GCF_022649565.1 - 19 region(s)

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Location: 62,765 - 156,464 nt. (total: 93,700 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

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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

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: acyltransferase aminotransferase glycosyltransferase

CPY53_RS00245: acyltransferase 3

smcogs: SMCOG1088: acyltransferase 3

CPY53_RS00370: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

CPY53_RS00420: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

Hydrolases: esterase hydrolase

CPY53_RS00310: thioesterase

smcogs: SMCOG1004: thioesterase

CPY53_RS00345: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase

CPY53_RS00325: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CPY53_RS00330: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CPY53_RS00335: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001843.2	0.83	NRPS	tridecaptin M	Paenibacillus sp. M-152
BGC0000449.5	0.82	NRPS	tridecaptin	Paenibacillus terrae
BGC0001758.4	0.75	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002071.2	0.74	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001133.4	0.73	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.72	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001843.2	0.83	NRPS	tridecaptin M	Paenibacillus sp. M-152
BGC0000449.5	0.82	NRPS	tridecaptin	Paenibacillus terrae
BGC0001758.4	0.75	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002071.2	0.74	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001133.4	0.73	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.72	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:

ToxT

Description: Regulator of MSHA biosynthesis
Species: Vibrio cholerae O395
Score: 17.13 out of 18.57

Confidence: medium

ArcA

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

Confidence: strong

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.87 out of 21.55

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.14 out of 25.31

Confidence: medium

Additional weak hits (4):

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 28.80 out of 39.62

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.46 out of 21.55

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.82 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 1, location 62764 - 156464:

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

Polymer prediction:: (D-Val - D-Dab - D-Gly - D-Ser - D-Trp - Ser) + (Dab - D-Dab - Trp - Glu - Val) + (D-Ile - Ala)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CPY53_RS00325: Val - Dab - Gly - Ser - Trp

Search NORINE for peptide: strict or relaxed

AMP-binding (464..896): 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:: LNTGFDASTFEGWLLVGGDINGYGPTENTTFSTT
Nearest Stachelhaus code(s):: Val DAFWLGGTFK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2026..2485): 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 (3618..4015): 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:: FGMTFDIFVLELQMMVGGEYNMYGPTETTVWSTV
Nearest Stachelhaus code(s):: Gly DILQMGMVWK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (5157..5570): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTFDVSVWEWHFFASGEVNLYGPTEATVDVSY
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (6691..7086): Trp

nrpys: Trp

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:: LYFAFDAACWEQALFTAGSYNGYGPTENSVATSI
Nearest Stachelhaus code(s):: Trp DAWAFAGVAK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

CPY53_RS00330: Ser - Dab - Dab - Trp - Glu

Search NORINE for peptide: strict or relaxed

AMP-binding (35..453): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTFDVSVWEWHFFASGEVNLYGPTEATVDVSY
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1125..1584): 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:: TAYAFDVFVGDQESITSSDINSYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISSIDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2230..2689): 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 (3807..4202): Trp

nrpys: Trp

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:: LYFAFDAACWEQALVTAGSYNGYGPTENSVATSI
Nearest Stachelhaus code(s):: Trp DAWAFAGVAK (97% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (4866..5291): Glu

nrpys: Glu

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: glu,gln (Glu, Gln)
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: LALSFDASVKQADGLIGGETNVYGPTEATVDATA
Nearest Stachelhaus code(s):: Glu DAKDLGVVDK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

CPY53_RS00335: Val - Ile - Ala

Search NORINE for peptide: strict or relaxed

AMP-binding (268..716): 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:: LNTGFDASTFEGWLLVGGDINGYGPTENTTFSTT
Nearest Stachelhaus code(s):: Val DAFWLGGTFK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1363..1770): 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:: N/A

Stachelhaus prediction details:

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

AMP-binding (2905..3298): Ala

nrpys: Ala

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: LNTCFDVSTFEGWLLVGGDINGYGPTENTTFSTT
Nearest Stachelhaus code(s):: Ala DVFWLGGTFK (100% 8Å match); Val DVFWLGGTFK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
ArcA	Repressor of carbon oxidation
CatR	H2O2-responsive repressor
ToxT	Regulator of MSHA biosynthesis

NZ_CP023711.1 - Region 2 - NRPS

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Location: 306,246 - 348,195 nt. (total: 41,950 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 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: amidase hydrolase

CPY53_RS01130: amidase

smcogs: SMCOG1105: amidase

CPY53_RS01220: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase synthase

CPY53_RS01180: carbamoyl phosphate synthase small subunit

smcogs: SMCOG1249: carbamoyl phosphate synthase small subunit

CPY53_RS01185: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.60	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000307.4	0.59	NRPS	AbT1	Aureobasidium pullulans
BGC0000342.4	0.59	NRPS	enniatin	Fusarium equiseti
BGC0001641.4	0.59	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.59	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001128.4	0.58	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.58	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.58	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.58	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.60	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0000307.4	0.59	NRPS	AbT1	Aureobasidium pullulans
BGC0000342.4	0.59	NRPS	enniatin	Fusarium equiseti
BGC0001641.4	0.59	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.59	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001128.4	0.58	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.58	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.58	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001132.4	0.58	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ArcA

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

Confidence: strong

ANR

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

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.64 out of 26.06

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.29 out of 26.06

Confidence: medium

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.32 out of 30.25

Confidence: medium

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.14 out of 27.18

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 20.57 out of 25.31

Confidence: medium

Additional weak hits (4):

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 27.57 out of 39.62

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.36 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.76 out of 36.54

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.16 out of 27.18

Confidence: weak

Detailed domain annotation

Selected features only

Show module domains

TFBS Finder

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
ArcA	Repressor of carbon oxidation
CatR	H2O2-responsive repressor
ColR	Phenol-responsive regulator
MogR	Repressor of flagellar motility genes
NrdR	Represses ribonucleotide reductase encoding genes

NZ_CP023711.1 - Region 3 - NRPS,T1PKS

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Location: 371,362 - 447,501 nt. (total: 76,140 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

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 oxidoreductase

CPY53_RS01390: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CPY53_RS01440: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CPY53_RS01460: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Transferases: aminotransferase phosphotransferase

CPY53_RS01425: aminotransferase

smcogs: SMCOG1019: aminotransferase

CPY53_RS01475: Glucose-specific phosphotransferase enzyme IIA

smcogs: SMCOG1145: Glucose-specific phosphotransferase enzyme IIA

Hydrolases: esterase

CPY53_RS01415: thioesterase

smcogs: SMCOG1004: thioesterase

Ligases: ligase synthase

CPY53_RS01400: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

CPY53_RS01405: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CPY53_RS01410: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.86	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.83	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.81	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.81	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002071.2	0.79	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
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
BGC0001825.4	0.75	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001641.4	0.71	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	0.75	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0002071.2	0.74	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001133.4	0.73	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001128.4	0.73	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002286.3	0.72	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.72	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:

RpoN

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

Confidence: strong

RpoN

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

Confidence: strong

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.54 out of 18.46

Confidence: medium

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.13 out of 26.85

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.79 out of 23.79

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46

Confidence: medium

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.62 out of 21.55

Confidence: strong

AfsR

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

Confidence: strong

AfsR

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

Confidence: medium

MexT

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

Confidence: medium

Additional weak hits (8):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.82 out of 27.55

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.00 out of 30.25

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 25.75

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.62 out of 21.55

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.06 out of 25.88

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.71 out of 30.97

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.60 out of 30.97

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 20.83 out of 29.65

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 3, location 371361 - 447501:

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

Polymer prediction:: (pk - X) + (Thr - Ser - Orn - Ser - D-Ala) + (Phe - Gln - Glu)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CPY53_RS01400: pk - X

PKS_AT (536..823): pk

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%; Methylmalonyl-CoA: 62.5%; Isobutyryl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 124.4
Methoxymalonyl-CoA: 114.4
Malonyl-CoA: 108.3
Isobutyryl-CoA: 96.1
trans-1,2-CPDA: 87.6
Ethylmalonyl-CoA: 85.7
Propionyl-CoA: 72.0
2-Methylbutyryl-CoA: 65.3
CHC-CoA: 55.3
3-Methylbutyryl-CoA: 46.4
Benzoyl-CoA: 46.3
Acetyl-CoA: 45.6
inactive: 35.1
fatty_acid: 19.3

AMP-binding (2281..2686): X

nrpys: (unknown)

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: HAESFDVSVWQAEVLITGEVNAYGPAEAADDITL
Nearest Stachelhaus code(s):: Dab DIWELTADDK (74% 8Å match); Ser DVWEMTADDK (71% 8Å match)
Stachelhaus code match:: 90% (moderate)

CPY53_RS01405: Thr - Ser - Orn - Ser - Ala

Search NORINE for peptide: strict or relaxed

AMP-binding (501..900): 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:: LNSHFDFSVWEGNQIFGGEINMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1542..1947): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTFDVSVWEWHFFASGEHNLYGPTEATVDVSY
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2591..2993): 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:: IAWAFDVFVGDRESILGSDVNSYGVTESTIDSSY
Nearest Stachelhaus code(s):: Orn DVGEIGSIDK (88% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3635..4040): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTFDVSVWEWHFFASGEHNLYGPTEATVDVSY
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (4722..5122): 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:: IALTFDVSVAEGNFFAAGEENIYGPTESTIYAAG
Nearest Stachelhaus code(s):: Ala DVANFAIIYK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

CPY53_RS01410: Phe - Gln - Glu

Search NORINE for peptide: strict or relaxed

AMP-binding (471..861): Phe

nrpys: Phe

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
Small clusters prediction:: Unpolar aromatic ring (Phe, Trp)
Single AA prediction:: phe (Phe)

Stachelhaus prediction details:

Stachelhaus sequence:: LFFAFDAAVWEMTLIAAGSINAYGPTETTVCATV
Nearest Stachelhaus code(s):: Phe DAWTIAAVCK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1505..1907): Gln

nrpys: Gln

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: glu,gln (Glu, Gln)
Single AA prediction:: gln (Gln)

Stachelhaus prediction details:

Stachelhaus sequence:: LGLAFDASVQQADGIIGGDTNVYGPTECCVDSTE
Nearest Stachelhaus code(s):: Gln DAQDLGVVDK (82% 8Å match); Glu DAKDIGVVDK (82% 8Å match); Ile DAQDLGVVDK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (2549..2951): Glu

nrpys: Glu

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: glu,gln (Glu, Gln)
Single AA prediction:: gln (Gln)

Stachelhaus prediction details:

Stachelhaus sequence:: LGLSFDASVKQADGIIGGETNVYGPTECCVDSTY
Nearest Stachelhaus code(s):: Glu DAKDIGVVDK (79% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
ArcA	Repressor of carbon oxidation
IolR	Regulator of the inositol catabolism
MexT	Global virulence regulator
RpoN	Regulator of nitrogen assimilation and virulence
RutR	Regulator of the pyrimidine and purine metabolism

NZ_CP023711.1 - Region 4 - betalactone

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Location: 521,767 - 552,702 nt. (total: 30,936 nt) Show pHMM detection rules used

betalactone: (HMGL-like and AMP-binding)

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

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

CPY53_RS01950: dehydrogenase

smcogs: SMCOG1181: dehydrogenase

Hydrolases: hydrolase

CPY53_RS01930: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

Ligases: synthase

CPY53_RS01915: 2-isopropylmalate synthase

smcogs: SMCOG1271: 2-isopropylmalate synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.59	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.59	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.59	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.59	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.58	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.58	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.58	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001844.4	0.44	NRPS	holrhizin A, holrhizin B, holrhizin C, holrhizin D	Paraburkholderia rhizoxinica HKI 454
BGC0002518.3	0.44	NRPS	syringafactin A, syringafactin C	Pseudomonas sp. SZ57
BGC0000426.5	0.44	NRPS	sevadicin	Paenibacillus larvae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.59	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.59	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.59	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.59	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	0.58	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.58	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.58	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001844.4	0.44	NRPS	holrhizin A, holrhizin B, holrhizin C, holrhizin D	Paraburkholderia rhizoxinica HKI 454
BGC0002518.3	0.44	NRPS	syringafactin A, syringafactin C	Pseudomonas sp. SZ57
BGC0000426.5	0.44	NRPS	sevadicin	Paenibacillus larvae

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

PerR

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

Confidence: strong

ToxT

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

Confidence: strong

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.44 out of 28.14

Confidence: medium

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.01 out of 32.93

Confidence: medium

Additional weak hits (5):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.50 out of 29.38

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.39 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.20 out of 26.06

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.42 out of 36.54

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.39 out of 32.93

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
LexA variant 3	Repressor of DNA damage response
PerR	Peroxide regulator
ToxT	Regulator of MSHA biosynthesis

NZ_CP023711.1 - Region 5 - cyclic-lactone-autoinducer

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Location: 593,418 - 613,966 nt. (total: 20,549 nt) Show pHMM detection rules used

cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

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

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

CPY53_RS02225: NADH:flavin oxidoreductase/NADH oxidase

smcogs: SMCOG1217: NADH:flavin oxidoreductase/NADH oxidase

Hydrolases: deacetylase hydrolase

CPY53_RS02150: amidohydrolase

smcogs: SMCOG1244: amidohydrolase

CPY53_RS02230: polysaccharide deacetylase

smcogs: SMCOG1235: polysaccharide deacetylase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000504.5	0.41	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0000916.5	0.39	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0000772.5	0.38	saccharide	lipopolysaccharide	Brucella melitensis
BGC0002442.3	0.36	ribosomal	toyoncin	Bacillus toyonensis
BGC0001304.3	0.36	PKS	aflavarin	Aspergillus flavus NRRL3357
BGC0000551.5	0.36	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000518.3	0.35	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0002698.2	0.35	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0001636.4	0.34	NRPS	KK-1	Curvularia clavata
BGC0000541.5	0.33	ribosomal	paenicidin A	Paenibacillus polymyxa

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000504.5	0.41	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0000916.5	0.39	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0000772.5	0.38	saccharide	lipopolysaccharide	Brucella melitensis
BGC0002442.3	0.36	ribosomal	toyoncin	Bacillus toyonensis
BGC0001304.3	0.36	PKS	aflavarin	Aspergillus flavus NRRL3357
BGC0000551.5	0.36	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000518.3	0.35	ribosomal	informatipeptin	Streptomyces viridochromogenes DSM 40736
BGC0002698.2	0.35	ribosomal	phaeornamide	Pseudophaeobacter arcticus DSM 23566
BGC0001636.4	0.34	NRPS	KK-1	Curvularia clavata
BGC0000541.5	0.33	ribosomal	paenicidin A	Paenibacillus polymyxa

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.99 out of 20.47

Confidence: medium

VqsM

Description: Regulator of quorum-sensing signalling systems
Species: Pseudomonas aeruginosa PAO1
Score: 17.88 out of 20.47

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.30 out of 27.78

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 24.68 out of 28.19

Confidence: strong

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.31 out of 24.78

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.08 out of 28.19

Confidence: medium

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 19.49 out of 20.01

Confidence: strong

Additional weak hits (4):

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 21.04 out of 30.22

Confidence: weak

CsoR

Description: Copper-responsive repressor
Species: Streptomyces lividans
Score: 22.48 out of 32.38

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.31 out of 25.75

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.71 out of 33.14

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
ArgR	Regulator of arginine biosynthesis genes
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2	Repressor of DNA damage response
VqsM	Regulator of quorum-sensing signalling systems
ZuR variant 1	Zinc-responsive repressor

NZ_CP023711.1 - Region 6 - terpene-precursor

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Location: 1,012,303 - 1,033,226 nt. (total: 20,924 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

CPY53_RS04390: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Ligases: synthase synthetase

CPY53_RS04345: 1-deoxy-D-xylulose-5-phosphate synthase

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

CPY53_RS04350: 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
BGC0000666.5	0.36	terpene	xiamycin A	Streptomyces sp. SCSIO 02999
BGC0001501.5	0.36	other (other)	ambiguine P	Fischerella sp. TAU

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
BGC0000666.5	0.36	terpene	xiamycin A	Streptomyces sp. SCSIO 02999
BGC0001501.5	0.36	other (other)	ambiguine P	Fischerella sp. TAU

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:

CPY53_RS04350: PT_FPPS_like

Domain 1 (41 - 307): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:: IPP, DMAPP → FPP

Transcription Factor Binding Sites

Binding sites found:

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.38 out of 26.06

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.03 out of 26.06

Confidence: medium

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.24 out of 25.88

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.85 out of 28.19

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.34 out of 24.78

Confidence: medium

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.60 out of 25.88

Confidence: medium

Additional weak hits (3):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.78 out of 29.38

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

MatP

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

Confidence: weak

Terpene

TFBS Finder

Glossary

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

TFBS definitions

Regulator	Description
LexA variant 2	Repressor of DNA damage response
MogR	Repressor of flagellar motility genes
PsrA	Oleic acid responsive regulator
ZuR variant 1	Zinc-responsive repressor

NZ_CP023711.1 - Region 7 - NRPS,PKS-like,T3PKS,transAT-PKS

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Location: 1,191,460 - 1,293,368 nt. (total: 101,909 nt) Show pHMM detection rules used

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)))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)
PKS-like: (t2pks2 or ksIII)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

NRPS/PKS modules

NRPS/PKS domains

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

CPY53_RS05215: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CPY53_RS05220: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CPY53_RS05230: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

CPY53_RS05365: dehydrogenase

smcogs: SMCOG1181: dehydrogenase

Transferases: PPTase acetyltransferase acylase

CPY53_RS05205: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CPY53_RS05210: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CPY53_RS05265: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

CPY53_RS05370: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase

CPY53_RS05275: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

Lyases: hydratase

CPY53_RS05225: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

CPY53_RS05240: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

CPY53_RS05245: enoyl-CoA hydratase

smcogs: SMCOG1023: enoyl-CoA hydratase

Ligases: ligase synthase

CPY53_RS05235: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CPY53_RS05250: hydroxymethylglutaryl-CoA synthase

smcogs: SMCOG1043: hydroxymethylglutaryl-CoA synthase

CPY53_RS05255: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CPY53_RS05375: 3-oxoacyl-(acyl carrier protein) synthase III

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

Translocases: transporter

CPY53_RS05145: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	1.45	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	1.33	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	1.31	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	1.31	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001758.4	1.28	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	1.26	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	1.24	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000205.3	1.12	PKS	bryostatin	Candidatus Endobugula sertula
BGC0001164.3	1.06	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0002518.3	0.79	NRPS	syringafactin A, syringafactin C	Pseudomonas sp. SZ57

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.69	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.66	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0000205.3	0.65	PKS	bryostatin	Candidatus Endobugula sertula
BGC0001758.4	0.65	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001244.3	0.62	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0002276.2	0.62	NRPS	choline	Aspergillus nidulans FGSC A4

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: 24.98 out of 27.55

Confidence: strong

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 25.77 out of 26.06

Confidence: strong

ANR

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

Confidence: medium

RpoN

Description: Regulator of nitrogen assimilation and virulence
Species: Salmonella & Vibrio sp.
Score: 16.16 out of 18.46

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.79 out of 20.97

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 23.09 out of 27.78

Confidence: medium

ColR

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

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.30 out of 27.78

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.75 out of 28.19

Confidence: medium

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.84 out of 32.93

Confidence: medium

Additional weak hits (16):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.92 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.29 out of 31.73

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.68 out of 30.25

Confidence: weak

CopR

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

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.47 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.14 out of 26.06

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.32 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.11 out of 29.38

Confidence: weak

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.51 out of 32.93

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.86 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.56 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.96 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.79 out of 26.06

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.96 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 22.84 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 7, location 1191459 - 1293368:

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

Polymer prediction:: (Acetyl-CoA - Gly - ohmal - Me-mal) + (ohmal - mal - ccmal - ccmal - mal) + (ccmal - Me-ccmal - ohmal) + (ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 8, location 1191459 - 1289056:

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

Polymer prediction:: (Acetyl-CoA - Gly - ohmal - Me-mal) + (ohmal - mal - ccmal - ccmal - mal) + (ccmal - Me-ccmal - ohmal) + (ccmal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 9, location 1250842 - 1292105:

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

Polymer prediction:: (Acetyl-CoA - Gly - ohmal - Me-mal) + (ohmal - mal - ccmal - ccmal - mal)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 10, location 1252120 - 1293368:

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

Polymer prediction:: (Acetyl-CoA - Gly - ohmal - Me-mal) + (ohmal - mal - ccmal - ccmal - mal)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CPY53_RS05205: mal

PKS_AT (4..283): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 66.7%; Methylmalonyl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 96.7
inactive: 35.3
Methoxymalonyl-CoA: 25.1
Methylmalonyl-CoA: 23.6
fatty_acid: 13.6
Propionyl-CoA: 12.2
2-Methylbutyryl-CoA: 11.3
CHC-CoA: 9.6
Isobutyryl-CoA: 9.0
trans-1,2-CPDA: 0.0
Ethylmalonyl-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

CPY53_RS05210: mal

PKS_AT (7..298): mal

ATSignature: (unknown)

No matches above 50%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 41.7
inactive: 29.1
Methoxymalonyl-CoA: 14.1
Methylmalonyl-CoA: 9.4
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Propionyl-CoA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

CPY53_RS05235: Acetyl-CoA - Gly

Search NORINE for peptide: strict or relaxed

CAL_domain (66..485): Acetyl-CoA

minowa: Acetyl-CoA

Prediction, score:

Acetyl-CoA: 102.1
fatty_acid: 15.5
NH2: 8.4
AHBA: 5.0
shikimic_acid: 0.0

AMP-binding (1159..1555): 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:: FSMTFDIAGLELQALCGGEWNMFGPTETTIWSTI
Nearest Stachelhaus code(s):: Gly DILQLGMIWK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
ColR	Phenol-responsive regulator
GnfM	Regulator of nitrogen-fixation genes
LexA variant 3	Repressor of DNA damage response
MogR	Repressor of flagellar motility genes
RpoN	Regulator of nitrogen assimilation and virulence
ZuR variant 1	Zinc-responsive repressor

NZ_CP023711.1 - Region 8 - terpene-precursor

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Location: 1,572,926 - 1,595,313 nt. (total: 22,388 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

Ligases: synthetase

CPY53_RS06730: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	terpene-precursor	Similarity score	Type	Compound(s)	Organism
BGC0001910.4		0.29	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0002007.2		0.24	terpene	atolypene A, atolypene B	Amycolatopsis tolypomycina

Reference	Aggregated	Similarity score	Type	Compound(s)	Organism
BGC0001910.4		0.29	terpene	cyslabdan A, cyslabdan B, cyslabdan C	Streptomyces cyslabdanicus
BGC0002007.2		0.24	terpene	atolypene A, atolypene B	Amycolatopsis tolypomycina

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:

CPY53_RS06730: PT_FPPS_like

Domain 1 (537 - 761): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

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

Transcription Factor Binding Sites

Binding sites found:

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.61 out of 24.78

Confidence: medium

Additional weak hits (3):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.60 out of 31.73

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.15 out of 23.43

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.85 out of 36.53

Confidence: weak

Terpene

TFBS Finder

Glossary

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

TFBS definitions

Regulator	Description
LexA variant 2	Repressor of DNA damage response

NZ_CP023711.1 - Region 9 - NRPS,transAT-PKS

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Location: 1,881,054 - 1,962,987 nt. (total: 81,934 nt) Show pHMM detection rules used

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)))
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: acylase aminotransferase methyltransferase

CPY53_RS07950: aminotransferase class V

smcogs: SMCOG1139: aminotransferase class V

CPY53_RS08050: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

CPY53_RS08060: O-methyltransferase

smcogs: SMCOG1042: O-methyltransferase

Ligases: ligase synthase

CPY53_RS08035: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CPY53_RS08040: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CPY53_RS08045: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CPY53_RS08070: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CPY53_RS08075: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001268.4	0.65	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0001276.3	0.62	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.62	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.62	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.61	PKS	asperlactone	Aspergillus ochraceus
BGC0001135.5	0.60	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.59	NRPS	peramine	Epichloe festucae
BGC0001254.3	0.59	PKS	ACT-Toxin II	Alternaria alternata
BGC0000342.4	0.59	NRPS	enniatin	Fusarium equiseti
BGC0000307.4	0.59	NRPS	AbT1	Aureobasidium pullulans

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001268.4	0.66	NRPS, PKS	fusarin C	Fusarium fujikuroi
BGC0001276.3	0.65	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001244.3	0.64	PKS	(-)-Mellein	Parastagonospora nodorum
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0002192.3	0.64	PKS	FR901512	fungal sp. No.14919
BGC0001135.5	0.63	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.63	NRPS	peramine	Epichloe festucae
BGC0001254.3	0.63	PKS	ACT-Toxin II	Alternaria alternata
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

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

Confidence: strong

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.02 out of 23.79

Confidence: medium

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 20.54 out of 26.33

Confidence: medium

Additional weak hits (9):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.56 out of 29.38

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.48 out of 21.55

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.50 out of 32.74

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.90 out of 25.88

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.76 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 23.51 out of 32.74

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 22.66 out of 26.12

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.92 out of 25.88

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.72 out of 29.38

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 12, location 1881053 - 1962987:

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

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

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CPY53_RS08050: mal

PKS_AT (4..281): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 91.4
Methoxymalonyl-CoA: 38.4
inactive: 31.3
Propionyl-CoA: 24.6
Methylmalonyl-CoA: 20.6
trans-1,2-CPDA: 0.0
fatty_acid: 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

CPY53_RS08070: Leu

Search NORINE for peptide: strict or relaxed

AMP-binding (273..674): Leu

nrpys: Leu

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: FAIAFDLFISEYMILIGGQVNVYGPTEATCLATS
Nearest Stachelhaus code(s):: Leu DLLHLGLILK (56% 8Å match)
Stachelhaus code match:: 60% (weak)

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
IolR	Regulator of the inositol catabolism
ToxT	Regulator of MSHA biosynthesis

NZ_CP023711.1 - Region 10 - ranthipeptide

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Location: 2,038,623 - 2,064,010 nt. (total: 25,388 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

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: kinase phosphotransferase

CPY53_RS08550: glycerol kinase

smcogs: SMCOG1210: glycerol kinase

CPY53_RS08560: Glucose-specific phosphotransferase enzyme IIA

smcogs: SMCOG1145: Glucose-specific phosphotransferase enzyme IIA

Translocases: transporter

CPY53_RS08565: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.50	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000558.5	0.42	ribosomal	sublancin 168	Bacillus subtilis subsp. subtilis str. 168
BGC0000916.5	0.41	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0001229.4	0.41	ribosomal	SBI-06990 A1, SBI-06989 A2	Streptomyces bingchenggensis BCW-1
BGC0000572.5	0.41	ribosomal	capistruin	Burkholderia thailandensis E444
BGC0000504.5	0.40	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0000552.3	0.39	ribosomal	SmbA, SmbB	Streptococcus mutans
BGC0000497.3	0.39	ribosomal	BHT-Aα, BHT-Aβ	Streptococcus ratti
BGC0002690.2	0.39	other (other)	FW0622	Verrucosispora sp. FIM060022
BGC0001364.3	0.38	ribosomal	cinnamycin B	Actinomadura atramentaria DSM 43919

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.50	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0000558.5	0.42	ribosomal	sublancin 168	Bacillus subtilis subsp. subtilis str. 168
BGC0000916.5	0.41	other (other)	molybdenum cofactor	Staphylococcus carnosus
BGC0001229.4	0.41	ribosomal	SBI-06990 A1, SBI-06989 A2	Streptomyces bingchenggensis BCW-1
BGC0000572.5	0.41	ribosomal	capistruin	Burkholderia thailandensis E444
BGC0000504.5	0.40	ribosomal	cytolysin ClyLl, cytolysin ClyLs	Plasmid pAD1
BGC0000552.3	0.39	ribosomal	SmbA, SmbB	Streptococcus mutans
BGC0000497.3	0.39	ribosomal	BHT-Aα, BHT-Aβ	Streptococcus ratti
BGC0002690.2	0.39	other (other)	FW0622	Verrucosispora sp. FIM060022
BGC0001364.3	0.38	ribosomal	cinnamycin B	Actinomadura atramentaria DSM 43919

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CRP

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

Confidence: medium

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 25.74 out of 30.25

Confidence: medium

Additional weak hits (5):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.40 out of 29.38

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.64 out of 30.97

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.42 out of 36.54

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 24.77 out of 30.97

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 22.98 out of 36.53

Confidence: weak

RREFinder

TFBS Finder

RRE predictions

: RRE type: Other_Sactipeptide_rSAM_RRE; Location: 5 - 135; Score: 29.1

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
ColR	Phenol-responsive regulator

NZ_CP023711.1 - Region 11 - NRPS

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Location: 2,439,635 - 2,519,204 nt. (total: 79,570 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: dehydrogenase

CPY53_RS10590: crotonyl-CoA reductase / alcohol dehydrogenase

smcogs: SMCOG1028: crotonyl-CoA reductase / alcohol dehydrogenase

Transferases: glycosyltransferase

CPY53_RS10455: glycosyltransferase, MGT family

smcogs: SMCOG1062: glycosyltransferase, MGT family

Hydrolases: deacetylase

CPY53_RS10505: polysaccharide deacetylase

smcogs: SMCOG1235: polysaccharide deacetylase

Ligases: ligase

CPY53_RS10550: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CPY53_RS10565: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CPY53_RS10570: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transporter

CPY53_RS10475: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001153.5	0.87	NRPS	polymyxin B	Paenibacillus polymyxa
BGC0001192.5	0.86	NRPS	colistin A, colistin B	Paenibacillus alvei
BGC0000408.5	0.86	NRPS	polymyxin	Paenibacillus polymyxa
BGC0002653.2	0.84	NRPS	macolacin	Paenibacillus xylanexedens
BGC0001758.4	0.75	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002286.3	0.73	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001153.5	0.87	NRPS	polymyxin B	Paenibacillus polymyxa
BGC0001192.5	0.86	NRPS	colistin A, colistin B	Paenibacillus alvei
BGC0000408.5	0.86	NRPS	polymyxin	Paenibacillus polymyxa
BGC0002653.2	0.84	NRPS	macolacin	Paenibacillus xylanexedens
BGC0001758.4	0.75	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002286.3	0.73	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:

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.26 out of 26.06

Confidence: strong

ToxT

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

Confidence: strong

CatR

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

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.06 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

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.46 out of 27.78

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.99 out of 26.06

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.50 out of 28.19

Confidence: medium

Additional weak hits (21):

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.45 out of 21.55

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.39 out of 20.01

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: 19.64 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.73 out of 26.06

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.52 out of 29.38

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.34 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.85 out of 30.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 19.86 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.00 out of 26.06

Confidence: weak

PerR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.49 out of 26.06

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.31 out of 36.54

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.74 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.46 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.47 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

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.28 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.18 out of 28.14

Confidence: weak

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.52 out of 28.19

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 21.45 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 14, location 2439634 - 2519204:

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

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

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CPY53_RS10550: 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:: LNDHFDFSVWEGNQIFGGEINMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2585..3039): 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 (3682..4094): 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 (4737..5154): 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)

CPY53_RS10565: 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:: LNDHFDFSVWEGNQIFGGEINMYGITETTVHVTY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (100% 8Å match)
Stachelhaus code match:: 100% (strong)

CPY53_RS10570: Leu - Leu - Dab - Dab

Search NORINE for peptide: strict or relaxed

AMP-binding (293..683): 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 (1800..2195): 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:: ile (Ile)

Stachelhaus prediction details:

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

AMP-binding (2837..3272): 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:: TGYAFDVFVGDRESITSSDVNAYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISAIDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (3917..4352): 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)

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_CP023711.1 - Region 12 - ranthipeptide

Download region SVG

Location: 3,636,649 - 3,658,070 nt. (total: 21,422 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

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Hydrolases: esterase

CPY53_RS15870: 2`,3`-cyclic-nucleotide 2`-phosphodiesterase

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

Translocases: transporter

CPY53_RS15815: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.54	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002116.3	0.45	ribosomal	darobactin A	Photorhabdus khanii HGB 1456
BGC0000600.3	0.43	ribosomal	thurincin H	Bacillus thuringiensis
BGC0000539.5	0.42	ribosomal	nukacin ISK-1	Staphylococcus warneri
BGC0001555.4	0.42	ribosomal	colicin V	Escherichia coli chi7122
BGC0001210.5	0.41	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000584.5	0.41	ribosomal	colicin V	Escherichia coli
BGC0001887.3	0.41	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0002667.2	0.40	ribosomal	estericin A	Clostridium estertheticum
BGC0001779.5	0.40	ribosomal	siamycin	Streptomyces nodosus

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.54	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002116.3	0.45	ribosomal	darobactin A	Photorhabdus khanii HGB 1456
BGC0000600.3	0.43	ribosomal	thurincin H	Bacillus thuringiensis
BGC0000539.5	0.42	ribosomal	nukacin ISK-1	Staphylococcus warneri
BGC0001555.4	0.42	ribosomal	colicin V	Escherichia coli chi7122
BGC0001210.5	0.41	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000584.5	0.41	ribosomal	colicin V	Escherichia coli
BGC0001887.3	0.41	ribosomal	huazacin	Bacillus thuringiensis serovar huazhongensis BGSC 4BD1
BGC0002667.2	0.40	ribosomal	estericin A	Clostridium estertheticum
BGC0001779.5	0.40	ribosomal	siamycin	Streptomyces nodosus

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: 18.04 out of 18.57

Confidence: strong

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.85 out of 28.14

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.15 out of 26.06

Confidence: medium

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.54 out of 21.55

Confidence: medium

DasR

Description: N-acetylglucosamine dependent repressor
Species: Streptomyces coelicolor
Score: 22.04 out of 27.04

Confidence: medium

Additional weak hits (8):

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.42 out of 28.14

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.77 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.46 out of 31.73

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 22.93 out of 30.97

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.67 out of 29.38

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 24.35 out of 33.73

Confidence: weak

RREFinder

TFBS Finder

RRE predictions

: RRE type: Ranthipeptide_rSAM_RRE; Location: 8 - 98; Score: 58.4

TFBS definitions

Regulator	Description
ArcA	Repressor of carbon oxidation
DasR	N-acetylglucosamine dependent repressor
MogR	Repressor of flagellar motility genes
PerR	Peroxide regulator
ToxT	Regulator of MSHA biosynthesis

NZ_CP023711.1 - Region 13 - cyclic-lactone-autoinducer,lanthipeptide-class-i

BGC0000517.4 (BAB04173.1):

Download region SVG

Location: 4,380,319 - 4,407,671 nt. (total: 27,353 nt) Show pHMM detection rules used

lanthipeptide-class-i: (((Lant_dehydr_N or Lant_dehydr_C) and cds(LANC_like and not Pkinase)) and not (YcaO or TIGR03604))
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

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

Oxidoreductases: oxidoreductase

CPY53_RS19325: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: protease

CPY53_RS19280: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Lyases: cyclase dehydratase

CPY53_RS19285: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

CPY53_RS19290: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

Ligases: synthase

CPY53_RS19270: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000540.5	1.51	ribosomal	paenibacillin	Paenibacillus polymyxa OSY-DF
BGC0002576.2	0.87	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0000510.3	0.77	ribosomal	epilancin K7	Staphylococcus epidermidis
BGC0000560.5	0.56	ribosomal	subtilomycin	Bacillus subtilis
BGC0000507.5	0.49	ribosomal	epicidin	Staphylococcus epidermidis
BGC0000543.5	0.48	ribosomal	pep5	Staphylococcus epidermidis
BGC0000509.4	0.43	ribosomal	epilancin 15x	Staphylococcus epidermidis
BGC0001289.5	0.39	ribosomal	penisin	Paenibacillus ehimensis
BGC0001727.3	0.32	ribosomal	paenilan	Paenibacillus polymyxa E681
BGC0000542.3	0.32	ribosomal	paenicidin B	Paenibacillus terrae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000540.5	0.91	ribosomal	paenibacillin	Paenibacillus polymyxa OSY-DF
BGC0002576.2	0.74	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0000510.3	0.71	ribosomal	epilancin K7	Staphylococcus epidermidis
BGC0000560.5	0.62	ribosomal	subtilomycin	Bacillus subtilis
BGC0000507.5	0.58	ribosomal	epicidin	Staphylococcus epidermidis
BGC0000543.5	0.57	ribosomal	pep5	Staphylococcus epidermidis
BGC0000509.4	0.55	ribosomal	epilancin 15x	Staphylococcus epidermidis
BGC0001289.5	0.52	ribosomal	penisin	Paenibacillus ehimensis
BGC0001727.3	0.48	ribosomal	paenilan	Paenibacillus polymyxa E681
BGC0000542.3	0.48	ribosomal	paenicidin B	Paenibacillus terrae

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CPY53_RS19285

CPY53_RS19275

Leader:

MFDLDLRKSYEASELSPQ

Core:

ASIIKTTIKVSKAVCKTLTCICTGSCSNCK

Core with dehydrations:

ADhaIIKDhbDhbIKVDhaKAVCysKDhbLDhbCysICysDhbGDhaCysDhaNCysK

antiSMASH-DB 4.0 matches for CPY53_RS19275

100.0%

NZ_CP023711.1and 11 others:

NZ_CP034141.1 Lanthipeptides: EGM68_RS25880_lanthipeptideNZ_CP040829.1 Lanthipeptides: FGY93_RS26165_lanthipeptideNZ_CP049598.1 Lanthipeptides: G7L40_RS03920_lanthipeptideNZ_CP071875.1 Lanthipeptides: J4I02_RS05145_lanthipeptideNZ_CP086373.1 Lanthipeptides: LMH85_RS04795_lanthipeptideNZ_CP092831.1 Lanthipeptides: MLD56_RS04795_lanthipeptideNZ_CP102865.1 Lanthipeptides: NWS42_RS17805_lanthipeptideNZ_JAFJXZ010000012.1 Lanthipeptides: JYU28_RS03620_lanthipeptideNZ_JAKVDC010000009.1 Lanthipeptides: MKN04_RS18550_lanthipeptideNZ_JWJJ01000002.1 Lanthipeptides: U707_RS25810_lanthipeptideNZ_POVT01000017.1 Lanthipeptides: C1T20_RS25545_lanthipeptide

Lanthipeptides: CPY53_RS19275_lanthipeptide

1

ASIIKTTIKVSKAVCKTLTCICTGSCSNCK

30

ASIIKTTIKVSKAVCKTLTCICTGSCSNCK

1

ASIIKTTIKVSKAVCKTLTCICTGSCSNCK

30

70.0%

NZ_KB976165.1:

Lanthipeptides: ICC_RS25590_lanthipeptide

5

KTTIKVSKAVCKTLTCICTGSCSNCK

30

TTI VS++VCKTLTCICT SCSNCK

1

PTTILVSRSVCKTLTCICTISCSNCK

26

70.0%

NZ_MOOT01000054.1:

Lanthipeptides: BK765_RS17665_lanthipeptide

5

KTTIKVSKAVCKTLTCICTGSCSNCK

30

TTI VS++VCKTLTCICT SCSNCK

1

PTTIFVSRSVCKTLTCICTISCSNCK

26

with 15 more sequence matches

Only the first 10 are displayed here.

70.0%

NZ_MOOT01000054.1and 1 other:

NZ_MOOT01000054.1 Lanthipeptides: BK765_RS17680_lanthipeptide

Lanthipeptides: BK765_RS17685_lanthipeptide

6

TTIKVSKAVCKTLTCICTGSCSNCK

30

T +KVSKAVCKT TCICT SCSNCK

4

TIVKVSKAVCKTGTCICTTSCSNCK

28

66.7%

NZ_CP036100.1and 5 others:

NZ_CP036100.1 Lanthipeptides: EXW47_RS29575_lanthipeptideNZ_CP036100.1 Lanthipeptides: EXW47_RS29570_lanthipeptideNZ_CP072062.1 Lanthipeptides: J5V93_RS29670_lanthipeptideNZ_CP072062.1 Lanthipeptides: J5V93_RS29665_lanthipeptideNZ_CP072062.1 Lanthipeptides: J5V93_RS29660_lanthipeptide

Lanthipeptides: EXW47_RS29580_lanthipeptide

6

TTIKVSKAVCKTLTCICTGSCSNCK

30

T IK SKA CKT TCICT SCSNCK

2

TVIKFSKAFCKTGTCICTTSCSNCK

26

66.7%

NZ_QNRN01000010.1:

Lanthipeptides: DET63_RS17955_lanthipeptide

6

TTIKVSKAVCKTLTCICTGSCSNCK

30

T +KVSKA+CKT TCICT SCSNCK

4

TVVKVSKAICKTGTCICTTSCSNCK

28

63.3%

NZ_CP036100.1and 1 other:

NZ_CP072062.1 Lanthipeptides: J5V93_RS29680_lanthipeptide

Lanthipeptides: EXW47_RS29590_lanthipeptide

8

IKVSKAVCKTLTCICTGSCSNCK

30

+KVS+AVCKT TCICT SCSNCK

6

LKVSRAVCKTGTCICTTSCSNCK

28

60.0%

NZ_KB976165.1and 1 other:

NZ_MOOT01000054.1 Lanthipeptides: BK765_RS17670_lanthipeptide

Lanthipeptides: ICC_RS25585_lanthipeptide

6

TTIKVSKAVCKTLTCICTGSCSNCK

30

T +KVSKA+CKT TCI T SC+NCK

2

TVVKVSKAICKTGTCIGTISCTNCK

26

56.7%

NZ_QNRN01000010.1:

Lanthipeptides: DET63_RS17960_lanthipeptide

7

TIKVSKAVCKTLTCICTGSCSNCK

30

TI +S+ +CKTLTC+CT SCSNCK

2

TILISRTICKTLTCVCTTSCSNCK

25

53.3%

NZ_KB976165.1and 1 other:

NZ_MOOT01000054.1 Lanthipeptides: BK765_RS17675_lanthipeptide

Lanthipeptides: ICC_RS37095_lanthipeptide

8

IKVSKAVCKTLTCICTGSCSNCK

30

+KVS+A CK+ TC+CT SCSNCK

6

LKVSRAPCKSGTCLCTTSCSNCK

28

53.1%

NZ_BDDH01000005.1and 2 others:

NZ_CP073265.1 Lanthipeptides: KCX77_RS01160_lanthipeptideNZ_JALAUD010000002.1 Lanthipeptides: MOE28_RS05435_lanthipeptide

Lanthipeptides: A7P71_RS15855_lanthipeptide

1

ASIIKTTIKVSKAVCKTLTCICT-GSCSNCK

30

A+I KT ++ K C+T TC C+ GSCSNCK

3

ATIGKTIVQSVKK-CRTFTCGCSLGSCSNCK

32

50.0%

NC_014976.1and 6 others:

NZ_CP029461.1 Lanthipeptides: DJ572_RS00745_lanthipeptideNZ_CP031675.1 Lanthipeptides: DYS67_RS00910_lanthipeptideNZ_CP045824.1 Lanthipeptides: GII78_RS01205_lanthipeptideNZ_CP046591.1 Lanthipeptides: GO004_RS12840_lanthipeptideNZ_CP049924.1 Lanthipeptides: G4G26_RS01205_lanthipeptideNZ_CP095736.1 Lanthipeptides: MX663_RS01330_lanthipeptide

Lanthipeptides: BSN5_RS12800_lanthipeptide

1

ASIIKTTIKVSKAVCKTLTCICT-GSCSNCK

30

A+I KT ++ K C+T TC C+ GSCSNC

3

ATIGKTIVQSVKK-CRTFTCGCSLGSCSNCN

32

33.3%

NZ_CP040417.1and 2 others:

NZ_SIYN01000015.1 Lanthipeptides: EY674_RS12755_lanthipeptideNZ_SIYN01000015.1 Lanthipeptides: EY674_RS12755_lanthipeptide

Lanthipeptides: FE328_RS05340_lanthipeptide

4

IKTTIKVSKAVCKTLTC

20

I T+ VS AVC TL C

5

IPCTVMVSAAVCPTLVC

21

MIBiG 4.0 matches for CPY53_RS19275

20.0%

Lanthipeptide: haloduracin β or haloduracin α

17

TLTCICTGSCS

27

TLT C SC+

18

TLTVECMPSCN

28

13.3%

BGC0000563.4 (AEA03263.1):

Lanthipeptide: venezuelin

19

TCICTG

24

TC C G

2

TCECVG

7

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.15 out of 20.01

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.72 out of 26.06

Confidence: medium

Additional weak hits (5):

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.85 out of 39.62

Confidence: weak

CopR

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

Confidence: weak

MogR

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

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 19.21 out of 23.43

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.33 out of 20.01

Confidence: weak

Lanthipeptides

RREFinder

TFBS Finder

Core peptide predictions

CPY53_RS19275 - Class I

Cleavage pHMM score: 14.70

RODEO score: 22

Monoisotopic mass: 2941.6 Da

Molecular weight: 2943.6 Da

Number of bridges: 5

Alternative weights: (assuming N unmodified Ser/Thr residues); 2961.6 Da N = 1; 2979.6 Da N = 2; 2997.7 Da N = 3; 3015.7 Da N = 4

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 149 - 242; Score: 43.9
: RRE type: Lanthipeptide_LanB_RRE; Location: 149 - 242; Score: 43.9

TFBS definitions

Regulator	Description
ArgR	Regulator of arginine biosynthesis genes
MogR	Repressor of flagellar motility genes

NZ_CP023711.1 - Region 14 - NRPS,transAT-PKS

Download region SVG

Location: 4,422,838 - 4,500,219 nt. (total: 77,382 nt) Show pHMM detection rules used

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)))
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

Oxidoreductases: oxidoreductase

CPY53_RS19410: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

Transferases: acylase

CPY53_RS19490: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase

CPY53_RS19480: hydrolase

smcogs: SMCOG1179: hydrolase

Ligases: ligase synthase

CPY53_RS19495: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CPY53_RS19500: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CPY53_RS19505: 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	0.81	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.77	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001133.4	0.73	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata
BGC0001166.5	0.72	NRPS	HC-toxin	Alternaria jesenskae
BGC0001128.4	0.70	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.69	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.73	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001833.4	0.71	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001133.4	0.71	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae
BGC0000402.4	0.70	NRPS	paenilarvin A, paenilarvin B, paenilarvin C	Paenibacillus larvae subsp. larvae DSM 25430
BGC0001261.3	0.69	NRPS	AM-toxin	Alternaria alternata
BGC0001128.4	0.69	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.68	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0002286.3	0.68	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

MexT

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

Confidence: medium

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.80 out of 25.88

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.73 out of 27.78

Confidence: medium

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.87 out of 21.55

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 22.44 out of 24.78

Confidence: strong

MexT

Description: Global virulence regulator
Species: Pseudomonas aeruginosa PAO1
Score: 19.86 out of 21.84

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.40 out of 26.06

Confidence: medium

Additional weak hits (11):

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 25.21 out of 32.74

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.06 out of 28.14

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.92 out of 25.88

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.93 out of 26.06

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.52 out of 30.11

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.19 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.16 out of 31.73

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.28 out of 39.62

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.06 out of 25.88

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.65 out of 31.73

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 19, location 4422837 - 4500219:

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

Polymer prediction:: (fatty_acid - mal - Tyr - D-X) + (Ser - D-Ser) + (Ser - D-Ile - Ser)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CPY53_RS19490: mal

PKS_AT (6..293): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 88.5
inactive: 38.0
Methoxymalonyl-CoA: 26.5
Propionyl-CoA: 14.1
Methylmalonyl-CoA: 13.9
Acetyl-CoA: 9.4
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

CPY53_RS19495: fatty_acid - Tyr - X

Search NORINE for peptide: strict or relaxed

CAL_domain (36..482): fatty_acid

minowa: fatty_acid

Prediction, score:

fatty_acid: 310.4
NH2: 17.3
shikimic_acid: 0.0
Acetyl-CoA: 0.0
AHBA: 0.0

AMP-binding (3153..3549): Tyr

nrpys: Tyr

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aromatic (Phe, Tyr, diOH-Bz, Ph-Gly, bOH-Tyr)
Large clusters prediction:: Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
Small clusters prediction:: Polar aromatic ring (Tyr, bOH-Tyr)
Single AA prediction:: tyr (Tyr)

Stachelhaus prediction details:

Stachelhaus sequence:: TWRLFDAFVGATVCTLGGEFNEYGPTENSVVTTM
Nearest Stachelhaus code(s):: Tyr DALTTGEVVK (71% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (4193..4596): X

nrpys: Asp, Asn, Glu, Gln, Aad

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTYDSAVWQWDFILGGETNLYGPTEASIGCVA
Nearest Stachelhaus code(s):: Glu DVWHIGSIGK (65% 8Å match); Orn DVWNIGLIHK (56% 8Å match)
Stachelhaus code match:: 70% (weak)

CPY53_RS19500: Ser - Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (469..873): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTFDVSVWEWHFFASGEHNLYGPTEATVDATW
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1523..1934): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTFDVSLWESHFFASGEHNLYGPTEATVEVAY
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (85% 8Å match)
Stachelhaus code match:: 90% (moderate)

CPY53_RS19505: Ser - Ile - Ser

Search NORINE for peptide: strict or relaxed

AMP-binding (470..881): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTFDVSLWESHFFASGEHNLYGPTEATVEVAY
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (85% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1533..1939): 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:: LNSSFDGSVFDGFILFGGELHMYGPTESTVFATC
Nearest Stachelhaus code(s):: Ile DGFFLGVVFK (82% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (3061..3470): Ser

nrpys: Ser

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Aliphatic chain or phenyl group with -OH (Ser, Thr, Dhpg, Hpg)
Small clusters prediction:: ser (Ser)
Single AA prediction:: ser (Ser)

Stachelhaus prediction details:

Stachelhaus sequence:: RWMTFDVSLWESHFFASGEHNLYGPTEATVEVAY
Nearest Stachelhaus code(s):: Ser DVWHFSLVDK (85% 8Å match)
Stachelhaus code match:: 90% (moderate)

TFBS definitions

Regulator	Description
ArcA	Repressor of carbon oxidation
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
LexA variant 2	Repressor of DNA damage response
MexT	Global virulence regulator
MogR	Repressor of flagellar motility genes
PsrA	Oleic acid responsive regulator

NZ_CP023711.1 - Region 15 - proteusin

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Location: 4,605,014 - 4,625,250 nt. (total: 20,237 nt) Show pHMM detection rules used

proteusin: (PoyD or TIGR03793)

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

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: acyltransferase

CPY53_RS20080: acyltransferase 3

smcogs: SMCOG1088: acyltransferase 3

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000889.5	0.32	other (other)	bagremycin A, bagremycin B	Streptomyces sp. WK-5344
BGC0001592.5	0.31	other (other)	ferroverdin, bagremycin	Streptomyces lunaelactis
BGC0001594.3	0.29	other (other)	fischerindole L	Fischerella muscicola UTEX 1829
BGC0001126.4	0.28	other (other), terpene	12-epi-hapalindole J isonitrile, ambiguine A isonitrile, ambiguine B isonitrile, ambiguine C isonitrile, ambiguine D isonitrile, ambiguine E isonitrile, ambiguine K isonitrile, ambiguine L isonitrile, ambiguine I isonitrile, ambiguine J isonitrile	Fischerella ambigua UTEX 1903
BGC0001612.3	0.28	other (other)	ambiguine H isonitrile	Fischerella ambigua UTEX 1903
BGC0001501.5	0.28	other (other)	ambiguine P	Fischerella sp. TAU
BGC0002443.3	0.27	PKS	mycemycin C, mycemycin A, mycemycin B	Streptomyces olivaceus
BGC0002713.2	0.26	NRPS	mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D	Photorhabdus laumondii subsp. laumondii
BGC0000668.5	0.25	other (other), terpene	12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole	Hapalosiphon welwitschii UTEX B 1830
BGC0002637.3	0.24	NRPS	rimomycin A, rimomycin B, rimomycin C	Streptomyces sp. WAC 06783

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000889.5	0.32	other (other)	bagremycin A, bagremycin B	Streptomyces sp. WK-5344
BGC0001592.5	0.31	other (other)	ferroverdin, bagremycin	Streptomyces lunaelactis
BGC0001594.3	0.29	other (other)	fischerindole L	Fischerella muscicola UTEX 1829
BGC0001126.4	0.28	other (other), terpene	12-epi-hapalindole J isonitrile, ambiguine A isonitrile, ambiguine B isonitrile, ambiguine C isonitrile, ambiguine D isonitrile, ambiguine E isonitrile, ambiguine K isonitrile, ambiguine L isonitrile, ambiguine I isonitrile, ambiguine J isonitrile	Fischerella ambigua UTEX 1903
BGC0001612.3	0.28	other (other)	ambiguine H isonitrile	Fischerella ambigua UTEX 1903
BGC0001501.5	0.28	other (other)	ambiguine P	Fischerella sp. TAU
BGC0002443.3	0.27	PKS	mycemycin C, mycemycin A, mycemycin B	Streptomyces olivaceus
BGC0002713.2	0.26	NRPS	mevalagmapeptide A, mevalagmapeptide B, mevalagmapeptide C, mevalagmapeptide D	Photorhabdus laumondii subsp. laumondii
BGC0000668.5	0.25	other (other), terpene	12-epi-hapalindole C isonitrile, 12-epi-hapalindole E, 12-epi-fischerindole U isonitrile, fischerindole L, 12-epi-fischerindole I isonitrile, welwitindolinone A isonitrile, welwitindolinone B isothiocyanate, welwitindolinone C isothiocyanate, N-methylwelwitindolinone C isothiocyanate, N-methylwelwitinsolinone C isonitrile, 3-epi-welwitindolinone B isothiocyanate, 3-(Z-2'-isocyanoethenyl)-indole	Hapalosiphon welwitschii UTEX B 1830
BGC0002637.3	0.24	NRPS	rimomycin A, rimomycin B, rimomycin C	Streptomyces sp. WAC 06783

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: 17.55 out of 18.46

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: 18.04 out of 18.57

Confidence: strong

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.33 out of 27.55

Confidence: medium

CcpA

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

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.68 out of 28.19

Confidence: medium

Additional weak hits (5):

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.60 out of 32.74

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.58 out of 26.12

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.72 out of 26.06

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.23 out of 30.11

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 26.64 out of 39.62

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
GnfM	Regulator of nitrogen-fixation genes
RpoN	Regulator of nitrogen assimilation and virulence
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_CP023711.1 - Region 16 - NRPS,transAT-PKS

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Location: 4,658,953 - 4,758,931 nt. (total: 99,979 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

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: dehydrogenase

CPY53_RS20490: dehydrogenase

smcogs: SMCOG1072: dehydrogenase

Transferases: acylase acyltransferase aminotransferase

CPY53_RS20420: aminotransferase

smcogs: SMCOG1019: aminotransferase

CPY53_RS20440: polyketide synthase associated protein papA3

smcogs: SMCOG1209: polyketide synthase associated protein papA3

CPY53_RS20445: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: hydrolase

CPY53_RS20385: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase synthase

CPY53_RS20380: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CPY53_RS20400: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

CPY53_RS20410: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CPY53_RS20415: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CPY53_RS20425: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CPY53_RS20430: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CPY53_RS20450: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

CPY53_RS20455: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002286.3	0.90	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.90	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.90	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.88	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.88	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.87	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	0.84	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001825.4	0.83	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001261.3	0.83	NRPS	AM-toxin	Alternaria alternata
BGC0001249.5	0.82	NRPS	dimethylcoprogen	Alternaria alternata

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002286.3	0.75	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.74	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002075.3	0.73	NRPS	pyreudione A, pyreudione B, pyreudione C, pyreudione D, pyreudione E	Pseudomonas fluorescens
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001261.3	0.73	NRPS	AM-toxin	Alternaria alternata
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.31 out of 26.06

Confidence: medium

CRP

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

Confidence: medium

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 23.44 out of 30.25

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 17.55 out of 19.26

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 24.59 out of 24.78

Confidence: strong

Additional weak hits (8):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.21 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.27 out of 32.74

Confidence: weak

HipB

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

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.68 out of 24.78

Confidence: weak

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 21.18 out of 29.65

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.98 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.45 out of 26.06

Confidence: weak

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 21.36 out of 27.18

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 4658952 - 4758931:

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

Polymer prediction:: (D-Asn) + (Gln - Me-ohmal) + (mal) + (X) + (ohmal) + (X - Gly) + (ccmal - Lys - X) + (X)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CPY53_RS20380: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (457..852): 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)

CPY53_RS20410: Gln

Search NORINE for peptide: strict or relaxed

AMP-binding (269..665): Gln

nrpys: Gln

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: QGLAFDPSVQQLNTIMAGEFNIYGPTEAAINTTL
Nearest Stachelhaus code(s):: Gln DAQNIAVINK (53% 8Å match); bOH-Gln DAQNIASINK (50% 8Å match)
Stachelhaus code match:: 80% (moderate)

CPY53_RS20425: X

AMP-binding (39..457): X

nrpys: Asp, Asn, Glu, Gln, Aad

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: TWLTFTDSVWEWQFFNGGEANIYGMTESAIYATC
Nearest Stachelhaus code(s):: Gln DAWQFGLIDK (62% 8Å match)
Stachelhaus code match:: 60% (weak)

CPY53_RS20440: X - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (472..903): X

nrpys: Asp, Asn, Glu, Gln, Aad

SVM prediction details:

Predicted physicochemical class:: hydrophilic (Arg, Asp, Glu, Asn, Lys, Gln, Orn, Aad)
Large clusters prediction:: Aliphatic chain with H-bond donor (Asp, Asn, Glu, Gln, Aad)
Small clusters prediction:: N/A
Single AA prediction:: N/A

Stachelhaus prediction details:

Stachelhaus sequence:: TWLTFTDSVWEWQFFNGGEANLYGMTESAIYATQ
Nearest Stachelhaus code(s):: Gln DAWQFGLIDK (65% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (1559..1953): 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:: LGITFDIFVLELQMMVGGEFNMYGPTETTVWSTV
Nearest Stachelhaus code(s):: Gly DILQMGMVWK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

CPY53_RS20445: mal

PKS_AT (6..293): mal

ATSignature: Malonyl-CoA

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

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 125.2
Methoxymalonyl-CoA: 46.3
inactive: 44.9
Methylmalonyl-CoA: 37.9
Ethylmalonyl-CoA: 17.3
fatty_acid: 13.9
Isobutyryl-CoA: 13.2
Propionyl-CoA: 11.8
Acetyl-CoA: 7.9
trans-1,2-CPDA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

CPY53_RS20450: Lys - X

Search NORINE for peptide: strict or relaxed

AMP-binding (2062..2459): Lys

nrpys: Lys

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: YAFAFDASVEEPSAISGGDYNTYGPTEATVCATY
Nearest Stachelhaus code(s):: Lys DAESIGSVCK (85% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (3046..3447): 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:: RWLAFDGSIVESFFMSGDELNLYGPTEASVFATA
Nearest Stachelhaus code(s):: Val DGYFLGVVFK (56% 8Å match); Ile DGFFLGVVFK (47% 8Å match)
Stachelhaus code match:: 70% (weak)

CPY53_RS20455: X

AMP-binding (459..851): 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:: LEPCFDVSVYEGWFMTGGDVNAYGPSENTIFTSF
Nearest Stachelhaus code(s):: Ala DVFWTGGIFK (65% 8Å match); norCMA DPYWWGATFK (53% 8Å match)
Stachelhaus code match:: 70% (weak)

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
ColR	Phenol-responsive regulator
LexA variant 2	Repressor of DNA damage response
MogR	Repressor of flagellar motility genes

NZ_CP023711.1 - Region 17 - lassopeptide

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Location: 4,794,168 - 4,818,238 nt. (total: 24,071 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

reset view

zoom to selection

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

Hydrolases: hydrolase

CPY53_RS20725: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001356.4	0.67	ribosomal	paeninodin	Paenibacillus dendritiformis C454
BGC0001634.3	0.53	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0001164.3	0.52	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001551.4	0.51	ribosomal	citrulassin E	Streptomyces glaucescens
BGC0001779.5	0.47	ribosomal	siamycin	Streptomyces nodosus
BGC0001496.3	0.47	ribosomal	actinokineosin	Actinokineospora spheciospongiae
BGC0000581.6	0.47	ribosomal	microcin J25	Escherichia coli AY25
BGC0001639.3	0.47	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0000579.4	0.45	ribosomal	SSV-2083	Streptomyces sviceus ATCC 29083
BGC0002575.2	0.44	ribosomal	cochonodin I	Streptococcus suis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001356.4	0.67	ribosomal	paeninodin	Paenibacillus dendritiformis C454
BGC0001634.3	0.53	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0001164.3	0.52	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001551.4	0.51	ribosomal	citrulassin E	Streptomyces glaucescens
BGC0001779.5	0.47	ribosomal	siamycin	Streptomyces nodosus
BGC0001496.3	0.47	ribosomal	actinokineosin	Actinokineospora spheciospongiae
BGC0000581.6	0.47	ribosomal	microcin J25	Escherichia coli AY25
BGC0001639.3	0.47	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0000579.4	0.45	ribosomal	SSV-2083	Streptomyces sviceus ATCC 29083
BGC0002575.2	0.44	ribosomal	cochonodin I	Streptococcus suis

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lasso peptide predictions

Lassopeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.67 out of 20.97

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.35 out of 27.55

Confidence: medium

Additional weak hits (5):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.86 out of 31.73

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.61 out of 28.14

Confidence: weak

PerR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.43 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.39 out of 26.06

Confidence: weak

Lasso peptides

RREFinder

TFBS Finder

Core peptide predictions

No core peptides found.

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 16 - 94; Score: 83.5

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
GnfM	Regulator of nitrogen-fixation genes

NZ_CP023711.1 - Region 18 - lanthipeptide-class-i

BGC0001229.4 (SBI_06989):

Download region SVG

Location: 5,101,749 - 5,128,758 nt. (total: 27,010 nt) Show pHMM detection rules used

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

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: PPTase

CPY53_RS22290: 4'-phosphopantetheinyl transferase

smcogs: SMCOG1012: 4'-phosphopantetheinyl transferase

Lyases: cyclase dehydratase

CPY53_RS22230: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

CPY53_RS22240: Lanthionine synthetase C family protein

smcogs: SMCOG1140: Lanthionine synthetase C family protein

CPY53_RS22250: Lantibiotic dehydratase domain protein

smcogs: SMCOG1155: Lantibiotic dehydratase domain protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001727.3	0.88	ribosomal	paenilan	Paenibacillus polymyxa E681
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0001289.5	0.57	ribosomal	penisin	Paenibacillus ehimensis
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0000556.5	0.54	ribosomal	streptin	Streptococcus pyogenes
BGC0002635.2	0.54	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000560.5	0.54	ribosomal	subtilomycin	Bacillus subtilis
BGC0000541.5	0.53	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000542.3	0.53	ribosomal	paenicidin B	Paenibacillus terrae
BGC0000506.4	0.52	ribosomal	entianin	Bacillus subtilis subsp. spizizenii

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001727.3	0.88	ribosomal	paenilan	Paenibacillus polymyxa E681
BGC0002576.2	0.76	ribosomal	mechercharmycin	Thermoactinomyces sp.
BGC0001289.5	0.57	ribosomal	penisin	Paenibacillus ehimensis
BGC0002640.2	0.56	ribosomal	thalassomonasin A, thalassomonasin B	Thalassomonas actiniarum
BGC0000556.5	0.54	ribosomal	streptin	Streptococcus pyogenes
BGC0002635.2	0.54	ribosomal	daspyromycin A, daspyromycin B	Actinokineospora diospyrosa
BGC0000560.5	0.54	ribosomal	subtilomycin	Bacillus subtilis
BGC0000541.5	0.53	ribosomal	paenicidin A	Paenibacillus polymyxa
BGC0000542.3	0.53	ribosomal	paenicidin B	Paenibacillus terrae
BGC0000506.4	0.52	ribosomal	entianin	Bacillus subtilis subsp. spizizenii

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for CPY53_RS22250

CPY53_RS22235

Leader:

MKNQFDLDLQVAKNEVAPKEVQPA

Core:

SGLICTPSCATGTLNCQVSLSFCKTC

Core with dehydrations:

DhaGLICysDhbPDhaCysADhbGDhbLNCysQVDhaLDhaFCysKDhbCys

antiSMASH-DB 4.0 matches for CPY53_RS22235

100.0%

NC_014483.2and 17 others:

NC_014622.2 Lanthipeptides: PPSC2_RS36205_lanthipeptideNC_017542.1 Lanthipeptides: PPM_RS07465_lanthipeptideNZ_CP006872.1 Lanthipeptides: PPSQR21_RS07740_lanthipeptideNZ_CP023711.1 Lanthipeptides: CPY53_RS22235_lanthipeptideNZ_CP025957.1 Lanthipeptides: C1A50_RS07530_lanthipeptideNZ_CP029370.1 Lanthipeptides: DI243_RS07495_lanthipeptideNZ_CP040829.1 Lanthipeptides: FGY93_RS00500_lanthipeptideNZ_CP049598.1 Lanthipeptides: G7L40_RS00115_lanthipeptideNZ_CP073682.1 Lanthipeptides: KAI36_RS07745_lanthipeptideNZ_CP084033.1 Lanthipeptides: LAZ93_RS07550_lanthipeptideNZ_CP085682.1 Lanthipeptides: LJR53_RS07370_lanthipeptideNZ_CP086373.1 Lanthipeptides: LMH85_RS07780_lanthipeptideNZ_CP092779.1 Lanthipeptides: MJ749_RS07440_lanthipeptideNZ_CP097766.1 Lanthipeptides: MF620_RS07485_lanthipeptideNZ_CP102865.1 Lanthipeptides: NWS42_RS21195_lanthipeptideNZ_JWJJ01000002.1 Lanthipeptides: U707_RS10390_lanthipeptideNZ_POVT01000009.1 Lanthipeptides: C1T20_RS05900_lanthipeptide

Lanthipeptides: PPE_RS07020_lanthipeptide

1

SGLICTPSCATGTLNCQVSLSFCKTC

26

SGLICTPSCATGTLNCQVSLSFCKTC

1

SGLICTPSCATGTLNCQVSLSFCKTC

26

96.2%

NZ_CP061172.1and 5 others:

NZ_CP109848.1 Lanthipeptides: OF859_RS22650_lanthipeptideNZ_CP113973.1 Lanthipeptides: OYT09_RS07785_lanthipeptideNZ_JAAMNR010000001.1 Lanthipeptides: G9G54_RS03500_lanthipeptideNZ_PNXQ01000013.1 Lanthipeptides: C1I60_RS14430_lanthipeptideNZ_POVS01000009.1 Lanthipeptides: C1T21_RS10630_lanthipeptide

Lanthipeptides: IAQ67_RS07480_lanthipeptide

1

SGLICTPSCATGTLNCQVSLSFCKTC

26

SGLICTPSCATGTLNCQVSL+FCKTC

1

SGLICTPSCATGTLNCQVSLTFCKTC

26

96.2%

NZ_JAKVDC010000001.1:

Lanthipeptides: MKN04_RS02755_lanthipeptide

1

SGLICTPSCATGTLNCQVSLSFCKTC

26

SG+ICTPSCATGTLNCQVSLSFCKTC

1

SGIICTPSCATGTLNCQVSLSFCKTC

26

with 59 more sequence matches

Only the first 10 are displayed here.

92.3%

NC_023037.2and 5 others:

NZ_CP017967.2 Lanthipeptides: PPYC1_RS07755_lanthipeptideNZ_CP017968.3 Lanthipeptides: PPYC2_RS08330_lanthipeptideNZ_CP073683.1 Lanthipeptides: KAI37_RS07495_lanthipeptideNZ_FOYG01000001.1 Lanthipeptides: BM358_RS03525_lanthipeptideNZ_PTJM01000020.1 Lanthipeptides: C5G87_RS02825_lanthipeptide

Lanthipeptides: X809_RS07820_lanthipeptide

1

SGLICTPSCATGTLNCQVSLSFCKTC

26

SG+ICTPSCATGTLNCQVSL+FCKTC

1

SGIICTPSCATGTLNCQVSLTFCKTC

26

84.6%

NZ_JAIFIS010000001.1:

Lanthipeptides: K1X09_RS26315_lanthipeptide

1

SGLICTPSCATGTLNCQVSLSFCKTC

26

SGLICTPSC TGTLNC++SLSFC+TC

1

SGLICTPSCLTGTLNCKISLSFCRTC

26

80.8%

NZ_WTWY01000020.1:

Lanthipeptides: GQY55_RS27090_lanthipeptide

1

SGLICTPSCATGTLNCQVSLSFCKTC

26

SG ICTPSC TGTLNC++SLSFC+TC

1

SGFICTPSCLTGTLNCKISLSFCRTC

26

76.9%

NZ_NIST01000001.1:

Lanthipeptides: CD001_RS09870_lanthipeptide

1

SGLICTPSCATGTLNCQVSLSFCKTC

26

+G ICTPSC TGTLNC+VSL+FC+TC

1

TGGICTPSCLTGTLNCRVSLTFCRTC

26

57.7%

NZ_CP029370.1:

Lanthipeptides: DI243_RS07485_lanthipeptide

1

SGLICTPSCATGTLNCQVSLSFCKTC

26

SG+ICTP+C T LNC S+S C C

1

SGIICTPTCLTSILNCYTSISHCGPC

26

38.5%

NZ_CP090942.1:

Lanthipeptides: LZT96_RS12010_lanthipeptide

1

SGLICTPSCA-TGTLN

15

S ICTP CA TG+ N

3

SKFICTPGCAKTGSFN

18

35.3%

NC_022237.1and 1 other:

NZ_JUZI01000019.1 Lanthipeptides: ADI02_RS09325_lanthipeptide

Lanthipeptides: SII_RS05025_lanthipeptide

1

SGLICTPSCATGTL----------NCQVSLS

21

S +CTP C TG L NC V +S

3

SVFMCTPGCVTGALMGCNLQTATCNCHVHIS

33

34.6%

NZ_CP094805.1:

Lanthipeptides: MUA37_RS13310_lanthipeptide

1

SGLICTPSCA-TGTLN

15

S +CTP CA TG+ N

3

SKFLCTPGCAKTGSFN

18

34.6%

NZ_NBBB01000022.1and 1 other:

NZ_NUOG01000083.1 Lanthipeptides: COE07_RS24905_lanthipeptide

Lanthipeptides: B6F67_RS25205_lanthipeptide

1

SGLICTPSCATGTLNCQVSLSFC

23

SG+ICTP T C+++ ++C

1

SGIICTP--GTCQTLCRITENWC

21

30.8%

NC_003923.1and 11 others:

NC_009641.1 Lanthipeptides: NWMN_RS09635_lanthipeptideNZ_AP019791.1 Lanthipeptides: RxyAA322_RS06460_lanthipeptideNZ_CP023076.1 Lanthipeptides: CJ017_RS08945_lanthipeptideNZ_CP054876.1 Lanthipeptides: HUW54_RS09150_lanthipeptideNZ_CP077098.1 Lanthipeptides: KSF82_RS09475_lanthipeptideNZ_CP092781.1 Lanthipeptides: ML436_RS08940_lanthipeptideNZ_CP102959.1 Lanthipeptides: NW979_RS08780_lanthipeptideNZ_CP102962.1 Lanthipeptides: NW971_RS09555_lanthipeptideNZ_LR133917.1 Lanthipeptides: ELZ45_RS09155_lanthipeptideNZ_LS483317.1 Lanthipeptides: DQL75_RS09700_lanthipeptideNZ_VKCY01000012.1 Lanthipeptides: FNK43_RS09020_lanthipeptide

Lanthipeptides: MW_RS09420_lanthipeptide

4

ICTPSCA-TGTLN

15

+CTP CA TG+ N

7

LCTPGCAKTGSFN

19

MIBiG 4.0 matches for CPY53_RS22235

21.6%

Lanthipeptide: SBI-06990 A1 or SBI-06989 A2

1

SGLICTPSCATGTLNCQVSLSFCKT

25

+GLI + VS +FC T

6

TGLILGIVAIQAGVAVGVSAAFCPT

30

20.6%

BGC0000535.4 (ADJ56352.1):

Lanthipeptide: nisin A

4

ICTPSCATGTL

14

+CTP C TG L

6

LCTPGCKTGAL

16

14.3%

BGC0000517.4 (BAB04173.1):

Lanthipeptide: haloduracin β or haloduracin α

5

CTPSC

9

C PSC

23

CMPSC

27

with 1 more sequence matches

10.7%

BGC0000517.4 (BAB04173.1):

Lanthipeptide: haloduracin β or haloduracin α

9

CATGTLNCQV

18

CA ++C++

1

CAWYNISCRL

10

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.33 out of 18.16

Confidence: strong

Additional weak hits (5):

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 23.88 out of 33.73

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.91 out of 28.14

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.91 out of 28.14

Confidence: weak

ClgR

Description: Caseinolytic protease gene regulator
Species: Corynebacterium glutamicum ATCC 13032
Score: 22.02 out of 30.22

Confidence: weak

OsdR

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

Confidence: weak

Lanthipeptides

RREFinder

TFBS Finder

Core peptide predictions

CPY53_RS22235 - Class I

Cleavage pHMM score: 5.70

RODEO score: 23

Monoisotopic mass: 2492.2 Da

Molecular weight: 2493.9 Da

Number of bridges: 5

Alternative weights: (assuming N unmodified Ser/Thr residues); 2511.9 Da N = 1; 2530.0 Da N = 2; 2548.0 Da N = 3

RRE predictions

: RRE type: Lanthipeptide_LanB_RRE; Location: 182 - 277; Score: 60.7

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator

NZ_CP023711.1 - Region 19 - NRPS-like,cyclic-lactone-autoinducer

Download region SVG

Location: 5,401,776 - 5,463,904 nt. (total: 62,129 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)
cyclic-lactone-autoinducer: (TIGR04223 or AgrB)

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: acetyltransferase acyltransferase

CPY53_RS23815: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

CPY53_RS23875: acyltransferase 3

smcogs: SMCOG1088: acyltransferase 3

Hydrolases: hydrolase

CPY53_RS23700: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase synthase

CPY53_RS23745: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

CPY53_RS23940: 3-oxoacyl-(acyl carrier protein) synthase III

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

Translocases: permease transporter

CPY53_RS23670: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

CPY53_RS23870: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002164.2	0.27	NRPS	peramine	Epichloe festucae
BGC0002135.2	0.27	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.27	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001249.5	0.26	NRPS	dimethylcoprogen	Alternaria alternata
BGC0000357.5	0.26	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001250.4	0.26	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.26	NRPS	epichloenin A	Epichloe festucae
BGC0000307.4	0.26	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.26	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001758.4	0.26	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002164.2	0.61	NRPS	peramine	Epichloe festucae
BGC0002135.2	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.60	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001249.5	0.60	NRPS	dimethylcoprogen	Alternaria alternata
BGC0000357.5	0.60	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0001250.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0001251.4	0.60	NRPS	epichloenin A	Epichloe festucae
BGC0000307.4	0.60	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.59	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii
BGC0001758.4	0.59	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: 18.57 out of 18.57

Confidence: strong

ToxT

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

Confidence: strong

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: 22.13 out of 27.78

Confidence: medium

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.68 out of 28.14

Confidence: medium

CRP

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

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.22 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.02 out of 28.19

Confidence: medium

Additional weak hits (18):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.19 out of 26.06

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.68 out of 26.12

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.98 out of 28.14

Confidence: weak

SypG

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.25 out of 26.06

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.48 out of 21.55

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 20.50 out of 26.12

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: 21.47 out of 26.06

Confidence: weak

MogR

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

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.27 out of 29.38

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.78 out of 21.55

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.02 out of 36.54

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.59 out of 36.54

Confidence: weak

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 22.53 out of 33.73

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.05 out of 33.14

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.59 out of 33.14

Confidence: weak

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 18.76 out of 23.43

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 24, location 5401775 - 5463904:

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

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 25, location 5401775 - 5445471:

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

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

NRPS/PKS substrate predictions

CPY53_RS23745: X

AMP-binding (224..633): 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:: Aromatic side chain (Phe, Trp, Ph-Gly, Tyr, bOH-Tyr)
Small clusters prediction:: Unpolar aromatic ring (Phe, Trp)
Single AA prediction:: phe (Phe)

Stachelhaus prediction details:

Stachelhaus sequence:: LVVAFDASVWDGTLTVAGEVNVYGPTECTVATTT
Nearest Stachelhaus code(s):: bMe-Phe DAWTTAVAAK (68% 8Å match)
Stachelhaus code match:: 90% (moderate)