GCF_015040335.1 - 7 region(s) - antiSMASH results

Identified secondary metabolite regions using strictness 'relaxed'

NZ_CP053549.1 (Paenarthrobacter sp. YJN-D)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1.1	RiPP-like	41,807	53,198	Low	streptamidine	ribosomal:unmodified
Region 1.2	lassopeptide	103,547	125,938	Low	siamycin	ribosomal:RiPP
Region 1.3	betalactone,terpene-precursor	211,439	247,886
Region 1.4	T3PKS	712,731	753,867
Region 1.5	NI-siderophore	1,149,873	1,179,714	High	desferrioxamine E	other:other
Region 1.6	terpene	1,200,932	1,226,201	Low	carotenoid	terpene
Region 1.7	NAPAA	2,539,183	2,573,139	Low	stenothricin	NRPS:Type I

No secondary metabolite regions were found in these records:: NZ_CP053550.1 (Paenarthrobacter sp. YJN-D); NZ_CP053551.1 (Paenarthrobacter sp. YJN-D); NZ_CP053552.1 (Paenarthrobacter sp. YJN-D)

Compact view

NZ_CP053549.1 - Region 1 - RiPP-like

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Location: 41,807 - 53,198 nt. (total: 11,392 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:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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Gene details

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Gene overview

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MIBiG comparison

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SubClusterBlast

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Gene/CDS overview

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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
BGC0002115.3	0.51	ribosomal	streptamidine	Streptomyces albidoflavus J1074
BGC0001638.4	0.51	ribosomal	klebsazolicin	Klebsiella pneumoniae subsp. ozaenae
BGC0000551.5	0.50	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000501.3	0.48	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0002698.2	0.47	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0002306.2	0.43	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0001555.4	0.42	ribosomal	colicin V	Escherichia coli chi7122
BGC0000513.3	0.41	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0001639.3	0.40	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0000588.5	0.40	ribosomal	microcin L	Escherichia coli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002115.3	0.51	ribosomal	streptamidine	Streptomyces albidoflavus J1074
BGC0001638.4	0.51	ribosomal	klebsazolicin	Klebsiella pneumoniae subsp. ozaenae
BGC0000551.5	0.50	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000501.3	0.48	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0002698.2	0.47	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0002306.2	0.43	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0001555.4	0.42	ribosomal	colicin V	Escherichia coli chi7122
BGC0000513.3	0.41	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0001639.3	0.40	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0000588.5	0.40	ribosomal	microcin L	Escherichia coli

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

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

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 27.61 out of 32.74

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.14 out of 29.38

Confidence: medium

CatR

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

Confidence: medium

Additional weak hits (7):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.46 out of 27.55

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.55 out of 29.25

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.22 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 18.30 out of 29.38

Confidence: weak

MatP

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

Confidence: weak

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 15.11 out of 18.57

Confidence: weak

ZuR variant 1

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

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
CatR	H2O2-responsive repressor
FuR variant 1	Ferric Uptake Regulator
FuR variant 2	Ferric Uptake Regulator

NZ_CP053549.1 - Region 2 - lassopeptide

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Location: 103,547 - 125,938 nt. (total: 22,392 nt) Show pHMM detection rules used

lassopeptide: (PF13471 and Asn_synthase or micJ25 or mcjC)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

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resistance

binding site

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Gene/CDS overview

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

Tailoring functions

Oxidoreductases: oxidoreductase

HMI60_RS00590: dihydropteridine reductase

smcogs: SMCOG1159: dihydropteridine reductase

Hydrolases: hydrolase

HMI60_RS00565: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: dehydratase

HMI60_RS00510: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001634.3	0.62	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0001176.4	0.61	ribosomal	streptomonomicin	Streptomonospora alba
BGC0001645.3	0.60	ribosomal	lagmysin	Streptomyces sp. NRRL S-118
BGC0001493.5	0.58	ribosomal	achromosin	Streptomyces achromogenes subsp. achromogenes
BGC0002053.3	0.58	ribosomal	ulleungdin	Streptomyces sp.
BGC0001506.5	0.58	ribosomal	anantin B1, anantin B2	Streptomyces sp. NRRL S-146
BGC0001779.5	0.56	ribosomal	siamycin	Streptomyces nodosus
BGC0001307.3	0.56	ribosomal	chaxapeptin	Streptomyces leeuwenhoekii
BGC0002074.2	0.56	ribosomal	huascopeptin	Streptomyces huasconensis
BGC0001655.3	0.56	ribosomal	LP2006	Nocardiopsis alba DSM 43377

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001634.3	0.62	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0001176.4	0.61	ribosomal	streptomonomicin	Streptomonospora alba
BGC0001645.3	0.60	ribosomal	lagmysin	Streptomyces sp. NRRL S-118
BGC0001493.5	0.58	ribosomal	achromosin	Streptomyces achromogenes subsp. achromogenes
BGC0002053.3	0.58	ribosomal	ulleungdin	Streptomyces sp.
BGC0001506.5	0.58	ribosomal	anantin B1, anantin B2	Streptomyces sp. NRRL S-146
BGC0001779.5	0.56	ribosomal	siamycin	Streptomyces nodosus
BGC0001307.3	0.56	ribosomal	chaxapeptin	Streptomyces leeuwenhoekii
BGC0002074.2	0.56	ribosomal	huascopeptin	Streptomyces huasconensis
BGC0001655.3	0.56	ribosomal	LP2006	Nocardiopsis alba DSM 43377

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lasso peptide predictions

Lassopeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: medium

Additional weak hits (4):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.21 out of 26.33

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.60 out of 26.06

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.31 out of 29.38

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 19.26 out of 33.14

Confidence: weak

Lasso peptides

RREFinder

TFBS Finder

Core peptide predictions

No core peptides found.

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 14 - 97; Score: 58.3

TFBS definitions

Regulator	Description
VqsM	Regulator of quorum-sensing signalling systems

NZ_CP053549.1 - Region 3 - betalactone,terpene-precursor

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Location: 211,439 - 247,886 nt. (total: 36,448 nt) Show pHMM detection rules used

betalactone: (HMGL-like and AMP-binding)
terpene-precursor: (PT_FPPS_like and not PT_HPP)

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core biosynthetic genes

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transport-related genes

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Terpene

TFBS Finder

Gene/CDS overview

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

Tailoring functions

Transferases: acyltransferase carboxylase

HMI60_RS01085: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

HMI60_RS01115: acyltransferase

smcogs: SMCOG1141: acyltransferase

Ligases: ligase synthetase

HMI60_RS01090: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

HMI60_RS01140: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000936.5	0.23	other (other)	pyocyanine	Pseudomonas aeruginosa PAO1
BGC0002274.2	0.23	NRPS	aspulvinone H, aspulvinone B1	Aspergillus terreus NIH2624
BGC0002561.3	0.22	other (other)	phenazine SA, phenazine SB, phenazine SC	Streptomyces sp.
BGC0001521.3	0.20	NRPS	auriculamide	Herpetosiphon aurantiacus DSM 785
BGC0001221.5	0.19	other (phenazine)	marinophenazine A, phenaziterpene A	Streptomyces sp. CNQ-509
BGC0001444.5	0.19	other (shikimate-derived)	caboxamycin	Streptomyces sp. NTK 937
BGC0000935.5	0.17	PKS, other (aminocoumarin)	esmeraldin	Streptomyces antibioticus
BGC0002492.3	0.17	NRPS	myxochelin B, myxochelin A	Myxococcus xanthus DK 1622
BGC0001080.5	0.17	other (phenazine)	endophenazine A, endophenazine B	Streptomyces anulatus
BGC0000934.4	0.17	other (phenazine)	5-acetyl-5,10-dihydrophenazine-1-carboxylic acid, 5-(2-hydroxyacetyl)-5,10-dihydrophenazine-1-carboxylic acid, endophenazine A1, endophenazine F, endophenazine G	Kitasatospora sp. HKI 714

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002274.2	0.56	NRPS	aspulvinone H, aspulvinone B1	Aspergillus terreus NIH2624
BGC0002309.2	0.47	terpene	cattleyene	Streptomyces cattleya NRRL 8057 = DSM 46488
BGC0000677.5	0.46	terpene	cyclooctatin	Streptomyces melanosporofaciens
BGC0001910.4	0.43	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0000664.5	0.43	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0001911.3	0.43	terpene	raimonol	Streptomyces anulatus
BGC0001456.3	0.42	terpene	isorenieratene	Streptomyces argillaceus
BGC0000649.3	0.42	terpene	carotenoid	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002284.3	0.42	other (other)	corynecin III, corynecin I, corynecin II	Rhodococcus sp. H-CA8f
BGC0000633.3	0.42	terpene	carotenoid	Streptomyces avermitilis

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:

HMI60_RS01140: PT_FPPS_like

Domain 1 (52 - 342): 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:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.45 out of 29.72

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.74 out of 29.72

Confidence: medium

Additional weak hits (7):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.59 out of 30.22

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.45 out of 30.97

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.81 out of 27.78

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 23.13 out of 29.51

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.55 out of 30.22

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.87 out of 30.25

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 18.50 out of 28.19

Confidence: weak

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
NtrC	Nitrogen regulatory protein C

NZ_CP053549.1 - Region 4 - T3PKS

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Location: 712,731 - 753,867 nt. (total: 41,137 nt) Show pHMM detection rules used

T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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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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

HMI60_RS03410: monooxygenase FAD-binding

smcogs: SMCOG1050: monooxygenase FAD-binding

Transferases: methyltransferase

HMI60_RS03390: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: deformylase

HMI60_RS03400: peptide deformylase

smcogs: SMCOG1275: peptide deformylase

Ligases: synthase

HMI60_RS03370: polyprenol-monophosphomannose synthase ppm1

smcogs: SMCOG1123: polyprenol-monophosphomannose synthase ppm1

HMI60_RS03420: 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	0.54	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
BGC0001962.3	0.51	PKS	hierridin B, hierridin C	Cyanobium sp. LEGE 06113
BGC0002403.2	0.49	PKS	β-Diketones	Hordeum vulgare subsp. vulgare
BGC0002332.2	0.48	PKS	4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A	Candidatus Entotheonella sp.
BGC0001831.3	0.45	PKS	alkylpyrone-407, alkylpyrone-393	Myxococcus xanthus DK 1622
BGC0001336.5	0.42	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0001903.3	0.40	other (other)	neocarazostatin A	Streptomyces sp. MA37
BGC0002482.2	0.37	other (other)	tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M	Symphyonema bifilamentata 97.28
BGC0001964.2	0.36	PKS	alkylpyrone-407, alkylpyrone-393	Cystobacterineae bacterium
BGC0001886.2	0.36	PKS	Secalonic acid B, Secalonic acid A, Secalonic acid C, Endocrocin, Clavorubin	Claviceps purpurea 20.1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000282.3	0.54	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
BGC0001962.3	0.51	PKS	hierridin B, hierridin C	Cyanobium sp. LEGE 06113
BGC0002403.2	0.49	PKS	β-Diketones	Hordeum vulgare subsp. vulgare
BGC0002332.2	0.48	PKS	4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A	Candidatus Entotheonella sp.
BGC0001831.3	0.45	PKS	alkylpyrone-407, alkylpyrone-393	Myxococcus xanthus DK 1622
BGC0001336.5	0.42	other (other)	erdasporine A, erdasporine B, erdasporine C	uncultured bacterium
BGC0001903.3	0.40	other (other)	neocarazostatin A	Streptomyces sp. MA37
BGC0002482.2	0.37	other (other)	tjipanazole D, tjipanazole I, tjipanazole L, tjipanazole K, tjipanazole M	Symphyonema bifilamentata 97.28
BGC0001964.2	0.36	PKS	alkylpyrone-407, alkylpyrone-393	Cystobacterineae bacterium
BGC0001886.2	0.36	PKS	Secalonic acid B, Secalonic acid A, Secalonic acid C, Endocrocin, Clavorubin	Claviceps purpurea 20.1

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

AbrC3

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

Confidence: strong

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 20.58 out of 23.05

Confidence: strong

VqsM

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

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 25.46 out of 27.04

Confidence: strong

Additional weak hits (5):

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 19.61 out of 26.33

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.09 out of 29.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 16.83 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 19.71 out of 30.25

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 20.95 out of 35.63

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
AfsR	Pleiotropic regulatory for antibiotic production
DasR	N-acetylglucosamine dependent repressor
VqsM	Regulator of quorum-sensing signalling systems

NZ_CP053549.1 - Region 5 - NI-siderophore

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Location: 1,149,873 - 1,179,714 nt. (total: 29,842 nt) Show pHMM detection rules used

NI-siderophore: IucA_IucC

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

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

HMI60_RS05470: lysine/ornithine N-monooxygenase

smcogs: SMCOG1080: lysine/ornithine N-monooxygenase

HMI60_RS05495: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: aminotransferase

HMI60_RS05535: aminotransferase

smcogs: SMCOG1019: aminotransferase

Lyases: decarboxylase

HMI60_RS05465: Decarboxylase, pyridoxal-dependent

smcogs: SMCOG1180: Decarboxylase, pyridoxal-dependent

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001478.5	0.81	other (other)	desferrioxamine E	Streptomyces sp. ID38640
BGC0000941.3	0.75	other (other)	desferrioxamin B	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2	0.71	other (other)	legonoxamine A, desferrioxamine B, legonoxamine B	Streptomyces sp.
BGC0001572.3	0.70	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0000940.5	0.65	other (other)	desferrioxamin B, desferrioxamine E	Streptomyces coelicolor A3(2)
BGC0002620.2	0.60	other (other)	fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4	Fulvivirga marina
BGC0001453.5	0.58	other (other)	desferrioxamine	Streptomyces argillaceus
BGC0002464.3	0.56	other (other)	alcaligin	Bordetella pertussis Tohama I
BGC0001531.5	0.55	other (other)	bisucaberin B	Tenacibaculum mesophilum
BGC0000244.4	0.55	PKS	nonactin, monactin, dinactin, trinactin, tetranactin	Streptomyces griseus subsp. griseus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001478.5	0.81	other (other)	desferrioxamine E	Streptomyces sp. ID38640
BGC0000941.3	0.75	other (other)	desferrioxamin B	Streptomyces griseus subsp. griseus NBRC 13350
BGC0002305.2	0.71	other (other)	legonoxamine A, desferrioxamine B, legonoxamine B	Streptomyces sp.
BGC0001572.3	0.70	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0000940.5	0.65	other (other)	desferrioxamin B, desferrioxamine E	Streptomyces coelicolor A3(2)
BGC0002620.2	0.60	other (other)	fulvivirgamide A2, fulvivirgamide B2, fulvivirgamide B3, fulvivirgamide B4	Fulvivirga marina
BGC0001453.5	0.58	other (other)	desferrioxamine	Streptomyces argillaceus
BGC0002464.3	0.56	other (other)	alcaligin	Bordetella pertussis Tohama I
BGC0001531.5	0.55	other (other)	bisucaberin B	Tenacibaculum mesophilum
BGC0000244.4	0.55	PKS	nonactin, monactin, dinactin, trinactin, tetranactin	Streptomyces griseus subsp. griseus

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: 17.92 out of 20.47

Confidence: medium

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.75 out of 18.57

Confidence: strong

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.33 out of 21.55

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.08 out of 23.43

Confidence: medium

AfsR

Description: Pleiotropic regulatory for antibiotic production
Species: Streptomyces coelicolor
Score: 19.59 out of 23.05

Confidence: medium

Additional weak hits (3):

MexT

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

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.54 out of 36.53

Confidence: weak

LuxO

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

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
ArcA	Repressor of carbon oxidation
BldD	Development and antibiotic global regulator
ToxT	Regulator of MSHA biosynthesis
VqsM	Regulator of quorum-sensing signalling systems

NZ_CP053549.1 - Region 6 - terpene

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Location: 1,200,932 - 1,226,201 nt. (total: 25,270 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)

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

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

HMI60_RS05745: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

Transferases: methyltransferase

HMI60_RS05715: methyltransferase

smcogs: SMCOG1248: methyltransferase

Hydrolases: hydrolase

HMI60_RS05695: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: synthetase

HMI60_RS05755: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000644.3	0.68	terpene	carotenoid	Dietzia sp. CQ4
BGC0000637.3	0.58	terpene	carotenoid	Corynebacterium glutamicum
BGC0000647.3	0.56	terpene	carotenoid	Rhodobacter sphaeroides
BGC0000648.3	0.55	terpene	carotenoid	Myxococcus xanthus
BGC0000650.3	0.50	terpene	carotenoid	Algoriphagus sp. KK10202C
BGC0000656.5	0.50	terpene	zeaxanthin	Xanthobacter autotrophicus Py2
BGC0000664.5	0.48	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000636.3	0.47	terpene	carotenoid	Brevibacterium linens
BGC0001456.3	0.47	terpene	isorenieratene	Streptomyces argillaceus
BGC0000633.3	0.47	terpene	carotenoid	Streptomyces avermitilis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000644.3	0.68	terpene	carotenoid	Dietzia sp. CQ4
BGC0000637.3	0.58	terpene	carotenoid	Corynebacterium glutamicum
BGC0000647.3	0.56	terpene	carotenoid	Rhodobacter sphaeroides
BGC0000648.3	0.55	terpene	carotenoid	Myxococcus xanthus
BGC0000650.3	0.50	terpene	carotenoid	Algoriphagus sp. KK10202C
BGC0000656.5	0.50	terpene	zeaxanthin	Xanthobacter autotrophicus Py2
BGC0000664.5	0.48	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000636.3	0.47	terpene	carotenoid	Brevibacterium linens
BGC0001456.3	0.47	terpene	isorenieratene	Streptomyces argillaceus
BGC0000633.3	0.47	terpene	carotenoid	Streptomyces avermitilis

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:

HMI60_RS05735: Lycopene_cycl

Domain 1 (2 - 97): Lycopene cyclase

Reactions:: C40_carotenoid → C40_carotenoid

HMI60_RS05740: Lycopene_cycl

Domain 1 (4 - 93): Lycopene cyclase

Reactions:: C40_carotenoid → C40_carotenoid

HMI60_RS05750: PT_phytoene_like

Domain 1 (19 - 296): Prenyltransferase; Phytoene synthase like

Subtype: unknown

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

HMI60_RS05755: PT_FPPS_like

Domain 1 (52 - 369): 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:

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.24 out of 19.26

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.36 out of 19.26

Confidence: medium

Additional weak hits (3):

MexT

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

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: 19.70 out of 31.73

Confidence: weak

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

NZ_CP053549.1 - Region 7 - NAPAA

Download region GenBank file

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Location: 2,539,183 - 2,573,139 nt. (total: 33,957 nt) Show pHMM detection rules used

NAPAA: (AMP-binding and TIGR02353)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

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 phosphate reductase

HMI60_RS11910: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

HMI60_RS11920: N-acetyl-gamma-glutamyl-phosphate reductase

smcogs: SMCOG1219: N-acetyl-gamma-glutamyl-phosphate reductase

Transferases: PPTase aminotransferase carbamoyltransferase kinase

HMI60_RS11895: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

HMI60_RS11930: acetylglutamate kinase

smcogs: SMCOG1174: acetylglutamate kinase

HMI60_RS11935: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

HMI60_RS11940: ornithine carbamoyltransferase

smcogs: SMCOG1114: ornithine carbamoyltransferase

Lyases: lyase

HMI60_RS11955: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase

HMI60_RS11905: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

HMI60_RS11950: argininosuccinate synthase

smcogs: SMCOG1291: argininosuccinate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002174.2	0.66	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001135.5	0.60	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0001251.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0002286.3	0.59	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.59	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000357.5	0.59	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
BGC0001641.4	0.59	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.59	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002174.2	0.66	NRPS	ε-Poly-L-lysine	Epichloe festucae
BGC0001135.5	0.60	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0001251.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0002286.3	0.59	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.59	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000357.5	0.59	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
BGC0001641.4	0.59	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.59	NRPS	icosalide A, icosalide B	Burkholderia gladioli

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: 28.63 out of 29.65

Confidence: strong

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 22.78 out of 24.78

Confidence: strong

Additional weak hits (4):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.07 out of 30.25

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.78 out of 21.55

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.88 out of 27.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.13 out of 21.55

Confidence: weak

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 9, location 2539182 - 2573139:

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

HMI60_RS11905: X

AMP-binding (38..413): 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:: FAELFDASCEELSTIFGGEWNTYGPTEATVVACA
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
LexA variant 2	Repressor of DNA damage response