GCF_021654795.1 - 17 region(s)

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Location: 189,538 - 213,425 nt. (total: 23,888 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

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

Lasso peptides

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

Transferases: glycosyltransferase

L6439_RS00885: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

Hydrolases: esterase hydrolase

L6439_RS00945: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

L6439_RS00960: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

smcogs: SMCOG1283: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

Lyases: dehydratase

L6439_RS00905: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001356.4	0.90	ribosomal	paeninodin	Paenibacillus dendritiformis C454
BGC0002312.2	0.53	ribosomal	ubonodin	Burkholderia ubonensis
BGC0001634.3	0.52	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0001176.4	0.52	ribosomal	streptomonomicin	Streptomonospora alba
BGC0000575.5	0.52	ribosomal	lariatin	Rhodococcus jostii
BGC0001552.3	0.52	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001549.3	0.52	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0001550.3	0.52	ribosomal	citrulassin D	Streptomyces katrae
BGC0000571.3	0.51	ribosomal	burhizin	Paraburkholderia rhizoxinica HKI 454
BGC0001645.3	0.51	ribosomal	lagmysin	Streptomyces sp. NRRL S-118

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001356.4	0.90	ribosomal	paeninodin	Paenibacillus dendritiformis C454
BGC0002312.2	0.53	ribosomal	ubonodin	Burkholderia ubonensis
BGC0001634.3	0.52	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0001176.4	0.52	ribosomal	streptomonomicin	Streptomonospora alba
BGC0000575.5	0.52	ribosomal	lariatin	Rhodococcus jostii
BGC0001552.3	0.52	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0001549.3	0.52	ribosomal	citrulassin B	Streptomyces aurantiacus JA 4570
BGC0001550.3	0.52	ribosomal	citrulassin D	Streptomyces katrae
BGC0000571.3	0.51	ribosomal	burhizin	Paraburkholderia rhizoxinica HKI 454
BGC0001645.3	0.51	ribosomal	lagmysin	Streptomyces sp. NRRL S-118

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lasso peptide predictions

Lassopeptide(s) for L6439_RS00940

L6439_RS00940

Leader:

MKKPYSKPSLEVLDVHQTMA

Full core:

GPGTSTPDAFQPDPDEDVHYDPMDS

Putative macrolactam:

GPGTSTPD

antiSMASH-DB 4.0 matches for L6439_RS00940

100.0%

Lassopeptides: L6439_RS00940_lassopeptide

1

GPGTSTPDAFQPDPDEDVHYDPMDS

25

GPGTSTPDAFQPDPDEDVHYDPMDS

1

GPGTSTPDAFQPDPDEDVHYDPMDS

25

96.0%

NZ_CP041405.1and 2 others:

NZ_CP094446.1 Lassopeptides: L3476_RS19330_lassopeptideNZ_CP106992.1 Lassopeptides: NDS46_RS02035_lassopeptide

Lassopeptides: FLT43_RS18930_lassopeptide

1

GPGTSTPDAFQPDPDEDVHYDPMDS

25

GPG STPDAFQPDPDEDVHYDPMDS

1

GPGLSTPDAFQPDPDEDVHYDPMDS

25

84.0%

NZ_OX216966.1:

Lassopeptides: NNL35_RS04670_lassopeptide

1

GPGTSTPDAFQPDPDEDVHYD

21

GPGTSTPDAFQPDPDEDVHYD

1

GPGTSTPDAFQPDPDEDVHYD

21

with 53 more sequence matches

Only the first 10 are displayed here.

68.0%

NC_017138.1and 11 others:

NZ_CP018874.1 Lassopeptides: BUW91_RS28875_lassopeptideNZ_CP028084.1 Lassopeptides: C1N54_RS05380_lassopeptideNZ_JANIOE010000001.1 Lassopeptides: NQ109_RS19625_lassopeptideNZ_NGUL01000003.1 Lassopeptides: CBE78_RS15420_lassopeptideNZ_NTZG01000008.1 Lassopeptides: CN510_RS30020_lassopeptideNZ_NUEC01000009.1 Lassopeptides: CN635_RS27505_lassopeptideNZ_NUOI01000031.1 Lassopeptides: COE08_RS30705_lassopeptideNZ_NVEG01000005.1 Lassopeptides: COL08_RS29985_lassopeptideNZ_NVEV01000001.1 Lassopeptides: COL23_RS28065_lassopeptideNZ_VDTN01000001.1 Lassopeptides: FS483_RS07665_lassopeptideNZ_VEEA01000001.1 Lassopeptides: FS744_RS11845_lassopeptide

Lassopeptides: BMWSH_RS26600_lassopeptide

1

GPGTSTPDAFQPDPDEDVHY

20

GPGTS PDA QPDPDE VHY

1

GPGTSIPDAVQPDPDETVHY

20

64.0%

NZ_SDLR01000004.1:

Lassopeptides: EIZ58_RS19635_lassopeptide

1

GPGTSTPDAFQPDPDEDVHYD

21

GPG +TPDAFQPDPDE +HY+

1

GPGVTTPDAFQPDPDETIHYE

21

60.0%

NZ_CM000754.1and 7 others:

NZ_CP020723.1 Lassopeptides: B7P25_RS28625_lassopeptideNZ_CP023179.1 Lassopeptides: CK938_RS28520_lassopeptideNZ_CP085399.1 Lassopeptides: LIS81_RS18060_lassopeptideNZ_FTLZ01000002.1 Lassopeptides: BW973_RS28715_lassopeptideNZ_PIYQ01000023.1 Lassopeptides: CW365_RS28935_lassopeptideNZ_VDNI01000012.1 Lassopeptides: FSV62_RS19525_lassopeptideNZ_WBPF01000005.1 Lassopeptides: F8162_RS06315_lassopeptide

Lassopeptides: BTHUR0009_RS30905_lassopeptide

1

GPGTSTPDAFQPDPDEDVHY

20

GPG TPDA QPD DE VHY

1

GPGLKTPDAVQPDIDEVVHY

20

60.0%

NZ_CP030028.1:

Lassopeptides: DOE78_RS20570_lassopeptide

1

GPGTSTPDAFQPDPDEDVHY

20

GPG TPDA QPD DE VHY

1

GPGIKTPDASQPDVDEVVHY

20

60.0%

NZ_CP032365.1and 8 others:

NZ_FMBE01000013.1 Lassopeptides: CCY88_RS31005_lassopeptideNZ_FMJI01000046.1 Lassopeptides: CCY61_RS30520_lassopeptideNZ_FMZR01000002.1 Lassopeptides: BLS53_RS31385_lassopeptideNZ_JH791975.1 Lassopeptides: IEI_RS31960_lassopeptideNZ_JYPF01000002.1 Lassopeptides: TU50_RS30650_lassopeptideNZ_NUFG01000001.1 Lassopeptides: CN694_RS29875_lassopeptideNZ_NURJ01000008.1 Lassopeptides: COE89_RS29040_lassopeptideNZ_QOSC01000009.1 Lassopeptides: DN392_RS14315_lassopeptide

Lassopeptides: D4A37_RS18780_lassopeptide

1

GPGTSTPDAFQPDPDEDVHY

20

GPG TPDA QPD DE VHY

1

GPGLKTPDAVQPDVDEVVHY

20

60.0%

NZ_JAIEZS010000055.1and 1 other:

NZ_JH792165.1 Lassopeptides: IIO_RS35460_lassopeptide

Lassopeptides: K0820_RS18465_lassopeptide

1

GPGTSTPDAFQPDPDEDVHY

20

GPG TPDA QPD DE VHY

1

GPGIKTPDAVQPDVDEVVHY

20

60.0%

NZ_JAQQWU010000003.1:

Lassopeptides: PQ511_RS07455_lassopeptide

1

GPGTSTPDAFQPDPDEDVHY

20

GPG TPDA QPD DE VHY

1

GPGIKTPDAVQPDVDEAVHY

20

60.0%

NZ_KI632505.1:

Lassopeptides: V180_RS32040_lassopeptide

1

GPGTSTPDAFQPDPD----EDVHY

20

GPG TPDA QPDPD + VHY

1

GPGIKTPDAVQPDPDAPLKDQVHY

24

60.0%

NZ_NUPF01000007.1:

Lassopeptides: COE35_RS26755_lassopeptide

1

GPGTSTPDAFQPDPDEDVHY

20

GPG S PDA Q DPDE VHY

1

GPGLSIPDAVQSDPDETVHY

20

56.0%

NC_021171.1:

Lassopeptides: B1NLA3E_RS24645_lassopeptide

1

GPGTSTPDAFQPDPD----EDVHY

20

GPG PDA QPDPD + VHY

1

GPGIRIPDAVQPDPDAPLNDVVHY

24

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 24.66 out of 29.51

Confidence: medium

Additional weak hits (2):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.90 out of 29.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.08 out of 28.14

Confidence: weak

Lasso peptides

RREFinder

TFBS Finder

Core peptide predictions

L6439_RS00940 - Class II: Cleavage pHMM score: -9.90; RODEO score: 16; Monoisotopic mass: 2671.1 Da; Molecular weight: 2672.7 Da; Number of bridges: 0

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 16 - 94; Score: 78.1

TFBS definitions

Regulator	Description
DosR	Hypoxia stress response regulator

NZ_AP025344.1 - Region 2 - NRPS,transAT-PKS-like

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Location: 560,420 - 640,064 nt. (total: 79,645 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
transAT-PKS-like: cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS) and not PKS_AT)

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

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

L6439_RS02715: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

L6439_RS02725: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

L6439_RS02780: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

L6439_RS02785: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acylase

L6439_RS02730: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase hydrolase

L6439_RS02695: thioesterase

smcogs: SMCOG1004: thioesterase

L6439_RS02705: thioesterase

smcogs: SMCOG1004: thioesterase

L6439_RS02710: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase synthase

L6439_RS02675: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS02680: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

L6439_RS02685: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

L6439_RS02690: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

L6439_RS02700: 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	0.86	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.85	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.81	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.81	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001641.4	0.78	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.77	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.76	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5	0.75	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	0.75	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.74	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.74	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.72	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001641.4	0.71	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.70	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.70	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

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: 18.16 out of 18.16

Confidence: strong

AbrC3

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

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.22 out of 20.97

Confidence: strong

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.22 out of 18.57

Confidence: strong

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.67 out of 27.78

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.83 out of 28.19

Confidence: medium

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.47 out of 20.01

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.31 out of 28.19

Confidence: medium

Additional weak hits (14):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.99 out of 30.25

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 20.55 out of 27.18

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.46 out of 32.93

Confidence: weak

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.49 out of 29.72

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.91 out of 26.06

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.26 out of 20.01

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.73 out of 30.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.54 out of 29.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.08 out of 26.06

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 22.40 out of 36.54

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.22 out of 29.38

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.44 out of 20.01

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.45 out of 26.06

Confidence: weak

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 21.63 out of 30.12

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 2, location 560419 - 640064:

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

Polymer prediction:: (Gly - Thr) + (Gly - Orn) + (ohmal - Val - Lys - Thr) + (Pro - X) + (D-Asn)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

L6439_RS02675: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (466..862): 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:: FSFSFDIFVVELQTLLGGEYNLYGPTETTVWSAV
Nearest Stachelhaus code(s):: Gly DILQLGLVWK (74% 8Å match)
Stachelhaus code match:: 90% (moderate)

L6439_RS02680: Thr - Gly - Orn

Search NORINE for peptide: strict or relaxed

AMP-binding (265..664): 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:: LNTHFDFSVWEGNQIFGGEVNMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1307..1703): 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:: N/A
Single AA prediction:: gly (Gly)

Stachelhaus prediction details:

Stachelhaus sequence:: FAMTFDIFFVELQLLVGGEYNLYGPTETTIWSTL
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (82% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2348..2750): Orn

nrpys: Orn

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: MVWAFDVFSGDRESIIGSDINSYGVTEAAVDASY
Nearest Stachelhaus code(s):: Orn DVGEIGSVDK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS02685: Val - Lys

Search NORINE for peptide: strict or relaxed

AMP-binding (1683..2078): 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:: LSDAFDAFTLEGFLLIGGEINGYGPTENTTFSTV
Nearest Stachelhaus code(s):: Val DALFLGGTFK (68% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2728..3127): Lys

nrpys: Lys

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: N/A
Single AA prediction:: lys (Lys)

Stachelhaus prediction details:

Stachelhaus sequence:: YAFSFDTSIEEPSCIAGGDFNSYGPTETTVCAAY
Nearest Stachelhaus code(s):: Lys DAESIGSVCK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

L6439_RS02690: Thr - Pro - X

Search NORINE for peptide: strict or relaxed

AMP-binding (645..948): 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:: LTAHFDFSVWEGSQVFGGEVNMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWSVGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1596..1993): Pro

nrpys: 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:: LHHSFDVCYQELFLVVAGEHNHYGPSETHVVSAL
Nearest Stachelhaus code(s):: Pro DVQFVAHVVK (65% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2640..3030): X

nrpys: Phe, Trp, Ph-Gly, Tyr, bOH-Tyr

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:: 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:: LFFAFDMALLETTVITAGEVNLYGPTETTIITTM
Nearest Stachelhaus code(s):: Phe DAWTIAAICK (65% 8Å match); Ala DILQISLIYK (62% 8Å match); Pro DMTFSAGIIK (56% 8Å match)
Stachelhaus code match:: 60% (weak)

L6439_RS02700: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (469..861): 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:: YWASFDLTVTSTKLIVGGEWNEYGPTEATVGCMI
Nearest Stachelhaus code(s):: Asn DLTKIGEVGK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS02730: mal

PKS_AT (6..289): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 62.5%; inactive: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 58.1
inactive: 32.4
Methoxymalonyl-CoA: 26.2
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Isobutyryl-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
Methylmalonyl-CoA: -0.4
Ethylmalonyl-CoA: -3.0

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
ArgR	Regulator of arginine biosynthesis genes
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_AP025344.1 - Region 3 - ranthipeptide

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Location: 790,778 - 812,403 nt. (total: 21,626 nt) Show pHMM detection rules used

ranthipeptide: (TIGR03973 or SCIFF or (cds(PF04055 and (TIGR04085 or SPASM)) 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]) and not (TIGR01716 or subtilosin or TIGR02111 or TIGR03966 or TIGR04103 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

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

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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

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.50	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000134.3	0.33	PKS	radicicol	Pochonia chlamydosporia
BGC0002187.3	0.33	PKS	monorden D, monocillin IV, monocillin VI, monocillin VII, pochonin M, monocillin V, monocillin II	Pochonia chlamydosporia 170
BGC0002012.4	0.23	PKS	julichrome Q3-3, julichrome Q3-5	Streptomyces afghaniensis 772
BGC0000360.5	0.22	NRPS	GE81112	Streptomyces sp. L-49973
BGC0002087.3	0.21	NRPS, PKS	gladiostatin A	Burkholderia gladioli 238
BGC0001119.5	0.19	PKS	divergolide A, divergolide B, divergolide C, divergolide D	Streptomyces sp. HKI0576

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.50	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000134.3	0.33	PKS	radicicol	Pochonia chlamydosporia
BGC0002187.3	0.33	PKS	monorden D, monocillin IV, monocillin VI, monocillin VII, pochonin M, monocillin V, monocillin II	Pochonia chlamydosporia 170
BGC0002012.4	0.23	PKS	julichrome Q3-3, julichrome Q3-5	Streptomyces afghaniensis 772
BGC0000360.5	0.22	NRPS	GE81112	Streptomyces sp. L-49973
BGC0002087.3	0.21	NRPS, PKS	gladiostatin A	Burkholderia gladioli 238
BGC0001119.5	0.19	PKS	divergolide A, divergolide B, divergolide C, divergolide D	Streptomyces sp. HKI0576

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

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

Confidence: strong

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.44 out of 18.16

Confidence: strong

Additional weak hits (4):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.79 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.10 out of 29.38

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.89 out of 30.25

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.25 out of 30.98

Confidence: weak

RREFinder

TFBS Finder

RRE predictions

: RRE type: Ranthipeptide_rSAM_RRE; Location: 0 - 99; Score: 104.8

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
ToxT	Regulator of MSHA biosynthesis

NZ_AP025344.1 - Region 4 - NRP-metallophore,NRPS

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Location: 850,378 - 902,311 nt. (total: 51,934 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

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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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

L6439_RS03785: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: hydrolase

L6439_RS03800: isochorismatase

smcogs: SMCOG1027: isochorismatase

Isomerases: isomerase

L6439_RS03790: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: ligase

L6439_RS03795: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS03805: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000401.5	1.10	NRPS	paenibactin	Paenibacillus elgii B69
BGC0001185.5	1.04	NRPS	bacillibactin	Bacillus velezensis FZB42
BGC0000309.5	1.01	NRPS	bacillibactin	Bacillus subtilis subsp. subtilis str. 168
BGC0002075.3	0.87	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0000343.5	0.87	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001833.4	0.76	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002695.2	0.76	NRPS	bacillibactin, bacillibactin E, bacillibactin F	Bacillus sp. WMMC1349
BGC0001825.4	0.75	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.74	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.73	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000401.5	0.81	NRPS	paenibactin	Paenibacillus elgii B69
BGC0001185.5	0.80	NRPS	bacillibactin	Bacillus velezensis FZB42
BGC0000309.5	0.79	NRPS	bacillibactin	Bacillus subtilis subsp. subtilis str. 168
BGC0002075.3	0.75	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0000343.5	0.74	NRPS	enterobactin	Pseudomonas sp. J465
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002695.2	0.70	NRPS	bacillibactin, bacillibactin E, bacillibactin F	Bacillus sp. WMMC1349
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.70	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 20.76 out of 21.84

Confidence: strong

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 26.61 out of 29.38

Confidence: strong

FuR variant 1

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

Confidence: strong

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 28.84 out of 29.38

Confidence: strong

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57

Confidence: strong

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.22 out of 18.57

Confidence: strong

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 26.49 out of 29.38

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 25.36 out of 28.19

Confidence: strong

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 28.19

Confidence: medium

Additional weak hits (31):

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 21.08 out of 30.11

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.39 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.04 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.12 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.33 out of 26.06

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.49 out of 32.74

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.08 out of 31.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.52 out of 29.38

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.61 out of 32.74

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.80 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.80 out of 28.14

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.94 out of 32.74

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.38 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.90 out of 28.14

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 21.58 out of 36.54

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.87 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.52 out of 29.38

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.64 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.62 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.84 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.62 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.22 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.41 out of 30.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.57 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.39 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.29 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.30 out of 27.78

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.97 out of 30.98

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.40 out of 30.98

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.89 out of 24.78

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 4, location 850377 - 902311:

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

Polymer prediction:: (Ala - Thr)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

L6439_RS03795: diOH-Bz

Search NORINE for peptide: strict or relaxed

AMP-binding (34..440): diOH-Bz

nrpys: diOH-Bz

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
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:: SVSLYPLSSPGGAVQVGGAQQVYGMAEGLVNYTR
Nearest Stachelhaus code(s):: diOH-Bz PLPAQGVVNK (91% 8Å match); diOH-Bz or Sal PLPAQGVVNK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS03805: Ala - Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (464..867): Ala

nrpys: Ala

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:: LCMTFDISVMELQAITGGENNQYGPTETTIYSTA
Nearest Stachelhaus code(s):: Ala DILQIGQIYK (91% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1529..1945): 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:: LSTHFDFSVWEGNQIFGGEINMYGITETTVHVSY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
FuR variant 1	Ferric Uptake Regulator
MexT	Global virulence regulator
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_AP025344.1 - Region 5 - NRPS,proteusin

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Location: 1,080,060 - 1,128,527 nt. (total: 48,468 nt) Show pHMM detection rules used

proteusin: (PoyD or TIGR03793)
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

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

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

Transferases: PPTase

L6439_RS04760: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Hydrolases: hydrolase

L6439_RS04695: hydrolase

smcogs: SMCOG1179: hydrolase

L6439_RS04825: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase

L6439_RS04765: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002164.2	0.36	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.33	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.32	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.32	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.31	NRPS	AbT1	Aureobasidium pullulans
BGC0002286.3	0.31	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.30	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0002135.2	0.30	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001641.4	0.30	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.29	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002164.2	0.69	NRPS	peramine	Epichloe festucae
BGC0001135.5	0.67	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001132.4	0.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.65	NRPS	AbT1	Aureobasidium pullulans
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001240.4	0.64	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57

Confidence: strong

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.71 out of 23.79

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.13 out of 20.97

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.39 out of 27.78

Confidence: medium

ToxT

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

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.19 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

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 28.57 out of 29.38

Confidence: strong

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 25.02 out of 29.38

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.18 out of 28.19

Confidence: medium

Additional weak hits (23):

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.33 out of 36.54

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.89 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.51 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.29 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.80 out of 28.14

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.33 out of 30.25

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.42 out of 33.14

Confidence: weak

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 20.61 out of 27.04

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.83 out of 23.43

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.12 out of 27.78

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.85 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.92 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.37 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.26 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.80 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.50 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.13 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 20.59 out of 31.73

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.15 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.65 out of 28.14

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 20.34 out of 30.97

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.52 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.76 out of 33.14

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 5, location 1080059 - 1128527:

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

Polymer prediction:: (Ile - Val)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 7, location 1081780 - 1128527:

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

Polymer prediction:: (Ile - Val)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

L6439_RS04765: Ile - Val

Search NORINE for peptide: strict or relaxed

AMP-binding (219..612): Ile

nrpys: Ile

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: ile (Ile)

Stachelhaus prediction details:

Stachelhaus sequence:: LNTGFDASTFEGFLFVGGESNIYGPTENTTFSTC
Nearest Stachelhaus code(s):: Ile DAFFLGITFK (91% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1253..1650): 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:: LNTGFDASTFEGWLLVGGDINGYGPTENTTFTAC
Nearest Stachelhaus code(s):: Val DAFWLGGTFK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1	Ferric Uptake Regulator
IolR	Regulator of the inositol catabolism
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_AP025344.1 - Region 6 - RiPP-like

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Location: 1,785,644 - 1,797,578 nt. (total: 11,935 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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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: oxidoreductase

L6439_RS07855: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

Transferases: aminotransferase

L6439_RS07875: aminotransferase

smcogs: SMCOG1019: aminotransferase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001174.4	0.37	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0000607.5	0.36	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0001173.5	0.36	ribosomal	plantazolicin	Bacillus pumilus ATCC 7061
BGC0000569.5	0.36	ribosomal	plantazolicin	Bacillus velezensis FZB42
BGC0001146.5	0.35	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000193.3	0.34	PKS	aclacinomycin	Streptomyces galilaeus
BGC0000605.5	0.34	ribosomal	GE37468	Streptomyces sp. ATCC 55365
BGC0000603.5	0.33	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0000606.5	0.33	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0000914.5	0.33	other (other)	methylenomycin A	Streptomyces coelicolor A3(2)

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001174.4	0.37	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0000607.5	0.36	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0001173.5	0.36	ribosomal	plantazolicin	Bacillus pumilus ATCC 7061
BGC0000569.5	0.36	ribosomal	plantazolicin	Bacillus velezensis FZB42
BGC0001146.5	0.35	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000193.3	0.34	PKS	aclacinomycin	Streptomyces galilaeus
BGC0000605.5	0.34	ribosomal	GE37468	Streptomyces sp. ATCC 55365
BGC0000603.5	0.33	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0000606.5	0.33	ribosomal	lactazole	Streptomyces lactacystinaeus
BGC0000914.5	0.33	other (other)	methylenomycin A	Streptomyces coelicolor A3(2)

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.73 out of 20.97

Confidence: medium

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.59 out of 18.57

Confidence: medium

Additional weak hits (5):

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.65 out of 20.01

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.53 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.51 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.12 out of 26.06

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.52 out of 33.14

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
ToxT	Regulator of MSHA biosynthesis

NZ_AP025344.1 - Region 7 - NRPS,NRPS-like,T1PKS

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Location: 2,124,746 - 2,224,206 nt. (total: 99,461 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)
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

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

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

L6439_RS09370: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

L6439_RS09380: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

L6439_RS09530: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: acylase

L6439_RS09390: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

L6439_RS09410: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase hydrolase phosphatase

L6439_RS09385: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

L6439_RS09460: isochorismatase

smcogs: SMCOG1027: isochorismatase

L6439_RS09510: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

L6439_RS09515: thioesterase

smcogs: SMCOG1004: thioesterase

L6439_RS09520: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

L6439_RS09570: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

Ligases: ligase synthase

L6439_RS09395: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

L6439_RS09415: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS09505: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS09535: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS09540: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

L6439_RS09545: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

L6439_RS09550: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

L6439_RS09555: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Translocases: transporter

L6439_RS09435: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	1.01	NRPS	enniatin	Fusarium equiseti
BGC0002135.2	1.00	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.98	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.97	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.97	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.97	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001261.3	0.97	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.97	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.96	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001166.5	0.95	NRPS	HC-toxin	Alternaria jesenskae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000342.4	0.69	NRPS	enniatin	Fusarium equiseti
BGC0001250.4	0.68	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.68	NRPS	epichloenin A	Epichloe festucae
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.68	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.67	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.67	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	0.67	NRPS	AM-toxin	Alternaria alternata

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: 17.62 out of 20.97

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.85 out of 20.97

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.67 out of 19.26

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 22.63 out of 24.78

Confidence: strong

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 22.56 out of 24.78

Confidence: strong

CatR

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

Confidence: medium

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 25.39 out of 30.25

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.48 out of 24.78

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.61 out of 24.78

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.49 out of 24.78

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.67 out of 28.19

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.71 out of 18.16

Confidence: strong

Additional weak hits (27):

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.99 out of 27.78

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.22 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.22 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.35 out of 28.14

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 18.82 out of 27.78

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 19.50 out of 29.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.41 out of 30.25

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.45 out of 29.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.25 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.52 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.74 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.31 out of 27.78

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.56 out of 24.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.04 out of 29.65

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 18.52 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 17.94 out of 26.06

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.11 out of 39.62

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: 19.55 out of 28.19

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.45 out of 29.65

Confidence: weak

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.12 out of 21.84

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.91 out of 28.14

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.42 out of 20.01

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.01 out of 26.06

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.20 out of 26.12

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.06 out of 26.06

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.13 out of 33.14

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 2124745 - 2224206:

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

Polymer prediction:: (ccmal - ohmal) + (Gly) + (D-Asn) + (Val - ccmal - Leu) + (ohmal) + (mal - ohmal) + (mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 2124745 - 2166494:

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

Polymer prediction:: (ccmal - ohmal) + (Gly) + (D-Asn)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 11, location 2144003 - 2224206:

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

Polymer prediction:: (Gly) + (D-Asn) + (Val - ccmal - Leu) + (ohmal) + (mal - ohmal) + (mal)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

L6439_RS09390: mal

PKS_AT (6..291): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 50.5
Methylmalonyl-CoA: 22.4
inactive: 21.5
Methoxymalonyl-CoA: 20.7
Propionyl-CoA: 18.0
Benzoyl-CoA: 13.3
Acetyl-CoA: 8.5
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

L6439_RS09410: mal

PKS_AT (9..294): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 54.2%

minowa: trans-1,2-CPDA

Prediction, score:

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
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
Malonyl-CoA: -1.7

L6439_RS09415: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (1..391): 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:: FGMTFDIFVLELQTMIGGEYNLYGPTETTIWSTV
Nearest Stachelhaus code(s):: Gly DILQLGLIWK (79% 8Å match)
Stachelhaus code match:: 90% (moderate)

L6439_RS09505: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (443..837): 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:: YWASFDLTVTSTKLIVGGEYNEYGPTETVVGCMI
Nearest Stachelhaus code(s):: Asn DLTKIGEVGK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS09535: Val - mal

Search NORINE for peptide: strict or relaxed

AMP-binding (479..872): 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:: LNTGFDALTFEGILIVAGDWNGYGPTENTVFSTC
Nearest Stachelhaus code(s):: Val DAFWIGGTFK (91% 8Å match); aIle DAFLYGGVFK (68% 8Å match); Leu DGYIIGGVFK (62% 8Å match); Tyr DAAIIAAVCK (59% 8Å match)
Stachelhaus code match:: 70% (weak)

PKS_AT (1612..1903): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%; inactive: 62.5%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 122.0
Methoxymalonyl-CoA: 75.9
inactive: 67.7
Methylmalonyl-CoA: 61.5
Isobutyryl-CoA: 41.5
Ethylmalonyl-CoA: 40.2
CHC-CoA: 25.5
Propionyl-CoA: 25.1
Benzoyl-CoA: 13.6
fatty_acid: 12.3
3-Methylbutyryl-CoA: 8.8
trans-1,2-CPDA: 0.0
Acetyl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

L6439_RS09540: Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (275..659): Leu

nrpys: Leu

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: leu (Leu)

Stachelhaus prediction details:

Stachelhaus sequence:: LWHAFDASVWEPFLLTGGDFNNYGPTENTVVTTC
Nearest Stachelhaus code(s):: Leu DAWFLGNVVK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS09545: mal

PKS_AT (535..830): mal

ATSignature: Malonyl-CoA, inactive

Top 3 matches:: Malonyl-CoA: 83.3%; inactive: 83.3%; Methylmalonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 155.7
inactive: 95.3
Methoxymalonyl-CoA: 73.2
Methylmalonyl-CoA: 55.3
Propionyl-CoA: 33.0
Ethylmalonyl-CoA: 25.6
2-Methylbutyryl-CoA: 14.2
trans-1,2-CPDA: 13.6
fatty_acid: 0.0
Isobutyryl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

L6439_RS09550: mal - mal

PKS_AT (533..824): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 79.2%; 2-Rhyd-Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 174.7
inactive: 113.3
Methoxymalonyl-CoA: 77.7
Methylmalonyl-CoA: 61.3
Propionyl-CoA: 45.5
Isobutyryl-CoA: 27.1
CHC-CoA: 26.6
Ethylmalonyl-CoA: 24.9
fatty_acid: 22.2
2-Methylbutyryl-CoA: 19.7
Acetyl-CoA: 9.3
trans-1,2-CPDA: 0.0
Benzoyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

PKS_AT (1580..1876): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 79.2%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 186.4
inactive: 117.8
Methoxymalonyl-CoA: 77.5
Methylmalonyl-CoA: 72.3
Ethylmalonyl-CoA: 38.2
Propionyl-CoA: 36.9
Isobutyryl-CoA: 36.8
2-Methylbutyryl-CoA: 23.2
Benzoyl-CoA: 19.7
CHC-CoA: 16.2
fatty_acid: 15.7
trans-1,2-CPDA: 12.5
Acetyl-CoA: 6.2
3-Methylbutyryl-CoA: 0.0

L6439_RS09555: mal

PKS_AT (535..832): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 91.7%; inactive: 79.2%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 172.5
inactive: 102.5
Methoxymalonyl-CoA: 78.8
Methylmalonyl-CoA: 77.6
Ethylmalonyl-CoA: 54.6
Propionyl-CoA: 54.0
2-Methylbutyryl-CoA: 41.1
Isobutyryl-CoA: 33.0
CHC-CoA: 30.1
Benzoyl-CoA: 28.1
fatty_acid: 23.1
trans-1,2-CPDA: 17.1
Acetyl-CoA: 8.0
3-Methylbutyryl-CoA: 0.0

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
CRP	Cyclic AMP receptor protein
CatR	H2O2-responsive repressor
CcpA	Catabolite control protein A
ColR	Phenol-responsive regulator
LexA variant 2	Repressor of DNA damage response
ZuR variant 1	Zinc-responsive repressor

NZ_AP025344.1 - Region 8 - lanthipeptide-class-iii

Download region SVG

Location: 2,702,981 - 2,725,587 nt. (total: 22,607 nt) Show pHMM detection rules used

lanthipeptide-class-iii: (micKC and not PKS_KS)

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

Lanthipeptides

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

Transferases: methyltransferase

L6439_RS11880: methyltransferase

smcogs: SMCOG1248: methyltransferase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002700.2	0.81	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0002701.2	0.59	ribosomal	paenithipeptin	Paenibacillus thiaminolyticus
BGC0000551.5	0.54	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000519.4	0.53	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000501.3	0.51	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000496.5	0.51	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.51	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000518.3	0.51	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0000553.3	0.49	ribosomal	SRO15-2212	Streptomyces filamentosus NRRL 15998
BGC0002111.3	0.47	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002700.2	0.81	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0002701.2	0.59	ribosomal	paenithipeptin	Paenibacillus thiaminolyticus
BGC0000551.5	0.54	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000519.4	0.53	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000501.3	0.51	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0000496.5	0.51	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000513.3	0.51	ribosomal	Ery-9, Ery-6, Ery-8, Ery-7, Ery-5, Ery-4, Ery-3	Saccharopolyspora erythraea NRRL 2338
BGC0000518.3	0.51	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0000553.3	0.49	ribosomal	SRO15-2212	Streptomyces filamentosus NRRL 15998
BGC0002111.3	0.47	ribosomal	andalusicin A, andalusicin B	Bacillus thuringiensis serovar andalousiensis NRRL B-23139

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for L6439_RS11915

L6439_RS11890

Leader:

MNTVLELQELAHDTDGKGQAAE

Core:

ATVISTIAATTCVTTTVITAGK

Core with dehydrations:

ADhbVIDhaDhbIAADhbDhbCysVDhbDhbDhbVIDhbAGK

antiSMASH-DB 4.0 matches for L6439_RS11890

100.0%

Lanthipeptides: L6439_RS11890_lanthipeptide

1

ATVISTIAATTCVTTTVITAGK

22

ATVISTIAATTCVTTTVITAGK

1

ATVISTIAATTCVTTTVITAGK

22

L6439_RS11920

Leader:

MNTVLELQKLAHDTDGKGQAVD

L6439_RS11930

Leader:

MNTVLELQKLAHDTDGKGQAVD

Shared core:

ATPTTVTVTTVTTTVAGWSTQSQHHC

Core with dehydrations:

ADhbPDhbDhbVDhbVDhbDhbVDhbDhbDhbVAGWDhaDhbQDhaQHHCys

antiSMASH-DB 4.0 matches for L6439_RS11920

100.0%

NZ_AP025344.1and 1 other:

NZ_AP025344.1 Lanthipeptides: L6439_RS11920_lanthipeptide

Lanthipeptides: L6439_RS11930_lanthipeptide

1

ATPTTVTVTTVTTTVAGWSTQSQHHC

26

ATPTTVTVTTVTTTVAGWSTQSQHHC

1

ATPTTVTVTTVTTTVAGWSTQSQHHC

26

46.2%

Lanthipeptides: L6439_RS11925_lanthipeptide

8

VTTVTTTVAGWSTQSQHHC

26

T + TT WSTQSQHHC

1

ATPILTTPTRWSTQSQHHC

19

28.6%

NZ_BMSZ01000006.1and 4 others:

NZ_BMSZ01000006.1 Lanthipeptides: IE135_RS12790_lanthipeptideNZ_CP021707.1 Lanthipeptides: CCZ36_RS18195_lanthipeptideNZ_LZRD01000017.1 Lanthipeptides: A3Q37_RS19730_lanthipeptideNZ_LZRD01000017.1 Lanthipeptides: A3Q37_RS19730_lanthipeptide

Lanthipeptides: IE135_RS12790_lanthipeptide

2

TPTTVTVTTVTTTVAGWSTQSQHHC

26

TPT V T VTT + G S Q C

9

TPTIVPATAVTTVIVGASAAMQGGC

33

with 2 more sequence matches

26.2%

NZ_BMRY01000003.1and 19 others:

NZ_BMRY01000003.1 Lanthipeptides: IE140_RS12360_lanthipeptideNZ_BNBJ01000003.1 Lanthipeptides: IE304_RS05295_lanthipeptideNZ_BNBJ01000003.1 Lanthipeptides: IE304_RS05295_lanthipeptideNZ_CP079114.1 Lanthipeptides: KV381_RS19415_lanthipeptideNZ_CP079114.1 Lanthipeptides: KV381_RS19415_lanthipeptideNZ_CP084357.1 Lanthipeptides: LEL86_RS34975_lanthipeptideNZ_CP084357.1 Lanthipeptides: LEL86_RS34975_lanthipeptideNZ_JALDPQ010000054.1 Lanthipeptides: MQC87_RS11030_lanthipeptideNZ_JALDPQ010000054.1 Lanthipeptides: MQC87_RS11030_lanthipeptideNZ_JAMFLF010000021.1 Lanthipeptides: M1212_RS32890_lanthipeptideNZ_JAMFLF010000021.1 Lanthipeptides: M1212_RS32890_lanthipeptideNZ_JNLT01000014.1 Lanthipeptides: CD02_RS0123035_lanthipeptideNZ_JNLT01000014.1 Lanthipeptides: CD02_RS0123035_lanthipeptideNZ_JNZV01000231.1 Lanthipeptides: BG84_RS0100135_lanthipeptideNZ_JNZV01000231.1 Lanthipeptides: BG84_RS0100135_lanthipeptideNZ_KZ819178.1 Lanthipeptides: DBP20_RS18445_lanthipeptideNZ_KZ819178.1 Lanthipeptides: DBP20_RS18445_lanthipeptideNZ_NNBN01000001.1 Lanthipeptides: CG717_RS03745_lanthipeptideNZ_NNBN01000001.1 Lanthipeptides: CG717_RS03745_lanthipeptide

Lanthipeptides: IE140_RS12360_lanthipeptide

2

TPTTVTVTTVTTTVAGWSTQSQHHC

26

TPT + T VTT + G S Q C

9

TPTIIPATAVTTVIVGASAAMQGGC

33

23.5%

NZ_BMVL01000013.1and 1 other:

NZ_BMVL01000013.1 Lanthipeptides: IE257_RS28650_lanthipeptide

Lanthipeptides: IE257_RS28650_lanthipeptide

10

TVTTTVAGWSTQSQHH

25

TVT TVA W+ + H

5

TVTYTVASWALGNNGH

20

L6439_RS11925

Leader:

MNAVLELQKLAHDTDGKGQAAD

Core:

ATPILTTPTRWSTQSQHHC

Core with dehydrations:

ADhbPILDhbDhbPDhbRWDhaDhbQDhaQHHCys

antiSMASH-DB 4.0 matches for L6439_RS11925

100.0%

Lanthipeptides: L6439_RS11925_lanthipeptide

1

ATPILTTPTRWSTQSQHHC

19

ATPILTTPTRWSTQSQHHC

1

ATPILTTPTRWSTQSQHHC

19

34.6%

NZ_AP025344.1and 1 other:

NZ_AP025344.1 Lanthipeptides: L6439_RS11920_lanthipeptide

Lanthipeptides: L6439_RS11930_lanthipeptide

11

WSTQSQHHC

19

WSTQSQHHC

18

WSTQSQHHC

26

33.3%

NZ_SMBT01000005.1:

Lanthipeptides: EV682_RS11315_lanthipeptide

7

TPTRWSTQSQH

17

TP WST S H

1

TPADWSTVSNH

11

with 2 more sequence matches

27.3%

NZ_SMBT01000005.1:

Lanthipeptides: EV682_RS11310_lanthipeptide

7

TPTRWSTQSQH

17

TP+ WST S +

1

TPSEWSTVSNY

11

20.7%

NZ_CP013140.1:

Lanthipeptides: allorf_2668303_2668419_lanthipeptide

2

TPILTTPTRWSTQSQH

17

TP+ + TRW ++ +H

14

TPLSPSKTRWCSRVEH

29

MIBiG 4.0 matches for L6439_RS11925

8.7%

BGC0002111.3 (EVG22_32245)and 1 other:

BGC0002111.3 (multiple genes) Lanthipeptide: andalusicin A or andalusicin B

Lanthipeptide: andalusicin A or andalusicin B

11

WSTQSQHHC

19

W++ ++C

15

WASTISNNC

23

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 25.44 out of 29.25

Confidence: medium

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.96 out of 30.25

Confidence: medium

Additional weak hits (4):

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.71 out of 25.75

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.28 out of 30.25

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.59 out of 30.97

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 24.24 out of 35.63

Confidence: weak

Lanthipeptides

TFBS Finder

Core peptide predictions

L6439_RS11890 - Class III

Cleavage pHMM score: 4.30

RODEO score: 0

Monoisotopic mass: 1960.2 Da

Molecular weight: 1961.3 Da

Number of bridges: 1

Alternative weights: (assuming N unmodified Ser/Thr residues); 1979.3 Da N = 1; 1997.3 Da N = 2; 2015.3 Da N = 3; 2033.4 Da N = 4; 2051.4 Da N = 5; 2069.4 Da N = 6; 2087.4 Da N = 7; 2105.4 Da N = 8

L6439_RS11920 - Class III

Cleavage pHMM score: -0.30

RODEO score: 0

Monoisotopic mass: 2498.3 Da

Molecular weight: 2499.7 Da

Number of bridges: 1

Alternative weights: (assuming N unmodified Ser/Thr residues); 2517.7 Da N = 1; 2535.7 Da N = 2; 2553.8 Da N = 3; 2571.8 Da N = 4; 2589.8 Da N = 5; 2607.8 Da N = 6; 2625.8 Da N = 7; 2643.9 Da N = 8; 2661.9 Da N = 9; 2679.9 Da N = 10; 2697.9 Da N = 11

L6439_RS11925 - Class III

Cleavage pHMM score: 4.30

RODEO score: 0

Monoisotopic mass: 2038.0 Da

Molecular weight: 2039.2 Da

Number of bridges: 1

Alternative weights: (assuming N unmodified Ser/Thr residues); 2057.3 Da N = 1; 2075.3 Da N = 2; 2093.3 Da N = 3; 2111.3 Da N = 4; 2129.3 Da N = 5; 2147.4 Da N = 6

L6439_RS11930 - Class III

Cleavage pHMM score: -0.30

RODEO score: 0

Monoisotopic mass: 2498.3 Da

Molecular weight: 2499.7 Da

Number of bridges: 1

Alternative weights: (assuming N unmodified Ser/Thr residues); 2517.7 Da N = 1; 2535.7 Da N = 2; 2553.8 Da N = 3; 2571.8 Da N = 4; 2589.8 Da N = 5; 2607.8 Da N = 6; 2625.8 Da N = 7; 2643.9 Da N = 8; 2661.9 Da N = 9; 2679.9 Da N = 10; 2697.9 Da N = 11

TFBS definitions

Regulator	Description
ColR	Phenol-responsive regulator
SypG	Regulator of biofilm formation and host colonization

NZ_AP025344.1 - Region 9 - NRPS

Download region SVG

Location: 2,771,103 - 2,844,921 nt. (total: 73,819 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

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

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

Hydrolases: esterase hydrolase

L6439_RS12315: thioesterase

smcogs: SMCOG1004: thioesterase

L6439_RS12350: hydrolase

smcogs: SMCOG1179: hydrolase

Lyases: decarboxylase

L6439_RS12230: Decarboxylase, pyridoxal-dependent

smcogs: SMCOG1180: Decarboxylase, pyridoxal-dependent

Isomerases: isomerase

L6439_RS12275: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: ligase synthase

L6439_RS12270: carbamoyl phosphate synthase small subunit

smcogs: SMCOG1249: carbamoyl phosphate synthase small subunit

L6439_RS12280: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS12285: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS12295: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS29305: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001758.4	0.74	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
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
BGC0001641.4	0.73	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.73	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001261.3	0.72	NRPS	AM-toxin	Alternaria alternata
BGC0001133.4	0.72	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001758.4	0.74	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
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
BGC0001641.4	0.73	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.73	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001261.3	0.72	NRPS	AM-toxin	Alternaria alternata
BGC0001133.4	0.72	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.31 out of 18.57

Confidence: strong

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.65 out of 27.78

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 23.16 out of 26.33

Confidence: medium

AfsR

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

Confidence: strong

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 20.76 out of 21.84

Confidence: strong

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 17.11 out of 19.52

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.33 out of 27.78

Confidence: medium

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 16.86 out of 18.57

Confidence: medium

Additional weak hits (19):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.25 out of 30.25

Confidence: weak

PsrA

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.26 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.64 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.08 out of 27.78

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.73 out of 31.73

Confidence: weak

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.06 out of 26.33

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.42 out of 31.73

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.05 out of 33.73

Confidence: weak

ANR

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

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.61 out of 30.25

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.60 out of 30.98

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.48 out of 29.65

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.79 out of 26.06

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 21.34 out of 29.25

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 20.96 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.17 out of 33.14

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.19 out of 20.01

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 13, location 2771102 - 2844921:

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

Polymer prediction:: (X - Thr) + (X) + (Ile - Ile - D-Ile) + (Ile - Val - X - X)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

L6439_RS12280: X

AMP-binding (95..533): 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:: NGIMGGLLTNHGWSLNVGQVPAYGMTEFSGSLCF
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

L6439_RS29305: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (39..441): 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:: LNDHFDFSVWEGNQIFGGEINMYGITETTVHATY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS12285: X - Ile - Ile - Ile

Search NORINE for peptide: strict or relaxed

AMP-binding (291..693): X

nrpys: Leu, 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:: TNNSFDGSTYEGFMFFGGEANGYGPTETTVFAAA
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (79% 8Å match); Leu DGYIIGGVFK (53% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1342..1734): Ile

nrpys: Ile

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: ile (Ile)

Stachelhaus prediction details:

Stachelhaus sequence:: TNNSFDGATFDGFMLFGGEMHMYGPTETTVFATS
Nearest Stachelhaus code(s):: Ile DGFFLGVVFK (79% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2397..2792): Ile

nrpys: Ile

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: ile (Ile)

Stachelhaus prediction details:

Stachelhaus sequence:: FNRSFDGSIFDGFMLVGGELNCYGPTETTVMATM
Nearest Stachelhaus code(s):: Ile or Val DGFFLGVVYK (71% 8Å match); Ile DGFFLGVVYK (68% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (3448..3850): Ile

nrpys: Ile

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: ile (Ile)

Stachelhaus prediction details:

Stachelhaus sequence:: TNNSFDGSTFEGFAFIGGEANAYGPTETTVFATT
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (79% 8Å match); Ile DGFFLGVVFK (68% 8Å match)
Stachelhaus code match:: 80% (moderate)

L6439_RS12295: Ile - Val - X - X

Search NORINE for peptide: strict or relaxed

AMP-binding (469..861): Ile

nrpys: Ile

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: ile (Ile)

Stachelhaus prediction details:

Stachelhaus sequence:: TNNSFDGATFDGFMLFGGELHMYGPTETTVYATC
Nearest Stachelhaus code(s):: Ile or Val DGFFLGVVYK (79% 8Å match); Leu DGFFLGVVYK (76% 8Å match); Ile DGFFLGVVYK (74% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1532..1933): 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:: TNNSFDGSTYEGFMFFGGEVNSYGPTETTVFATT
Nearest Stachelhaus code(s):: Val DGYFLGVVFK (76% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (2595..2991): X

nrpys: Leu, 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:: TRNSFDGSTYEGFMFFGGEANGYGPTETTVFATT
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (82% 8Å match); Leu DGYIIGGVFK (56% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (3645..4041): X

nrpys: Leu, 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:: TRNSFDGSTYEGFMFFGGEANGYGPTETTVFATT
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (82% 8Å match); Leu DGYIIGGVFK (56% 8Å match)
Stachelhaus code match:: 80% (moderate)

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
AfsR	Pleiotropic regulatory for antibiotic production
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
MexT	Global virulence regulator
ToxT	Regulator of MSHA biosynthesis

NZ_AP025344.1 - Region 10 - azole-containing-RiPP,terpene-precursor

Download region SVG

Location: 3,048,791 - 3,090,931 nt. (total: 42,141 nt) Show pHMM detection rules used

terpene-precursor: (PT_FPPS_like and not PT_HPP)
azole-containing-RiPP: ((YcaO or TIGR03604) and (((thio_amide and (PF06968 or PF04055 or PF07366)) or Lant_dehydr_C or Lant_dehydr_N or (PF06968 or PF04055 or PF07366)) or (goadsporin_like or PF00881 or TIGR03605)) or TIGR03882 or TIGR03603 or thiostrepton or TIGR03602)

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

Terpene

TFBS Finder

Azole RiPPs

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

L6439_RS13385: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

L6439_RS13430: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Hydrolases: esterase

L6439_RS13390: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: synthetase

L6439_RS13405: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002218.2	0.26	terpene	(-)-Cyatha-3,12-diene	Dentipellis sp. KUC8613
BGC0000616.4	0.24	ribosomal	amylocyclicin	Bacillus velezensis FZB42
BGC0001810.3	0.24	PKS	trehangelin	Polymorphospora rubra
BGC0000671.3	0.24	terpene	momilactone B	Oryza sativa Japonica Group
BGC0002496.3	0.23	NRPS	serratiochelin A, serratiochelin C, serratiochelin B	Serratia plymuthica
BGC0000502.5	0.21	ribosomal	cerecidin, cerecidin A1, cerecidin A2, cerecidin A3, cerecidin A4, cerecidin A5, cerecidin A6, cerecidin A7	Bacillus cereus
BGC0002062.2	0.21	PKS	agnestin A, agnestin B	Paecilomyces divaricatus
BGC0001789.3	0.21	ribosomal	suicin 90-1330	Streptococcus suis
BGC0002474.2	0.21	NRPS	agrobactin	Agrobacterium tumefaciens
BGC0000537.3	0.21	ribosomal	nisin U	Streptococcus uberis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002667.2	0.48	ribosomal	estericin A	Clostridium estertheticum
BGC0001173.5	0.47	ribosomal	plantazolicin	Bacillus pumilus ATCC 7061
BGC0001174.4	0.47	ribosomal	corynazolicin	Corynebacterium urealyticum DSM 7111
BGC0000600.3	0.46	ribosomal	thurincin H	Bacillus thuringiensis
BGC0001145.5	0.46	ribosomal	cyclothiazomycin b1	Streptomyces mobaraensis NBRC 13819 = DSM 40847
BGC0000603.5	0.45	ribosomal	cyclothiazomycin	Streptomyces hygroscopicus
BGC0001146.5	0.45	ribosomal	cyclothiazomycin C	Streptomyces sp. NRRL WC-3908
BGC0000607.5	0.45	ribosomal	micrococcin P1	Macrococcus caseolyticus
BGC0000589.5	0.44	ribosomal	microcin M	Escherichia coli Nissle 1917
BGC0002218.2	0.44	terpene	(-)-Cyatha-3,12-diene	Dentipellis sp. KUC8613

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:

L6439_RS13405: PT_FPPS_like

Domain 1 (536 - 759): 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:

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 18.82 out of 21.84

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 23.00 out of 29.72

Confidence: medium

Additional weak hits (10):

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 20.90 out of 29.25

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.94 out of 28.14

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.77 out of 31.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.12 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.60 out of 26.06

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.90 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 28.36 out of 36.54

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.81 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.98 out of 26.06

Confidence: weak

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 23.04 out of 30.12

Confidence: weak

(Thi)azol(in)e containing peptide predictions

No core peptides found.

RREFinder

Terpene

TFBS Finder

Azole RiPPs

RRE predictions

: RRE type: Heterocycloanthracin_C_RRE; Location: 1 - 91; Score: 154.4; RRE type: Thiopeptide_F_RRE; Location: 0 - 82; Score: 43.9

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
MexT	Global virulence regulator
NtrC	Nitrogen regulatory protein C

Core peptide predictions

No core peptides found.

NZ_AP025344.1 - Region 11 - HR-T2PKS,NRPS

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Location: 3,341,711 - 3,399,437 nt. (total: 57,727 nt) Show pHMM detection rules used

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

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

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 oxygenase

L6439_RS14880: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

L6439_RS14935: cytochrome P450

smcogs: SMCOG1034: cytochrome P450

Transferases: acetyltransferase aminotransferase

L6439_RS14780: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

L6439_RS14785: aminotransferase

smcogs: SMCOG1019: aminotransferase

L6439_RS14840: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Isomerases: mutase

L6439_RS14835: phosphoglycerate mutase

smcogs: SMCOG1101: phosphoglycerate mutase

Ligases: ligase synthase

L6439_RS14855: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

L6439_RS14860: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS14865: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

L6439_RS14870: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

L6439_RS14895: 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	0.87	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.80	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.79	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.78	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.77	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001050.5	0.76	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis
BGC0001133.4	0.76	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0000426.5	0.75	NRPS	sevadicin	Paenibacillus larvae
BGC0001166.5	0.75	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	0.74	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.72	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.71	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001050.5	0.70	NRPS, PKS	thalassospiramide A	Tistrella bauzanensis
BGC0001133.4	0.70	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0000426.5	0.70	NRPS	sevadicin	Paenibacillus larvae
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 26.68 out of 32.74

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 27.57 out of 29.38

Confidence: strong

ToxT

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

Confidence: strong

ToxT

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

Confidence: strong

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 27.99 out of 32.74

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.93 out of 29.38

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

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.06 out of 19.26

Confidence: strong

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.00 out of 26.06

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.72 out of 27.78

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.52 out of 26.06

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.70 out of 28.19

Confidence: medium

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 26.61 out of 30.98

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.40 out of 28.19

Confidence: medium

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.20 out of 20.01

Confidence: medium

Additional weak hits (12):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.14 out of 29.38

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 23.98 out of 30.22

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.80 out of 29.38

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.47 out of 21.55

Confidence: weak

ANR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.18 out of 26.06

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.15 out of 21.55

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.89 out of 29.65

Confidence: weak

MatP

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.74 out of 26.06

Confidence: weak

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 20.57 out of 30.12

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.18 out of 29.25

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 17, location 3341710 - 3399437:

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

Polymer prediction:: (Leu - D-Ala) + (Ile - Leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 18, location 3341710 - 3397043:

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

Polymer prediction:: (Leu - D-Ala) + (Ile - Leu)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 19, location 3357057 - 3399437:

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

Polymer prediction:: (Leu - D-Ala) + (Ile - Leu)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

L6439_RS14855: Ala - Ile - Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (266..666): 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:: TQLTFDVSVTEGNFFAAGEINVYGPTETTIYASE
Nearest Stachelhaus code(s):: Ala DVTNFALIYK (82% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1780..2175): Ile

nrpys: Ile

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: Aliphatic, branched hydrophobic (Val, Leu, Ile, Abu, Ival)
Single AA prediction:: ile (Ile)

Stachelhaus prediction details:

Stachelhaus sequence:: VNTSFDGSTFDGFMLFGGEKHVYGPTESTVFATC
Nearest Stachelhaus code(s):: Ile DGFFLGVVFK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2817..3207): 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:: Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
Small clusters prediction:: Unpolar aromatic ring (Phe, Trp)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: LMFAFDAACWEKIMITGGSFNAYGPTEASIVTAL
Nearest Stachelhaus code(s):: Leu DAWIIGAIVK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS14860: Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (467..857): 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:: Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
Small clusters prediction:: Unpolar aromatic ring (Phe, Trp)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: LMFAFDAACWEKIMITGGSFNAYGPTEASIVTAL
Nearest Stachelhaus code(s):: Leu DAWIIGAIVK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS14895: X

AMP-binding (10..398): 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:: DRIAFGLICGCAMALSSTAHNIYGSSEAGGISIK
Nearest Stachelhaus code(s):
Stachelhaus code match:: 0% (weak)

TFBS definitions

Regulator	Description
ArgR	Regulator of arginine biosynthesis genes
CRP	Cyclic AMP receptor protein
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
FuR variant 1	Ferric Uptake Regulator
FuR variant 2	Ferric Uptake Regulator
MogR	Repressor of flagellar motility genes
NuR	Nickel-responsive regulator
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_AP025344.1 - Region 12 - terpene-precursor

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Location: 3,766,518 - 3,787,393 nt. (total: 20,876 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

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

Transferases: carboxylase

L6439_RS16800: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Ligases: synthase synthetase

L6439_RS16750: 1-deoxy-D-xylulose-5-phosphate synthase

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

L6439_RS16760: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001361.3	0.49	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0002283.2	0.49	terpene	sodorifen	Serratia plymuthica
BGC0002397.2	0.47	terpene	astallatene	Arabidopsis thaliana
BGC0002400.2	0.44	terpene	boleracene	Brassica oleracea var. oleracea
BGC0002398.2	0.38	terpene	(-)-ent-quiannulatene	Arabidopsis thaliana
BGC0000665.5	0.38	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0002284.3	0.38	other (other)	corynecin III, corynecin I, corynecin II	Rhodococcus sp. H-CA8f
BGC0001594.3	0.37	other (other)	fischerindole L	Fischerella muscicola UTEX 1829
BGC0000635.3	0.36	terpene	carotenoid	Paracoccus sp. N81106
BGC0000666.5	0.36	terpene	xiamycin A	Streptomyces sp. SCSIO 02999

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001361.3	0.49	terpene	sodorifen	Serratia plymuthica 4Rx13
BGC0002283.2	0.49	terpene	sodorifen	Serratia plymuthica
BGC0002397.2	0.47	terpene	astallatene	Arabidopsis thaliana
BGC0002400.2	0.44	terpene	boleracene	Brassica oleracea var. oleracea
BGC0002398.2	0.38	terpene	(-)-ent-quiannulatene	Arabidopsis thaliana
BGC0000665.5	0.38	other (other), terpene	xiamycin, indosespene, sespenine, dixiamycin A, dixiamycin B, sulfadixiamycin A, sulfadixiamycin B, sulfadixiamycin C	Streptomyces sp. HKI0576
BGC0002284.3	0.38	other (other)	corynecin III, corynecin I, corynecin II	Rhodococcus sp. H-CA8f
BGC0001594.3	0.37	other (other)	fischerindole L	Fischerella muscicola UTEX 1829
BGC0000635.3	0.36	terpene	carotenoid	Paracoccus sp. N81106
BGC0000666.5	0.36	terpene	xiamycin A	Streptomyces sp. SCSIO 02999

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 precursor		FPP	C15	acyclic	PP

Genes with terpene domains:

L6439_RS16760: PT_FPPS_like

Domain 1 (25 - 290): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:: DMAPP, IPP → FPP

Transcription Factor Binding Sites

Binding sites found:

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 18.04 out of 18.57

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.94 out of 20.97

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.76 out of 24.78

Confidence: medium

AfsR

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

Confidence: medium

Additional weak hits (10):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 19.62 out of 29.38

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.38 out of 21.55

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.48 out of 25.88

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.21 out of 29.38

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.00 out of 32.93

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.14 out of 39.62

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 21.23 out of 30.98

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 21.80 out of 30.11

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.80 out of 24.78

Confidence: weak

LuxO

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

Confidence: weak

Terpene

TFBS Finder

Glossary

Acronym	Full name
DMAPP	Dimethylallyl diphosphate
FPP	Farnesyl diphosphate
IPP	Isopentenyl diphosphate
PP	Diphosphate

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
CcpA	Catabolite control protein A
LexA variant 2	Repressor of DNA damage response
ToxT	Regulator of MSHA biosynthesis

NZ_AP025344.1 - Region 13 - NRPS,T1PKS

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Location: 3,965,809 - 4,024,594 nt. (total: 58,786 nt) Show pHMM detection rules used

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

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

Transferases: methyltransferase

L6439_RS17655: methyltransferase

smcogs: SMCOG1089: methyltransferase

Hydrolases: hydrolase

L6439_RS17745: HAD-superfamily hydrolase, subfamily IA, variant

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

Ligases: ligase synthase

L6439_RS17660: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

L6439_RS17665: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

L6439_RS17670: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

L6439_RS17675: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

L6439_RS17680: 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	0.85	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.79	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.79	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000342.4	0.78	NRPS	enniatin	Fusarium equiseti
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.75	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	0.74	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.73	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.73	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.72	NRPS	AM-toxin	Alternaria alternata
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000342.4	0.71	NRPS	enniatin	Fusarium equiseti
BGC0001132.4	0.70	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.70	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	0.70	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.99 out of 27.55

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.51 out of 23.79

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 18.21 out of 20.47

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.51 out of 20.97

Confidence: medium

ZuR variant 1

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

Confidence: medium

Additional weak hits (21):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.47 out of 26.06

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.19 out of 27.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.76 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.15 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.25 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.22 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.68 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.63 out of 26.06

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.62 out of 29.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.16 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

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 21.71 out of 33.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.52 out of 31.73

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.41 out of 35.63

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.23 out of 20.01

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.53 out of 26.06

Confidence: weak

LuxO

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

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.45 out of 23.43

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.63 out of 32.74

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.06 out of 27.78

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 23.27 out of 30.98

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 21, location 3965808 - 4024594:

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

Polymer prediction:: (pk) + (X - X) + (mal) + (NMe-Thr)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

L6439_RS17660: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (507..921): 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:: LATHFDFSVWEGNQIFGGEINMYGITEITVHATF
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS17665: mal

PKS_AT (530..822): mal

ATSignature: Malonyl-CoA, inactive

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 87.5%; Propionyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 141.0
inactive: 96.8
Methoxymalonyl-CoA: 59.6
Methylmalonyl-CoA: 50.1
Propionyl-CoA: 30.9
Ethylmalonyl-CoA: 21.0
2-Methylbutyryl-CoA: 16.4
CHC-CoA: 13.2
fatty_acid: 8.4
Isobutyryl-CoA: 6.6
trans-1,2-CPDA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

L6439_RS17670: X - X

AMP-binding (501..893): 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:: Apolar, aliphatic (Gly, Ala, Val, Leu, Ile, Abu, Ival)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: MAQAFDAWVFEMVLISAGEYNAYGPSEATVWVTV
Nearest Stachelhaus code(s):: Phe DAFTVAAVWK (74% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1560..1979): 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:: FWQSHDPLLRDVHLFFGGDLNGYGATETQIMGIY
Nearest Stachelhaus code(s):: Htia DPHHFGLIGK (41% 8Å match)
Stachelhaus code match:: 70% (weak)

L6439_RS17675: pk

PKS_AT (613..906): pk

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; Methylmalonyl-CoA: 70.8%; Methoxymalonyl-CoA: 70.8%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 120.2
Methoxymalonyl-CoA: 116.2
Malonyl-CoA: 115.8
Isobutyryl-CoA: 81.5
Ethylmalonyl-CoA: 81.4
Propionyl-CoA: 70.0
2-Methylbutyryl-CoA: 58.5
trans-1,2-CPDA: 49.7
3-Methylbutyryl-CoA: 49.3
inactive: 42.3
Acetyl-CoA: 37.6
CHC-CoA: 30.7
Benzoyl-CoA: 28.4
fatty_acid: 22.1

L6439_RS17680: NH2

CAL_domain (147..466): NH2

minowa: NH2

Prediction, score:

NH2: 125.2
Acetyl-CoA: 52.2
fatty_acid: 37.0
AHBA: 19.7
shikimic_acid: 15.7

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
GnfM	Regulator of nitrogen-fixation genes
IolR	Regulator of the inositol catabolism
VqsM	Regulator of quorum-sensing signalling systems
ZuR variant 1	Zinc-responsive repressor

NZ_AP025344.1 - Region 14 - RiPP-like

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Location: 4,538,711 - 4,549,940 nt. (total: 11,230 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

reset view

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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

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
BGC0000616.4	0.40	ribosomal	amylocyclicin	Bacillus velezensis FZB42
BGC0001887.3	0.39	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0000563.4	0.36	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001579.4	0.35	ribosomal	duramycin	Streptomyces cinnamoneus
BGC0001173.5	0.33	ribosomal	plantazolicin	Bacillus pumilus ATCC 7061
BGC0000569.5	0.33	ribosomal	plantazolicin	Bacillus velezensis FZB42
BGC0001210.5	0.32	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000626.3	0.32	ribosomal	thuricin	Bacillus thuringiensis
BGC0002005.2	0.32	ribosomal	RaxX	Xanthomonas oryzae pv. oryzae
BGC0000539.5	0.31	ribosomal	nukacin ISK-1	Staphylococcus warneri

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000616.4	0.40	ribosomal	amylocyclicin	Bacillus velezensis FZB42
BGC0001887.3	0.39	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0000563.4	0.36	ribosomal	venezuelin	Streptomyces venezuelae ATCC 10712
BGC0001579.4	0.35	ribosomal	duramycin	Streptomyces cinnamoneus
BGC0001173.5	0.33	ribosomal	plantazolicin	Bacillus pumilus ATCC 7061
BGC0000569.5	0.33	ribosomal	plantazolicin	Bacillus velezensis FZB42
BGC0001210.5	0.32	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000626.3	0.32	ribosomal	thuricin	Bacillus thuringiensis
BGC0002005.2	0.32	ribosomal	RaxX	Xanthomonas oryzae pv. oryzae
BGC0000539.5	0.31	ribosomal	nukacin ISK-1	Staphylococcus warneri

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: 16.07 out of 18.46

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.69 out of 27.55

Confidence: medium

Additional weak hits (1):

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.04 out of 29.65

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
GnfM	Regulator of nitrogen-fixation genes
RpoN	Regulator of nitrogen assimilation and virulence

NZ_AP025344.1 - Region 15 - NRPS,transAT-PKS

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Location: 4,934,325 - 5,000,082 nt. (total: 65,758 nt) Show pHMM detection rules used

NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
transAT-PKS: (cds(PKS_AT and not (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) and (cds(ATd and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS)) or cds(tra_KS and PP-binding)))

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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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

L6439_RS22025: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Transferases: acylase methyltransferase

L6439_RS21920: methyltransferase

smcogs: SMCOG1089: methyltransferase

L6439_RS21995: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase hydrolase peptidase

L6439_RS21905: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

L6439_RS21970: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

L6439_RS22005: thioesterase

smcogs: SMCOG1004: thioesterase

L6439_RS22055: methionine aminopeptidase

smcogs: SMCOG1172: methionine aminopeptidase

Ligases: ligase synthase

L6439_RS21975: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

L6439_RS21980: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

L6439_RS21985: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

L6439_RS22000: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS22010: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter

L6439_RS22040: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

L6439_RS22045: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001251.4	0.70	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.70	NRPS	epichloenin A	Epichloe festucae
BGC0000342.4	0.70	NRPS	enniatin	Fusarium equiseti
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001273.3	0.67	PKS	asperlactone	Aspergillus ochraceus
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.67	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001825.4	0.69	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001251.4	0.68	NRPS	epichloenin A	Epichloe festucae
BGC0001250.4	0.68	NRPS	epichloenin A	Epichloe festucae
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001273.3	0.67	PKS	asperlactone	Aspergillus ochraceus
BGC0001132.4	0.67	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.67	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.80 out of 26.33

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.62 out of 18.16

Confidence: strong

ToxT

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

Confidence: strong

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.04 out of 27.78

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 20.10 out of 23.79

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 22.84 out of 24.78

Confidence: strong

AfsR

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

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.30 out of 24.78

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.80 out of 18.16

Confidence: strong

Additional weak hits (6):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.90 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.96 out of 26.06

Confidence: weak

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 23.87 out of 30.12

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.46 out of 35.63

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.00 out of 30.98

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.47 out of 33.14

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 23, location 4934324 - 5000082:

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

Polymer prediction:: (D-Asn) + (Gly) + (ccmal) + (mal - bAla)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

L6439_RS21980: bAla

Search NORINE for peptide: strict or relaxed

AMP-binding (1215..1616): bAla

nrpys: 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:: RWMTFVDSICEGTLVSSGEINLYGSSEVSADVTC
Nearest Stachelhaus code(s):: bAla VDWVVSLADK (76% 8Å match)
Stachelhaus code match:: 80% (moderate)

L6439_RS21995: mal

PKS_AT (6..287): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 120.5
inactive: 57.1
Methylmalonyl-CoA: 56.8
Methoxymalonyl-CoA: 55.5
Isobutyryl-CoA: 31.7
Propionyl-CoA: 24.5
Acetyl-CoA: 21.5
Ethylmalonyl-CoA: 20.3
Benzoyl-CoA: 14.8
fatty_acid: 13.6
CHC-CoA: 13.6
2-Methylbutyryl-CoA: 9.6
trans-1,2-CPDA: 0.0
3-Methylbutyryl-CoA: 0.0

L6439_RS22000: X - bAla - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (464..847): 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:: LELTCGLSITEGNFMVSGGVSFYGFTESAIYALC
Nearest Stachelhaus code(s):: Cys DLQNMSLIWK (38% 8Å match)
Stachelhaus code match:: 60% (weak)

AMP-binding (1118..1514): bAla

nrpys: 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:: RWMTFVDSIWEGTLMASGELNLYGSSEVSADVCC
Nearest Stachelhaus code(s):: bAla VDWVTSLADK (85% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (2146..2536): 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:: FGITFDIFALEIQAMVGGEYNMYGPTETTVWSTL
Nearest Stachelhaus code(s):: Gly DILQMGMVWK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS22010: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (461..854): 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:: YWASFDLTVTSTKLIVGGEYNEYGPTEATVGCMY
Nearest Stachelhaus code(s):: Asn DLTKIGEVGK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
AbrC3	Antibiotic production activator
AfsR	Pleiotropic regulatory for antibiotic production
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
IolR	Regulator of the inositol catabolism
LexA variant 2	Repressor of DNA damage response
ToxT	Regulator of MSHA biosynthesis

NZ_AP025344.1 - Region 16 - ectoine

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Location: 5,419,929 - 5,430,312 nt. (total: 10,384 nt) Show pHMM detection rules used

ectoine: ectoine_synt

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

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

Transferases: aminotransferase

L6439_RS24090: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002052.3	0.80	other (ectoine)	ectoine	Streptomyces sp.
BGC0000853.3	0.80	other (other)	ectoine	Streptomyces anulatus
BGC0000858.3	0.73	other (other)	ectoine	Methylobacter marinus
BGC0000855.3	0.72	other (other)	ectoine	Methylomicrobium kenyense
BGC0000852.5	0.71	other (other)	ectoine	Sporosarcina pasteurii
BGC0000859.3	0.66	other (other)	ectoine	Methylomicrobium alcaliphilum
BGC0000856.3	0.66	other (other)	ectoine	Methylophaga thalassica
BGC0000857.3	0.60	other (other)	ectoine	Methylophaga alcalica
BGC0000854.3	0.60	other (other)	ectoine	Methylomicrobium alcaliphilum 20Z
BGC0000860.3	0.59	other (other)	ectoine	Methylarcula marina

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002052.3	0.80	other (ectoine)	ectoine	Streptomyces sp.
BGC0000853.3	0.80	other (other)	ectoine	Streptomyces anulatus
BGC0000858.3	0.73	other (other)	ectoine	Methylobacter marinus
BGC0000855.3	0.72	other (other)	ectoine	Methylomicrobium kenyense
BGC0000852.5	0.71	other (other)	ectoine	Sporosarcina pasteurii
BGC0000859.3	0.66	other (other)	ectoine	Methylomicrobium alcaliphilum
BGC0000856.3	0.66	other (other)	ectoine	Methylophaga thalassica
BGC0000857.3	0.60	other (other)	ectoine	Methylophaga alcalica
BGC0000854.3	0.60	other (other)	ectoine	Methylomicrobium alcaliphilum 20Z
BGC0000860.3	0.59	other (other)	ectoine	Methylarcula marina

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (1):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.00 out of 31.73

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description

NZ_AP025344.1 - Region 17 - NRPS

Download region SVG

Location: 5,484,109 - 5,565,023 nt. (total: 80,915 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

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

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: oxidoreductase

L6439_RS24430: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

Transferases: aminotransferase

L6439_RS24520: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Ligases: ligase

L6439_RS24495: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

L6439_RS24510: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

L6439_RS24515: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000408.5	0.89	NRPS	polymyxin	Paenibacillus polymyxa
BGC0001192.5	0.88	NRPS	colistin A, colistin B	Paenibacillus alvei
BGC0001153.5	0.88	NRPS	polymyxin B	Paenibacillus polymyxa
BGC0002653.2	0.85	NRPS	macolacin	Paenibacillus xylanexedens
BGC0000426.5	0.76	NRPS	sevadicin	Paenibacillus larvae
BGC0001758.4	0.76	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002071.2	0.74	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001133.4	0.74	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000408.5	0.89	NRPS	polymyxin	Paenibacillus polymyxa
BGC0001192.5	0.88	NRPS	colistin A, colistin B	Paenibacillus alvei
BGC0001153.5	0.88	NRPS	polymyxin B	Paenibacillus polymyxa
BGC0002653.2	0.85	NRPS	macolacin	Paenibacillus xylanexedens
BGC0000426.5	0.76	NRPS	sevadicin	Paenibacillus larvae
BGC0001758.4	0.76	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002071.2	0.74	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001133.4	0.74	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004

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: 18.48 out of 20.97

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.24 out of 27.78

Confidence: medium

ToxT

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

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.17 out of 27.78

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: 19.26 out of 19.26

Confidence: strong

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.87 out of 27.55

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.41 out of 20.97

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.15 out of 27.78

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.59 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.25 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.45 out of 28.19

Confidence: medium

OsdR

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

Confidence: medium

Additional weak hits (29):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 20.41 out of 29.38

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.54 out of 31.73

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.98 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.75 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 25.02 out of 31.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.83 out of 29.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.51 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.31 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.06 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.76 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.47 out of 30.25

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.93 out of 30.25

Confidence: weak

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 19.75 out of 27.78

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 21.79 out of 32.93

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.62 out of 28.14

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 20.66 out of 30.25

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.03 out of 32.93

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.70 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.75 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.89 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 19.24 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 18.97 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.47 out of 26.06

Confidence: weak

OsdR

Description: Development and stress management regulator
Species: Streptomyces coelicolor
Score: 22.15 out of 30.12

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.89 out of 35.63

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 19.94 out of 28.19

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 21.88 out of 35.63

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 22.43 out of 29.65

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.97 out of 33.14

Confidence: weak

Module view

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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 25, location 5484108 - 5565023:

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

Polymer prediction:: (D-Leu - Thr - Dab - Dab - Thr) + (Dab - Thr - D-Dab - Dab - Dab)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

L6439_RS24495: Dab - Thr - Dab - Dab - Dab

Search NORINE for peptide: strict or relaxed

AMP-binding (466..878): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: Orn and hydroxy-Orn specific (Orn, OH-Orn)
Single AA prediction:: orn (Orn)

Stachelhaus prediction details:

Stachelhaus sequence:: TAYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISSIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1520..1927): 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:: LNEHFDFSVWEGNQIFGGEINMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2585..3018): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: Orn and hydroxy-Orn specific (Orn, OH-Orn)
Single AA prediction:: orn (Orn)

Stachelhaus prediction details:

Stachelhaus sequence:: TGYAFDVFVGDRESITSSDINSYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISSIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4138..4577): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: Orn and hydroxy-Orn specific (Orn, OH-Orn)
Single AA prediction:: orn (Orn)

Stachelhaus prediction details:

Stachelhaus sequence:: TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISAIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5220..5659): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: Orn and hydroxy-Orn specific (Orn, OH-Orn)
Single AA prediction:: orn (Orn)

Stachelhaus prediction details:

Stachelhaus sequence:: TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISAIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS24510: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (269..676): 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:: LNEHFDFSVWEGNQIFGGEINMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

L6439_RS24515: Leu - Thr - Dab - Dab

Search NORINE for peptide: strict or relaxed

AMP-binding (279..668): 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:: Cyclic aliphatic chain (polar NH2 group) (Pro, Hpr)
Small clusters prediction:: Unpolar aromatic ring (Phe, Trp)
Single AA prediction:: N/A

Stachelhaus prediction details:

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

AMP-binding (1787..2194): 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:: LNEHFDFSVWEGNQIFGGEINMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2836..3275): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: Orn and hydroxy-Orn specific (Orn, OH-Orn)
Single AA prediction:: orn (Orn)

Stachelhaus prediction details:

Stachelhaus sequence:: TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISAIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3920..4359): Dab

nrpys: Dab

SVM prediction details:

Predicted physicochemical class:: N/A
Large clusters prediction:: Long positively charged side chain (Orn, Lys, Arg)
Small clusters prediction:: Orn and hydroxy-Orn specific (Orn, OH-Orn)
Single AA prediction:: orn (Orn)

Stachelhaus prediction details:

Stachelhaus sequence:: TGYAFDVFVGDRESITSSDINAYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISAIDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)