 out of 23.05

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.03 out of 26.85

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47

Confidence: medium

Additional weak hits (42):

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.99 out of 26.85

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.20 out of 20.97

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.59 out of 25.88

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.69 out of 21.55

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.99 out of 29.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.12 out of 27.78

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.48 out of 27.55

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.62 out of 25.75

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.57 out of 26.33

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.40 out of 29.38

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.88 out of 19.26

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.54 out of 20.97

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.58 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.13 out of 27.78

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.03 out of 24.78

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.64 out of 32.93

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 21.84 out of 32.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.42 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.95 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.68 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.07 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.37 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.07 out of 26.06

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.68 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.41 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.74 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.60 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 15.83 out of 33.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.04 out of 29.65

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.25 out of 27.04

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.58 out of 27.18

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.61 out of 23.43

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.44 out of 26.85

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.47 out of 26.85

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.26 out of 29.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.67 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.99 out of 28.14

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 22.35 out of 36.54

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.43 out of 26.06

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.37 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.63 out of 32.93

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 97189 - 231151:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (Me-mal - Me-ohmal - Me-ohmal) + (ccmal - ohmal) + (ohmal - ohmal - mal - Me-ohmal - ccmal) + (ohmal - Me-ohmal) + (ccmal)
Non-colinear ordering:: CDS_02637 + CDS_02648 + CDS_02645 + CDS_02644 + CDS_02643

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 100384 - 197148:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (Me-mal - Me-ohmal - Me-ohmal) + (ohmal - ohmal - mal - Me-ohmal - ccmal) + (ohmal - Me-ohmal) + (ccmal)
Non-colinear ordering:: CDS_02637 + CDS_02645 + CDS_02644 + CDS_02643

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 181731 - 231151:

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

Polymer prediction:: (ccmal - ohmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_02637: mmal - mmal - mmal

PKS_AT (511..799): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 87.5%; Methoxymalonyl-CoA: 79.2%; Malonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 187.4
Ethylmalonyl-CoA: 185.0
Methoxymalonyl-CoA: 156.8
2-Methylbutyryl-CoA: 124.8
Propionyl-CoA: 112.7
trans-1,2-CPDA: 110.4
Malonyl-CoA: 95.4
CHC-CoA: 90.0
Isobutyryl-CoA: 80.6
Benzoyl-CoA: 47.5
3-Methylbutyryl-CoA: 41.1
Acetyl-CoA: 39.4
fatty_acid: 36.0
inactive: 24.0

PKS_AT (1472..1744): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Methoxymalonyl-CoA: 91.7%; Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 214.6
Ethylmalonyl-CoA: 198.6
Methoxymalonyl-CoA: 170.3
2-Methylbutyryl-CoA: 164.6
trans-1,2-CPDA: 115.4
Propionyl-CoA: 111.0
Malonyl-CoA: 93.9
CHC-CoA: 80.5
Isobutyryl-CoA: 78.1
Benzoyl-CoA: 62.5
Acetyl-CoA: 47.4
3-Methylbutyryl-CoA: 37.0
fatty_acid: 28.0
inactive: 26.7

PKS_AT (2956..3228): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 91.7%; Methoxymalonyl-CoA: 87.5%; Ethylmalonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 185.7
Ethylmalonyl-CoA: 175.2
Methoxymalonyl-CoA: 146.4
2-Methylbutyryl-CoA: 115.5
trans-1,2-CPDA: 101.0
Propionyl-CoA: 90.7
CHC-CoA: 84.0
Malonyl-CoA: 71.7
Isobutyryl-CoA: 54.8
Acetyl-CoA: 39.0
3-Methylbutyryl-CoA: 33.0
Benzoyl-CoA: 31.3
inactive: 22.2
fatty_acid: 21.9

CDS_02643: mal

PKS_AT (553..824): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 224.1
inactive: 126.1
Methoxymalonyl-CoA: 67.0
Methylmalonyl-CoA: 58.0
Propionyl-CoA: 37.7
Acetyl-CoA: 27.2
Ethylmalonyl-CoA: 26.5
Isobutyryl-CoA: 26.3
Benzoyl-CoA: 25.0
2-Methylbutyryl-CoA: 24.0
fatty_acid: 20.0
trans-1,2-CPDA: 14.9
CHC-CoA: 2.0
3-Methylbutyryl-CoA: 0.0

CDS_02644: mal - mmal

PKS_AT (550..819): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 214.5
inactive: 117.5
Methoxymalonyl-CoA: 54.9
Methylmalonyl-CoA: 45.8
Propionyl-CoA: 26.4
Acetyl-CoA: 24.4
Benzoyl-CoA: 23.0
Isobutyryl-CoA: 15.0
fatty_acid: 14.2
Ethylmalonyl-CoA: 13.4
2-Methylbutyryl-CoA: 12.5
CHC-CoA: 8.5
trans-1,2-CPDA: 8.4
3-Methylbutyryl-CoA: 0.0

PKS_AT (2026..2299): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Methoxymalonyl-CoA: 91.7%; Malonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 216.6
Ethylmalonyl-CoA: 207.4
Methoxymalonyl-CoA: 170.5
2-Methylbutyryl-CoA: 159.3
trans-1,2-CPDA: 128.4
Propionyl-CoA: 109.7
Malonyl-CoA: 105.3
CHC-CoA: 87.6
Isobutyryl-CoA: 86.4
Benzoyl-CoA: 64.9
Acetyl-CoA: 52.9
3-Methylbutyryl-CoA: 36.8
inactive: 35.2
fatty_acid: 29.8

CDS_02645: mal - mal - mal - mmal - mal

PKS_AT (561..837): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 83.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 224.1
inactive: 128.7
Methoxymalonyl-CoA: 70.3
Methylmalonyl-CoA: 57.8
Propionyl-CoA: 34.5
Isobutyryl-CoA: 30.0
Acetyl-CoA: 27.1
Benzoyl-CoA: 25.6
Ethylmalonyl-CoA: 21.2
2-Methylbutyryl-CoA: 17.8
fatty_acid: 15.5
CHC-CoA: 14.5
trans-1,2-CPDA: 8.6
3-Methylbutyryl-CoA: 0.0

PKS_AT (2032..2300): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 234.0
inactive: 133.9
Methoxymalonyl-CoA: 70.3
Methylmalonyl-CoA: 62.0
Propionyl-CoA: 40.4
Isobutyryl-CoA: 38.6
Acetyl-CoA: 28.2
Benzoyl-CoA: 27.5
Ethylmalonyl-CoA: 24.5
CHC-CoA: 19.6
2-Methylbutyryl-CoA: 19.5
fatty_acid: 16.6
trans-1,2-CPDA: 10.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (3485..3753): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 227.0
inactive: 126.2
Methoxymalonyl-CoA: 60.1
Methylmalonyl-CoA: 55.1
Propionyl-CoA: 35.0
Acetyl-CoA: 26.8
Isobutyryl-CoA: 26.6
Ethylmalonyl-CoA: 24.6
Benzoyl-CoA: 22.9
fatty_acid: 21.0
2-Methylbutyryl-CoA: 20.7
CHC-CoA: 19.9
trans-1,2-CPDA: 13.4
3-Methylbutyryl-CoA: 0.0

PKS_AT (4766..5057): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Methoxymalonyl-CoA: 91.7%; Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 197.7
Ethylmalonyl-CoA: 187.9
Methoxymalonyl-CoA: 147.3
2-Methylbutyryl-CoA: 135.5
trans-1,2-CPDA: 111.6
Propionyl-CoA: 98.1
CHC-CoA: 84.1
Malonyl-CoA: 79.9
Isobutyryl-CoA: 67.4
Benzoyl-CoA: 55.1
Acetyl-CoA: 33.5
3-Methylbutyryl-CoA: 31.3
fatty_acid: 26.4
inactive: 21.4

PKS_AT (6279..6553): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 239.0
inactive: 137.9
Methoxymalonyl-CoA: 65.8
Methylmalonyl-CoA: 60.0
Propionyl-CoA: 43.8
Isobutyryl-CoA: 32.9
2-Methylbutyryl-CoA: 27.7
Benzoyl-CoA: 27.2
Acetyl-CoA: 26.4
Ethylmalonyl-CoA: 23.6
CHC-CoA: 14.2
fatty_acid: 13.5
trans-1,2-CPDA: 9.7
3-Methylbutyryl-CoA: 0.0

CDS_02648: mal - mal

PKS_AT (554..829): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 83.3%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 207.1
inactive: 104.6
Methoxymalonyl-CoA: 59.4
Methylmalonyl-CoA: 46.1
Acetyl-CoA: 21.2
Benzoyl-CoA: 18.7
Ethylmalonyl-CoA: 18.1
Isobutyryl-CoA: 17.1
Propionyl-CoA: 15.2
2-Methylbutyryl-CoA: 12.0
fatty_acid: 9.2
CHC-CoA: 3.0
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (2161..2429): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 237.9
inactive: 126.9
Methoxymalonyl-CoA: 66.9
Methylmalonyl-CoA: 58.7
Propionyl-CoA: 40.8
Isobutyryl-CoA: 35.7
Benzoyl-CoA: 33.1
Acetyl-CoA: 29.9
Ethylmalonyl-CoA: 25.0
fatty_acid: 20.5
2-Methylbutyryl-CoA: 18.8
trans-1,2-CPDA: 13.9
CHC-CoA: 13.9
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
AfsR	Pleiotropic regulatory for antibiotic production
BldD	Development and antibiotic global regulator
IolR	Regulator of the inositol catabolism
OsdR	Development and stress management regulator
RutR	Regulator of the pyrimidine and purine metabolism
ToxT	Regulator of MSHA biosynthesis
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0006 - Region 3 - terpene

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Location: 343,580 - 364,443 nt. (total: 20,864 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_02778: monooxygenase FAD-binding

smcogs: SMCOG1246: monooxygenase FAD-binding

CDS_02782: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Lyases: hydratase

CDS_02767: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

CDS_02768: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

Ligases: ligase

CDS_02770: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002276.2	0.58	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0002174.2	0.56	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001135.5	0.56	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.56	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.55	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.55	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.55	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.55	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.55	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.55	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002276.2	0.58	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0002174.2	0.56	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001135.5	0.56	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.56	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.55	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.55	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.55	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.55	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.55	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.55	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
triterpene	C30 carotenoid	diapophytoene	C30	acyclic	none
triterpene		squalene	C30	acyclic	none
triterpene		PSPP	C30	acyclic	PP
tetraterpene	C40 carotenoid	phytoene	C40	acyclic	none
triterpene		hydroxysqualene	C30	acyclic	OH

Genes with terpene domains:

CDS_02772: PT_phytoene_like

Domain 1 (3 - 285): Prenyltransferase; Phytoene synthase like

Subtype: unknown

Reactions:: FPP → diapophytoene; FPP → squalene; FPP → PSPP; GGPP → phytoene; PSPP → hydroxysqualene

Transcription Factor Binding Sites

Binding sites found:

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52

Confidence: medium

Additional weak hits (6):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.73 out of 29.38

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.48 out of 29.25

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.14 out of 30.22

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.88 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.28 out of 32.93

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
FPP	Farnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
PP	Diphosphate
PSPP	Presqualene diphosphate

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production

NPDC052558.ctg-0007 - Region 1 - terpene

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Location: 177,663 - 198,721 nt. (total: 21,059 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: acetyltransferase aminotransferase

CDS_03020: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CDS_03026: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

Ligases: ligase

CDS_03017: carboxylate-amine ligase

smcogs: SMCOG1165: carboxylate-amine ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000877.5	0.34	other (other)	polyoxin A, polyoxin H	Streptomyces cacaoi subsp. asoensis
BGC0002261.2	0.33	PKS	lucilactaene	Fusarium sp.
BGC0000689.3	0.31	saccharide	2-deoxystreptamine	Micromonospora echinospora
BGC0002172.3	0.31	NRPS	fusatrixin, fusapentaxin, fusaoctaxin A	Fusarium graminearum PH-1
BGC0000269.5	0.30	PKS, saccharide	SF2575	Streptomyces sp. SF2575
BGC0001108.5	0.30	NRPS, PKS	pederin, pseudopederin, pederone	Uncultured bacterium
BGC0001109.4	0.28	NRPS, PKS	pederin	unidentified unclassified sequences.
BGC0001603.3	0.27	saccharide	gentamicin	Micromonospora echinospora
BGC0002087.3	0.27	NRPS, PKS	gladiostatin A	Burkholderia gladioli 238
BGC0002082.3	0.27	NRPS, PKS	sesbanimide C, sesbanimide F, sesbanimide E	Stappia indica

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000877.5	0.34	other (other)	polyoxin A, polyoxin H	Streptomyces cacaoi subsp. asoensis
BGC0002261.2	0.33	PKS	lucilactaene	Fusarium sp.
BGC0000689.3	0.31	saccharide	2-deoxystreptamine	Micromonospora echinospora
BGC0002172.3	0.31	NRPS	fusatrixin, fusapentaxin, fusaoctaxin A	Fusarium graminearum PH-1
BGC0000269.5	0.30	PKS, saccharide	SF2575	Streptomyces sp. SF2575
BGC0001108.5	0.30	NRPS, PKS	pederin, pseudopederin, pederone	Uncultured bacterium
BGC0001109.4	0.28	NRPS, PKS	pederin	unidentified unclassified sequences.
BGC0001603.3	0.27	saccharide	gentamicin	Micromonospora echinospora
BGC0002087.3	0.27	NRPS, PKS	gladiostatin A	Burkholderia gladioli 238
BGC0002082.3	0.27	NRPS, PKS	sesbanimide C, sesbanimide F, sesbanimide E	Stappia indica

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
tetraterpene	C40 carotenoid		C40	unknown	unknown

Genes with terpene domains:

CDS_03015: Lycopene_cycl

Domain 1 (1 - 338): Lycopene cyclase

Reactions:: C40_carotenoid → C40_carotenoid

Transcription Factor Binding Sites

Binding sites found:

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 25.93 out of 29.65

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 22.33 out of 24.78

Confidence: medium

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.58 out of 21.84

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

Additional weak hits (6):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.56 out of 21.55

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.46 out of 27.78

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 21.09 out of 36.53

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.49 out of 32.93

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.29 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.62 out of 33.14

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

No acronyms to display

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
LexA variant 1	Repressor of DNA damage response
LexA variant 2	Repressor of DNA damage response
MexT	Global virulence regulator

NPDC052558.ctg-0007 - Region 2 - NRP-metallophore,NRPS

Download region GenBank file

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Location: 275,791 - 338,376 nt. (total: 62,586 nt) Show pHMM detection rules used

NRP-metallophore: (VibH_like or Cy_tandem or (cds(Condensation and AMP-binding) and ((IBH_Asp and not SBH_Asp) or IBH_His or TBH_Asp or CyanoBH_Asp1 or CyanoBH_Asp2 or IPL or SalSyn or (EntA and EntC) or (GrbD and GrbE) or (FbnL and FbnM) or PvdO or PvdP or (Orn_monoox and not (KtzT or MetRS-like)) or Lys_monoox or VbsL)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_03118: lysine/ornithine N-monooxygenase

smcogs: SMCOG1080: lysine/ornithine N-monooxygenase

CDS_03124: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_03129: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: PPTase aminotransferase methyltransferase

CDS_03114: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_03120: aminotransferase

smcogs: SMCOG1019: aminotransferase

CDS_03125: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1060: 4'-phosphopantetheinyl transferase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.76	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.74	NRPS	AM-toxin	Alternaria alternata
BGC0000307.4	0.71	NRPS	AbT1	Aureobasidium pullulans
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.67	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.64	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.64	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.70	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.70	NRPS	AM-toxin	Alternaria alternata
BGC0000307.4	0.68	NRPS	AbT1	Aureobasidium pullulans
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.67	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.65	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.57 out of 36.53

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.57 out of 36.53

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 26.57 out of 36.53

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 27.86 out of 36.53

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.63 out of 18.46

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

Additional weak hits (9):

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.61 out of 23.43

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.56 out of 39.62

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.95 out of 27.78

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 24.57 out of 36.53

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.57 out of 36.53

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.62 out of 29.38

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.16 out of 31.73

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.62 out of 25.75

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.63 out of 18.57

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 275790 - 338376:

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

Polymer prediction:: (NMe-Fo-OH-Orn - NMe-Ser - NMe-Fo-OH-Orn - X - OH-Orn)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03114: Fo-OH-Orn - Ser - Fo-OH-Orn - X - OH-Orn

Search NORINE for peptide: strict or relaxed

AMP-binding (233..619): Fo-OH-Orn

nrpys: Fo-OH-Orn

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

AMP-binding (1637..2031): 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:: DVWHVSLVDK
Nearest Stachelhaus code(s):: Ser DVWHVSLVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3042..3430): Fo-OH-Orn

nrpys: Fo-OH-Orn

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

AMP-binding (4446..4827): X

nrpys: me-bAla, bAla

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:: IDTTISLGDK
Nearest Stachelhaus code(s):: me-bAla LDTTVSLGDK (76% 8Å match); bAla VDTVISLGDK (59% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (5478..5869): OH-Orn

nrpys: OH-Orn

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:: DAQEGGLVDK
Nearest Stachelhaus code(s):: OH-Orn DAQEGGLVDK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
DmdR1	Iron(II)-dependent repressor
RpoN	Regulator of nitrogen assimilation and virulence
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0008 - Region 1 - T1PKS,hglE-KS

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Location: 146,302 - 197,169 nt. (total: 50,868 nt) Show pHMM detection rules used

hglE-KS: (hglE or hglD)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

Legend:

core biosynthetic genes

additional biosynthetic genes

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other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

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TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: glycosyltransferase sulfhydrylase

CDS_03355: O-succinylhomoserine sulfhydrylase

smcogs: SMCOG1168: O-succinylhomoserine sulfhydrylase

CDS_03366: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: deacetylase deaminase hydrolase protease

CDS_03359: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

CDS_03365: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_03371: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

CDS_03374: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

CDS_03375: polysaccharide deacetylase

smcogs: SMCOG1235: polysaccharide deacetylase

Lyases: cyclase

CDS_03369: diguanylate cyclase

smcogs: SMCOG1025: diguanylate cyclase

Ligases: synthase

CDS_03362: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_03363: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.59	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.58	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.57	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.57	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001160.5	0.54	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.52	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002192.3	0.51	PKS	FR901512	fungal sp. No.14919
BGC0001254.3	0.49	PKS	ACT-Toxin II	Alternaria alternata
BGC0001268.4	0.44	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0000863.3	0.39	other (other)	eicosapentaenoic acid	Pseudoalteromonas sp. DS-12

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.63	PKS	asperlactone	Aspergillus ochraceus
BGC0001276.3	0.62	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001275.3	0.62	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001244.3	0.62	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001160.5	0.61	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.59	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002192.3	0.59	PKS	FR901512	fungal sp. No.14919
BGC0001254.3	0.58	PKS	ACT-Toxin II	Alternaria alternata
BGC0001268.4	0.55	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0000863.3	0.52	other (other)	eicosapentaenoic acid	Pseudoalteromonas sp. DS-12

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26

Confidence: strong

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.65 out of 18.46

Confidence: strong

Additional weak hits (8):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.79 out of 29.38

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.85 out of 30.97

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.84 out of 27.78

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 24.83 out of 32.38

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.58 out of 29.25

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.81 out of 21.84

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.72 out of 23.43

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.93 out of 36.53

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 146301 - 197169:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (mal) + (pk)
Non-colinear ordering:: CDS_03362 + CDS_03363 + CDS_03364

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 146301 - 193117:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (mal) + (pk)
Non-colinear ordering:: CDS_03362 + CDS_03363 + CDS_03364

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 153122 - 197169:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (mal) + (pk)
Non-colinear ordering:: CDS_03362 + CDS_03363 + CDS_03364

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03362: mal

PKS_AT (1183..1465): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 79.2%; inactive: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 55.3
inactive: 27.5
Methoxymalonyl-CoA: 18.4
fatty_acid: 15.8
Methylmalonyl-CoA: 12.0
trans-1,2-CPDA: 0.0
Propionyl-CoA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

CDS_03363: pk

PKS_AT (596..806): pk

ATSignature: (unknown)

No matches above 50%

minowa: inactive

Prediction, score:

inactive: 15.2
Malonyl-CoA: 7.1
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Methylmalonyl-CoA: 0.0
Methoxymalonyl-CoA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
RpoN	Regulator of nitrogen assimilation and virulence

NPDC052558.ctg-0009 - Region 1 - CDPS

Download region GenBank file

Download region SVG

Location: 191,202 - 211,918 nt. (total: 20,717 nt) Show pHMM detection rules used

CDPS: CDPS

Legend:

core biosynthetic genes

additional biosynthetic genes

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regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_03738: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_03741: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_03750: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_03755: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: formyltransferase

CDS_03735: methionyl-tRNA formyltransferase

smcogs: SMCOG1228: methionyl-tRNA formyltransferase

Hydrolases: hydrolase

CDS_03744: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000706.3	0.45	saccharide	kanamycin	Streptomyces kanamyceticus
BGC0001223.5	0.42	other (other)	hydroxysporine	uncultured bacterium
BGC0001336.5	0.41	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0002482.2	0.41	other (other)	tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M	Symphyonema bifilamentata 97.28
BGC0000679.5	0.41	terpene	diazepinomicin	Micromonospora sp. M42
BGC0001483.4	0.41	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0000003.3	0.40	PKS	AF-toxin	Alternaria alternata
BGC0002347.3	0.40	other (other)	cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D	Actinoalloteichus caeruleus WH1-2216-6
BGC0002000.4	0.40	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0002343.3	0.39	other (other), ribosomal	ammosester A, ammosester B, ammosester C, ammosamaic acid cogener	Streptomyces uncialis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000706.3	0.45	saccharide	kanamycin	Streptomyces kanamyceticus
BGC0001223.5	0.42	other (other)	hydroxysporine	uncultured bacterium
BGC0001336.5	0.41	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0002482.2	0.41	other (other)	tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M	Symphyonema bifilamentata 97.28
BGC0000679.5	0.41	terpene	diazepinomicin	Micromonospora sp. M42
BGC0001483.4	0.41	other (other)	5-isoprenylindole-3-carboxylate β-D-glycosyl ester	Streptomyces sp. RM-5-8
BGC0000003.3	0.40	PKS	AF-toxin	Alternaria alternata
BGC0002347.3	0.40	other (other)	cyanogramide, cyanogramide B, cyanogramide C, cyanogramide D	Actinoalloteichus caeruleus WH1-2216-6
BGC0002000.4	0.40	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0002343.3	0.39	other (other), ribosomal	ammosester A, ammosester B, ammosester C, ammosamaic acid cogener	Streptomyces uncialis

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.10 out of 27.78

Confidence: medium

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 28.62 out of 36.53

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.62 out of 27.04

Confidence: medium

Additional weak hits (16):

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.66 out of 31.73

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 25.30 out of 36.53

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.08 out of 36.53

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.48 out of 29.25

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.51 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.38 out of 36.54

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.42 out of 26.85

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.48 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.92 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.55 out of 29.38

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 17.30 out of 21.84

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.49 out of 30.97

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.72 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 25.09 out of 35.63

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
DasR	N-acetylglucosamine dependent repressor
DmdR1	Iron(II)-dependent repressor
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0009 - Region 2 - NRPS-like,T1PKS

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Location: 269,967 - 316,110 nt. (total: 46,144 nt) Show pHMM detection rules used

NRPS-like: cds((PP-binding or NAD_binding_4) 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))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_03821: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_03837: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_03840: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase glycosyltransferase

CDS_03823: glycosyltransferase

smcogs: SMCOG1102: glycosyltransferase

CDS_03848: aminotransferase

smcogs: SMCOG1019: aminotransferase

Hydrolases: deformylase dehalogenase hydrolase

CDS_03828: peptide deformylase

smcogs: SMCOG1275: peptide deformylase

CDS_03838: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_03844: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Ligases: synthase

CDS_03835: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.86	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001160.5	0.69	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.69	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001273.3	0.60	PKS	asperlactone	Aspergillus ochraceus
BGC0002191.2	0.59	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0002192.3	0.57	PKS	FR901512	fungal sp. No.14919
BGC0001284.4	0.57	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001254.3	0.56	PKS	ACT-Toxin II	Alternaria alternata
BGC0001268.4	0.54	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0001257.3	0.54	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.74	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001160.5	0.68	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.68	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0002192.3	0.62	PKS	FR901512	fungal sp. No.14919
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata
BGC0001268.4	0.61	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0001257.3	0.60	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47

Confidence: medium

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 21.40 out of 23.05

Confidence: strong

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.13 out of 23.43

Confidence: medium

Additional weak hits (18):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.56 out of 29.38

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.20 out of 29.65

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.60 out of 26.12

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.69 out of 35.63

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.97 out of 24.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.66 out of 29.65

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 18.10 out of 25.88

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.47 out of 27.04

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 16.16 out of 28.14

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 18.12 out of 26.12

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.86 out of 26.85

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.50 out of 26.85

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.84 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.34 out of 33.14

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.48 out of 30.98

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 2, location 269966 - 316110:

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

Polymer prediction:: (AHBA - ccmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03835: AHBA - mal

CAL_domain (42..379): AHBA

minowa: AHBA

Prediction, score:

AHBA: 163.7
shikimic_acid: 123.0
fatty_acid: 0.0
NH2: 0.0
Acetyl-CoA: 0.0

PKS_AT (1044..1312): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 70.8%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 167.0
inactive: 96.7
Methoxymalonyl-CoA: 72.6
Methylmalonyl-CoA: 53.7
Isobutyryl-CoA: 39.9
Ethylmalonyl-CoA: 20.8
Propionyl-CoA: 18.4
Benzoyl-CoA: 18.1
fatty_acid: 14.2
CHC-CoA: 13.6
trans-1,2-CPDA: 11.3
Acetyl-CoA: 10.5
2-Methylbutyryl-CoA: 6.6
3-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
AfsR	Pleiotropic regulatory for antibiotic production
BldD	Development and antibiotic global regulator
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0010 - Region 1 - T1PKS

Download region GenBank file

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Location: 53,530 - 148,640 nt. (total: 95,111 nt) Show pHMM detection rules used

T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidase

CDS_03936: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

CDS_03939: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_03946: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

CDS_03954: FAD linked oxidase domain protein

smcogs: SMCOG1138: FAD linked oxidase domain protein

Transferases: transketolase

CDS_03920: transketolase

smcogs: SMCOG1204: transketolase

Hydrolases: esterase

CDS_03934: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: synthase

CDS_03933: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_03952: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Translocases: transport

CDS_03929: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.42	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001160.5	0.32	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.32	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001273.3	0.30	PKS	asperlactone	Aspergillus ochraceus
BGC0002154.2	0.30	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.30	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0001244.3	0.30	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0000107.3	0.30	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002191.2	0.29	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001275.3	0.29	PKS	6-methylsalicyclic acid	Glarea lozoyensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.76	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.66	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.66	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.66	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001160.5	0.65	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.65	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002154.2	0.63	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.35 out of 20.47

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.46 out of 20.47

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.37 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.00 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.25 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.70 out of 23.79

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.98 out of 23.79

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.22 out of 26.85

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.88 out of 28.19

Confidence: medium

Additional weak hits (29):

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.38 out of 26.85

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.89 out of 21.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.89 out of 21.55

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.46 out of 25.88

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 26.33

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.59 out of 21.55

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.67 out of 23.43

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.75 out of 29.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.88 out of 30.25

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.07 out of 33.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.34 out of 31.73

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.99 out of 35.63

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.96 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.69 out of 24.78

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.89 out of 29.25

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.10 out of 39.62

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.72 out of 24.78

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.48 out of 26.06

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.37 out of 30.98

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.46 out of 33.14

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.04 out of 29.65

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.49 out of 33.14

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.79 out of 22.40

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.24 out of 29.65

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.44 out of 29.65

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.94 out of 26.85

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.93 out of 27.18

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 53529 - 148640:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (Me-mal - Me-ccmal - ccmal - ohmal - ccmal - ccmal) + (Me-ccmal)
Non-colinear ordering:: CDS_03952 + CDS_03933

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 53529 - 98749:

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

Polymer prediction:: (Me-ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 82090 - 148640:

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

Polymer prediction:: (Me-mal - Me-ccmal - ccmal - ohmal - ccmal - ccmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03933: mmal

PKS_AT (531..828): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 83.3%; Ethylmalonyl-CoA: 70.8%; Malonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 133.7
Methoxymalonyl-CoA: 114.2
Ethylmalonyl-CoA: 110.5
2-Methylbutyryl-CoA: 85.3
Malonyl-CoA: 78.4
Propionyl-CoA: 75.3
Isobutyryl-CoA: 73.4
trans-1,2-CPDA: 71.9
Acetyl-CoA: 49.8
fatty_acid: 45.2
CHC-CoA: 43.5
Benzoyl-CoA: 43.5
3-Methylbutyryl-CoA: 35.2
inactive: 32.4

CDS_03952: mmal - mmal - mal - mal - mal - mal

PKS_AT (516..813): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Methoxymalonyl-CoA: 91.7%; Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 207.1
Ethylmalonyl-CoA: 205.2
Methoxymalonyl-CoA: 172.6
2-Methylbutyryl-CoA: 152.8
trans-1,2-CPDA: 115.9
Propionyl-CoA: 111.8
Isobutyryl-CoA: 105.2
Malonyl-CoA: 101.9
CHC-CoA: 80.4
Benzoyl-CoA: 70.2
Acetyl-CoA: 58.6
fatty_acid: 46.8
3-Methylbutyryl-CoA: 39.3
inactive: 33.0

PKS_AT (1494..1785): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Methoxymalonyl-CoA: 95.8%; Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 202.1
Ethylmalonyl-CoA: 188.7
Methoxymalonyl-CoA: 166.8
2-Methylbutyryl-CoA: 111.0
trans-1,2-CPDA: 107.9
Malonyl-CoA: 97.5
Propionyl-CoA: 91.1
CHC-CoA: 72.1
Isobutyryl-CoA: 71.6
Benzoyl-CoA: 52.0
Acetyl-CoA: 35.0
3-Methylbutyryl-CoA: 26.5
fatty_acid: 26.2
inactive: 15.3

PKS_AT (3127..3403): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 70.8%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 196.6
inactive: 96.5
Methoxymalonyl-CoA: 65.3
Methylmalonyl-CoA: 55.9
Propionyl-CoA: 27.8
Acetyl-CoA: 22.2
Isobutyryl-CoA: 22.1
Ethylmalonyl-CoA: 19.0
2-Methylbutyryl-CoA: 11.8
fatty_acid: 8.5
Benzoyl-CoA: 7.3
3-Methylbutyryl-CoA: 4.3
CHC-CoA: 4.1
trans-1,2-CPDA: 0.0

PKS_AT (4673..4958): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 83.3%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 198.1
inactive: 114.6
Methoxymalonyl-CoA: 66.3
Methylmalonyl-CoA: 53.2
Isobutyryl-CoA: 42.6
Propionyl-CoA: 29.4
Acetyl-CoA: 18.9
Ethylmalonyl-CoA: 16.6
2-Methylbutyryl-CoA: 10.1
Benzoyl-CoA: 9.5
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
3-Methylbutyryl-CoA: 0.0
CHC-CoA: -0.3

PKS_AT (6049..6326): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 83.3%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 208.3
inactive: 107.4
Methoxymalonyl-CoA: 73.7
Methylmalonyl-CoA: 55.8
Isobutyryl-CoA: 43.2
Propionyl-CoA: 36.4
Acetyl-CoA: 23.2
Ethylmalonyl-CoA: 18.8
2-Methylbutyryl-CoA: 13.8
Benzoyl-CoA: 11.5
CHC-CoA: 11.1
trans-1,2-CPDA: 9.7
fatty_acid: 9.1
3-Methylbutyryl-CoA: 0.0

PKS_AT (7685..7966): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 75.0%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 207.3
inactive: 114.5
Methoxymalonyl-CoA: 74.5
Methylmalonyl-CoA: 65.6
Propionyl-CoA: 34.1
Isobutyryl-CoA: 33.7
Acetyl-CoA: 26.8
Ethylmalonyl-CoA: 25.4
2-Methylbutyryl-CoA: 22.8
Benzoyl-CoA: 12.1
fatty_acid: 10.4
3-Methylbutyryl-CoA: 9.8
CHC-CoA: 8.7
trans-1,2-CPDA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
IolR	Regulator of the inositol catabolism
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems
ZuR variant 1	Zinc-responsive repressor

NPDC052558.ctg-0010 - Region 2 - T1PKS,arylpolyene

Download region GenBank file

Download region SVG

Location: 182,258 - 329,639 nt. (total: 147,382 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))
arylpolyene: (APE_KS1 or APE_KS2)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase reductase

CDS_03981: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

CDS_03986: aldehyde oxidase and xanthine dehydrogenase

smcogs: SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

CDS_03998: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_03999: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_04002: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_04003: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_04021: alkyl hydroperoxide reductase/ Thiol specific

smcogs: SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

CDS_04028: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

CDS_04034: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_04057: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_04060: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acylase glycosyltransferase transferase

CDS_04005: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_04041: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_04064: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs: SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

CDS_04067: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

Hydrolases: dehalogenase hydrolase

CDS_04017: alpha/beta hydrolase domain-containing protein

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

CDS_04055: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

CDS_04056: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_04069: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Lyases: cyclase decarboxylase dehydratase hydratase

CDS_03990: putative carboxymuconolactone decarboxylase

smcogs: SMCOG1298: putative carboxymuconolactone decarboxylase

CDS_04038: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

CDS_04039: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

CDS_04063: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_04065: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_04071: Diels-Alderase cyclase

extras: DA_cyclase: Diels-Alderase cyclase

Ligases: synthase

CDS_04000: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04001: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04037: hydroxymethylglutaryl-CoA synthase

smcogs: SMCOG1043: hydroxymethylglutaryl-CoA synthase

CDS_04040: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04042: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04043: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_04045: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04072: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04073: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	1.04	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.92	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.90	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.90	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001164.3	0.88	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.88	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002154.2	0.87	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0000107.3	0.86	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0001258.3	0.86	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0001257.3	0.86	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.77	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.67	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.67	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.67	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001164.3	0.66	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.66	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002154.2	0.64	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.64	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0001258.3	0.64	PKS	1,3,6,8-tetrahydroxynaphthalene	Glarea lozoyensis
BGC0000107.3	0.64	PKS	naphthopyrone	Aspergillus nidulans FGSC A4

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.86 out of 28.19

Confidence: medium

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.25 out of 20.01

Confidence: medium

Additional weak hits (16):

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.11 out of 29.51

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.45 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.12 out of 29.38

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 26.85

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.16 out of 30.25

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.01 out of 27.78

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 19.59 out of 33.73

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.02 out of 27.78

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 19.13 out of 30.97

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.27 out of 20.97

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.22 out of 21.55

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.82 out of 22.40

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.46 out of 26.85

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.09 out of 28.19

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 19.14 out of 22.40

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 4, location 182257 - 329639:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (Me-mal - Me-redmal) + (ccmal - Me-redmal) + (pk - redmal) + (mal) + (Me-ohmal - redmal) + (ccemal)
Non-colinear ordering:: CDS_03999 + CDS_04000 + CDS_04073 + CDS_04072 + CDS_04001 + CDS_04002

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 182257 - 258504:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (Me-mal - Me-redmal) + (ccmal - Me-redmal) + (Me-ohmal - redmal) + (ccemal)
Non-colinear ordering:: CDS_03999 + CDS_04000 + CDS_04001 + CDS_04002

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 295500 - 329639:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (pk - redmal) + (mal)
Non-colinear ordering:: CDS_04073 + CDS_04072

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_03999: mmal - mmal

PKS_AT (514..805): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Methoxymalonyl-CoA: 95.8%; Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 214.2
Ethylmalonyl-CoA: 200.5
Methoxymalonyl-CoA: 173.5
2-Methylbutyryl-CoA: 158.9
trans-1,2-CPDA: 130.4
CHC-CoA: 123.5
Malonyl-CoA: 118.9
Propionyl-CoA: 115.1
Isobutyryl-CoA: 62.7
Benzoyl-CoA: 47.4
Acetyl-CoA: 47.3
fatty_acid: 29.2
3-Methylbutyryl-CoA: 27.8
inactive: 24.0

PKS_AT (1473..1758): mmal

ATSignature: Methylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 91.7%; Methoxymalonyl-CoA: 91.7%; Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 195.2
Ethylmalonyl-CoA: 193.2
Methoxymalonyl-CoA: 164.4
2-Methylbutyryl-CoA: 118.2
trans-1,2-CPDA: 107.8
CHC-CoA: 102.7
Propionyl-CoA: 98.0
Malonyl-CoA: 96.9
Benzoyl-CoA: 78.3
Isobutyryl-CoA: 73.0
Acetyl-CoA: 47.6
inactive: 37.7
3-Methylbutyryl-CoA: 33.0
fatty_acid: 28.7

CDS_04000: mal - mmal

PKS_AT (550..821): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 189.9
inactive: 105.6
Methoxymalonyl-CoA: 61.8
Methylmalonyl-CoA: 52.8
Ethylmalonyl-CoA: 24.0
Isobutyryl-CoA: 23.7
Propionyl-CoA: 22.6
fatty_acid: 22.2
Benzoyl-CoA: 17.7
Acetyl-CoA: 17.5
2-Methylbutyryl-CoA: 15.7
trans-1,2-CPDA: 12.4
CHC-CoA: 11.9
3-Methylbutyryl-CoA: 0.0

PKS_AT (2175..2458): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Malonyl-CoA: 91.7%; Methoxymalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 196.4
Ethylmalonyl-CoA: 182.5
Methoxymalonyl-CoA: 158.1
2-Methylbutyryl-CoA: 121.6
trans-1,2-CPDA: 105.6
CHC-CoA: 100.2
Malonyl-CoA: 99.2
Propionyl-CoA: 96.7
Isobutyryl-CoA: 53.7
Benzoyl-CoA: 53.2
Acetyl-CoA: 30.6
inactive: 26.6
3-Methylbutyryl-CoA: 25.4
fatty_acid: 14.2

CDS_04001: mmal - mal

PKS_AT (555..847): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Methoxymalonyl-CoA: 95.8%; Ethylmalonyl-CoA: 91.7%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 197.9
Ethylmalonyl-CoA: 183.8
Methoxymalonyl-CoA: 160.2
2-Methylbutyryl-CoA: 120.7
trans-1,2-CPDA: 103.0
Propionyl-CoA: 99.7
CHC-CoA: 99.4
Malonyl-CoA: 79.6
Isobutyryl-CoA: 57.1
Acetyl-CoA: 48.1
Benzoyl-CoA: 44.5
fatty_acid: 25.6
inactive: 22.7
3-Methylbutyryl-CoA: 21.8

PKS_AT (1953..2225): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 70.8%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 188.0
inactive: 77.3
Methoxymalonyl-CoA: 62.9
Methylmalonyl-CoA: 59.7
Propionyl-CoA: 32.0
Ethylmalonyl-CoA: 30.5
Acetyl-CoA: 25.2
Isobutyryl-CoA: 17.0
Benzoyl-CoA: 16.4
CHC-CoA: 15.0
fatty_acid: 12.0
2-Methylbutyryl-CoA: 11.2
trans-1,2-CPDA: 10.2
3-Methylbutyryl-CoA: 2.2

CDS_04002: emal

PKS_AT (552..835): emal

ATSignature: Ethylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:: Ethylmalonyl-CoA: 83.3%; Methoxymalonyl-CoA: 83.3%; Methylmalonyl-CoA: 79.2%

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 204.1
Methylmalonyl-CoA: 199.0
Methoxymalonyl-CoA: 165.5
2-Methylbutyryl-CoA: 119.2
trans-1,2-CPDA: 111.5
CHC-CoA: 99.5
Propionyl-CoA: 97.6
Malonyl-CoA: 87.6
Benzoyl-CoA: 74.4
Isobutyryl-CoA: 69.6
Acetyl-CoA: 50.3
3-Methylbutyryl-CoA: 35.8
fatty_acid: 29.9
inactive: 28.7

CDS_04041: mal

PKS_AT (5..281): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 93.0
inactive: 31.6
Methoxymalonyl-CoA: 27.9
Methylmalonyl-CoA: 15.7
Propionyl-CoA: 9.9
fatty_acid: 8.7
trans-1,2-CPDA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

CDS_04072: mal

PKS_AT (563..862): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 79.2%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 191.6
inactive: 82.8
Methoxymalonyl-CoA: 60.0
Methylmalonyl-CoA: 54.1
Propionyl-CoA: 46.1
Isobutyryl-CoA: 36.7
2-Methylbutyryl-CoA: 32.1
Ethylmalonyl-CoA: 21.2
Acetyl-CoA: 15.7
Benzoyl-CoA: 15.3
fatty_acid: 12.3
CHC-CoA: 11.6
trans-1,2-CPDA: 9.1
3-Methylbutyryl-CoA: 0.0

CDS_04073: pk - mal

PKS_AT (564..859): pk

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 100.0%; Methoxymalonyl-CoA: 95.8%; Ethylmalonyl-CoA: 91.7%

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 222.5
Methylmalonyl-CoA: 218.0
Methoxymalonyl-CoA: 177.8
2-Methylbutyryl-CoA: 153.3
trans-1,2-CPDA: 128.5
Propionyl-CoA: 127.6
CHC-CoA: 110.9
Malonyl-CoA: 101.2
Isobutyryl-CoA: 96.8
Benzoyl-CoA: 80.0
Acetyl-CoA: 59.7
3-Methylbutyryl-CoA: 41.5
fatty_acid: 35.1
inactive: 29.6

PKS_AT (1855..2125): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 75.0%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 202.6
inactive: 90.4
Methoxymalonyl-CoA: 77.5
Methylmalonyl-CoA: 67.3
Propionyl-CoA: 35.7
Ethylmalonyl-CoA: 29.4
Isobutyryl-CoA: 20.0
Benzoyl-CoA: 19.8
Acetyl-CoA: 15.2
fatty_acid: 14.0
CHC-CoA: 12.2
2-Methylbutyryl-CoA: 11.5
3-Methylbutyryl-CoA: 9.2
trans-1,2-CPDA: 6.3

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
ArgR	Regulator of arginine biosynthesis genes
ZuR variant 1	Zinc-responsive repressor

NPDC052558.ctg-0011 - Region 1 - RiPP-like,terpene-precursor

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Location: 237,893 - 258,933 nt. (total: 21,041 nt) Show pHMM detection rules used

terpene-precursor: (PT_FPPS_like and not PT_HPP)
RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_04295: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

Ligases: synthetase

CDS_04300: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002397.2	0.39	terpene	astallatene	Arabidopsis thaliana
BGC0000677.5	0.27	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002309.2	0.26	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3	0.22	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.20	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0000313.4	0.20	NRPS	beauvericin	Beauveria bassiana
BGC0000664.5	0.20	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001227.3	0.19	terpene	isorenieratene	Streptomyces collinus Tu 365
BGC0000648.3	0.19	terpene	carotenoid	Myxococcus xanthus
BGC0001456.3	0.19	terpene	isorenieratene	Streptomyces argillaceus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002397.2	0.52	terpene	astallatene	Arabidopsis thaliana
BGC0000677.5	0.42	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002309.2	0.42	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3	0.38	terpene	raimonol	Streptomyces anulatus
BGC0001910.4	0.36	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0000313.4	0.36	NRPS	beauvericin	Beauveria bassiana
BGC0000664.5	0.35	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001227.3	0.35	terpene	isorenieratene	Streptomyces collinus Tu 365
BGC0000648.3	0.34	terpene	carotenoid	Myxococcus xanthus
BGC0001456.3	0.34	terpene	isorenieratene	Streptomyces argillaceus

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene precursor	FPP	C15	acyclic	PP
diterpene precursor	GGPP	C20	acyclic	PP
sesterterpene precursor	GFPP	C25	acyclic	PP
triterpene precursor	HPP	C30	acyclic	PP

Genes with terpene domains:

CDS_04300: PT_FPPS_like

Domain 1 (48 - 324): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 19.19 out of 20.47

Confidence: strong

Additional weak hits (4):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.77 out of 21.55

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.66 out of 27.04

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.52 out of 27.04

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0012 - Region 1 - terpene

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Location: 33,759 - 56,979 nt. (total: 23,221 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene overview

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Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Hydrolases: esterase

CDS_04418: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: cyclase

CDS_04413: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: synthetase

CDS_04412: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.80	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0002397.2	0.58	terpene	astallatene	Arabidopsis thaliana
BGC0000657.5	0.57	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0002400.2	0.54	terpene	boleracene	Brassica oleracea var. oleracea
BGC0002162.3	0.53	terpene	sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8	Aspergillus fischeri NRRL 181
BGC0000677.5	0.48	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002398.2	0.48	terpene	(-)-ent-quiannulatene	Arabidopsis thaliana
BGC0002309.2	0.46	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3	0.43	terpene	raimonol	Streptomyces anulatus
BGC0000678.5	0.40	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001181.4	0.80	terpene	geosmin	Streptomyces coelicolor A3(2)
BGC0002397.2	0.58	terpene	astallatene	Arabidopsis thaliana
BGC0000657.5	0.57	terpene	2-methylisoborneol	Pseudanabaena sp. dqh15
BGC0002400.2	0.54	terpene	boleracene	Brassica oleracea var. oleracea
BGC0002162.3	0.53	terpene	sesterfisherol, sesterfisheric acid, compound 6, compound 7a, compound 5, compound 8	Aspergillus fischeri NRRL 181
BGC0000677.5	0.48	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0002398.2	0.48	terpene	(-)-ent-quiannulatene	Arabidopsis thaliana
BGC0002309.2	0.46	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0001911.3	0.43	terpene	raimonol	Streptomyces anulatus
BGC0000678.5	0.40	terpene	pentalenolactone	Streptomyces avermitilis MA-4680 = NBRC 14893

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene		germacradienol	C15	C1-C10	OH
sesquiterpene		geosmin	C12	C1-C10	OH

Genes with terpene domains:

CDS_04412: PT_FPPS_like

Domain 1 (65 - 349): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

CDS_04413: T1TS + T1TS

Domain 1 (2 - 331): Type 1 terpene synthase

Subtype: Geosmin synthase, N terminal domain

Reactions:: FPP → germacradienol

Domain 2 (332 - 693): Type 1 terpene synthase

Subtype: Geosmin synthase, C terminal domain

Reactions:: germacradienol → geosmin

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

Additional weak hits (3):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.21 out of 29.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.76 out of 30.25

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.27 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
AfsR	Pleiotropic regulatory for antibiotic production
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0013 - Region 1 - oligosaccharide

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Location: 40,546 - 64,047 nt. (total: 23,502 nt) Show pHMM detection rules used

oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: glycosyltransferase

CDS_04691: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_04692: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_04693: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: hydrolase

CDS_04688: hydrolase

smcogs: SMCOG1179: hydrolase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000277.5	0.53	PKS	urdamycin	Streptomyces fradiae
BGC0001496.3	0.45	ribosomal	actinokineosin	Actinokineospora spheciospongiae
BGC0002573.2	0.44	other (other)	phosphoramidon	Streptomyces mozunensis
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0001226.4	0.42	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0000563.4	0.42	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0002575.2	0.42	ribosomal	cochonodin I	Streptococcus suis
BGC0001552.3	0.41	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000277.5	0.53	PKS	urdamycin	Streptomyces fradiae
BGC0001496.3	0.45	ribosomal	actinokineosin	Actinokineospora spheciospongiae
BGC0002573.2	0.44	other (other)	phosphoramidon	Streptomyces mozunensis
BGC0002150.2	0.43	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.43	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0001226.4	0.42	ribosomal	streptocollin	Streptomyces collinus Tu 365
BGC0000563.4	0.42	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0002575.2	0.42	ribosomal	cochonodin I	Streptococcus suis
BGC0001552.3	0.41	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 19.02 out of 25.31

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 23.31 out of 27.04

Confidence: medium

Additional weak hits (6):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.41 out of 26.33

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.96 out of 30.25

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.90 out of 28.19

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.86 out of 19.52

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.91 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
DasR	N-acetylglucosamine dependent repressor

NPDC052558.ctg-0014 - Region 1 - HR-T2PKS

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Location: 45,976 - 87,094 nt. (total: 41,119 nt) Show pHMM detection rules used

HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-synt))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxidoreductase

CDS_04974: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Hydrolases: dehalogenase hydrolase

CDS_04978: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

CDS_05006: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Lyases: dehydratase hydratase lyase

CDS_04979: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

CDS_04997: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_04999: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase

CDS_04990: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_04993: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_04995: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002458.3	0.65	NRPS	alazopeptin	Streptacidiphilus griseoplanus
BGC0002826.2	0.54	other (other)	closoxazole A, closoxazole B	Clostridium cavendishii DSM 21758
BGC0001592.5	0.50	other (other)	ferroverdin, bagremycin	Streptomyces lunaelactis
BGC0000889.5	0.50	other (other)	bagremycin A, bagremycin B	Streptomyces sp. WK-5344
BGC0001850.4	0.50	other (shikimate-derived)	diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G	Streptomyces sp. F001
BGC0001965.4	0.49	other (other)	nybomycin	Streptomyces albus subsp. chlorinus
BGC0000662.5	0.49	terpene	grixazone A	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002591.2	0.46	PKS, terpene	aurachin C, aurachin D, aurachin SS	Streptomyces sp.
BGC0000885.3	0.46	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0001295.5	0.46	other (other)	cremeomycin	Streptomyces cremeus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002458.3	0.65	NRPS	alazopeptin	Streptacidiphilus griseoplanus
BGC0002826.2	0.54	other (other)	closoxazole A, closoxazole B	Clostridium cavendishii DSM 21758
BGC0001592.5	0.50	other (other)	ferroverdin, bagremycin	Streptomyces lunaelactis
BGC0000889.5	0.50	other (other)	bagremycin A, bagremycin B	Streptomyces sp. WK-5344
BGC0001850.4	0.50	other (shikimate-derived)	diazaquinomycin A, diazaquinomycin E, diazaquinomycin F, diazaquinomycin G	Streptomyces sp. F001
BGC0001965.4	0.49	other (other)	nybomycin	Streptomyces albus subsp. chlorinus
BGC0000662.5	0.49	terpene	grixazone A	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002591.2	0.46	PKS, terpene	aurachin C, aurachin D, aurachin SS	Streptomyces sp.
BGC0000885.3	0.46	other (other)	4-hydroxy-3-nitrosobenzamide	Streptomyces murayamaensis
BGC0001295.5	0.46	other (other)	cremeomycin	Streptomyces cremeus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.39 out of 19.26

Confidence: strong

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 24.42 out of 27.04

Confidence: strong

Additional weak hits (11):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.19 out of 18.57

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 17.72 out of 29.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.86 out of 30.25

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.67 out of 18.57

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.93 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.21 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.55 out of 30.25

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.60 out of 21.84

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.19 out of 28.19

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.19 out of 32.93

Confidence: weak

Detailed Pfam domain annotation

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Detailed domain annotation

Selected features only

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NRPS/PKS substrates

TFBS Finder

NRPS/PKS substrate predictions

CDS_04990: X

AMP-binding (9..362): X

nrpys: Val, Leu, Ile, Abu, Ival

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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: GLGFVGSVIK
Nearest Stachelhaus code(s):: nohBza GLGLVGAIIK (79% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_04995: X

AMP-binding (48..440): X

nrpys: (unknown)

SVM prediction details:

NOTE: uncertain match

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:: AMMFYT-LGK
Nearest Stachelhaus code(s):: Trp or Tyr DVMFYTALVK (24% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
DasR	N-acetylglucosamine dependent repressor

NPDC052558.ctg-0016 - Region 1 - T1PKS

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Location: 1 - 43,987 nt. (total: 43,987 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))

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Gene/CDS overview

Filter:

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_05362: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_05364: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_05382: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase

CDS_05367: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: phosphatase

CDS_05361: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

Ligases: synthase

CDS_05365: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_05366: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_05368: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.76	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.75	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.74	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002191.2	0.64	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002192.3	0.63	PKS	FR901512	fungal sp. No.14919
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001164.3	0.62	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.62	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001273.3	0.76	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.75	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.74	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002191.2	0.64	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002192.3	0.63	PKS	FR901512	fungal sp. No.14919
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001164.3	0.62	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.62	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.75 out of 20.97

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

Additional weak hits (3):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.90 out of 30.22

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.02 out of 30.22

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.19 out of 28.19

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 43987:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (mal) + (ohemal) + (Me-ccmal - pk)
Non-colinear ordering:: CDS_05368 + CDS_05367 + CDS_05366

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_05366: mmal - pk

PKS_AT (558..853): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Methoxymalonyl-CoA: 91.7%; Ethylmalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 199.7
Ethylmalonyl-CoA: 188.9
Methoxymalonyl-CoA: 168.0
2-Methylbutyryl-CoA: 122.3
CHC-CoA: 110.6
trans-1,2-CPDA: 107.0
Malonyl-CoA: 91.4
Propionyl-CoA: 91.1
Isobutyryl-CoA: 75.7
Benzoyl-CoA: 53.8
3-Methylbutyryl-CoA: 51.5
Acetyl-CoA: 43.4
fatty_acid: 24.1
inactive: 20.5

PKS_AT (1965..2263): pk

ATSignature: Ethylmalonyl-CoA

Top 3 matches:: Ethylmalonyl-CoA: 79.2%; Methylmalonyl-CoA: 75.0%; Methoxymalonyl-CoA: 75.0%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 167.6
Ethylmalonyl-CoA: 160.6
Methoxymalonyl-CoA: 140.2
2-Methylbutyryl-CoA: 130.3
trans-1,2-CPDA: 110.4
Propionyl-CoA: 108.0
Malonyl-CoA: 87.4
CHC-CoA: 78.3
Isobutyryl-CoA: 62.9
Benzoyl-CoA: 50.1
Acetyl-CoA: 42.2
fatty_acid: 40.4
inactive: 37.7
3-Methylbutyryl-CoA: 34.8

CDS_05367: emal

PKS_AT (545..842): emal

ATSignature: Methylmalonyl-CoA, Ethylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 87.5%; Ethylmalonyl-CoA: 87.5%; Methoxymalonyl-CoA: 87.5%

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 185.8
Methylmalonyl-CoA: 182.0
Methoxymalonyl-CoA: 170.1
2-Methylbutyryl-CoA: 127.7
trans-1,2-CPDA: 114.7
Propionyl-CoA: 102.3
CHC-CoA: 101.5
Malonyl-CoA: 96.9
Isobutyryl-CoA: 60.4
Benzoyl-CoA: 58.7
inactive: 47.7
Acetyl-CoA: 35.5
fatty_acid: 26.3
3-Methylbutyryl-CoA: 16.2

CDS_05368: mal

PKS_AT (633..910): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 83.3%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 214.2
inactive: 99.9
Methoxymalonyl-CoA: 59.9
Methylmalonyl-CoA: 51.3
Propionyl-CoA: 32.6
Isobutyryl-CoA: 28.5
Benzoyl-CoA: 27.7
Ethylmalonyl-CoA: 24.0
fatty_acid: 18.2
Acetyl-CoA: 14.9
CHC-CoA: 12.1
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0016 - Region 2 - butyrolactone

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Location: 100,164 - 111,135 nt. (total: 10,972 nt) Show pHMM detection rules used

butyrolactone: AfsA

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_05445: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Ligases: synthase

CDS_05440: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_05441: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000850.5	0.54	other (other)	γ-butyrolactone	Streptomyces acidiscabies
BGC0000866.5	0.50	other (other)	polyhydroxyalkanoate	Burkholderia sp. DSM 9242
BGC0000231.5	0.45	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000234.5	0.45	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0002510.2	0.44	PKS	youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4	Streptomyces sp.
BGC0002547.2	0.44	PKS	youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4	Streptomyces youssoufiensis
BGC0001723.5	0.43	PKS	oviedomycin	Streptomyces antibioticus
BGC0001987.2	0.43	PKS	koreenceine A, koreenceine B, koreenceine C, koreenceine D	Pseudomonas koreensis
BGC0001197.5	0.43	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0000903.3	0.43	other (other)	fluorometabolite	Streptomyces cattleya

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000850.5	0.54	other (other)	γ-butyrolactone	Streptomyces acidiscabies
BGC0000866.5	0.50	other (other)	polyhydroxyalkanoate	Burkholderia sp. DSM 9242
BGC0000231.5	0.45	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000234.5	0.45	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0002510.2	0.44	PKS	youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4	Streptomyces sp.
BGC0002547.2	0.44	PKS	youssoufene A1, youssoufene B1, youssoufene B2, youssoufene B3, youssoufene B4	Streptomyces youssoufiensis
BGC0001723.5	0.43	PKS	oviedomycin	Streptomyces antibioticus
BGC0001987.2	0.43	PKS	koreenceine A, koreenceine B, koreenceine C, koreenceine D	Pseudomonas koreensis
BGC0001197.5	0.43	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0000903.3	0.43	other (other)	fluorometabolite	Streptomyces cattleya

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97

Confidence: medium

Additional weak hits (4):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.94 out of 27.55

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.88 out of 19.26

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.76 out of 24.78

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.93 out of 32.93

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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TFBS Finder

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
ToxT	Regulator of MSHA biosynthesis

NPDC052558.ctg-0016 - Region 3 - RiPP-like

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Location: 179,577 - 190,716 nt. (total: 11,140 nt) Show pHMM detection rules used

RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

Legend:

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Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: methyltransferase

CDS_05521: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

Hydrolases: hydrolase

CDS_05526: isochorismatase

smcogs: SMCOG1027: isochorismatase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000468.5	0.35	ribosomal	bottromycin A2	Streptomyces bottropensis DSM40262
BGC0001157.6	0.35	ribosomal	bottromycin A2	Streptomyces scabiei 87.22
BGC0000470.6	0.35	ribosomal	bottromycin D	Streptomyces sp. WMMB272
BGC0000469.6	0.33	ribosomal	bottromycin A2	Streptomyces sp. BC16019
BGC0002147.2	0.27	NRPS	bohemamine A, bohemamine B, bohemamine C	Streptomyces sp. CB02009
BGC0000877.5	0.26	other (other)	polyoxin A, polyoxin H	Streptomyces cacaoi subsp. asoensis
BGC0000925.5	0.26	other (other)	quinolobactin	Pseudomonas fluorescens
BGC0000177.5	0.24	PKS	iso-migrastatin, migrastatin, dorrigocin A, dorrigocin B, 13-epi-dorrigocin A	Streptomyces platensis subsp. rosaceus
BGC0000935.5	0.24	PKS, other (aminocoumarin)	esmeraldin	Streptomyces antibioticus
BGC0001902.3	0.24	NRPS, PKS	bengamide	Myxococcus virescens

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000468.5	0.35	ribosomal	bottromycin A2	Streptomyces bottropensis DSM40262
BGC0001157.6	0.35	ribosomal	bottromycin A2	Streptomyces scabiei 87.22
BGC0000470.6	0.35	ribosomal	bottromycin D	Streptomyces sp. WMMB272
BGC0000469.6	0.33	ribosomal	bottromycin A2	Streptomyces sp. BC16019
BGC0002147.2	0.27	NRPS	bohemamine A, bohemamine B, bohemamine C	Streptomyces sp. CB02009
BGC0000877.5	0.26	other (other)	polyoxin A, polyoxin H	Streptomyces cacaoi subsp. asoensis
BGC0000925.5	0.26	other (other)	quinolobactin	Pseudomonas fluorescens
BGC0000177.5	0.24	PKS	iso-migrastatin, migrastatin, dorrigocin A, dorrigocin B, 13-epi-dorrigocin A	Streptomyces platensis subsp. rosaceus
BGC0000935.5	0.24	PKS, other (aminocoumarin)	esmeraldin	Streptomyces antibioticus
BGC0001902.3	0.24	NRPS, PKS	bengamide	Myxococcus virescens

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97

Confidence: medium

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05

Confidence: medium

Additional weak hits (9):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.61 out of 26.33

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.34 out of 36.54

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.06 out of 27.78

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.43 out of 26.85

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.92 out of 39.62

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.03 out of 30.22

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.64 out of 29.65

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.59 out of 26.85

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.13 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
CcpA	Catabolite control protein A
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0020 - Region 1 - T1PKS

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Location: 94,472 - 140,615 nt. (total: 46,144 nt) Show pHMM detection rules used

T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))

Legend:

core biosynthetic genes

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resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

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TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: acetyltransferase glycosyltransferase methyltransferase

CDS_06196: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

CDS_06197: Chloramphenicol acetyltransferase

smcogs: SMCOG1156: Chloramphenicol acetyltransferase

CDS_06202: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: glucanase glucosidase

CDS_06205: Pullulanase, type I

smcogs: SMCOG1297: Pullulanase, type I

CDS_06221: Alpha-glucosidase

smcogs: SMCOG1257: Alpha-glucosidase

CDS_06222: Alpha-glucosidase

smcogs: SMCOG1257: Alpha-glucosidase

CDS_06224: Alpha-glucosidase

smcogs: SMCOG1257: Alpha-glucosidase

Lyases: dehydratase hydratase

CDS_06203: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

CDS_06216: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase

CDS_06217: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001160.5	0.66	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.65	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.64	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0002192.3	0.62	PKS	FR901512	fungal sp. No.14919
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata
BGC0001268.4	0.61	NRPS, PKS	fusarin C	Fusarium fujikuroi

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001160.5	0.66	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.65	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001276.3	0.64	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.64	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.63	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0002192.3	0.62	PKS	FR901512	fungal sp. No.14919
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata
BGC0001268.4	0.61	NRPS, PKS	fusarin C	Fusarium fujikuroi

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (8):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 19.18 out of 27.55

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 16.99 out of 30.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.09 out of 29.38

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.60 out of 31.73

Confidence: weak

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.73 out of 19.26

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.68 out of 32.74

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.63 out of 27.18

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.59 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 94471 - 140615:

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

Polymer prediction:: (Me-redmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_06217: mmal

PKS_AT (538..823): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 79.2%; Ethylmalonyl-CoA: 70.8%; Malonyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 131.6
Ethylmalonyl-CoA: 112.1
Methoxymalonyl-CoA: 99.8
2-Methylbutyryl-CoA: 84.6
Malonyl-CoA: 79.2
Propionyl-CoA: 77.3
trans-1,2-CPDA: 67.0
CHC-CoA: 57.9
Isobutyryl-CoA: 55.5
3-Methylbutyryl-CoA: 46.3
fatty_acid: 40.4
Acetyl-CoA: 38.8
Benzoyl-CoA: 30.8
inactive: 23.8

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description

NPDC052558.ctg-0021 - Region 1 - terpene

Download region GenBank file

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Location: 37,409 - 58,278 nt. (total: 20,870 nt) Show pHMM detection rules used

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

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Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxidase

CDS_06298: pyruvate oxidase/decarboxylase

smcogs: SMCOG1055: pyruvate oxidase/decarboxylase

Transferases: glycosyltransferase

CDS_06313: glycosyltransferase

smcogs: SMCOG1102: glycosyltransferase

Lyases: dehydratase

CDS_06297: L-carnitine dehydratase/bile acid-inducible

smcogs: SMCOG1189: L-carnitine dehydratase/bile acid-inducible

Ligases: ligase

CDS_06312: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001164.3	0.52	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.52	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002554.2	0.43	other (other)	carquinostatin A, carquinostatin B	Streptomyces exfoliatus
BGC0000641.3	0.42	terpene	carotenoid	Enterobacteriaceae bacterium DC416
BGC0000646.5	0.42	terpene	β-carotein	uncultured bacterium
BGC0000642.3	0.42	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0000649.3	0.42	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000645.3	0.42	terpene	carotenoid	Halobacillus halophilus DSM 2266
BGC0001456.3	0.41	terpene	isorenieratene	Streptomyces argillaceus
BGC0000664.5	0.41	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001164.3	0.52	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.52	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002554.2	0.43	other (other)	carquinostatin A, carquinostatin B	Streptomyces exfoliatus
BGC0000641.3	0.42	terpene	carotenoid	Enterobacteriaceae bacterium DC416
BGC0000646.5	0.42	terpene	β-carotein	uncultured bacterium
BGC0000642.3	0.42	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0000649.3	0.42	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000645.3	0.42	terpene	carotenoid	Halobacillus halophilus DSM 2266
BGC0001456.3	0.41	terpene	isorenieratene	Streptomyces argillaceus
BGC0000664.5	0.41	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Subclass	Product name	Chain length	Initial cyclisations	Functional groups
triterpene	C30 carotenoid	diapophytoene	C30	acyclic	none
triterpene		squalene	C30	acyclic	none
triterpene		PSPP	C30	acyclic	PP
tetraterpene	C40 carotenoid	phytoene	C40	acyclic	none
triterpene		hydroxysqualene	C30	acyclic	OH

Genes with terpene domains:

CDS_06305: PT_phytoene_like

Domain 1 (15 - 284): Prenyltransferase; Phytoene synthase like

Subtype: unknown

Reactions:: FPP → diapophytoene; FPP → squalene; FPP → PSPP; GGPP → phytoene; PSPP → hydroxysqualene

Transcription Factor Binding Sites

Binding sites found:

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 30.00 out of 36.54

Confidence: medium

Additional weak hits (7):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 22.41 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.75 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.66 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 20.74 out of 36.54

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.27 out of 30.22

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 18.14 out of 33.14

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 32.93

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
FPP	Farnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
PP	Diphosphate
PSPP	Presqualene diphosphate

TFBS definitions

Regulator	Description
HgtR	Hydrogen-dependent regulator

NPDC052558.ctg-0022 - Region 1 - NRPS-like

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Location: 86,865 - 130,941 nt. (total: 44,077 nt) Show pHMM detection rules used

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

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core biosynthetic genes

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NRPS/PKS modules

Pfam domains

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NRPS/PKS domains

Gene/CDS overview

Filter:

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: acetyltransferase aminotransferase

CDS_06538: aminotransferase

smcogs: SMCOG1019: aminotransferase

CDS_06559: acetyl-CoA acetyltransferase

smcogs: SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: protease

CDS_06521: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Lyases: hydratase

CDS_06560: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

Ligases: ligase

CDS_06540: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0001261.3	0.60	NRPS	AM-toxin	Alternaria alternata
BGC0002174.2	0.60	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001240.4	0.60	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001758.4	0.60	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001251.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0001132.4	0.59	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.61	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0001261.3	0.60	NRPS	AM-toxin	Alternaria alternata
BGC0002174.2	0.60	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001240.4	0.60	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001758.4	0.60	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001251.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0001132.4	0.59	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.38 out of 19.26

Confidence: medium

Additional weak hits (19):

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.50 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.54 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.64 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 15.21 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.35 out of 29.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.12 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.22 out of 31.73

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.98 out of 32.93

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.39 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.93 out of 28.14

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.52 out of 29.25

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.07 out of 26.85

Confidence: weak

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 16.94 out of 19.52

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.84 out of 31.73

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 14.70 out of 21.55

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.00 out of 29.38

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 24.02 out of 30.22

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.86 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 18.97 out of 35.63

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 86864 - 130941:

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

Polymer prediction:: (Glu)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_06540: Glu

Search NORINE for peptide: strict or relaxed

AMP-binding (14..409): Glu

nrpys: Glu

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:: glu (Glu)

Stachelhaus prediction details:

Stachelhaus sequence:: DSECYGGVTK
Nearest Stachelhaus code(s):: OH-Orn DGEGSGGVTK (41% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NPDC052558.ctg-0024 - Region 1 - redox-cofactor

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Location: 121,206 - 143,212 nt. (total: 22,007 nt) Show pHMM detection rules used

redox-cofactor: (cds(PF04055 and (TIGR04085 or SPASM)) and (TIGR02111 or TIGR03966) and minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE]))

Legend:

core biosynthetic genes

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Select a gene to view the details available for it

Gene overview

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Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Transferases: acetyltransferase

CDS_06895: acetyl-CoA acetyltransferase

smcogs: SMCOG1124: acetyl-CoA acetyltransferase

Hydrolases: hydrolase

CDS_06882: alpha/beta hydrolase domain-containing protein

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

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002318.2	0.42	ribosomal	canucin A, canucin B	Streptomyces canus
BGC0002013.4	0.41	ribosomal	curacozole	Streptomyces curacoi
BGC0000866.5	0.37	other (other)	polyhydroxyalkanoate	Burkholderia sp. DSM 9242
BGC0002316.2	0.36	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0000867.3	0.36	other (other)	polyhydroxyalkanoic acids	Ectothiorhodospira shaposhnikovii
BGC0001100.5	0.36	NRPS, PKS	lankacidin C	Streptomyces rochei
BGC0000528.5	0.32	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001561.4	0.30	NRPS	curacomycin	Streptomyces curacoi
BGC0000820.5	0.29	other (other)	physostigmine	Streptomyces griseofuscus
BGC0000219.4	0.27	PKS, saccharide	elloramycin	Streptomyces olivaceus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002318.2	0.42	ribosomal	canucin A, canucin B	Streptomyces canus
BGC0002013.4	0.41	ribosomal	curacozole	Streptomyces curacoi
BGC0000866.5	0.37	other (other)	polyhydroxyalkanoate	Burkholderia sp. DSM 9242
BGC0002316.2	0.36	ribosomal	cebulantin	Saccharopolyspora cebuensis
BGC0000867.3	0.36	other (other)	polyhydroxyalkanoic acids	Ectothiorhodospira shaposhnikovii
BGC0001100.5	0.36	NRPS, PKS	lankacidin C	Streptomyces rochei
BGC0000528.5	0.32	ribosomal	michiganin A	Clavibacter michiganensis subsp. michiganensis NCPPB 382
BGC0001561.4	0.30	NRPS	curacomycin	Streptomyces curacoi
BGC0000820.5	0.29	other (other)	physostigmine	Streptomyces griseofuscus
BGC0000219.4	0.27	PKS, saccharide	elloramycin	Streptomyces olivaceus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.77 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.74 out of 20.47

Confidence: medium

Additional weak hits (7):

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.96 out of 23.43

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.33 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.26 out of 27.78

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.15 out of 32.93

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.27 out of 18.57

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.17 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.26 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

RREFinder

TFBS Finder

RRE predictions

: RRE type: PqqD_RRE; Location: 2 - 86; Score: 74.2

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0026 - Region 1 - indole

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Location: 25,172 - 48,312 nt. (total: 23,141 nt) Show pHMM detection rules used

indole: (indsynth or dmat or indole_PTase)

Legend:

core biosynthetic genes

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Gene details

Select a gene to view the details available for it

Gene overview

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxidoreductase oxygenase

CDS_07094: Oxidation

MITE: MITE0000070Oxidation (identity: 60.00%)
smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_07097: flavin reductase domain protein FMN-binding

smcogs: SMCOG1160: flavin reductase domain protein FMN-binding

CDS_07101: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_07106: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_07108: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Transferases: glycosyltransferase halogenase methyltransferase

CDS_07099: flavin-dependent trp 5 halogenase

halogenases: flavin-dependent trp 5 halogenase
MITE: MITE0000030Halogenation (identity: 66.30%)
smcogs: SMCOG1119: halogenase

CDS_07100: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_07103: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_07105: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001333.5	0.70	other (other)	BE-54017	uncultured bacterium AB1650
BGC0001334.5	0.67	other (other)	caldoniamide A, cladoniamide B, cladoniamide C7, cladoniamide D, cladoniamide E, cladoniamide F, cladoniamide G	Streptomyces uncialis
BGC0000817.4	0.59	other (other)	methylarcyriarubin	uncultured bacterium
BGC0001224.5	0.57	other (other)	reductasporine	uncultured bacterium
BGC0001336.5	0.55	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0000829.5	0.55	other (other)	violacein	Chromobacterium violaceum
BGC0001223.5	0.53	other (other)	hydroxysporine	uncultured bacterium
BGC0000830.5	0.49	other (aminocoumarin)	violacein	uncultured bacterium
BGC0000924.5	0.48	other (other)	pyrrolnitrin	Pseudomonas chlororaphis
BGC0000821.5	0.48	other (other)	rebeccamycin	Lechevalieria aerocolonigenes

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001333.5	0.70	other (other)	BE-54017	uncultured bacterium AB1650
BGC0001334.5	0.67	other (other)	caldoniamide A, cladoniamide B, cladoniamide C7, cladoniamide D, cladoniamide E, cladoniamide F, cladoniamide G	Streptomyces uncialis
BGC0000817.4	0.59	other (other)	methylarcyriarubin	uncultured bacterium
BGC0001224.5	0.57	other (other)	reductasporine	uncultured bacterium
BGC0001336.5	0.55	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0000829.5	0.55	other (other)	violacein	Chromobacterium violaceum
BGC0001223.5	0.53	other (other)	hydroxysporine	uncultured bacterium
BGC0000830.5	0.49	other (aminocoumarin)	violacein	uncultured bacterium
BGC0000924.5	0.48	other (other)	pyrrolnitrin	Pseudomonas chlororaphis
BGC0000821.5	0.48	other (other)	rebeccamycin	Lechevalieria aerocolonigenes

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.83 out of 20.47

Confidence: medium

Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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TFBS Finder

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0026 - Region 2 - T2PKS

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Location: 62,032 - 134,493 nt. (total: 72,462 nt) Show pHMM detection rules used

T2PKS: (t2ks and t2clf)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

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TFBS Finder

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_07145: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07148: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07149: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_07156: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07157: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_07162: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Transferases: methyltransferase

CDS_07158: Methylation

MITE: MITE0000023Methylation (identity: 65.90%)
smcogs: SMCOG1042: O-methyltransferase

Lyases: cyclase decarboxylase

CDS_07143: diguanylate cyclase

smcogs: SMCOG1025: diguanylate cyclase

CDS_07147: cyclase/dehydrase

smcogs: SMCOG1128: cyclase/dehydrase

CDS_07164: putative carboxymuconolactone decarboxylase

smcogs: SMCOG1298: putative carboxymuconolactone decarboxylase

Ligases: ligase synthase

CDS_07146: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07153: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_07154: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000231.5	0.78	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000234.5	0.69	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0002276.2	0.60	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000272.3	0.60	PKS	spore pigment	Streptomyces collinus
BGC0002137.3	0.58	PKS	mutaxanthene A, mutaxanthene B, mutaxanthene D	Streptomyces sp. NRRL F-3213
BGC0001197.5	0.57	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0002000.4	0.56	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0000197.5	0.56	PKS, saccharide	aranciamycin	Streptomyces echinatus
BGC0000235.5	0.55	PKS	kiamycin	Streptomyces sp. W007
BGC0002477.3	0.55	PKS	thioangucycline A, thioangucycline B	Streptomyces sp. CB00072

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000231.5	0.78	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0000234.5	0.69	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0002276.2	0.60	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000272.3	0.60	PKS	spore pigment	Streptomyces collinus
BGC0002137.3	0.58	PKS	mutaxanthene A, mutaxanthene B, mutaxanthene D	Streptomyces sp. NRRL F-3213
BGC0001197.5	0.57	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0002000.4	0.56	PKS	setomimycin	Streptomyces aurantiacus JA 4570
BGC0000197.5	0.56	PKS, saccharide	aranciamycin	Streptomyces echinatus
BGC0000235.5	0.55	PKS	kiamycin	Streptomyces sp. W007
BGC0002477.3	0.55	PKS	thioangucycline A, thioangucycline B	Streptomyces sp. CB00072

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.54 out of 26.33

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52

Confidence: strong

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.22 out of 26.85

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.67 out of 23.79

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 27.52 out of 30.11

Confidence: strong

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 26.66 out of 30.11

Confidence: medium

Additional weak hits (9):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.28 out of 26.33

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.22 out of 20.97

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.60 out of 29.65

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.83 out of 26.06

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.52 out of 27.04

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.57 out of 26.85

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS substrates

Type II PKS

TFBS Finder

NRPS/PKS substrate predictions

CDS_07146: X

AMP-binding (7..360): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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:: TYMYAGGPLK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

Link to PARAS substrate predictor

Type II PKS gene cluster prediction details

Cluster section:: 62031 to 134493
Starter unit(s):: acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:: 8|9 (Score: 646.9; E-value: 2.4e-197)
Product class(es):: anthracycline
aureolic acid
tetracycline
Product molecular weight(s):: acetyl-CoA_8: 384 Da
acetyl-CoA_9: 426 Da

CDS_07144: CYC C5-C14/C3-C16 (Score: 408.9; E-value: 1.9e-125)
CDS_07145: KR (Score: 124.1; E-value: 1.8e-38)
CDS_07147: CYC C7-C12 (Score: 460.6; E-value: 4.4e-141)
CDS_07148: KR C9 (Score: 471.3; E-value: 1.8e-144)
CDS_07149: OXY (Score: 157.8; E-value: 1.1e-48)
CDS_07151: CYC C1-C18|C2-C19 (Score: 197.9; E-value: 1.5e-61)
CDS_07152: ACP (Score: 113.2; E-value: 1e-35)
CDS_07153: CLF 8|9 (Score: 646.9; E-value: 2.4e-197)
CDS_07154: KS (Score: 764.7; E-value: 5.2e-233)
CDS_07156: KR (Score: 167.9; E-value: 7.9e-52)
CDS_07157: OXY (Score: 401.6; E-value: 1.2e-122)
CDS_07158: MET C2O|C2N (Score: 428.8; E-value: 3.2e-131)
CDS_07162: OXY (Score: 483.7; E-value: 1.6e-147)

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
CelR	Cellobiose uptake repressor
IolR	Regulator of the inositol catabolism
RutR	Regulator of the pyrimidine and purine metabolism

NPDC052558.ctg-0027 - Region 1 - NRPS,betalactone

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Location: 13,991 - 106,274 nt. (total: 92,284 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_07232: dioxygenase, TauD/TfdA

smcogs: SMCOG1121: dioxygenase, TauD/TfdA

CDS_07239: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_07250: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

CDS_07273: dioxygenase, TauD/TfdA

smcogs: SMCOG1121: dioxygenase, TauD/TfdA

Transferases: aminotransferase glycosyltransferase

CDS_07224: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_07288: aminotransferase

smcogs: SMCOG1019: aminotransferase

Hydrolases: esterase

CDS_07286: thioesterase superfamily protein

smcogs: SMCOG1144: thioesterase superfamily protein

Lyases: dehydratase lyase

CDS_07237: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_07258: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase

CDS_07235: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07236: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07238: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07240: polyprenol-monophosphomannose synthase ppm1

smcogs: SMCOG1123: polyprenol-monophosphomannose synthase ppm1

CDS_07241: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_07242: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07247: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

CDS_07256: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

CDS_07269: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07271: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07275: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

Translocases: permease

CDS_07251: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	1.13	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001128.4	0.99	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.99	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.98	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.98	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001641.4	0.96	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.95	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.95	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	0.92	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001251.4	0.92	NRPS	epichloenin A	Epichloe festucae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001878.2	0.73	NRPS, PKS	detoxin N2, detoxin N3	Streptomyces sp. NRRL B-1347
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.68	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001251.4	0.68	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.68	NRPS	epichloenin A	Epichloe festucae
BGC0001758.4	0.67	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97

Confidence: medium

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.86 out of 25.88

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26

Confidence: strong

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.24 out of 19.26

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.07 out of 25.31

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.34 out of 23.43

Confidence: medium

Additional weak hits (12):

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.92 out of 39.62

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.42 out of 39.62

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.45 out of 30.22

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.27 out of 27.18

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.06 out of 23.43

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.14 out of 23.43

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.03 out of 26.06

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.50 out of 30.22

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.93 out of 27.18

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.99 out of 28.19

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.89 out of 23.43

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.15 out of 33.14

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 13990 - 106274:

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

Polymer prediction:: (X - X) + (Val) + (Orn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 13990 - 66427:

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

Polymer prediction:: (X - X) + (Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 62107 - 106274:

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

Polymer prediction:: (Orn)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07235: X - X

AMP-binding (9..416): X

nrpys: Leu, Ile, 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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DAFFLGGTFK
Nearest Stachelhaus code(s):: Ile DAFFLGITFK (79% 8Å match); Leu or Ile DAFFLGMTFK (68% 8Å match); Val DAFWLGGTFK (65% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1027..1409): X

nrpys: 4Me-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:: Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
Small clusters prediction:: pro (Pro)
Single AA prediction:: pro (Pro)

Stachelhaus prediction details:

Stachelhaus sequence:: DVQFIAHVAK
Nearest Stachelhaus code(s):: 4Me-Pro DVQFIAHVAK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_07236: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (460..847): 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:: N/A
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: val (Val)

Stachelhaus prediction details:

Stachelhaus sequence:: DAHFLGGLYK
Nearest Stachelhaus code(s):: Val DALFLGGTFK (59% 8Å match); Ile DAMFLGCTYK (56% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_07238: X

AMP-binding (9..402): X

nrpys: Val, Leu, Ile, Abu, Ival

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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DGAYLGVPIK
Nearest Stachelhaus code(s):: Ile DGFYLGVVFK (29% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_07269: Orn

Search NORINE for peptide: strict or relaxed

AMP-binding (453..835): Orn

nrpys: Orn

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:: DTEDAGLVDK
Nearest Stachelhaus code(s):: Orn DTEDMGLVDK (79% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_07271: X

AMP-binding (20..412): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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:: GFGCVGINTK
Nearest Stachelhaus code(s):: Val DFFCVGIVHK (38% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
BldD	Development and antibiotic global regulator
CRP	Cyclic AMP receptor protein
CatR	H2O2-responsive repressor
CcpA	Catabolite control protein A
PsrA	Oleic acid responsive regulator

NPDC052558.ctg-0029 - Region 1 - terpene

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Location: 111,367 - 130,048 nt. (total: 18,682 nt) Show pHMM detection rules used

Region on contig edge.

terpene: (PT_phytoene_like or phytoene_synt or Lycopene_cycl or Lycopene_cycl_fung or T1TS or T1TS_KS or T2TS or TS_UbiA or TS_Pyr4)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_07566: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

CDS_07573: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

Lyases: cyclase

CDS_07574: Terpene synthase/cyclase metal-binding domain protein

smcogs: SMCOG1052: Terpene synthase/cyclase metal-binding domain protein

Ligases: synthase synthetase

CDS_07576: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

CDS_07578: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs: SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000677.5	0.58	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000660.5	0.58	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0000674.5	0.57	terpene	(-)-δ-cadinene	Streptomyces clavuligerus ATCC 27064
BGC0002043.3	0.54	ribosomal	cittilin A, cittilin B	Myxococcus xanthus DK 1622
BGC0001361.3	0.53	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0002283.2	0.53	terpene	sodorifen	Serratia plymuthica
BGC0000673.3	0.53	terpene	pimara-8(14),15-diene	Aspergillus nidulans FGSC A4
BGC0000675.5	0.52	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0001911.3	0.50	terpene	raimonol	Streptomyces anulatus
BGC0002309.2	0.47	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000677.5	0.58	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000660.5	0.58	terpene	albaflavenone	Streptomyces coelicolor A3(2)
BGC0000674.5	0.57	terpene	(-)-δ-cadinene	Streptomyces clavuligerus ATCC 27064
BGC0002043.3	0.54	ribosomal	cittilin A, cittilin B	Myxococcus xanthus DK 1622
BGC0001361.3	0.53	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0002283.2	0.53	terpene	sodorifen	Serratia plymuthica
BGC0000673.3	0.53	terpene	pimara-8(14),15-diene	Aspergillus nidulans FGSC A4
BGC0000675.5	0.52	terpene	(+)-T-muurolol	Streptomyces clavuligerus ATCC 27064
BGC0001911.3	0.50	terpene	raimonol	Streptomyces anulatus
BGC0002309.2	0.47	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene precursor	FPP	C15	acyclic	PP
diterpene precursor	GGPP	C20	acyclic	PP
sesterterpene precursor	GFPP	C25	acyclic	PP
triterpene precursor	HPP	C30	acyclic	PP

Genes with terpene domains:

CDS_07574: T1TS

Domain 1 (6 - 314): Type 1 terpene synthase

Subtype: unknown

CDS_07576: PT_FPPS_like

Domain 1 (53 - 339): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 21.90 out of 23.79

Confidence: strong

Additional weak hits (7):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 20.95 out of 32.74

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.50 out of 21.55

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.62 out of 18.57

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.22 out of 27.04

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism

NPDC052558.ctg-0030 - Region 1 - NRPS,NRPS-like,T1PKS

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Location: 1 - 127,449 nt. (total: 127,449 nt) Show pHMM detection rules used

Region on contig edge.

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
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))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_07586: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_07592: Dioxygenase TauD/TfdA

smcogs: SMCOG1046: Dioxygenase TauD/TfdA

CDS_07596: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07605: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_07618: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_07629: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

CDS_07633: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Transferases: acylase aminotransferase carbamoyltransferase glycosyltransferase transferase

CDS_07602: ornithine carbamoyltransferase

smcogs: SMCOG1114: ornithine carbamoyltransferase

CDS_07624: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_07626: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs: SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CDS_07628: glucose-1-phosphate adenylyl/thymidylyltransferase

smcogs: SMCOG1064: glucose-1-phosphate adenylyl/thymidylyltransferase

CDS_07631: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_07634: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: amidase deaminase dehalogenase esterase

CDS_07591: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

CDS_07597: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_07600: amidase

smcogs: SMCOG1105: amidase

CDS_07625: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Lyases: decarboxylase

CDS_07620: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase synthase

CDS_07590: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

CDS_07593: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07598: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07599: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07619: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07621: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07622: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07630: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_07632: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter

CDS_07582: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002075.3	1.56	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001833.4	1.53	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	1.53	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	1.52	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	1.52	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	1.51	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002135.2	1.49	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	1.45	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	1.42	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001261.3	1.42	NRPS	AM-toxin	Alternaria alternata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.75	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002075.3	0.74	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001758.4	0.73	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.46 out of 23.05

Confidence: medium

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 18.76 out of 23.05

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.79 out of 20.97

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.90 out of 20.47

Confidence: medium

Additional weak hits (25):

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.31 out of 25.88

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.76 out of 26.85

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.03 out of 29.38

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.84 out of 21.84

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.23 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.06 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.11 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.33 out of 30.25

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.06 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.58 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.59 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.90 out of 26.06

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.51 out of 20.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.06 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 14.91 out of 27.78

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 17.11 out of 27.78

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.96 out of 27.04

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.65 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.76 out of 29.38

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.21 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.81 out of 29.65

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.33 out of 35.63

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 16.07 out of 33.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.81 out of 28.19

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 127449:

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

Polymer prediction:: (Me-redmal) + (redmal) + (ohemal) + (pk - redmal) + (Gln - Thr - Gly - D-Phe) + (Glu - Asn - X) + (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 40001:

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

Polymer prediction:: (Gln - Thr - Gly - D-Phe) + (Glu - Asn - X) + (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 639 - 44305:

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

Polymer prediction:: (Gln - Thr - Gly - D-Phe) + (Glu - Asn - X) + (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 5141 - 77138:

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

Polymer prediction:: (Gln - Thr - Gly - D-Phe) + (Glu - Asn - X) + (X) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 5, location 59579 - 127449:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (pk - redmal) + (Me-redmal) + (redmal) + (ohemal)
Non-colinear ordering:: CDS_07619 + CDS_07633 + CDS_07632 + CDS_07631

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07593: X

AMP-binding (210..608): X

nrpys: Dpr

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:: DIWQSTADDK
Nearest Stachelhaus code(s):: Dpr DIWQSTADDK (94% 8Å match); Asp DIWQSTADDK (82% 8Å match); dnmeProp or Dab DIWQSTADDK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_07596: X

AMP-binding (97..528): 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:: GIFWLGASGK
Nearest Stachelhaus code(s):: 2S-Hic GILWLGASGK (74% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_07598: Glu - Asn - X

Search NORINE for peptide: strict or relaxed

AMP-binding (455..828): 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:: glu,gln (Glu, Gln)
Single AA prediction:: glu (Glu)

Stachelhaus prediction details:

Stachelhaus sequence:: DVWHYGGVDK
Nearest Stachelhaus code(s):: Glu DAWHFGGVDK (71% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1468..1843): 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:: DLTKVGEIGK
Nearest Stachelhaus code(s):: OH-Asn DLTKVGEVGK (85% 8Å match); Asn DLTKVGEVGK (79% 8Å match); Asp DLTKVGHIGK (68% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2475..2839): 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:: DVAHIGACDK
Nearest Stachelhaus code(s):: Arg DVADVGAIDK (38% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_07599: Gln - Thr - Gly - Phe

Search NORINE for peptide: strict or relaxed

AMP-binding (20..412): Gln

nrpys: Gln

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:: DASQFALVDK
Nearest Stachelhaus code(s):: Gln DAWQFGLVDK (56% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (2653..3052): 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:: DFWNVGMVHK
Nearest Stachelhaus code(s):: Thr DFWNVGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5341..5732): 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:: DILQLGLVWK
Nearest Stachelhaus code(s):: Gly DILQLGLVWK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (6370..6746): Phe

nrpys: Phe

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:: DAWTVAAVCK
Nearest Stachelhaus code(s):: Phe DAWTVAAVCK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_07619: pk - mal

PKS_AT (654..949): pk

ATSignature: Methoxymalonyl-CoA

Top 3 matches:: Methoxymalonyl-CoA: 91.7%; Ethylmalonyl-CoA: 87.5%; Methylmalonyl-CoA: 83.3%

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 186.5
Methylmalonyl-CoA: 180.0
Methoxymalonyl-CoA: 153.4
2-Methylbutyryl-CoA: 120.5
CHC-CoA: 98.1
trans-1,2-CPDA: 97.7
Propionyl-CoA: 97.2
Malonyl-CoA: 81.7
Isobutyryl-CoA: 75.8
Benzoyl-CoA: 54.4
Acetyl-CoA: 38.5
fatty_acid: 38.4
inactive: 33.8
3-Methylbutyryl-CoA: 15.7

PKS_AT (2656..2940): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 62.5%; Ethylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 226.0
inactive: 96.9
Methoxymalonyl-CoA: 91.1
Methylmalonyl-CoA: 78.4
Propionyl-CoA: 51.2
Isobutyryl-CoA: 40.1
Ethylmalonyl-CoA: 32.9
Acetyl-CoA: 30.7
2-Methylbutyryl-CoA: 28.9
Benzoyl-CoA: 26.9
CHC-CoA: 24.2
fatty_acid: 23.8
trans-1,2-CPDA: 16.5
3-Methylbutyryl-CoA: 0.0

CDS_07621: Asp

Search NORINE for peptide: strict or relaxed

AMP-binding (17..414): 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:: DYYPTTMRVK
Nearest Stachelhaus code(s):: Asp DYYPTTMRVK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_07622: Ala

Search NORINE for peptide: strict or relaxed

AMP-binding (12..400): 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:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DCFFLALITK
Nearest Stachelhaus code(s):: bMe-Asp DCFFFALITK (82% 8Å match); Ala DCFFFALITK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_07624: pk

PKS_AT (12..245): pk

ATSignature: (unknown)

No matches above 50%

minowa: CHC-CoA

Prediction, score:

CHC-CoA: 11.0
trans-1,2-CPDA: 0.0
inactive: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Methylmalonyl-CoA: 0.0
Methoxymalonyl-CoA: 0.0
Malonyl-CoA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

CDS_07631: emal

PKS_AT (561..859): emal

ATSignature: Ethylmalonyl-CoA, Methoxymalonyl-CoA

Top 3 matches:: Ethylmalonyl-CoA: 91.7%; Methoxymalonyl-CoA: 91.7%; Methylmalonyl-CoA: 87.5%

minowa: Ethylmalonyl-CoA

Prediction, score:

Ethylmalonyl-CoA: 195.1
Methylmalonyl-CoA: 191.2
Methoxymalonyl-CoA: 167.4
2-Methylbutyryl-CoA: 133.0
trans-1,2-CPDA: 106.9
Malonyl-CoA: 101.5
Propionyl-CoA: 93.6
CHC-CoA: 83.6
Isobutyryl-CoA: 81.9
Benzoyl-CoA: 64.2
Acetyl-CoA: 52.6
3-Methylbutyryl-CoA: 44.6
inactive: 40.1
fatty_acid: 37.4

CDS_07632: mal

PKS_AT (553..837): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 75.0%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 210.2
inactive: 110.6
Methoxymalonyl-CoA: 82.9
Methylmalonyl-CoA: 73.1
Isobutyryl-CoA: 44.1
Propionyl-CoA: 43.0
Ethylmalonyl-CoA: 31.0
fatty_acid: 29.2
Benzoyl-CoA: 26.4
Acetyl-CoA: 25.4
2-Methylbutyryl-CoA: 17.6
CHC-CoA: 14.4
trans-1,2-CPDA: 12.9
3-Methylbutyryl-CoA: -0.1

CDS_07633: mmal

PKS_AT (551..849): mmal

ATSignature: Methoxymalonyl-CoA, Methylmalonyl-CoA

Top 3 matches:: Methoxymalonyl-CoA: 87.5%; Methylmalonyl-CoA: 87.5%; Malonyl-CoA: 79.2%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 176.8
Ethylmalonyl-CoA: 157.9
Methoxymalonyl-CoA: 144.8
2-Methylbutyryl-CoA: 111.3
trans-1,2-CPDA: 102.3
Malonyl-CoA: 101.2
Propionyl-CoA: 95.2
CHC-CoA: 77.6
Isobutyryl-CoA: 61.8
3-Methylbutyryl-CoA: 47.7
Benzoyl-CoA: 42.4
Acetyl-CoA: 39.4
inactive: 37.5
fatty_acid: 18.5

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
CcpA	Catabolite control protein A
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0031 - Region 1 - thioamitides

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Location: 19,994 - 42,422 nt. (total: 22,429 nt) Show pHMM detection rules used

thioamitides: ((YcaO or TIGR03604) and TfuA)

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_07660: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_07670: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: methyltransferase

CDS_07659: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: amidase

CDS_07671: amidase

smcogs: SMCOG1105: amidase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001849.4	0.54	ribosomal	thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D	Streptomyces varsoviensis
BGC0001310.5	0.51	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0001201.3	0.51	terpene	eremophilene	Sorangium cellulosum So ce56
BGC0000844.5	0.50	other (other)	clavulanic acid	Streptomyces clavuligerus
BGC0002127.3	0.48	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0000902.4	0.47	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0001224.5	0.46	other (other)	reductasporine	uncultured bacterium
BGC0000285.5	0.44	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0001605.3	0.44	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0001485.4	0.43	other (other)	chuangxinmycin	Actinoplanes tsinanensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001849.4	0.54	ribosomal	thiovarsolin A, thiovarsolin B, thiovarsolin C, thiovarsolin D	Streptomyces varsoviensis
BGC0001310.5	0.51	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0001201.3	0.51	terpene	eremophilene	Sorangium cellulosum So ce56
BGC0000844.5	0.50	other (other)	clavulanic acid	Streptomyces clavuligerus
BGC0002127.3	0.48	PKS	flaviolin, 1,3,6,8-tetrahydroxynaphthalene	Streptomyces coelicolor A3(2)
BGC0000902.4	0.47	PKS	flaviolin	Saccharopolyspora erythraea NRRL 2338
BGC0001224.5	0.46	other (other)	reductasporine	uncultured bacterium
BGC0000285.5	0.44	PKS, saccharide	flaviolin, flaviolin rhamnoside, 3,3'-diflaviolin	Saccharopolyspora erythraea
BGC0001605.3	0.44	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0001485.4	0.43	other (other)	chuangxinmycin	Actinoplanes tsinanensis

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.13 out of 29.72

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97

Confidence: medium

Additional weak hits (2):

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.11 out of 32.74

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.42 out of 26.33

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

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TFBS Finder

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
NtrC	Nitrogen regulatory protein C

NPDC052558.ctg-0031 - Region 2 - oligosaccharide

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Location: 73,051 - 97,797 nt. (total: 24,747 nt) Show pHMM detection rules used

oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase

CDS_07711: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

CDS_07717: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Transferases: aminotransferase glycosyltransferase methyltransferase

CDS_07718: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_07719: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_07720: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs: SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

CDS_07721: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_07722: methyltransferase

smcogs: SMCOG1248: methyltransferase

CDS_07723: methyltransferase

smcogs: SMCOG1248: methyltransferase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000277.5	0.48	PKS	urdamycin	Streptomyces fradiae
BGC0000772.5	0.43	saccharide	lipopolysaccharide	Brucella melitensis
BGC0000898.5	0.42	saccharide	desosamine, pikromycin, neomethymycin, narbomycin	Streptomyces venezuelae
BGC0000587.5	0.41	ribosomal	microcin H47	Escherichia coli
BGC0000586.5	0.40	ribosomal	microcin E492	Klebsiella pneumoniae RYC492
BGC0000019.5	0.40	PKS	angolamycin	Streptomyces eurythermus
BGC0000820.5	0.40	other (other)	physostigmine	Streptomyces griseofuscus
BGC0000875.4	0.39	other (nucleoside), saccharide	caprazamycin, caprazamycin aglycon	Streptomyces sp. MK730-62F2
BGC0000899.4	0.39	saccharide	desosamine	Streptomyces narbonensis
BGC0000214.5	0.38	PKS	cosmomycin B	Streptomyces olindensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000277.5	0.48	PKS	urdamycin	Streptomyces fradiae
BGC0000772.5	0.43	saccharide	lipopolysaccharide	Brucella melitensis
BGC0000898.5	0.42	saccharide	desosamine, pikromycin, neomethymycin, narbomycin	Streptomyces venezuelae
BGC0000587.5	0.41	ribosomal	microcin H47	Escherichia coli
BGC0000586.5	0.40	ribosomal	microcin E492	Klebsiella pneumoniae RYC492
BGC0000019.5	0.40	PKS	angolamycin	Streptomyces eurythermus
BGC0000820.5	0.40	other (other)	physostigmine	Streptomyces griseofuscus
BGC0000875.4	0.39	other (nucleoside), saccharide	caprazamycin, caprazamycin aglycon	Streptomyces sp. MK730-62F2
BGC0000899.4	0.39	saccharide	desosamine	Streptomyces narbonensis
BGC0000214.5	0.38	PKS	cosmomycin B	Streptomyces olindensis

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

Additional weak hits (4):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.64 out of 21.55

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.92 out of 30.22

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 16.96 out of 22.40

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.85 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

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TFBS Finder

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0032 - Region 1 - T3PKS

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Location: 2,772 - 43,788 nt. (total: 41,017 nt) Show pHMM detection rules used

T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: oxygenase

CDS_07783: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Hydrolases: glucanase glucosidase

CDS_07768: Pullulanase, type I

smcogs: SMCOG1297: Pullulanase, type I

CDS_07769: Alpha-glucosidase

smcogs: SMCOG1257: Alpha-glucosidase

CDS_07770: Pullulanase, type I

smcogs: SMCOG1297: Pullulanase, type I

Lyases: dehydratase

CDS_07775: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: synthase

CDS_07771: chalcone and stilbene synthase domain protein

smcogs: SMCOG1024: chalcone and stilbene synthase domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000282.3	0.55	PKS	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001285.5	0.48	other (fatty acid)	pseudopyronine A, pseudopyronine B	Pseudomonas putida
BGC0001077.4	0.47	PKS	6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone	Actinoplanes missouriensis 431
BGC0001735.5	0.46	other (other)	pentostatine, vidarabine	Streptomyces antibioticus
BGC0002362.3	0.45	PKS	loseolamycin A1, loseolamycin A2	Micromonospora endolithica
BGC0002407.3	0.44	other (other), saccharide	angustmycin A, angustmycin C	Streptomyces angustmyceticus
BGC0002690.2	0.42	other (other)	FW0622	Verrucosispora sp. FIM060022
BGC0002621.2	0.42	other (other)	angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine	Streptomyces angustmyceticus
BGC0001964.2	0.40	PKS	alkylpyrone-407, alkylpyrone-393	Cystobacterineae bacterium
BGC0000918.3	0.40	other (other)	ochronotic pigment	Streptomyces avermitilis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000282.3	0.55	PKS	2-methoxy-5-methyl-6-(13-methyltetradecyl)-1,4-benzoquinone, 2-methoxy-5-methyl-6-(13-methyltetradecyl)phenol	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001285.5	0.48	other (fatty acid)	pseudopyronine A, pseudopyronine B	Pseudomonas putida
BGC0001077.4	0.47	PKS	6-anteisoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrogeranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-geranyl-2-methoxyhydroquinone, 6-palmityl-4-O-geranyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-geranyl-2-methoxyhydroquinone, 6-isopalmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-palmityl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-anteisoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone, 6-isoheptadecyl-4-O-dihydrofarnesyl-2-methoxyhydroquinone	Actinoplanes missouriensis 431
BGC0001735.5	0.46	other (other)	pentostatine, vidarabine	Streptomyces antibioticus
BGC0002362.3	0.45	PKS	loseolamycin A1, loseolamycin A2	Micromonospora endolithica
BGC0002407.3	0.44	other (other), saccharide	angustmycin A, angustmycin C	Streptomyces angustmyceticus
BGC0002690.2	0.42	other (other)	FW0622	Verrucosispora sp. FIM060022
BGC0002621.2	0.42	other (other)	angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine	Streptomyces angustmyceticus
BGC0001964.2	0.40	PKS	alkylpyrone-407, alkylpyrone-393	Cystobacterineae bacterium
BGC0000918.3	0.40	other (other)	ochronotic pigment	Streptomyces avermitilis

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (6):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.72 out of 20.97

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.86 out of 26.85

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.40 out of 21.84

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.64 out of 36.54

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.70 out of 26.33

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.59 out of 22.40

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description

NPDC052558.ctg-0033 - Region 1 - NRPS,NRPS-like,PKS-like,T1PKS,butyrolactone

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Location: 1 - 64,145 nt. (total: 64,145 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))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
PKS-like: (t2pks2 or ksIII)
butyrolactone: AfsA

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Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidase oxygenase

CDS_07852: FAD linked oxidase domain protein

smcogs: SMCOG1138: FAD linked oxidase domain protein

CDS_07858: Dioxygenase TauD/TfdA

smcogs: SMCOG1046: Dioxygenase TauD/TfdA

CDS_07876: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_07877: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

CDS_07878: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07882: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_07888: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase

CDS_07864: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase

CDS_07874: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Ligases: ligase synthase

CDS_07859: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07862: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07865: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_07867: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_07868: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_07879: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_07883: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_07885: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000848.5	1.81	other (other)	A-factor	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001249.5	1.69	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	1.56	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	1.45	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	1.44	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002135.2	1.43	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002164.2	1.39	NRPS	peramine	Epichloe festucae
BGC0001128.4	1.38	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	1.38	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4	1.37	NRPS	enniatin	Fusarium equiseti

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000848.5	0.75	other (other)	A-factor	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001249.5	0.74	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata
BGC0002135.2	0.71	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001135.5	0.71	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.69	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001166.5	0.69	NRPS	HC-toxin	Alternaria jesenskae

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 17.31 out of 18.46

Confidence: strong

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 19.26

Confidence: strong

Additional weak hits (12):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.02 out of 26.06

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.09 out of 21.55

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.01 out of 31.73

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.60 out of 21.55

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.55 out of 32.93

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 16.65 out of 20.01

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 14.07 out of 28.14

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.16 out of 30.25

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 17.73 out of 33.14

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.20 out of 32.93

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.63 out of 26.06

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 19.53 out of 35.63

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 64145:

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

Polymer prediction:: (X) + (Val) + (ohmal) + (Asp) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 48425:

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

Polymer prediction:: (X) + (Val) + (ohmal) + (Asp) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 12013 - 53762:

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

Polymer prediction:: (X) + (Val) + (ohmal) + (Asp) + (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 23131 - 64145:

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

Polymer prediction:: (X) + (Val) + (ohmal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07859: X

AMP-binding (1043..1420): X

nrpys: meSer

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:: DVFESGGVAK
Nearest Stachelhaus code(s):: meSer DVFESGGVAK (82% 8Å match); Lys DVFESGGVAK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_07862: Asp

Search NORINE for peptide: strict or relaxed

AMP-binding (460..836): Asp

nrpys: Asp

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:: DSTKIGHIGK
Nearest Stachelhaus code(s):: Asp DLTKIGHIGK (62% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_07864: mal

PKS_AT (530..814): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 95.8%; inactive: 87.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 187.1
inactive: 109.1
Methoxymalonyl-CoA: 75.6
Methylmalonyl-CoA: 67.1
Propionyl-CoA: 55.7
Isobutyryl-CoA: 55.6
Ethylmalonyl-CoA: 39.2
Benzoyl-CoA: 35.8
2-Methylbutyryl-CoA: 32.2
Acetyl-CoA: 29.1
trans-1,2-CPDA: 24.8
fatty_acid: 24.0
CHC-CoA: 23.1
3-Methylbutyryl-CoA: 9.8

CDS_07865: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (6..379): 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:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DGLFLGLVAK
Nearest Stachelhaus code(s):: Val DALFVGLVAK (50% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_07868: X

AMP-binding (8..391): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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:: DMTHLGGFIK
Nearest Stachelhaus code(s):: Pro DMTFSAGIIK (47% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
RpoN	Regulator of nitrogen assimilation and virulence

NPDC052558.ctg-0034 - Region 1 - NRPS

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Location: 1 - 48,962 nt. (total: 48,962 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_07946: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_07951: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: aminotransferase

CDS_07950: aminotransferase

smcogs: SMCOG1019: aminotransferase

Ligases: ligase

CDS_07930: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_07931: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.76	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	0.75	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.74	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.74	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.74	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002071.2	0.73	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001132.4	0.72	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.76	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	0.75	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.74	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.74	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.74	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002071.2	0.73	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001132.4	0.72	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.40 out of 20.97

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 19.52 out of 19.52

Confidence: strong

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.13 out of 23.79

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.27 out of 23.79

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.31 out of 26.85

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.44 out of 23.79

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

Additional weak hits (7):

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.29 out of 20.97

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 19.96 out of 29.65

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.92 out of 25.75

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.35 out of 26.85

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.85 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.57 out of 29.65

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.47 out of 29.65

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 48962:

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

Polymer prediction:: (D-Glu) + (Val - Val - X - Val - Val - X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_07930: Val - Val - X - Val - Val - X

Search NORINE for peptide: strict or relaxed

AMP-binding (465..846): Val

nrpys: Val

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:: DALHMGGIFK
Nearest Stachelhaus code(s):: Val DALWMGGTFK (50% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1497..1872): 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:: DGLWMGGVFK
Nearest Stachelhaus code(s):: Val DALWMGGVFK (47% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2517..2894): X

nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:

Stachelhaus sequence:: DGLQVGGGFK
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (47% 8Å match); cycHexAla DLLSVGGVFK (44% 8Å match); 3OH-Leu DTLWWGGGFK (44% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (3521..3913): 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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DGLWLGGVFK
Nearest Stachelhaus code(s):: Val DALWLGGVFK (59% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (4568..4950): Val

nrpys: Val

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:: DALHMGGIFK
Nearest Stachelhaus code(s):: Val DALWMGGTFK (50% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (5600..5980): X

nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:

Stachelhaus sequence:: DGLQVGGGFK
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (47% 8Å match); cycHexAla DLLSVGGVFK (44% 8Å match); 3OH-Leu DTLWWGGGFK (44% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_07931: Glu

Search NORINE for peptide: strict or relaxed

AMP-binding (10..402): 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:: N/A
Single AA prediction:: glu (Glu)

Stachelhaus prediction details:

Stachelhaus sequence:: DVRHLGVVHK
Nearest Stachelhaus code(s):: Dpr DVRHLSMVEK (62% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CcpA	Catabolite control protein A
IolR	Regulator of the inositol catabolism
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0035 - Region 1 - NRPS,thioamide-NRP

Download region GenBank file

Download region SVG

Location: 1 - 49,908 nt. (total: 49,908 nt) Show pHMM detection rules used

Region on contig edge.

thioamide-NRP: (ATP-grasp and AMP-binding and PP-binding and (DUF98 or Orn_Arg_deC_N or Orn_DAP_Arg_deC))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_08012: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_08024: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_08033: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

CDS_08042: dehydrogenase

smcogs: SMCOG1072: dehydrogenase

CDS_08048: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Transferases: aminotransferase

CDS_08011: aminotransferase

smcogs: SMCOG1019: aminotransferase

Hydrolases: hydrolase

CDS_08021: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_08032: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_08037: alpha/beta hydrolase domain-containing protein

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

Lyases: decarboxylase lyase

CDS_08016: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

CDS_08026: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase

CDS_08014: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_08015: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.73	NRPS	enniatin	Fusarium equiseti
BGC0001833.4	0.69	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.68	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001758.4	0.67	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.65	NRPS	AM-toxin	Alternaria alternata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001758.4	0.67	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (8):

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.61 out of 32.74

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.90 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.53 out of 29.38

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 20.94 out of 33.73

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.12 out of 30.25

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.42 out of 18.57

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.47 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.64 out of 35.63

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 49908:

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

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_08014: X

AMP-binding (469..864): X

nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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

Stachelhaus prediction details:

Stachelhaus sequence:: DLAGLGGIGK
Nearest Stachelhaus code(s):: Z-ahmohOrn DVDGGGGIGK (53% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_08015: X

AMP-binding (15..418): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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:: DYNPCSMRSK
Nearest Stachelhaus code(s):: Asp DYYPTTMRAK (47% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description

NPDC052558.ctg-0036 - Region 1 - NRPS-like,T1PKS,T3PKS

Download region GenBank file

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Location: 6,709 - 71,403 nt. (total: 64,695 nt) Show pHMM detection rules used

T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidase oxidoreductase

CDS_08140: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_08153: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_08154: pyruvate oxidase/decarboxylase

smcogs: SMCOG1055: pyruvate oxidase/decarboxylase

Hydrolases: hydrolase

CDS_08146: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: hydratase

CDS_08149: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

CDS_08150: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

CDS_08151: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase

CDS_08142: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_08143: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_08144: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_08145: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_08152: chalcone and stilbene synthase domain protein

smcogs: SMCOG1024: chalcone and stilbene synthase domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.84	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.84	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.84	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.83	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0000041.3	0.81	PKS	oronofacic acid	Pseudomonas syringae
BGC0001160.5	0.80	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001164.3	0.79	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002154.2	0.60	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.60	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0000107.3	0.59	PKS	naphthopyrone	Aspergillus nidulans FGSC A4

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001276.3	0.73	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.73	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.73	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.73	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0000041.3	0.66	PKS	oronofacic acid	Pseudomonas syringae
BGC0002154.2	0.64	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001257.3	0.63	PKS	1,3,6,8-tetrahydroxynaphthalene	Nodulisporium sp. ATCC74245
BGC0000107.3	0.63	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0002175.3	0.63	PKS	YWA1	Aspergillus oryzae RIB40
BGC0001268.4	0.63	NRPS, PKS	fusarin C	Fusarium fujikuroi

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.85 out of 20.97

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.26 out of 19.26

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.07 out of 20.47

Confidence: medium

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 22.05 out of 22.40

Confidence: strong

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.01 out of 25.31

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 18.16 out of 18.16

Confidence: strong

Additional weak hits (7):

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.06 out of 29.25

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 21.66 out of 32.74

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 16.03 out of 27.78

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.91 out of 31.73

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.43 out of 32.93

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.47 out of 32.93

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 6708 - 71403:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (AHBA - ccmal - Me-ccmal) + (ccmal)
Non-colinear ordering:: CDS_08145 + CDS_08144

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 6708 - 64162:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (AHBA - ccmal - Me-ccmal) + (ccmal)
Non-colinear ordering:: CDS_08145 + CDS_08144

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 30341 - 71403:

Rough prediction of core scaffold based on assumed PKS linker matching; tailoring reactions not taken into account

Polymer prediction:: (AHBA - ccmal - Me-ccmal) + (ccmal)
Non-colinear ordering:: CDS_08145 + CDS_08144

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_08142: X

AMP-binding (102..332): X

nrpys: Val, Leu, Ile, Abu, Ival

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:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: SH-VVSATIK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

CDS_08144: mal

PKS_AT (517..804): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 75.0%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 202.3
inactive: 113.0
Methylmalonyl-CoA: 74.0
Methoxymalonyl-CoA: 67.6
fatty_acid: 32.4
Isobutyryl-CoA: 32.4
Propionyl-CoA: 30.6
Ethylmalonyl-CoA: 30.4
Benzoyl-CoA: 25.2
CHC-CoA: 20.5
Acetyl-CoA: 19.2
trans-1,2-CPDA: 16.2
2-Methylbutyryl-CoA: 14.3
3-Methylbutyryl-CoA: 0.0

CDS_08145: AHBA - mal - mmal

CAL_domain (33..437): AHBA

minowa: AHBA

Prediction, score:

AHBA: 324.5
shikimic_acid: 247.8
fatty_acid: 0.0
NH2: 0.0
Acetyl-CoA: 0.0

PKS_AT (1320..1588): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 75.0%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 201.1
inactive: 115.3
Methylmalonyl-CoA: 75.2
Methoxymalonyl-CoA: 69.2
fatty_acid: 35.5
Ethylmalonyl-CoA: 34.7
Propionyl-CoA: 33.2
Isobutyryl-CoA: 31.3
Benzoyl-CoA: 27.7
CHC-CoA: 19.7
Acetyl-CoA: 18.7
trans-1,2-CPDA: 15.4
2-Methylbutyryl-CoA: 14.9
3-Methylbutyryl-CoA: 3.8

PKS_AT (2873..3155): mmal

ATSignature: Methylmalonyl-CoA

Top 3 matches:: Methylmalonyl-CoA: 95.8%; Malonyl-CoA: 91.7%; Methoxymalonyl-CoA: 87.5%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 197.6
Ethylmalonyl-CoA: 188.3
Methoxymalonyl-CoA: 157.4
2-Methylbutyryl-CoA: 121.9
trans-1,2-CPDA: 119.3
Propionyl-CoA: 104.0
Malonyl-CoA: 100.0
CHC-CoA: 95.9
Benzoyl-CoA: 61.3
Isobutyryl-CoA: 60.1
Acetyl-CoA: 52.0
fatty_acid: 38.4
inactive: 32.7
3-Methylbutyryl-CoA: 29.4

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
CRP	Cyclic AMP receptor protein
CatR	H2O2-responsive repressor
CcpA	Catabolite control protein A
HypR	L-hydroxyproline utilization repressor
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0039 - Region 1 - NRPS

Download region GenBank file

Download region SVG

Location: 41,541 - 86,322 nt. (total: 44,782 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_08457: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_08470: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_08472: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

CDS_08474: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Transferases: carboxylase

CDS_08451: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Hydrolases: amidase hydrolase peptidase

CDS_08447: isochorismatase

smcogs: SMCOG1027: isochorismatase

CDS_08452: amidase

smcogs: SMCOG1105: amidase

CDS_08471: methionine aminopeptidase

smcogs: SMCOG1172: methionine aminopeptidase

Ligases: ligase

CDS_08458: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_08459: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_08463: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease

CDS_08448: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2	0.66	NRPS	peramine	Epichloe festucae
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.66	NRPS	AbT1	Aureobasidium pullulans

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002164.2	0.66	NRPS	peramine	Epichloe festucae
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.66	NRPS	AbT1	Aureobasidium pullulans

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 20.47 out of 20.47

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97

Confidence: medium

Additional weak hits (7):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 16.34 out of 31.73

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.54 out of 30.97

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.26 out of 27.78

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 18.75 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 17.67 out of 30.25

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.63 out of 27.04

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 23.43

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 41540 - 86322:

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

Polymer prediction:: (Phe - X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_08459: Phe - X

Search NORINE for peptide: strict or relaxed

AMP-binding (39..401): Phe

nrpys: Phe

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:: DAFVMMGIAK
Nearest Stachelhaus code(s):: Phe DAFVLAGVAK (68% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (1055..1415): X

nrpys: Val, Leu, Ile, Abu, Ival

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:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DVYFMGAVIK
Nearest Stachelhaus code(s):: Leu DALFMGAVAK (62% 8Å match); Trp or Pro DVMFIGAVNK (53% 8Å match)
Stachelhaus code match:: 70% (weak)

CDS_08463: X

AMP-binding (18..414): 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:: NAANVGAVAK
Nearest Stachelhaus code(s):: Leu DALFVGAVAK (35% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0042 - Region 1 - lanthipeptide-class-ii

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Location: 5,876 - 28,959 nt. (total: 23,084 nt) Show pHMM detection rules used

Region on contig edge.

lanthipeptide-class-ii: cds(LANC_like and DUF4135)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

Lanthipeptides

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_08645: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: acetyltransferase

CDS_08648: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase

CDS_08647: alpha/beta hydrolase domain-containing protein

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

Lyases: cyclase hydratase

CDS_08656: lanthionine synthetase C family protein

smcogs: SMCOG1070: lanthionine synthetase C family protein

CDS_08663: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

Isomerases: mutase

CDS_08649: phosphoglycerate mutase

smcogs: SMCOG1101: phosphoglycerate mutase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000525.5	0.50	ribosomal	lichenicidin VK21 A1, lichenicidin VK21 A2	Bacillus licheniformis
BGC0002704.2	0.46	ribosomal	archalan β	Halorussus salinus
BGC0002703.2	0.45	ribosomal	archalan α	Halorussus salinus
BGC0000554.4	0.43	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0001407.5	0.41	ribosomal	bicereucin	Bacillus cereus SJ1
BGC0000500.5	0.41	ribosomal	carnolysin A1, carnolysin A2	Carnobacterium maltaromaticum
BGC0001229.4	0.41	ribosomal	SBI-06990 A1, SBI-06989 A2	Streptomyces bingchenggensis BCW-1
BGC0000527.5	0.41	ribosomal	mersacidin	Bacillus sp. HIL-Y85/54728
BGC0000516.4	0.40	ribosomal	geobacillin II	Geobacillus thermodenitrificans
BGC0001210.5	0.40	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000525.5	0.50	ribosomal	lichenicidin VK21 A1, lichenicidin VK21 A2	Bacillus licheniformis
BGC0002704.2	0.46	ribosomal	archalan β	Halorussus salinus
BGC0002703.2	0.45	ribosomal	archalan α	Halorussus salinus
BGC0000554.4	0.43	ribosomal	SRO15-3108	Streptomyces filamentosus NRRL 15998
BGC0001407.5	0.41	ribosomal	bicereucin	Bacillus cereus SJ1
BGC0000500.5	0.41	ribosomal	carnolysin A1, carnolysin A2	Carnobacterium maltaromaticum
BGC0001229.4	0.41	ribosomal	SBI-06990 A1, SBI-06989 A2	Streptomyces bingchenggensis BCW-1
BGC0000527.5	0.41	ribosomal	mersacidin	Bacillus sp. HIL-Y85/54728
BGC0000516.4	0.40	ribosomal	geobacillin II	Geobacillus thermodenitrificans
BGC0001210.5	0.40	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CDS_08656

CDS_08651

Leader:

MTINWGGLGEVFVVSIVAA

Core:

VLFVSLFSVGIGAWTRRGEAVLNNVLAIVSFALCAAIVGYGIFAIAHK

Core with dehydrations:

VLFVDhaLFDhaVGIGAWDhbRRGEAVLNNVLAIVDhaFALCysAAIVGYGIFAIAHK

antiSMASH-DB 4.0 matches for CDS_08651

87.5%

NZ_CP073318.1:

Lanthipeptides: JJ691_RS04905_lanthipeptide

1

VLFVSLFSVGIGAWTRRGEAVLNNVLAIVSFALCAAIVGYGIFAIAHK

48

VLFV LFSVGIGAWTRRGEAVLNNVLAI F LCA I+GYGIFAIAHK

1

VLFVGLFSVGIGAWTRRGEAVLNNVLAIGCFVLCAVIIGYGIFAIAHK

48

75.0%

NZ_CP097263.1:

Lanthipeptides: M3Q35_RS17960_lanthipeptide

1

VLFVSLFSVGIGAWTRRGEAVLNNVLAIVSFALCAAIVGYGIFAIAHK

48

VLFV LFSVGI +WTRRGEA LNNVLAI F LCA IVGYG++AIA +

1

VLFVGLFSVGINSWTRRGEAALNNVLAIGCFVLCAGIVGYGLYAIAFR

48

14.6%

NZ_CP096658.1:

Lanthipeptides: allorf_3198246_3198419_lanthipeptide

19

EAVLNNVLAIVSFALCA

35

EAV+ +LA+ S ++C+

2

EAVVATILAVSSQSICS

18

with 1 more sequence matches

14.6%

NZ_QOIL01000028.1and 3 others:

NZ_QOIL01000028.1 Lanthipeptides: allorf_055366_055542_lanthipeptideNZ_QOIL01000028.1 Lanthipeptides: allorf_055366_055542_lanthipeptideNZ_QOIL01000028.1 Lanthipeptides: allorf_055366_055542_lanthipeptide

Lanthipeptides: allorf_055366_055542_lanthipeptide

4

VSLFSVGIGAWTRRGEAVLNNV

25

V ++ G+G+W RRG +++ +

12

VPVWGRGVGSWDRRGSVLVSGL

33

allorf_23698_23859

Leader:

MTPSRRPAHRLQPGRSPVLAG

Core:

PHSPSDAAHRSAVPHRDRCRSESIFELSSPRC

Core with dehydrations:

PHDhaPDhaDAAHRDhaAVPHRDRCysRDhaEDhaIFELDhaDhaPRCys

antiSMASH-DB 4.0 matches for allorf_23698_23859

21.2%

NZ_CP100763.1:

Lanthipeptides: NKH51_RS03980_lanthipeptide

6

DAAHRSAVPHRDRC

19

D AH HRD C

9

DEAHEETADHRDGC

22

20.9%

NZ_CP049945.1:

Lanthipeptides: allorf_6834514_6834684_lanthipeptide

10

RSAVPHRDRCRSESIFELSSPR

31

R AVP +DR + ++ L +PR

21

RRAVPVQDRPLAAAVRRLPAPR

42

15.6%

NC_021362.1and 25 others:

NC_021362.1 Lanthipeptides: allorf_0175505_0175678_lanthipeptideNZ_AP025342.1 Lanthipeptides: allorf_1470598_1470771_lanthipeptideNZ_AP025342.1 Lanthipeptides: allorf_1470598_1470771_lanthipeptideNZ_CABJBE010000012.1 Lanthipeptides: allorf_05598_05771_lanthipeptideNZ_CP010524.1 Lanthipeptides: allorf_0175655_0175828_lanthipeptideNZ_CP010524.1 Lanthipeptides: allorf_0175655_0175828_lanthipeptideNZ_CP020352.1 Lanthipeptides: allorf_0181382_0181555_lanthipeptideNZ_CP020352.1 Lanthipeptides: allorf_0181382_0181555_lanthipeptideNZ_CP023168.1 Lanthipeptides: allorf_0181439_0181612_lanthipeptideNZ_CP023168.1 Lanthipeptides: allorf_0181439_0181612_lanthipeptideNZ_CP118744.1 Lanthipeptides: allorf_0181347_0181520_lanthipeptideNZ_CP118744.1 Lanthipeptides: allorf_0181347_0181520_lanthipeptideNZ_JAHHXA010000013.1 Lanthipeptides: allorf_76220_76393_lanthipeptideNZ_JAHHXA010000013.1 Lanthipeptides: allorf_76220_76393_lanthipeptideNZ_KN125579.1 Lanthipeptides: allorf_0761255_0761428_lanthipeptideNZ_KN125579.1 Lanthipeptides: allorf_0761255_0761428_lanthipeptideNZ_NIKL01000035.1 Lanthipeptides: allorf_04826_04999_lanthipeptideNZ_NIKT01000033.1 Lanthipeptides: allorf_75882_76055_lanthipeptideNZ_NIKT01000033.1 Lanthipeptides: allorf_75882_76055_lanthipeptideNZ_NILF01000041.1 Lanthipeptides: allorf_04794_04967_lanthipeptideNZ_NILF01000041.1 Lanthipeptides: allorf_04794_04967_lanthipeptideNZ_NIMP01000010.1 Lanthipeptides: allorf_72951_73124_lanthipeptideNZ_NIMP01000010.1 Lanthipeptides: allorf_72951_73124_lanthipeptideNZ_NKBC01000001.1 Lanthipeptides: allorf_05089_05262_lanthipeptideNZ_QXII01000007.1 Lanthipeptides: allorf_05067_05240_lanthipeptide

Lanthipeptides: allorf_0175505_0175678_lanthipeptide

15

HRDRCRSESIFEL

27

H+ C+ +S+F L

7

HKVFCKGKSVFSL

19

with 2 more sequence matches

15.4%

NZ_CP102267.1:

Lanthipeptides: allorf_0904640_0904792_lanthipeptide

20

RSESIFELSSPRC

32

R+E +F L RC

6

RTEYVFILGEVRC

18

13.2%

NZ_AUBB01000029.1:

Lanthipeptides: G406_RS56815_lanthipeptide

6

DAAHRSAVPH

15

DA RSA PH

33

DAQQRSAFPH

42

allorf_26112_26252

Leader:

MSKYLWHLALREWLISLQGA

Core:

PEPLTCGEGDSREWVRWLRGRNEPLT

Core with dehydrations:

PEPLDhbCysGEGDDhaREWVRWLRGRNEPLDhb

antiSMASH-DB 4.0 matches for allorf_26112_26252

22.2%

NZ_LIPB01000002.1and 2 others:

NZ_LIPB01000002.1 Lanthipeptides: allorf_1142638_1142808_lanthipeptideNZ_LIPB01000002.1 Lanthipeptides: allorf_1142638_1142808_lanthipeptide

Lanthipeptides: allorf_1142638_1142808_lanthipeptide

1

PEPLTCGEGDSREWVRWLRGRNEP

24

P+P G G R+W+ L R EP

10

PQPPATGGGGFRKWL-LLDCRAEP

32

14.6%

NZ_CP025249.1and 1 other:

NZ_CP025249.1 Lanthipeptides: allorf_0098430_0098639_lanthipeptide

Lanthipeptides: allorf_0098430_0098639_lanthipeptide

5

TCGEGDSREWVRW

17

TC R W+RW

14

TCAVTSYRLWIRW

26

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26

Confidence: medium

Additional weak hits (8):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.22 out of 21.55

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.37 out of 30.25

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.57 out of 20.97

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.77 out of 21.55

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.42 out of 28.19

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.07 out of 30.11

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.74 out of 28.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.15 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Lanthipeptides

TFBS Finder

Core peptide predictions

CDS_08651 - Class II

Cleavage pHMM score: -5.30

RODEO score: 0

Monoisotopic mass: 4960.8 Da

Molecular weight: 4963.9 Da

Number of bridges: 1

Alternative weights: (assuming N unmodified Ser/Thr residues); 4981.9 Da N = 1; 4999.9 Da N = 2; 5017.9 Da N = 3

allorf_23698_23859 - Class II

Cleavage pHMM score: -6.00

RODEO score: 0

Monoisotopic mass: 3460.7 Da

Molecular weight: 3462.8 Da

Number of bridges: 2

Alternative weights: (assuming N unmodified Ser/Thr residues); 3480.8 Da N = 1; 3498.8 Da N = 2; 3516.8 Da N = 3; 3534.8 Da N = 4; 3552.9 Da N = 5

allorf_26112_26252 - Class II

Cleavage pHMM score: -5.90

RODEO score: 0

Monoisotopic mass: 2998.5 Da

Molecular weight: 3000.3 Da

Number of bridges: 1

Alternative weights: (assuming N unmodified Ser/Thr residues); 3018.3 Da N = 1; 3036.3 Da N = 2

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein

NPDC052558.ctg-0044 - Region 1 - T1PKS

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Location: 45,732 - 71,995 nt. (total: 26,264 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))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001275.3	0.77	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.77	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.77	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	0.67	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002192.3	0.61	PKS	FR901512	fungal sp. No.14919
BGC0001160.5	0.60	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002154.2	0.60	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001164.3	0.60	PKS	1-heptadecene	Cyanothece sp. PCC 7822

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001275.3	0.77	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.77	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.77	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	0.67	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0002192.3	0.61	PKS	FR901512	fungal sp. No.14919
BGC0001160.5	0.60	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0002154.2	0.60	PKS	1,3,5,8-tetrahydroxynapthalene, 1-(alpha-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene	Pyricularia oryzae 70-15
BGC0001164.3	0.60	PKS	1-heptadecene	Cyanothece sp. PCC 7822

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.18 out of 27.04

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.99 out of 20.47

Confidence: medium

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.86 out of 18.57

Confidence: medium

Additional weak hits (10):

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.11 out of 26.12

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.45 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.15 out of 29.38

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.52 out of 20.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.05 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.21 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 13.59 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.28 out of 26.06

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.00 out of 18.57

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 45731 - 71995:

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

Polymer prediction:: (pk)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_08848: pk

PKS_AT (540..829): pk

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 58.3%; Methylmalonyl-CoA: 54.2%; Ethylmalonyl-CoA: 54.2%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 103.6
Methoxymalonyl-CoA: 89.6
Ethylmalonyl-CoA: 76.9
Isobutyryl-CoA: 52.1
CHC-CoA: 51.4
2-Methylbutyryl-CoA: 50.2
trans-1,2-CPDA: 48.3
Propionyl-CoA: 46.7
Benzoyl-CoA: 42.4
Malonyl-CoA: 38.0
3-Methylbutyryl-CoA: 33.3
Acetyl-CoA: 24.7
fatty_acid: 24.4
inactive: 10.4

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
DasR	N-acetylglucosamine dependent repressor
ToxT	Regulator of MSHA biosynthesis
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0045 - Region 1 - NRPS,NRPS-like,other

Download region GenBank file

Download region SVG

Location: 6,208 - 64,790 nt. (total: 58,583 nt) Show pHMM detection rules used

other: (Neocarzinostat or bcpB or frbD or mitE or prnB or CaiA or bacilysin or orf2_PTase)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_08865: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_08870: acyl-CoA dehydrogenase type 2

smcogs: SMCOG1191: acyl-CoA dehydrogenase type 2

Transferases: glycosyltransferase

CDS_08881: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

Hydrolases: amidase hydrolase

CDS_08872: amidase

smcogs: SMCOG1105: amidase

CDS_08873: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

CDS_08886: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

CDS_08895: HAD-superfamily hydrolase, subfamily IA, variant

smcogs: SMCOG1115: HAD-superfamily hydrolase, subfamily IA, variant

Lyases: cyclase dehydratase

CDS_08857: diguanylate cyclase

smcogs: SMCOG1025: diguanylate cyclase

CDS_08871: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

CDS_08874: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_08875: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_08876: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_08879: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs: SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

CDS_08892: 1-deoxy-D-xylulose-5-phosphate synthase

smcogs: SMCOG1110: 1-deoxy-D-xylulose-5-phosphate synthase

CDS_08896: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	1.35	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	1.25	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	1.24	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001249.5	1.23	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002286.3	1.19	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	1.19	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	1.18	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	1.17	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001166.5	1.15	NRPS	HC-toxin	Alternaria jesenskae
BGC0002164.2	1.12	NRPS	peramine	Epichloe festucae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001534.3	0.81	other (other)	branched-chain fatty acids	Streptomyces filamentosus
BGC0001535.3	0.79	other (other)	branched-chain fatty acids	Streptomyces filamentosus
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002286.3	0.72	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.71	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.80 out of 20.47

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.13 out of 19.26

Confidence: medium

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 23.67 out of 30.11

Confidence: medium

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 28.14 out of 30.98

Confidence: medium

Additional weak hits (13):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.79 out of 27.78

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.74 out of 30.22

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.91 out of 27.04

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.46 out of 29.38

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 17.87 out of 24.78

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.34 out of 25.88

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.63 out of 25.75

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.31 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.20 out of 29.65

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 18.78 out of 24.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.63 out of 26.06

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 18.93 out of 29.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.52 out of 28.19

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

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Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 6207 - 64790:

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

Polymer prediction:: (Ala - Gly - X) + (Asn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 12078 - 61225:

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

Polymer prediction:: (Ala - Gly - X) + (Asn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 22966 - 64790:

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

Polymer prediction:: (Ala - Gly - X) + (Asn)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_08874: Ala - Gly - X

Search NORINE for peptide: strict or relaxed

AMP-binding (458..834): 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 (91% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1470..1842): 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:: DIVQLGVIWK
Nearest Stachelhaus code(s):: Gly DILQLGVIWK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2473..2846): X

nrpys: Hpg, 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:: N/A
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: DALHVGLLAK
Nearest Stachelhaus code(s):: Val DALFVGLVAK (47% 8Å match); Hpg DALHLGLLCK (41% 8Å match)
Stachelhaus code match:: 80% (moderate)

CDS_08876: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (16..400): 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:: DLTKVGEVAK
Nearest Stachelhaus code(s):: Asn DLTKVGEVGK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CelR	Cellobiose uptake repressor
NuR	Nickel-responsive regulator
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0046 - Region 1 - T2PKS,oligosaccharide

Download region GenBank file

Download region SVG

Location: 1 - 68,177 nt. (total: 68,177 nt) Show pHMM detection rules used

Region on contig edge.

T2PKS: (t2ks and t2clf)
oligosaccharide: (repeatable(3, [DUF1205, Glyco_transf_28, Glycos_transf_1, Glycos_transf_2, MGT]) and minscore(MGT, 150))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase oxygenase

CDS_08907: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

CDS_08908: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

CDS_08936: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_08944: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

CDS_08958: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

CDS_08960: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_08964: 3-hydroxyisobutyrate dehydrogenase

smcogs: SMCOG1100: 3-hydroxyisobutyrate dehydrogenase

CDS_08966: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: glycosyltransferase methyltransferase

CDS_08932: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_08933: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

CDS_08945: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_08954: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_08955: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_08956: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_08957: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

CDS_08961: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Lyases: cyclase dehydratase

CDS_08930: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_08931: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

CDS_08938: cyclase/dehydrase

smcogs: SMCOG1128: cyclase/dehydrase

CDS_08943: Polyketide synthesis cyclase

smcogs: SMCOG1225: Polyketide synthesis cyclase

Ligases: synthase

CDS_08940: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CDS_08941: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000231.5	0.77	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0001197.5	0.57	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0000234.5	0.51	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0001723.5	0.48	PKS	oviedomycin	Streptomyces antibioticus
BGC0000217.5	0.44	PKS	daunorubicin	Streptomyces sp.
BGC0000215.5	0.44	PKS	curamycin	Streptomyces cyaneus
BGC0000277.5	0.43	PKS	urdamycin	Streptomyces fradiae
BGC0000218.5	0.41	PKS	doxorubicin	Streptomyces peucetius
BGC0000271.5	0.40	PKS	spore pigment	Streptomyces avermitilis
BGC0000275.4	0.40	PKS	tetracenomycin C	Streptomyces glaucescens

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000231.5	0.71	PKS	griseusin A, griseusin B	Streptomyces griseus
BGC0001197.5	0.62	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0000234.5	0.59	PKS	jadomycin	Streptomyces venezuelae ATCC 10712
BGC0001723.5	0.57	PKS	oviedomycin	Streptomyces antibioticus
BGC0000217.5	0.55	PKS	daunorubicin	Streptomyces sp.
BGC0000215.5	0.55	PKS	curamycin	Streptomyces cyaneus
BGC0000277.5	0.55	PKS	urdamycin	Streptomyces fradiae
BGC0001895.4	0.54	PKS	huanglongmycin A, huanglongmycin B, huanglongmycin C	Streptomyces sp. CB09001
BGC0002047.2	0.54	PKS	brasiliquinone A, brasiliquinone B	Nocardia brasiliensis
BGC0001596.3	0.53	PKS	fluostatin M, fluostatin N, fluostatin O, fluostatin P, fluostatin Q	Streptomyces albus

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.06 out of 28.19

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 18.86 out of 25.31

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 21.42 out of 27.04

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.92 out of 20.47

Confidence: medium

Additional weak hits (10):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 14.00 out of 26.06

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.22 out of 21.55

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.25 out of 29.65

Confidence: weak

HypR

Description: L-hydroxyproline utilization repressor
Species: Streptomyces coelicolor
Score: 18.94 out of 22.40

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.64 out of 18.57

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 16.58 out of 26.12

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.40 out of 30.98

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.95 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.85 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.36 out of 29.65

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS substrates

Type II PKS

TFBS Finder

NRPS/PKS substrate predictions

CDS_08911: X

AMP-binding (132..292): 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:: DVCSQGNPVK
Nearest Stachelhaus code(s):: Trp DVASVGAVVK (38% 8Å match); Phe or Trp DVLSIGAVVK (35% 8Å match)
Stachelhaus code match:: 60% (weak)

Link to PARAS substrate predictor

Type II PKS gene cluster prediction details

Cluster section:: 0 to 68177
Starter unit(s):: acetyl-CoA (Score: 0.0; E-value: 0)
Malonyl elongations:: 11|12 (Score: 653.2; E-value: 2.7e-199)
Product class(es):: pentangular polyphenol
Product molecular weight(s):: acetyl-CoA_11: 1574 Da
acetyl-CoA_12: 1616 Da

CDS_08932: MET (Score: 35.9; E-value: 1e-11)
CDS_08933: MET C13O|C17O (Score: 450.9; E-value: 5.3e-138)
CDS_08936: KR C19 (Score: 407.9; E-value: 3.6e-125)
CDS_08938: CYC C9-C14 (Score: 243.8; E-value: 1.3e-75)
CDS_08939: ACP (Score: 80.7; E-value: 1.4e-25)
CDS_08940: CLF 11|12 (Score: 653.2; E-value: 2.7e-199)
CDS_08941: KS (Score: 741.3; E-value: 6.6e-226)
CDS_08942: CYC C5-C18 (Score: 222.2; E-value: 3.8e-69)
CDS_08943: CYC C4-C21/C2-C23|C2-C19 (Score: 158.2; E-value: 1.3e-49)
CDS_08944: OXY (Score: 313.7; E-value: 5.7e-96)
CDS_08945: GT (Score: 423.0; E-value: 3.5e-129)
CDS_08954: GT (Score: 429.3; E-value: 4.1e-131)
CDS_08955: GT (Score: 423.9; E-value: 1.8e-129)
CDS_08956: GT (Score: 437.0; E-value: 1.9e-133)
CDS_08957: GT (Score: 225.2; E-value: 4.2e-69)
CDS_08960: KR (Score: 110.6; E-value: 2.3e-34)
CDS_08961: GT (Score: 350.0; E-value: 5e-107)
CDS_08966: KR C11 (Score: 376.5; E-value: 1.2e-115)

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CatR	H2O2-responsive repressor
DasR	N-acetylglucosamine dependent repressor
VqsM	Regulator of quorum-sensing signalling systems
ZuR variant 1	Zinc-responsive repressor

NPDC052558.ctg-0048 - Region 1 - NRPS,lanthipeptide-class-i

Download region GenBank file

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Location: 10,871 - 62,898 nt. (total: 52,028 nt) Show pHMM detection rules used

Region on contig edge.

lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

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TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase reductase

CDS_09049: alkyl hydroperoxide reductase/ Thiol specific

smcogs: SMCOG1196: alkyl hydroperoxide reductase/ Thiol specific

CDS_09070: nucleotide sugar dehydrogenase

smcogs: SMCOG1152: nucleotide sugar dehydrogenase

Transferases: acylase aminotransferase methyltransferase transketolase

CDS_09037: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CDS_09047: transketolase

smcogs: SMCOG1204: transketolase

CDS_09071: methyltransferase

smcogs: SMCOG1248: methyltransferase

CDS_09074: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs: SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: deacetylase

CDS_09051: acetylornithine deacetylase

smcogs: SMCOG1247: acetylornithine deacetylase

Lyases: cyclase dehydratase

CDS_09044: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

CDS_09069: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase synthase

CDS_09034: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_09036: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

CDS_09060: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.36	NRPS	enniatin	Fusarium equiseti
BGC0001833.4	0.34	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.34	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002135.2	0.34	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.34	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.34	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.33	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.33	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.33	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.33	NRPS	AM-toxin	Alternaria alternata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001833.4	0.67	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.67	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.66	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.92 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.58 out of 23.79

Confidence: medium

Additional weak hits (8):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.18 out of 26.33

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 19.31 out of 31.73

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.24 out of 29.51

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 15.91 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.04 out of 29.38

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 17.11 out of 29.38

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.28 out of 32.93

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

Lanthipeptides

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Core peptide predictions

No core peptides found.

Predicted core structure(s)

For candidate cluster 1, location 10870 - 62898:

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

Polymer prediction:: (Cys - Gly)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 18786 - 62898:

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

Polymer prediction:: (Cys - Gly)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_09037: mal

PKS_AT (29..271): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 74.6
Methylmalonyl-CoA: 30.5
Methoxymalonyl-CoA: 27.9
inactive: 23.0
Propionyl-CoA: 20.0
Ethylmalonyl-CoA: 7.7
fatty_acid: 5.2
2-Methylbutyryl-CoA: 4.6
Isobutyryl-CoA: 2.4
CHC-CoA: 0.3
trans-1,2-CPDA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

CDS_09060: Cys - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (8..400): Cys

nrpys: Cys

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:: Polar, uncharged (aliphatic with -SH) (Cys)
Small clusters prediction:: Polar, uncharged (aliphatic with -SH) (Cys)
Single AA prediction:: Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:

Stachelhaus sequence:: DLYHVSMINK
Nearest Stachelhaus code(s):: Cys DLYNMSMIWK (68% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (1064..1442): 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:: DILQLGLIWK
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0051 - Region 1 - terpene-precursor

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Location: 35,514 - 56,662 nt. (total: 21,149 nt) Show pHMM detection rules used

terpene-precursor: (PT_FPPS_like and not PT_HPP)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

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resistance

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Gene details

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Gene overview

Tailoring

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Terpene

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_09210: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

Transferases: acyltransferase

CDS_09211: acyltransferase

smcogs: SMCOG1141: acyltransferase

Ligases: synthetase

CDS_09209: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000664.5	0.49	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3	0.49	terpene	isorenieratene	Streptomyces argillaceus
BGC0000633.3	0.47	terpene	carotenoid	Streptomyces avermitilis
BGC0001227.3	0.47	terpene	isorenieratene	Streptomyces collinus Tu 365
BGC0000649.3	0.45	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000677.5	0.42	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000648.3	0.42	terpene	carotenoid	Myxococcus xanthus
BGC0001910.4	0.39	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0001911.3	0.38	terpene	raimonol	Streptomyces anulatus
BGC0002309.2	0.37	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000664.5	0.49	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001456.3	0.49	terpene	isorenieratene	Streptomyces argillaceus
BGC0000633.3	0.47	terpene	carotenoid	Streptomyces avermitilis
BGC0001227.3	0.47	terpene	isorenieratene	Streptomyces collinus Tu 365
BGC0000649.3	0.45	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000677.5	0.42	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0000648.3	0.42	terpene	carotenoid	Myxococcus xanthus
BGC0001910.4	0.39	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0001911.3	0.38	terpene	raimonol	Streptomyces anulatus
BGC0002309.2	0.37	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

Class	Product name	Chain length	Initial cyclisations	Functional groups
sesquiterpene precursor	FPP	C15	acyclic	PP
diterpene precursor	GGPP	C20	acyclic	PP
sesterterpene precursor	GFPP	C25	acyclic	PP
triterpene precursor	HPP	C30	acyclic	PP

Genes with terpene domains:

CDS_09209: PT_FPPS_like

Domain 1 (64 - 366): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

Reactions:: IPP, DMAPP → FPP; IPP, DMAPP → GGPP; IPP, DMAPP → GFPP; IPP, DMAPP → HPP

Transcription Factor Binding Sites

Binding sites found:

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 25.27 out of 29.65

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.07 out of 24.78

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.94 out of 23.43

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.18 out of 20.47

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.21 out of 23.79

Confidence: medium

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 25.84 out of 30.12

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.02 out of 26.85

Confidence: medium

Additional weak hits (4):

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.94 out of 23.43

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.78 out of 29.65

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 19.62 out of 27.04

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
GFPP	Geranylfarnesyl diphosphate
GGPP	Geranylgeranyl diphosphate
HPP	Hexaprenyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
BldD	Development and antibiotic global regulator
IolR	Regulator of the inositol catabolism
LexA variant 1	Repressor of DNA damage response
LexA variant 2	Repressor of DNA damage response
OsdR	Development and stress management regulator
RutR	Regulator of the pyrimidine and purine metabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0052 - Region 1 - HR-T2PKS,NRPS,NRPS-like

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Location: 1 - 44,563 nt. (total: 44,563 nt) Show pHMM detection rules used

Region on contig edge.

NRPS-like: cds((PP-binding or NAD_binding_4) and (AMP-binding or A-OX) and not alpha_am_amid)
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
HR-T2PKS: (hr-t2pks-ksa and (t2fas or APE_KS2 or ketoacyl-synt))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

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KnownClusterBlast

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TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxygenase

CDS_09220: Dioxygenase TauD/TfdA

smcogs: SMCOG1046: Dioxygenase TauD/TfdA

CDS_09226: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_09233: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_09242: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

Transferases: methyltransferase

CDS_09239: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: deaminase esterase

CDS_09221: ornithine cyclodeaminase

smcogs: SMCOG1158: ornithine cyclodeaminase

CDS_09224: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase synthase

CDS_09222: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

CDS_09223: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_09225: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_09229: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_09230: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	1.34	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002075.3	1.31	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002286.3	1.25	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	1.25	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	1.22	NRPS	AM-toxin	Alternaria alternata
BGC0001833.4	1.22	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	1.22	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001249.5	1.21	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002135.2	1.16	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	1.13	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002075.3	0.75	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0002286.3	0.73	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.73	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.72	NRPS	AM-toxin	Alternaria alternata
BGC0001833.4	0.72	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001249.5	0.72	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002135.2	0.71	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.70	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.99 out of 20.97

Confidence: medium

Additional weak hits (6):

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 13.92 out of 18.57

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 15.52 out of 20.97

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.72 out of 30.25

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.34 out of 29.65

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.66 out of 33.14

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.35 out of 32.93

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 44563:

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

Polymer prediction:: (Val) + (X - X - Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 0 - 40882:

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

Polymer prediction:: (Val) + (X - X - Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 3, location 0 - 37670:

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

Polymer prediction:: (Val) + (X - X - Asp)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 4, location 2269 - 44563:

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

Polymer prediction:: (Val) + (X - X - Asp)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_09223: X - X - Asp

Search NORINE for peptide: strict or relaxed

AMP-binding (456..846): 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 (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2117..2503): 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 (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3146..3528): Asp

nrpys: Asp

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:: DLTKLGVVNK
Nearest Stachelhaus code(s):: Asp DLTKLGVVNK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

CDS_09225: Val

Search NORINE for peptide: strict or relaxed

AMP-binding (284..661): 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:: 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:: DFWNVGMVHK
Nearest Stachelhaus code(s):: Val DFWNVGMVHK (94% 8Å match); Thr DFWNVGMVHK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A

NPDC052558.ctg-0054 - Region 1 - NRPS

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Location: 1 - 52,097 nt. (total: 52,097 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

reset view

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

Pfam domains

TIGRFAM domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidase oxygenase

CDS_09316: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

CDS_09317: cytochrome P450

smcogs: SMCOG1007: cytochrome P450

CDS_09323: aldehyde oxidase and xanthine dehydrogenase

smcogs: SMCOG1293: aldehyde oxidase and xanthine dehydrogenase

CDS_09324: pyruvate oxidase/decarboxylase

smcogs: SMCOG1055: pyruvate oxidase/decarboxylase

CDS_09339: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase halogenase methyltransferase

CDS_09314: methyltransferase

smcogs: SMCOG1089: methyltransferase

CDS_09333: halogenase

smcogs: SMCOG1119: halogenase

CDS_09342: DegT/DnrJ/EryC1/StrS aminotransferase

smcogs: SMCOG1056: DegT/DnrJ/EryC1/StrS aminotransferase

Hydrolases: esterase phosphatase

CDS_09329: thioesterase

smcogs: SMCOG1004: thioesterase

CDS_09340: inositol monophosphatase

smcogs: SMCOG1207: inositol monophosphatase

Lyases: dehydratase

CDS_09343: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Ligases: ligase

CDS_09326: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_09327: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_09331: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_09332: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_09337: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_09338: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CDS_09344: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
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
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001133.4	0.65	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.65	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.65	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.65	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.65	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Reference	Similarity score	Type	Compound(s)	Organism
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
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001133.4	0.65	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.65	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.65	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.65	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.65	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 18.79 out of 23.79

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.52 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.42 out of 20.47

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.40 out of 19.26

Confidence: medium

Additional weak hits (12):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.11 out of 26.33

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 17.22 out of 31.73

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.14 out of 21.84

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 16.50 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.73 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 13.59 out of 28.14

Confidence: weak

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 16.21 out of 20.97

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 18.92 out of 26.33

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.14 out of 27.04

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.33 out of 25.75

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 17.62 out of 26.12

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 16.73 out of 28.19

Confidence: weak

Module view

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Detailed Pfam domain annotation

Selected features only

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Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 52097:

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

Polymer prediction:: (X - D-X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_09326: X - X

AMP-binding (7..393): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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:: ALLPLGTSVK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

AMP-binding (1052..1355): X

nrpys: Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr

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:: DRA-VAEPVK
Nearest Stachelhaus code(s):: His DSALVAEVWK (26% 8Å match); Trp DVAVVGEVVK (24% 8Å match)
Stachelhaus code match:: 60% (weak)

CDS_09327: X

AMP-binding (399..673): 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:: Polar, uncharged (aliphatic with -SH) (Cys)
Small clusters prediction:: Polar, uncharged (aliphatic with -SH) (Cys)
Single AA prediction:: Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:

Stachelhaus sequence:: DLYDLSLVWK
Nearest Stachelhaus code(s):: Cys DLYNLSLVWK (65% 8Å match)
Stachelhaus code match:: 90% (moderate)

CDS_09332: X

AMP-binding (24..383): 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:: DMGAIGALAK
Nearest Stachelhaus code(s):: Phe DAGALGACAK (35% 8Å match)
Stachelhaus code match:: 70% (weak)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems

NPDC052558.ctg-0055 - Region 1 - RiPP-like

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Location: 35,830 - 46,645 nt. (total: 10,816 nt) Show pHMM detection rules used

Region on contig edge.

RiPP-like: (strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Cloacin or Linocin_M18 or TIGR03651 or TIGR03693 or TIGR03601 or TIGR03795 or TIGR03975 or DUF692 or TIGR01193 or (YcaO or TIGR03604))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

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MIBiG comparison

ClusterBlast

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SubClusterBlast

TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase

CDS_09387: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000706.3	0.38	saccharide	kanamycin	Streptomyces kanamyceticus
BGC0002284.3	0.37	other (other)	corynecin III, corynecin I, corynecin II	Rhodococcus sp. H-CA8f
BGC0000131.5	0.33	PKS	pyrrolomycin	Streptomyces sp. UC 11065
BGC0002535.2	0.32	NRPS	γ-poly-L-2,4-diaminobutyric acid	Streptomyces celluloflavus
BGC0000274.5	0.30	PKS	tetarimycin A, tetarimycin B	uncultured bacterium
BGC0002147.2	0.30	NRPS	bohemamine A, bohemamine B, bohemamine C	Streptomyces sp. CB02009
BGC0000595.3	0.29	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0002091.3	0.29	NRPS	holomycin	Yersinia ruckeri ATCC 29473
BGC0002381.3	0.28	PKS, other (other)	tambjamine BE-18591	Streptomyces albus subsp. albus
BGC0000373.5	0.28	NRPS	holomycin	Streptomyces clavuligerus ATCC 27064

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000706.3	0.38	saccharide	kanamycin	Streptomyces kanamyceticus
BGC0002284.3	0.37	other (other)	corynecin III, corynecin I, corynecin II	Rhodococcus sp. H-CA8f
BGC0000131.5	0.33	PKS	pyrrolomycin	Streptomyces sp. UC 11065
BGC0002535.2	0.32	NRPS	γ-poly-L-2,4-diaminobutyric acid	Streptomyces celluloflavus
BGC0000274.5	0.30	PKS	tetarimycin A, tetarimycin B	uncultured bacterium
BGC0002147.2	0.30	NRPS	bohemamine A, bohemamine B, bohemamine C	Streptomyces sp. CB02009
BGC0000595.3	0.29	ribosomal	SCO-2138	Streptomyces coelicolor A3(2)
BGC0002091.3	0.29	NRPS	holomycin	Yersinia ruckeri ATCC 29473
BGC0002381.3	0.28	PKS, other (other)	tambjamine BE-18591	Streptomyces albus subsp. albus
BGC0000373.5	0.28	NRPS	holomycin	Streptomyces clavuligerus ATCC 27064

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 25.15 out of 29.65

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.93 out of 24.78

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.25 out of 29.72

Confidence: medium

Additional weak hits (8):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.99 out of 26.06

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 16.68 out of 29.25

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.77 out of 25.88

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.52 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 17.81 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 18.98 out of 36.54

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.82 out of 29.65

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 16.64 out of 21.84

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

TFBS Finder

TFBS definitions

Regulator	Description
LexA variant 1	Repressor of DNA damage response
LexA variant 2	Repressor of DNA damage response
NtrC	Nitrogen regulatory protein C

NPDC052558.ctg-0060 - Region 1 - PKS-like,T1PKS,amglyccycl

Download region GenBank file

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Location: 1 - 28,309 nt. (total: 28,309 nt) Show pHMM detection rules used

Region on contig edge.

PKS-like: (t2pks2 or ksIII)
T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
amglyccycl: (DOIS or ValA or salQ or strH or strK1 or strK2 or NeoL or SpcFG or SpcDK_glyc)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

KnownClusterBlast

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TFBS Finder

NRPS/PKS modules

Pfam domains

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Oxidoreductases: dehydrogenase oxidase

CDS_09536: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CDS_09537: FAD linked oxidase domain protein

smcogs: SMCOG1138: FAD linked oxidase domain protein

Ligases: ligase synthase

CDS_09538: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CDS_09539: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CDS_09542: 3-oxoacyl-(acyl carrier protein) synthase III

smcogs: SMCOG1084: 3-oxoacyl-(acyl carrier protein) synthase III

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001275.3	1.45	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	1.44	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	1.43	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	1.05	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002191.2	0.89	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001284.4	0.87	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001254.3	0.85	PKS	ACT-Toxin II	Alternaria alternata
BGC0002192.3	0.84	PKS	FR901512	fungal sp. No.14919
BGC0001160.5	0.83	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001268.4	0.81	NRPS, PKS	fusarin C	Fusarium fujikuroi

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001275.3	0.78	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.77	PKS	asperlactone	Aspergillus ochraceus
BGC0001244.3	0.77	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001276.3	0.68	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0002191.2	0.63	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1
BGC0001284.4	0.62	PKS	alternariol	Parastagonospora nodorum SN15
BGC0001254.3	0.62	PKS	ACT-Toxin II	Alternaria alternata
BGC0002192.3	0.62	PKS	FR901512	fungal sp. No.14919
BGC0001160.5	0.61	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001268.4	0.61	NRPS, PKS	fusarin C	Fusarium fujikuroi

Similar known clusters

Similar known clusters from MIBiG 4.0

Similar subclusters

Transcription Factor Binding Sites

Binding sites found:

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.68 out of 19.52

Confidence: medium

Additional weak hits (2):

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.13 out of 39.62

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.16 out of 30.22

Confidence: weak

Module view

Legend

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 28309:

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

Polymer prediction:: (pk)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

CDS_09538: pk

PKS_AT (527..820): pk

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; Methylmalonyl-CoA: 75.0%; Propionyl-CoA: 66.7%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 110.5
Methoxymalonyl-CoA: 98.8
Malonyl-CoA: 92.1
Ethylmalonyl-CoA: 80.5
Propionyl-CoA: 45.6
Isobutyryl-CoA: 45.5
2-Methylbutyryl-CoA: 43.1
trans-1,2-CPDA: 42.7
3-Methylbutyryl-CoA: 32.6
Benzoyl-CoA: 29.0
Acetyl-CoA: 27.5
fatty_acid: 22.7
CHC-CoA: 16.0
inactive: 15.1

CDS_09539: X

AMP-binding (27..435): X

nrpys: Sal

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
Small clusters prediction:: Hydroxy-benzoic acid derivates (diOH-Bz, Sal)
Single AA prediction:: dhb (diOH-Bz)

Stachelhaus prediction details:

Stachelhaus sequence:: PLPAQGVLNK
Nearest Stachelhaus code(s):: Sal PLPAQGVLNK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production

NPDC052558.ctg-0063 - Region 1 - RRE-containing

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Location: 1 - 20,201 nt. (total: 20,201 nt) Show pHMM detection rules used

Region on contig edge.

RRE-containing: minimum(1, [Bottromycin_Methyltransferase_RRE, Cyanobactin_D_RRE, Cytolysin_C_RRE, Goadsporin_CD_RRE, Heterocycloanthracin_C_RRE, Lanthipeptide_LanB_RRE, Lasso_Fused_RRE, Mycofactocin_RRE, NHLP_CD_RRE, Other_Sactipeptide_rSAM_RRE, Pantocin_Microcin_RRE, Plantazolicin_C_RRE, PlpY_RRE, PqqD_RRE, Proteusin_Epimerase_RRE, Proteusin_Methyltransferase_RRE, Quinohemoprotein_rSAM_RRE, Ranthipeptide_rSAM_RRE, Stand_Alone_Lasso_RRE, Streptide_RRE, Subtilosin_rSAM_RRE, Thiaglutamate_B_RRE, Thiaglutamate_G_RRE, Thiaglutamate_I_RRE, Thiopeptide_F_RRE, Thuricin_rSAM_RRE, Thurincin_rSAM_RRE, Trifolitoxin_RRE])

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

TTA codons

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

ClusterBlast

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TFBS Finder

Pfam domains

TIGRFAM domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

Identifier	Product	Length		Function	Sequence		NCBI Blast	Filter details
		NT	AA		NT	AA

Tailoring functions

Hydrolases: hydrolase peptidase

CDS_09604: gamma-glutamyltranspeptidase

smcogs: SMCOG1274: gamma-glutamyltranspeptidase

CDS_09605: alpha/beta hydrolase fold protein

smcogs: SMCOG1036: alpha/beta hydrolase fold protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000585.5	0.46	ribosomal	microcin C7	Escherichia coli
BGC0002407.3	0.43	other (other), saccharide	angustmycin A, angustmycin C	Streptomyces angustmyceticus
BGC0002621.2	0.39	other (other)	angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine	Streptomyces angustmyceticus
BGC0001485.4	0.34	other (other)	chuangxinmycin	Actinoplanes tsinanensis
BGC0000249.5	0.33	PKS	nogalamycin	Streptomyces nogalater
BGC0001591.4	0.32	other (other)	fatty acid enol ester, N-tetradecanoyl tyrosine	uncultured bacterium CSLC2
BGC0000916.5	0.32	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0000306.5	0.31	NRPS	arylomycin	Streptomyces filamentosus NRRL 11379
BGC0001565.4	0.28	NRPS	cyclosporin C	Beauveria felina
BGC0001190.3	0.28	PKS	fusaric acid	Fusarium verticillioides 7600

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000585.5	0.46	ribosomal	microcin C7	Escherichia coli
BGC0002407.3	0.43	other (other), saccharide	angustmycin A, angustmycin C	Streptomyces angustmyceticus
BGC0002621.2	0.39	other (other)	angustmycin A, angustmycin B, angustmycin C, aristeromycin, arabinofuranosyladenine	Streptomyces angustmyceticus
BGC0001485.4	0.34	other (other)	chuangxinmycin	Actinoplanes tsinanensis
BGC0000249.5	0.33	PKS	nogalamycin	Streptomyces nogalater
BGC0001591.4	0.32	other (other)	fatty acid enol ester, N-tetradecanoyl tyrosine	uncultured bacterium CSLC2
BGC0000916.5	0.32	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0000306.5	0.31	NRPS	arylomycin	Streptomyces filamentosus NRRL 11379
BGC0001565.4	0.28	NRPS	cyclosporin C	Beauveria felina
BGC0001190.3	0.28	PKS	fusaric acid	Fusarium verticillioides 7600

Similar known clusters

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (7):

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 15.91 out of 21.84

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 14.45 out of 18.57

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 15.20 out of 26.06

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 17.15 out of 30.97

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 15.02 out of 21.55

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 17.01 out of 28.19

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.08 out of 28.19

Confidence: weak

Detailed Pfam domain annotation

Selected features only

Expand to show all names

Detailed TIGRFAM domain annotation

Selected features only

Expand to show all names

RREFinder

TFBS Finder

RRE predictions

: RRE type: Pantocin_Microcin_RRE; Location: 0 - 82; Score: 30.3

TFBS definitions

Regulator	Description