GCF_003719335.1 - 21 region(s)

Identified secondary metabolite regions using strictness 'relaxed'

NZ_RIAS01000010.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1.1	T1PKS,NRPS,lanthipeptide-class-ii	72,470	130,512
Region 1.2	lanthipeptide-class-iv	214,099	236,849

NZ_RIAS01000011.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 2.1	NRPS,transAT-PKS	138,721	202,016	Low	paenilipoheptin	NRPS:Type I+PKS

NZ_RIAS01000012.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 3.1	NRPS	170,955	218,012	Low	octapeptin C4	NRPS:Type I

NZ_RIAS01000001.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 11.1	terpene-precursor	56,040	76,945
Region 11.2	NRPS	101,972	175,777
Region 11.3	cyclic-lactone-autoinducer	309,537	330,064
Region 11.4	transAT-PKS,NRPS,T1PKS	594,506	657,816	Low	pellasoren/pellasoren B	NRPS:Type I+PKS:Type I

NZ_RIAS01000002.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 22.1	NI-siderophore	99,037	134,932	Low	schizokinen	NRPS:Type IV
Region 22.2	proteusin	334,730	354,975

NZ_RIAS01000033.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 26.1	NRPS	1	25,963	High	colistin A/colistin B	NRPS:Type I

NZ_RIAS01000038.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 31.1	NRPS	1	2,271

NZ_RIAS01000003.1 (Paenibacillus amylolyticus)

Region	Type	From	To
Region 32.1	T3PKS	152,263	193,420
Region 32.2	terpene-precursor	248,396	270,777
Region 32.3	RRE-containing	428,626	450,158

NZ_RIAS01000005.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 37.1	NRPS-like	242,291	285,995

NZ_RIAS01000006.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 38.1	NRPS,transAT-PKS	71,593	138,252

NZ_RIAS01000007.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 39.1	NRPS,T1PKS,transAT-PKS	72,623	204,156	Low	xenocoumacin 1/xenocoumacin II	NRPS:Type I+PKS:Type I
Region 39.2	ranthipeptide	229,203	250,829

NZ_RIAS01000008.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 40.1	lassopeptide	31,192	55,173	Low	paeninodin	ribosomal:unmodified

NZ_RIAS01000009.1 (Paenibacillus amylolyticus)

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 41.1	terpene	68,633	89,505	Low	carotenoid	terpene

Region	Type	From	To	Similarity Confidence	Most similar known cluster
Region 1.1	T1PKS,NRPS,lanthipeptide-class-ii	72,470	130,512
Region 1.2	lanthipeptide-class-iv	214,099	236,849
Region 2.1	NRPS,transAT-PKS	138,721	202,016	Low	paenilipoheptin	NRPS:Type I+PKS
Region 3.1	NRPS	170,955	218,012	Low	octapeptin C4	NRPS:Type I
Region 11.1	terpene-precursor	56,040	76,945
Region 11.2	NRPS	101,972	175,777
Region 11.3	cyclic-lactone-autoinducer	309,537	330,064
Region 11.4	transAT-PKS,NRPS,T1PKS	594,506	657,816	Low	pellasoren/pellasoren B	NRPS:Type I+PKS:Type I
Region 22.1	NI-siderophore	99,037	134,932	Low	schizokinen	NRPS:Type IV
Region 22.2	proteusin	334,730	354,975
Region 26.1	NRPS	1	25,963	High	colistin A/colistin B	NRPS:Type I
Region 31.1	NRPS	1	2,271
Region 32.1	T3PKS	152,263	193,420
Region 32.2	terpene-precursor	248,396	270,777
Region 32.3	RRE-containing	428,626	450,158
Region 37.1	NRPS-like	242,291	285,995
Region 38.1	NRPS,transAT-PKS	71,593	138,252
Region 39.1	NRPS,T1PKS,transAT-PKS	72,623	204,156	Low	xenocoumacin 1/xenocoumacin II	NRPS:Type I+PKS:Type I
Region 39.2	ranthipeptide	229,203	250,829
Region 40.1	lassopeptide	31,192	55,173	Low	paeninodin	ribosomal:unmodified
Region 41.1	terpene	68,633	89,505	Low	carotenoid	terpene

No secondary metabolite regions were found in these records:: NZ_RIAS01000013.1 (Paenibacillus amylolyticus); NZ_RIAS01000014.1 (Paenibacillus amylolyticus); NZ_RIAS01000015.1 (Paenibacillus amylolyticus); NZ_RIAS01000016.1 (Paenibacillus amylolyticus); NZ_RIAS01000017.1 (Paenibacillus amylolyticus); NZ_RIAS01000018.1 (Paenibacillus amylolyticus); NZ_RIAS01000019.1 (Paenibacillus amylolyticus); NZ_RIAS01000020.1 (Paenibacillus amylolyticus); NZ_RIAS01000021.1 (Paenibacillus amylolyticus); NZ_RIAS01000022.1 (Paenibacillus amylolyticus); NZ_RIAS01000023.1 (Paenibacillus amylolyticus); NZ_RIAS01000024.1 (Paenibacillus amylolyticus); NZ_RIAS01000025.1 (Paenibacillus amylolyticus); NZ_RIAS01000026.1 (Paenibacillus amylolyticus); NZ_RIAS01000027.1 (Paenibacillus amylolyticus); NZ_RIAS01000028.1 (Paenibacillus amylolyticus); NZ_RIAS01000029.1 (Paenibacillus amylolyticus); NZ_RIAS01000030.1 (Paenibacillus amylolyticus); NZ_RIAS01000031.1 (Paenibacillus amylolyticus); NZ_RIAS01000032.1 (Paenibacillus amylolyticus); NZ_RIAS01000034.1 (Paenibacillus amylolyticus); NZ_RIAS01000035.1 (Paenibacillus amylolyticus); NZ_RIAS01000036.1 (Paenibacillus amylolyticus); NZ_RIAS01000037.1 (Paenibacillus amylolyticus); NZ_RIAS01000039.1 (Paenibacillus amylolyticus); NZ_RIAS01000040.1 (Paenibacillus amylolyticus); NZ_RIAS01000041.1 (Paenibacillus amylolyticus); NZ_RIAS01000004.1 (Paenibacillus amylolyticus)

Compact view

NZ_RIAS01000010.1 - Region 1 - NRPS,T1PKS,lanthipeptide-class-ii

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Location: 72,470 - 130,512 nt. (total: 58,043 nt) Show pHMM detection rules used

T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))
NRPS: cds(Condensation and (AMP-binding or A-OX) and not alpha_am_amid)
lanthipeptide-class-ii: cds(LANC_like and DUF4135)

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

Lanthipeptides

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

EC604_RS18155: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Hydrolases: esterase

EC604_RS18170: thioesterase

smcogs: SMCOG1004: thioesterase

Lyases: cyclase dehydratase

EC604_RS18185: NAD-dependent epimerase/dehydratase

smcogs: SMCOG1010: NAD-dependent epimerase/dehydratase

EC604_RS18230: lanthionine synthetase C family protein

smcogs: SMCOG1070: lanthionine synthetase C family protein

Ligases: ligase synthase

EC604_RS18160: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

EC604_RS18165: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Translocases: transporter

EC604_RS18090: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002135.2	0.66	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.66	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001210.5	0.65	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0001128.4	0.65	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000539.5	0.65	ribosomal	nukacin ISK-1	Staphylococcus warneri
BGC0001833.4	0.65	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001276.3	0.65	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.64	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.64	PKS	6-methylsalicyclic acid	Glarea lozoyensis

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	0.66	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002135.2	0.66	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001825.4	0.66	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001128.4	0.66	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.66	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001276.3	0.66	PKS	6-methylsalicyclic acid	Aspergillus terreus
BGC0001273.3	0.66	PKS	asperlactone	Aspergillus ochraceus
BGC0001275.3	0.66	PKS	6-methylsalicyclic acid	Glarea lozoyensis
BGC0002286.3	0.65	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001758.4	0.65	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptide(s) for EC604_RS18230

EC604_RS18225

Leader:

MKQFNLEALAAIEDISDDELMVVTGA

Core:

LAAIEDKKSGGVFCTVSHECHYNSVSPSSWLTCC

Core with dehydrations:

LAAIEDKKDhaGGVFCysDhbVDhaHECysHYNDhaVDhaPDhaDhaWLDhbCysCys

antiSMASH-DB 4.0 matches for EC604_RS18225

100.0%

NZ_FMVM01000006.1and 2 others:

NZ_RIAS01000010.1 Lanthipeptides: EC604_RS18225_lanthipeptideNZ_VEJI01000010.1 Lanthipeptides: FS576_RS22075_lanthipeptide

Lanthipeptides: BLQ13_RS10365_lanthipeptide

1

LAAIEDKKSGGVFCTVSHECHYNSVSPSSWLTCC

34

LAAIEDKKSGGVFCTVSHECHYNSVSPSSWLTCC

1

LAAIEDKKSGGVFCTVSHECHYNSVSPSSWLTCC

34

91.2%

NZ_CAKMMP010000011.1:

Lanthipeptides: L6H98_RS19925_lanthipeptide

1

LAAIEDKKSGGVFCTVSHECHYNSVSPSSWLTCC

34

+AAIE KSGGVFCTVSHECHYNSVSPSSWLTCC

1

VAAIEAAKSGGVFCTVSHECHYNSVSPSSWLTCC

34

79.4%

NZ_CP018620.1and 1 other:

NZ_CP062165.1 Lanthipeptides: JNUCC31_RS16755_lanthipeptide

Lanthipeptides: BS614_RS05680_lanthipeptide

1

LAAIEDKKSGGVFCTVSHECHYNSVSPSSWLTCC

34

++ I+ + SGGVFCTVSHECHYNSVSPSSWLTCC

1

VSVIDAQASGGVFCTVSHECHYNSVSPSSWLTCC

34

with 108 more sequence matches

Only the first 10 are displayed here.

61.8%

NZ_CP034248.1:

Lanthipeptides: EIM92_RS14995_lanthipeptide

7

KKSGGVFCTVSHECHYNSVSPSSWLTCC

34

SGGV CT+SHECHYNSVSP++W TCC

4

AASGGVICTISHECHYNSVSPAAWATCC

31

50.0%

NZ_CP086142.1and 3 others:

NZ_CP086142.1 Lanthipeptides: LL065_RS25460_lanthipeptideNZ_CP086142.1 Lanthipeptides: LL065_RS25455_lanthipeptideNZ_CP086142.1 Lanthipeptides: LL065_RS25450_lanthipeptide

Lanthipeptides: LL065_RS25465_lanthipeptide

9

SGGVFCTVSHECHYNSVSPSSWLTCC

34

GGV T +HEC+YNSVSP+SW CC

1

GGGVITTFTHECYYNSVSPASWGGCC

26

47.1%

NZ_CP077726.1and 12 others:

NZ_CP077726.1 Lanthipeptides: KTC92_RS18420_lanthipeptideNZ_CP077726.1 Lanthipeptides: KTC92_RS18415_lanthipeptideNZ_CP077726.1 Lanthipeptides: KTC92_RS18410_lanthipeptideNZ_CP077726.1 Lanthipeptides: KTC92_RS18405_lanthipeptideNZ_CP086248.1 Lanthipeptides: LL036_RS19070_lanthipeptideNZ_CP086248.1 Lanthipeptides: LL036_RS19065_lanthipeptideNZ_CP086248.1 Lanthipeptides: LL036_RS19060_lanthipeptideNZ_CP086248.1 Lanthipeptides: LL036_RS19055_lanthipeptideNZ_CP086248.1 Lanthipeptides: LL036_RS19050_lanthipeptideNZ_CP086248.1 Lanthipeptides: LL036_RS19045_lanthipeptideNZ_CP086248.1 Lanthipeptides: LL036_RS19040_lanthipeptideNZ_CP086248.1 Lanthipeptides: LL036_RS19035_lanthipeptide

Lanthipeptides: KTC92_RS18425_lanthipeptide

11

GVFCTVSHECHYNSVSPSSWLTCC

34

GV T +HEC+YNSVSP+SW CC

3

GVITTFTHECYYNSVSPASWGGCC

26

44.1%

NZ_CP051645.1and 2 others:

NZ_JAKVFF010000018.1 Lanthipeptides: MKR34_RS11425_lanthipeptideNZ_VDOJ01000018.1 Lanthipeptides: FSV48_RS11975_lanthipeptide

Lanthipeptides: HHJ99_RS13350_lanthipeptide

7

KKSGGVFCTVSHECHYNSVSPSSWLTCC

34

KK GV TVSH+CH NS TCC

1

KKKSGVIPTVSHDCHMNSF--QFVFTCC

26

41.2%

NZ_CP046304.1:

Lanthipeptides: FOC54_RS00030_lanthipeptide

7

KKSGGVFCTVSHECHYNSVSPSSWLTCC

34

KK GV TVSH+CH N+ TCC

1

KKKSGVIPTVSHDCHMNTF--QFMFTCC

26

41.2%

NZ_CP060646.1:

Lanthipeptides: H7789_RS06845_lanthipeptide

11

GVFCTVSHECHYNSVSPSSWLTCC

34

GVF T+SHECH N+ +S TCC

4

GVFKTISHECHLNTW--ASLATCC

25

41.2%

NZ_GL985606.1:

Lanthipeptides: HMPREF9062_RS00700_lanthipeptide

11

GVFCTVSHECHYNSVSPSSWLTCC

34

GVF T+SHEC+YNS + TCC

3

GVFHTISHECYYNSWAFI--FTCC

24

41.2%

NZ_JAEEGA010000010.1:

Lanthipeptides: I6N95_RS15660_lanthipeptide

11

GVFCTVSHECHYNSVSPSSWL-TCC

34

GV T+SHECH NS W+ TCC

3

GVIKTISHECHMNSW---QWIFTCC

24

41.2%

NZ_NWMU01000024.1and 3 others:

NZ_NWMU01000024.1 Lanthipeptides: CO197_RS09145_lanthipeptideNZ_VMMF01000004.1 Lanthipeptides: HT717_RS01575_lanthipeptideNZ_VMMF01000004.1 Lanthipeptides: HT717_RS01570_lanthipeptide

Lanthipeptides: CO197_RS09150_lanthipeptide

11

GVFCTVSHECHYNSVSPSSWLTCC

34

GVF T+SHECH NS + TCC

4

GVFKTISHECHMNSF--QFFFTCC

25

38.2%

NZ_CP031746.1:

Lanthipeptides: DCC27_RS08165_lanthipeptide

11

GVFCTVSHECHYNSVSPSSWLTCC

34

GV T++HECH N S LTCC

2

GVISTLTHECHMN--SWQGLLTCC

23

MIBiG 4.0 matches for EC604_RS18225

17.6%

BGC0002110.3 (QKV49893.1):

Lanthipeptide: birimositide

9

SGGVFCTVSHECHYN

23

+ G +CT++ EC N

14

NNGGWCTLTKECQPN

28

15.4%

BGC0001229.4 (SBI_06990):

Lanthipeptide: SBI-06990 A1 or SBI-06989 A2

14

CTVSHECHYN

23

CT+S EC N

28

CTLSKECQPN

37

14.7%

BGC0000517.4 (BAB04173.1):

Lanthipeptide: haloduracin β or haloduracin α

11

GVFCTVSHEC

20

G +CT++ EC

14

GAYCTLTVEC

23

allorf_125129_125284

Leader:

MCHMRMAHVVCKASHLNSEYA

Core:

LTKKKEFAAKRGYPVCCKLLCASYYNILFG

Core with dehydrations:

LDhbKKKEFAAKRGYPVCysCysKLLCysADhaYYNILFG

antiSMASH-DB 4.0 matches for allorf_125129_125284

100.0%

NZ_RIAS01000010.1:

Lanthipeptides: allorf_125129_125284_lanthipeptide

1

LTKKKEFAAKRGYPVCCKLLCASYYNILFG

30

LTKKKEFAAKRGYPVCCKLLCASYYNILFG

1

LTKKKEFAAKRGYPVCCKLLCASYYNILFG

30

23.3%

NC_014306.1:

Lanthipeptides: allorf_2538546_2538659_lanthipeptide

16

CCKLLCASYYNI

27

C +LL SYY I

5

CNRLLLTSYYQI

16

Legend:

Dha: Didehydroalanine
Dhb: Didehydrobutyrine

Transcription Factor Binding Sites

Binding sites found:

ToxT

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

Confidence: strong

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 23.57 out of 27.55

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.24 out of 18.16

Confidence: strong

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.11 out of 28.19

Confidence: medium

Additional weak hits (4):

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.97 out of 25.88

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.55 out of 28.14

Confidence: weak

SypG

Description: Regulator of biofilm formation and host colonization
Species: Vibrio fischeri ES114
Score: 22.38 out of 29.25

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.27 out of 26.06

Confidence: weak

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

Lanthipeptides

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Core peptide predictions

EC604_RS18225 - Class II

Cleavage pHMM score: 1.70

RODEO score: 0

Monoisotopic mass: 3513.6 Da

Molecular weight: 3515.9 Da

Number of bridges: 4

Alternative weights: (assuming N unmodified Ser/Thr residues); 3534.0 Da N = 1; 3552.0 Da N = 2; 3570.0 Da N = 3; 3588.0 Da N = 4

allorf_125129_125284 - Class II

Cleavage pHMM score: -7.00

RODEO score: 0

Monoisotopic mass: 3390.8 Da

Molecular weight: 3393.1 Da

Number of bridges: 2

Predicted core structure(s)

For candidate cluster 1, location 72469 - 130512:

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

Polymer prediction:: (pk) + (Orn - Cys)

Direct lookup in NORINE database: strict or relaxed

For candidate cluster 2, location 72469 - 124533:

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

Polymer prediction:: (pk) + (Orn - Cys)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

EC604_RS18160: pk

PKS_AT (551..847): pk

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; Methylmalonyl-CoA: 62.5%; CE-Malonyl-CoA: 58.3%

minowa: Methylmalonyl-CoA

Prediction, score:

Methylmalonyl-CoA: 105.2
Methoxymalonyl-CoA: 88.3
Isobutyryl-CoA: 85.8
Malonyl-CoA: 72.8
Ethylmalonyl-CoA: 65.2
trans-1,2-CPDA: 54.1
Propionyl-CoA: 53.8
2-Methylbutyryl-CoA: 52.4
Benzoyl-CoA: 48.2
Acetyl-CoA: 42.5
CHC-CoA: 39.1
inactive: 35.4
3-Methylbutyryl-CoA: 24.5
fatty_acid: 24.1

EC604_RS18165: Orn - Cys

Search NORINE for peptide: strict or relaxed

AMP-binding (521..926): 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:: AGWAFDVFVGDREFIVGSDISSYGLTEATIDSSY
Nearest Stachelhaus code(s):: Orn DVGEIGSIDK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1600..1994): Cys

nrpys: Cys

SVM prediction details:

Predicted physicochemical class:: hydrophobic-aliphatic (Ala, Gly, Val, Leu, Ile, Abu, Ival, Ser, Thr, Hpg, Dhpg, Cys, Pro, Hpr)
Large clusters prediction:: Polar, uncharged (aliphatic with -SH) (Cys)
Small clusters prediction:: Polar, uncharged (aliphatic with -SH) (Cys)
Single AA prediction:: Polar, uncharged (aliphatic with -SH) (Cys)

Stachelhaus prediction details:

Stachelhaus sequence:: TDVSFDLSVYDGNSLLSGDVSLGGATEASIWSIF
Nearest Stachelhaus code(s):: Cys DLYNLSLIWK (97% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
GnfM	Regulator of nitrogen-fixation genes
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_RIAS01000010.1 - Region 2 - lanthipeptide-class-iv

Download region GenBank file

Download region SVG

Location: 214,099 - 236,849 nt. (total: 22,751 nt) Show pHMM detection rules used

lanthipeptide-class-iv: (cds(LANC_like and Pkinase) and not micKC)

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

No tailoring functions detected.

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000519.4	0.48	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0002701.2	0.38	ribosomal	paenithipeptin	Paenibacillus thiaminolyticus
BGC0000874.5	0.30	other (other)	blasticidin S	Streptomyces griseochromogenes
BGC0002556.2	0.24	other (other)	cervinomycin B3, cervinomycin C1, cervinomycin C2, cervinomycin C3, cervinomycin C4	Streptomyces sp.
BGC0001199.5	0.20	PKS	akaeolide	Streptomyces sp. NBRC 109706

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000519.4	0.48	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0002701.2	0.38	ribosomal	paenithipeptin	Paenibacillus thiaminolyticus
BGC0000874.5	0.30	other (other)	blasticidin S	Streptomyces griseochromogenes
BGC0002556.2	0.24	other (other)	cervinomycin B3, cervinomycin C1, cervinomycin C2, cervinomycin C3, cervinomycin C4	Streptomyces sp.
BGC0001199.5	0.20	PKS	akaeolide	Streptomyces sp. NBRC 109706

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Lanthipeptide predictions

Lanthipeptides - No core peptides found.

Transcription Factor Binding Sites

Binding sites found:

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.14 out of 18.16

Confidence: strong

ToxT

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

Confidence: strong

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.27 out of 21.55

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.16 out of 26.06

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 20.75 out of 23.43

Confidence: medium

BldD

Description: Development and antibiotic global regulator
Species: Streptomyces coelicolor
Score: 21.71 out of 23.43

Confidence: medium

Additional weak hits (8):

MatP

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

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.39 out of 31.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.00 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.91 out of 26.06

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 21.95 out of 31.73

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 22.92 out of 32.74

Confidence: weak

ANR

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

Confidence: weak

RicR

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

Confidence: weak

Lanthipeptides

TFBS Finder

Core peptide predictions

No core peptides found.

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
ArcA	Repressor of carbon oxidation
BldD	Development and antibiotic global regulator
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis

NZ_RIAS01000011.1 - Region 1 - NRPS,transAT-PKS

Download region GenBank file

Download region SVG

Location: 138,721 - 202,016 nt. (total: 63,296 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

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

EC604_RS19655: alcohol dehydrogenase

smcogs: SMCOG1040: alcohol dehydrogenase

Transferases: acylase acyltransferase aminotransferase phosphotransferase

EC604_RS19650: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

EC604_RS19680: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

EC604_RS19715: Glucose-specific phosphotransferase enzyme IIA

smcogs: SMCOG1145: Glucose-specific phosphotransferase enzyme IIA

EC604_RS19730: acyltransferase 3

smcogs: SMCOG1088: acyltransferase 3

EC604_RS19755: Glucose-specific phosphotransferase enzyme IIA

smcogs: SMCOG1145: Glucose-specific phosphotransferase enzyme IIA

Hydrolases: hydrolase protease

EC604_RS19660: HAD-superfamily hydrolase, subfamily IA, variant

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

EC604_RS19685: hydrolase

smcogs: SMCOG1179: hydrolase

EC604_RS19700: alkaline serine protease, subtilase family

smcogs: SMCOG1075: alkaline serine protease, subtilase family

Ligases: ligase synthase

EC604_RS19640: Pseudouridine synthase

smcogs: SMCOG1154: Pseudouridine synthase

EC604_RS19670: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS19675: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.68	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.65	NRPS	AM-toxin	Alternaria alternata
BGC0001133.4	0.65	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.64	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001825.4	0.63	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0000402.4	0.63	NRPS	paenilarvin A, paenilarvin B, paenilarvin C	Paenibacillus larvae subsp. larvae DSM 25430
BGC0001132.4	0.62	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000307.4	0.62	NRPS	AbT1	Aureobasidium pullulans
BGC0001128.4	0.62	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.61	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.67	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001261.3	0.66	NRPS	AM-toxin	Alternaria alternata
BGC0001133.4	0.66	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001825.4	0.65	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0000402.4	0.65	NRPS	paenilarvin A, paenilarvin B, paenilarvin C	Paenibacillus larvae subsp. larvae DSM 25430
BGC0001132.4	0.65	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0000307.4	0.64	NRPS	AbT1	Aureobasidium pullulans
BGC0001128.4	0.64	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.64	NRPS	icosalide A, icosalide B	Burkholderia gladioli

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 22.03 out of 29.72

Confidence: medium

IolR

Description: Regulator of the inositol catabolism
Species: Caulobacter crescentus CB15
Score: 19.11 out of 23.79

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.67 out of 26.06

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.33 out of 27.78

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.49 out of 20.97

Confidence: medium

CRP

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

Confidence: strong

ANR

Description: Anaerobic transcriptional regulator
Species: Pseudomonas putida KT2440
Score: 21.28 out of 26.33

Confidence: medium

Additional weak hits (9):

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.45 out of 30.25

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.16 out of 27.55

Confidence: weak

LuxO

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

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.20 out of 26.85

Confidence: weak

RicR

Description: Copper-responsive regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.72 out of 32.93

Confidence: weak

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.16 out of 27.55

Confidence: weak

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 18.53 out of 21.55

Confidence: weak

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 17.40 out of 20.01

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.72 out of 24.78

Confidence: weak

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 138720 - 202016:

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

Polymer prediction:: (fatty_acid - mal - Glu - D-Tyr) + (D-Thr)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

EC604_RS19670: Tyr - Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (266..660): Tyr

nrpys: Tyr

SVM prediction details:

Predicted physicochemical class:: N/A
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:: SWKNFDSFITHGQSVAAGECNEYGPTENSVVSTV
Nearest Stachelhaus code(s):: Trp DPTQVGEVVK (74% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1779..2178): 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)

EC604_RS19675: fatty_acid - Glu

Search NORINE for peptide: strict or relaxed

CAL_domain (36..479): fatty_acid

minowa: fatty_acid

Prediction, score:

fatty_acid: 394.7
NH2: 22.5
shikimic_acid: 0.0
Acetyl-CoA: 0.0
AHBA: 0.0

AMP-binding (2948..3355): 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:: LSLAFDASVKQGDGLIGGEINVYGPTECCVDAAT
Nearest Stachelhaus code(s):: Glu DAKDLGVVDK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

EC604_RS19680: mal

PKS_AT (6..291): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 62.5%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 63.9
Methoxymalonyl-CoA: 31.4
inactive: 29.8
Propionyl-CoA: 15.1
Methylmalonyl-CoA: 13.5
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

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ANR	Anaerobic transcriptional regulator
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
IolR	Regulator of the inositol catabolism
MogR	Repressor of flagellar motility genes
NtrC	Nitrogen regulatory protein C

NZ_RIAS01000012.1 - Region 1 - NRPS

Download region GenBank file

Download region SVG

Location: 170,955 - 218,012 nt. (total: 47,058 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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: aminotransferase

EC604_RS20745: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Ligases: ligase

EC604_RS20740: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: permease

EC604_RS20705: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

EC604_RS20715: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.70	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.68	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001833.4	0.67	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.65	NRPS	AbT1	Aureobasidium pullulans

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.70	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0001132.4	0.68	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001135.5	0.68	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001166.5	0.68	NRPS	HC-toxin	Alternaria jesenskae
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001833.4	0.67	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001128.4	0.67	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002286.3	0.66	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.65	NRPS	AbT1	Aureobasidium pullulans

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 24.80 out of 27.78

Confidence: strong

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 24.53 out of 26.06

Confidence: strong

ToxT

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

Confidence: strong

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.21 out of 27.78

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.49 out of 27.78

Confidence: medium

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.94 out of 21.55

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.87 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 23.43 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.95 out of 28.19

Confidence: medium

Additional weak hits (9):

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.65 out of 26.06

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.70 out of 26.06

Confidence: weak

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.58 out of 29.72

Confidence: weak

CopR

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

Confidence: weak

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 19.63 out of 26.12

Confidence: weak

MogR

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

Confidence: weak

ArcA

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.30 out of 26.06

Confidence: weak

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 22.88 out of 30.98

Confidence: weak

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 170954 - 218012:

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

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

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

EC604_RS20740: Leu - Leu - Dab

Search NORINE for peptide: strict or relaxed

AMP-binding (282..672): 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 (1789..2184): 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 (2828..3246): 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)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
ArcA	Repressor of carbon oxidation
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_RIAS01000001.1 - Region 1 - terpene-precursor

Download region GenBank file

Download region SVG

Location: 56,040 - 76,945 nt. (total: 20,906 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

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

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

EC604_RS00375: acetyl-CoA carboxylase biotin carboxylase

smcogs: SMCOG1090: acetyl-CoA carboxylase biotin carboxylase

Ligases: synthase synthetase

EC604_RS00330: 1-deoxy-D-xylulose-5-phosphate synthase

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

EC604_RS00335: 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:

EC604_RS00335: PT_FPPS_like

Domain 1 (36 - 301): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: Farnesyl diphosphate synthase, bacterial

Reactions:: IPP, DMAPP → FPP

Transcription Factor Binding Sites

Binding sites found:

VqsM

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

Confidence: strong

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.93 out of 30.25

Confidence: medium

NrdR

Description: Represses ribonucleotide reductase encoding genes
Species: Streptomyces coelicolor
Score: 22.03 out of 27.18

Confidence: medium

Additional weak hits (2):

PerR

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

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 21.84 out of 30.25

Confidence: weak

Terpene

TFBS Finder

Glossary

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

TFBS definitions

Regulator	Description
ColR	Phenol-responsive regulator
NrdR	Represses ribonucleotide reductase encoding genes
VqsM	Regulator of quorum-sensing signalling systems

NZ_RIAS01000001.1 - Region 2 - NRPS

Download region GenBank file

Download region SVG

Location: 101,972 - 175,777 nt. (total: 73,806 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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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

EC604_RS00535: aldehyde dehydrogenase

smcogs: SMCOG1017: aldehyde dehydrogenase

EC604_RS00570: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

EC604_RS00585: oxidoreductase

smcogs: SMCOG1079: oxidoreductase

Hydrolases: esterase

EC604_RS00600: thioesterase

smcogs: SMCOG1004: thioesterase

Isomerases: isomerase

EC604_RS00635: isochorismate synthase

smcogs: SMCOG1018: isochorismate synthase

Ligases: ligase synthase

EC604_RS00615: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS00620: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS00625: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS00630: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS00640: carbamoyl phosphate synthase small subunit

smcogs: SMCOG1249: carbamoyl phosphate synthase small subunit

EC604_RS00675: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.74	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	0.72	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.72	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002071.2	0.72	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001133.4	0.72	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.71	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	0.74	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.74	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001135.5	0.72	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001641.4	0.72	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.72	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002071.2	0.72	NRPS	virginiafactin A, virginiafactin B, virginiafactin C, virginiafactin D	Pseudomonas sp. QS1027
BGC0001133.4	0.72	NRPS	taxlllaid A	Xenorhabdus bovienii SS-2004
BGC0002286.3	0.71	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.71	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.71	NRPS	xenematide	Xenorhabdus nematophila AN6/1

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: 19.26 out of 19.26

Confidence: strong

CRP

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

Confidence: strong

CRP

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

Confidence: strong

CRP

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

Confidence: medium

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.06 out of 25.88

Confidence: medium

RutR

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

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.66 out of 27.78

Confidence: medium

MexT

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

Confidence: medium

MogR

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

Confidence: medium

MogR

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

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.76 out of 20.97

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.11 out of 20.97

Confidence: medium

IolR

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

Confidence: medium

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 26.45 out of 33.14

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 20.84 out of 24.78

Confidence: medium

Additional weak hits (7):

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.02 out of 29.72

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.16 out of 30.25

Confidence: weak

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 20.26 out of 26.85

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 24.12 out of 28.14

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.11 out of 26.06

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.53 out of 30.25

Confidence: weak

PerR

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

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 2, location 101971 - 175777:

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

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

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

EC604_RS00615: Ile - Ile - Ile - X

Search NORINE for peptide: strict or relaxed

AMP-binding (470..863): 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:: TNNSFDGATFDGFMLFGGELHMYGPTETTVYATY
Nearest Stachelhaus code(s):: Ile or Val DGFFLGVVYK (82% 8Å match); Leu DGFFLGVVYK (79% 8Å match); Ile DGFFLGVVYK (76% 8Å match)
Stachelhaus code match:: 90% (moderate)

AMP-binding (1528..1926): 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:: THNSFDGSTYEGFMFFGGEVNAYGPTETTVFAAT
Nearest Stachelhaus code(s):: Val DGYFLGVVFK (74% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (2587..2983): 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:: TQNSFDGSTYDGFMFFGGEINCYGPTETTVFATT
Nearest Stachelhaus code(s):: Val DGYFLGVVFK (76% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (3632..4030): X

nrpys: Leu, Val

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: TNNSFDGSTYEGFMFFGGEANGYGPTETTVFAAT
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (82% 8Å match); Leu DGYIIGGVFK (53% 8Å match)
Stachelhaus code match:: 80% (moderate)

EC604_RS00620: X - Ile - Val - Val

Search NORINE for peptide: strict or relaxed

AMP-binding (295..693): X

nrpys: Leu, Val

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: TNNSFDGSTYEGFMFFGGEANGYGPTETTVFAAT
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (82% 8Å match); Leu DGYIIGGVFK (53% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1344..1746): 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:: THNSFDGSTFDGFMLFGGEIHVYGPTETTVFATF
Nearest Stachelhaus code(s):: Ile DGFFLGVVFK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (2409..2802): Val

nrpys: Val

SVM prediction details:

Predicted physicochemical class:: N/A
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:: TNNSFDGATYEGFMFIGGEVNGYGPTETTVFAAT
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (79% 8Å match); Leu DGYIIGGVFK (56% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (3465..3867): Val

nrpys: Val

SVM prediction details:

Predicted physicochemical class:: N/A
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:: TNNSFDGSTYEGFVFVGGEANGYGPTETTVFATT
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (79% 8Å match); Leu DGYIIGGVFK (53% 8Å match)
Stachelhaus code match:: 80% (moderate)

EC604_RS00625: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (39..442): 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)

EC604_RS00630: fatty_acid

CAL_domain (235..550): fatty_acid

minowa: fatty_acid

Prediction, score:

fatty_acid: 31.0
AHBA: 8.7
shikimic_acid: 0.0
NH2: 0.0
Acetyl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
IolR	Regulator of the inositol catabolism
LexA variant 2	Repressor of DNA damage response
MexT	Global virulence regulator
MogR	Repressor of flagellar motility genes
PsrA	Oleic acid responsive regulator
RutR	Regulator of the pyrimidine and purine metabolism
ZuR variant 2	Zinc-responsive repressor

NZ_RIAS01000001.1 - Region 3 - cyclic-lactone-autoinducer

Download region GenBank file

Download region SVG

Location: 309,537 - 330,064 nt. (total: 20,528 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

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

No tailoring functions detected.

Similar gene clusters

No matches found.

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: 24.16 out of 26.06

Confidence: strong

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.67 out of 26.06

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 24.63 out of 24.78

Confidence: strong

Additional weak hits (6):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.92 out of 27.55

Confidence: weak

HipB

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

Confidence: weak

ANR

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

Confidence: weak

DmdR1

Description: Iron(II)-dependent repressor
Species: Streptomyces coelicolor
Score: 23.12 out of 36.53

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 23.97 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

TFBS Finder

TFBS definitions

Regulator	Description
LexA variant 2	Repressor of DNA damage response
MogR	Repressor of flagellar motility genes

NZ_RIAS01000001.1 - Region 4 - NRPS,T1PKS,transAT-PKS

Download region GenBank file

Download region SVG

Location: 594,506 - 657,816 nt. (total: 63,311 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)
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

EC604_RS02730: pyridine nucleotide-disulfide oxidoreductase

smcogs: SMCOG1175: pyridine nucleotide-disulfide oxidoreductase

EC604_RS02790: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

EC604_RS02805: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

EC604_RS02890: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

EC604_RS02895: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

EC604_RS02900: oxidoreductase

smcogs: SMCOG1083: oxidoreductase

Transferases: acylase aminotransferase

EC604_RS02795: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

EC604_RS02800: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: dehalogenase esterase phosphatase

EC604_RS02770: thioesterase

smcogs: SMCOG1004: thioesterase

EC604_RS02785: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

EC604_RS02860: haloalkane dehalogenase

smcogs: SMCOG1262: haloalkane dehalogenase

Ligases: ligase synthase

EC604_RS02815: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS02820: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

Translocases: permease

EC604_RS02885: phenylalanine-specific permease

smcogs: SMCOG1038: phenylalanine-specific permease

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	1.07	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	1.05	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.98	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.93	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002175.3	0.90	PKS	YWA1	Aspergillus oryzae RIB40
BGC0000107.3	0.90	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0001164.3	0.87	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.86	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001876.2	0.80	NRPS	thalassospiramide A	Thalassospira sp. CNJ-328
BGC0002191.2	0.80	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	0.69	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001825.4	0.68	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0001758.4	0.66	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.64	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002175.3	0.64	PKS	YWA1	Aspergillus oryzae RIB40
BGC0000107.3	0.64	PKS	naphthopyrone	Aspergillus nidulans FGSC A4
BGC0001164.3	0.62	PKS	1-heptadecene	Cyanothece sp. PCC 7822
BGC0001160.5	0.62	PKS	1-nonadecene, (14Z)-1,14-nonadecadiene	Synechococcus sp. PCC 7002
BGC0001876.2	0.60	NRPS	thalassospiramide A	Thalassospira sp. CNJ-328
BGC0002191.2	0.60	PKS	prolipyrone B, gibepyrone D	Fusarium graminearum PH-1

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CRP

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

Confidence: strong

CRP

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

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.26 out of 24.78

Confidence: medium

Additional weak hits (6):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.47 out of 31.73

Confidence: weak

ANR

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

Confidence: weak

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 23.25 out of 30.97

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.23 out of 31.73

Confidence: weak

LexA variant 1

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

Confidence: weak

CelR

Description: Cellobiose uptake repressor
Species: Streptomyces coelicolor
Score: 20.25 out of 30.11

Confidence: weak

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 4, location 594505 - 657816:

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

Polymer prediction:: (X - mal - Gly - Val) + (fatty_acid - mal)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

EC604_RS02800: mal

PKS_AT (5..291): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 66.7%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 55.5
Methoxymalonyl-CoA: 40.4
Methylmalonyl-CoA: 32.1
Ethylmalonyl-CoA: 24.7
inactive: 16.4
Benzoyl-CoA: 11.5
CHC-CoA: 10.1
2-Methylbutyryl-CoA: 9.9
fatty_acid: 9.8
trans-1,2-CPDA: 0.0
Propionyl-CoA: 0.0
Isobutyryl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0

EC604_RS02815: fatty_acid

CAL_domain (49..480): fatty_acid

minowa: fatty_acid

Prediction, score:

fatty_acid: 66.7
shikimic_acid: 0.0
Acetyl-CoA: 0.0
AHBA: 0.0
NH2: -2.8

EC604_RS02820: X - mal - Gly - Val

Search NORINE for peptide: strict or relaxed

AMP-binding (461..866): X

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

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: TDLTFDVSCTEGNFFVGGEDNVYGPTECTIWVSH
Nearest Stachelhaus code(s):: Ala DVTNFALIYK (68% 8Å match); Gly DILQFGVIWK (62% 8Å match)
Stachelhaus code match:: 70% (weak)

PKS_AT (1587..1884): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 87.5%; inactive: 83.3%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 110.5
inactive: 67.4
Methoxymalonyl-CoA: 51.8
Methylmalonyl-CoA: 42.1
Propionyl-CoA: 30.2
Ethylmalonyl-CoA: 16.5
Isobutyryl-CoA: 11.2
fatty_acid: 10.6
trans-1,2-CPDA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

AMP-binding (2524..2919): 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:: FDITFDIFGFEALSLTGGEFNMYGPTETTIWSTT
Nearest Stachelhaus code(s):: Gly DILQLGMIWK (68% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (4528..4929): Val

nrpys: Val

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: VKSSFDGSIFDAFIMFGGELNGYGPTEATFFASY
Nearest Stachelhaus code(s):: Val DGFFVGGVFK (65% 8Å match)
Stachelhaus code match:: 80% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CRP	Cyclic AMP receptor protein
LexA variant 2	Repressor of DNA damage response

NZ_RIAS01000002.1 - Region 1 - NI-siderophore

Download region GenBank file

Download region SVG

Location: 99,037 - 134,932 nt. (total: 35,896 nt) Show pHMM detection rules used

NI-siderophore: IucA_IucC

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Transferases: aminotransferase

EC604_RS04300: aminotransferase class-III

smcogs: SMCOG1013: aminotransferase class-III

Hydrolases: glucosidase

EC604_RS04265: Alpha-glucosidase

smcogs: SMCOG1257: Alpha-glucosidase

Lyases: decarboxylase

EC604_RS04325: diaminopimelate decarboxylase

smcogs: SMCOG1264: diaminopimelate decarboxylase

Ligases: ligase

EC604_RS04260: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000946.5	0.59	other (other)	vibrioferrin	Vibrio parahaemolyticus
BGC0000943.5	0.58	other (other)	staphyloferrin B	Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002471.3	0.56	other (other)	baumannoferrin A, baumannoferrin B	Acinetobacter baumannii AYE
BGC0002682.2	0.56	other (other)	aerobactin	Vibrio mimicus
BGC0000939.5	0.55	other (other)	aerobactin	Grimontia hollisae
BGC0002073.3	0.55	NRPS	dehydroxynocardamine	Corynebacterium propinquum
BGC0000947.5	0.54	other (other)	vibrioferrin	Vibrio alginolyticus
BGC0001870.3	0.54	other (other)	putrebactin, avaroferrin	Xenorhabdus budapestensis
BGC0001572.3	0.52	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0002683.2	0.51	NRPS	schizokinen	Nostoc sp. PCC 7120 = FACHB-418

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000946.5	0.59	other (other)	vibrioferrin	Vibrio parahaemolyticus
BGC0000943.5	0.58	other (other)	staphyloferrin B	Staphylococcus aureus subsp. aureus NCTC 8325
BGC0002471.3	0.56	other (other)	baumannoferrin A, baumannoferrin B	Acinetobacter baumannii AYE
BGC0002682.2	0.56	other (other)	aerobactin	Vibrio mimicus
BGC0000939.5	0.55	other (other)	aerobactin	Grimontia hollisae
BGC0002073.3	0.55	NRPS	dehydroxynocardamine	Corynebacterium propinquum
BGC0000947.5	0.54	other (other)	vibrioferrin	Vibrio alginolyticus
BGC0001870.3	0.54	other (other)	putrebactin, avaroferrin	Xenorhabdus budapestensis
BGC0001572.3	0.52	other (other)	desferrioxamine E	Pantoea agglomerans
BGC0002683.2	0.51	NRPS	schizokinen	Nostoc sp. PCC 7120 = FACHB-418

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 26.54 out of 29.38

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.15 out of 20.97

Confidence: strong

CatR

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

Confidence: medium

NtrC

Description: Nitrogen regulatory protein C
Species: Pseudomonas putida KT2440
Score: 21.87 out of 29.72

Confidence: medium

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 24.54 out of 29.38

Confidence: medium

FuR variant 1

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

Confidence: medium

MexT

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

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.81 out of 28.19

Confidence: medium

ZuR variant 1

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

Confidence: medium

Additional weak hits (14):

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.62 out of 31.73

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 20.64 out of 28.14

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.33 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.15 out of 29.38

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 23.61 out of 29.38

Confidence: weak

FuR variant 2

Description: Ferric Uptake Regulator
Species: Caulobacter crescentus CB15
Score: 24.43 out of 32.74

Confidence: weak

PerR

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

Confidence: weak

PerR

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

Confidence: weak

PerR

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

Confidence: weak

ANR

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

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.88 out of 39.62

Confidence: weak

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 25.59 out of 39.62

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.95 out of 33.14

Confidence: weak

LexA variant 1

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

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
CatR	H2O2-responsive repressor
CcpA	Catabolite control protein A
FuR variant 1	Ferric Uptake Regulator
MexT	Global virulence regulator
NtrC	Nitrogen regulatory protein C
ZuR variant 1	Zinc-responsive repressor

NZ_RIAS01000002.1 - Region 2 - proteusin

Download region GenBank file

Download region SVG

Location: 334,730 - 354,975 nt. (total: 20,246 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

reset view

zoom to selection

Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

TFBS Finder

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

EC604_RS05245: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

Transferases: acyltransferase

EC604_RS05300: acyltransferase 3

smcogs: SMCOG1088: acyltransferase 3

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000888.5	0.49	other (other)	bacilysin	Bacillus sp. CS93
BGC0001928.2	0.48	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0001184.4	0.44	other (other)	bacilysin	Bacillus velezensis FZB42
BGC0000894.4	0.41	other (other)	citrinin	Monascus aurantiacus
BGC0002496.3	0.39	NRPS	serratiochelin A, serratiochelin C, serratiochelin B	Serratia plymuthica
BGC0001197.5	0.37	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0000671.3	0.36	terpene	momilactone B	Oryza sativa Japonica Group
BGC0000384.6	0.36	NRPS	lyngbyatoxin	Lyngbya majuscula
BGC0001605.3	0.35	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0000188.5	0.35	other (other)	saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2	Cylindrospermopsis raciborskii T3

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000888.5	0.49	other (other)	bacilysin	Bacillus sp. CS93
BGC0001928.2	0.48	other (other)	(2R,3S,4S)-5-fluoro-2,3,4-trihydroxypentanoic acid	Streptomyces sp. MA37
BGC0001184.4	0.44	other (other)	bacilysin	Bacillus velezensis FZB42
BGC0000894.4	0.41	other (other)	citrinin	Monascus aurantiacus
BGC0002496.3	0.39	NRPS	serratiochelin A, serratiochelin C, serratiochelin B	Serratia plymuthica
BGC0001197.5	0.37	PKS	frankiamicin	Frankia sp. EAN1pec
BGC0000671.3	0.36	terpene	momilactone B	Oryza sativa Japonica Group
BGC0000384.6	0.36	NRPS	lyngbyatoxin	Lyngbya majuscula
BGC0001605.3	0.35	terpene	gibberellin	Sinorhizobium fredii NGR234
BGC0000188.5	0.35	other (other)	saxitoxin, neosaxitoxin, decarbamoylsaxitoxin, gonyautoxin 3, gonyautoxin 2	Cylindrospermopsis raciborskii T3

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

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

Confidence: strong

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.95 out of 27.78

Confidence: medium

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.49 out of 25.88

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 18.11 out of 20.97

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 21.90 out of 27.78

Confidence: medium

Additional weak hits (1):

MntR

Description: Manganese transport regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 24.56 out of 39.62

Confidence: weak

TFBS Finder

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
PsrA	Oleic acid responsive regulator
ToxT	Regulator of MSHA biosynthesis

NZ_RIAS01000033.1 - Region 1 - NRPS

Download region GenBank file

Download region SVG

Location: 1 - 25,963 nt. (total: 25,963 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

Ligases: ligase

EC604_RS29090: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

EC604_RS29095: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001153.5	0.81	NRPS	polymyxin B	Paenibacillus polymyxa
BGC0001192.5	0.81	NRPS	colistin A, colistin B	Paenibacillus alvei
BGC0000408.5	0.81	NRPS	polymyxin	Paenibacillus polymyxa
BGC0002653.2	0.79	NRPS	macolacin	Paenibacillus xylanexedens
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.74	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001153.5	0.81	NRPS	polymyxin B	Paenibacillus polymyxa
BGC0001192.5	0.81	NRPS	colistin A, colistin B	Paenibacillus alvei
BGC0000408.5	0.81	NRPS	polymyxin	Paenibacillus polymyxa
BGC0002653.2	0.79	NRPS	macolacin	Paenibacillus xylanexedens
BGC0001132.4	0.75	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.75	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001833.4	0.75	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0002286.3	0.74	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001825.4	0.73	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

No hits above weak threshold.

Weak hits (1):

NuR

Description: Nickel-responsive regulator
Species: Streptomyces coelicolor
Score: 24.18 out of 30.98

Confidence: weak

Module view

Legend

Detailed domain annotation

Selected features only

Show module domains

NRPS/PKS products

NRPS/PKS substrates

TFBS Finder

Predicted core structure(s)

For candidate cluster 1, location 0 - 25963:

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

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

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

EC604_RS29075: Dab - Thr - Dab - Dab

Search NORINE for peptide: strict or relaxed

AMP-binding (485..894): 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 (1536..1943): 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 (2601..3059): 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 (4180..4598): 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)

EC604_RS29090: Thr

Search NORINE for peptide: strict or relaxed

AMP-binding (268..675): 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)

EC604_RS29095: Dab

Search NORINE for peptide: strict or relaxed

AMP-binding (9..235): 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:: ---AFDVFVGDRESITSSDINAYGVTEAAIDSSF
Nearest Stachelhaus code(s):: Dab DVGEISAIDK (91% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description

NZ_RIAS01000038.1 - Region 1 - NRPS

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Location: 1 - 2,271 nt. (total: 2,271 nt) Show pHMM detection rules used

Region on contig edge.

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

Legend:

core biosynthetic genes

additional biosynthetic genes

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regulatory genes

other genes

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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

Ligases: ligase

EC604_RS29285: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.63	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.63	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.62	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.62	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.65	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.64	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0000307.4	0.63	NRPS	AbT1	Aureobasidium pullulans
BGC0000342.4	0.63	NRPS	enniatin	Fusarium equiseti
BGC0001758.4	0.63	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001641.4	0.63	NRPS	kolossin	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001128.4	0.63	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.63	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001833.4	0.62	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.62	NRPS	xenematide	Xenorhabdus nematophila AN6/1

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Detailed domain annotation

Selected features only

Show module domains

NZ_RIAS01000003.1 - Region 1 - T3PKS

Download region GenBank file

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Location: 152,263 - 193,420 nt. (total: 41,158 nt) Show pHMM detection rules used

T3PKS: (Chal_sti_synt_C or Chal_sti_synt_N)

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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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

Oxidoreductases: oxidoreductase

EC604_RS07555: oxidoreductase

smcogs: SMCOG1161: oxidoreductase

EC604_RS07645: FAD dependent oxidoreductase

smcogs: SMCOG1103: FAD dependent oxidoreductase

Transferases: acetyltransferase aminotransferase methyltransferase

EC604_RS07545: aminotransferase

smcogs: SMCOG1019: aminotransferase

EC604_RS07595: methyltransferase

smcogs: SMCOG1089: methyltransferase

EC604_RS07635: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

Hydrolases: hydrolase

EC604_RS07575: alpha/beta hydrolase domain-containing protein

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

EC604_RS07615: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: synthase

EC604_RS07565: chalcone and stilbene synthase domain protein

smcogs: SMCOG1024: chalcone and stilbene synthase domain protein

Translocases: transporter

EC604_RS07520: sugar-binding lipoprotein

smcogs: SMCOG1143: sugar-binding lipoprotein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001310.5	0.53	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0001962.3	0.50	PKS	hierridin B, hierridin C	Cyanobium sp. LEGE 06113
BGC0000584.5	0.47	ribosomal	colicin V	Escherichia coli
BGC0002332.2	0.45	PKS	4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A	Candidatus Entotheonella sp.
BGC0001831.3	0.44	PKS	alkylpyrone-407, alkylpyrone-393	Myxococcus xanthus DK 1622
BGC0000589.5	0.44	ribosomal	microcin M	Escherichia coli Nissle 1917
BGC0001374.5	0.44	other (other)	thienodolin	Streptomyces albogriseolus
BGC0001964.2	0.44	PKS	alkylpyrone-407, alkylpyrone-393	Cystobacterineae bacterium
BGC0002313.3	0.43	other (other)	streptozotocin	Streptomyces achromogenes subsp. streptozoticus
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001310.5	0.53	PKS	naringenin	Streptomyces clavuligerus ATCC 27064
BGC0001962.3	0.50	PKS	hierridin B, hierridin C	Cyanobium sp. LEGE 06113
BGC0000584.5	0.47	ribosomal	colicin V	Escherichia coli
BGC0002332.2	0.45	PKS	4-hydroxy-6-pentadecylpyran-2-one, 4-hydroxy-6-(2-oxoheptadecyl)pyran-2-one, Adipostatin A	Candidatus Entotheonella sp.
BGC0001831.3	0.44	PKS	alkylpyrone-407, alkylpyrone-393	Myxococcus xanthus DK 1622
BGC0000589.5	0.44	ribosomal	microcin M	Escherichia coli Nissle 1917
BGC0001374.5	0.44	other (other)	thienodolin	Streptomyces albogriseolus
BGC0001964.2	0.44	PKS	alkylpyrone-407, alkylpyrone-393	Cystobacterineae bacterium
BGC0002313.3	0.43	other (other)	streptozotocin	Streptomyces achromogenes subsp. streptozoticus
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

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

Confidence: strong

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.06 out of 24.78

Confidence: medium

ArgR

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

Confidence: medium

LexA variant 1

Description: Repressor of DNA damage response
Species: Streptomyces coelicolor
Score: 24.34 out of 29.65

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.19 out of 24.78

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.05 out of 26.06

Confidence: medium

Additional weak hits (4):

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 22.53 out of 29.38

Confidence: weak

PerR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.35 out of 26.06

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 23.65 out of 36.54

Confidence: weak

Detailed domain annotation

Selected features only

Show module domains

TFBS Finder

TFBS definitions

Regulator	Description
ArgR	Regulator of arginine biosynthesis genes
LexA variant 1	Repressor of DNA damage response
LexA variant 2	Repressor of DNA damage response
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis

NZ_RIAS01000003.1 - Region 2 - terpene-precursor

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Location: 248,396 - 270,777 nt. (total: 22,382 nt) Show pHMM detection rules used

terpene-precursor: (PT_FPPS_like and not PT_HPP)

Legend:

core biosynthetic genes

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TFBS Finder

Gene/CDS overview

Filter:

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

Tailoring functions

Oxidoreductases: dehydrogenase oxidoreductase reductase

EC604_RS07875: alkyl hydroperoxide reductase subunit

smcogs: SMCOG1176: alkyl hydroperoxide reductase subunit

EC604_RS07915: short-chain dehydrogenase/reductase SDR

smcogs: SMCOG1001: short-chain dehydrogenase/reductase SDR

EC604_RS07930: aldo/keto reductase family oxidoreductase

smcogs: SMCOG1039: aldo/keto reductase family oxidoreductase

Ligases: synthetase

EC604_RS07905: Polyprenyl synthetase

smcogs: SMCOG1182: Polyprenyl synthetase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002150.2	0.42	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.42	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002707.2	0.42	terpene	(+)-δ-cadinol	Coniophora puteana RWD-64-598 SS2
BGC0000551.5	0.41	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000501.3	0.41	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0001210.5	0.41	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000519.4	0.40	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000592.5	0.40	ribosomal	microviridin B	Microcystis aeruginosa NIES-298
BGC0000496.5	0.40	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002150.2	0.42	ribosomal	triculamin	Streptomyces triculaminicus
BGC0002151.2	0.42	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0002306.2	0.42	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002707.2	0.42	terpene	(+)-δ-cadinol	Coniophora puteana RWD-64-598 SS2
BGC0000551.5	0.41	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000501.3	0.41	ribosomal	catenulipeptin	Catenulispora acidiphila DSM 44928
BGC0001210.5	0.41	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442
BGC0000519.4	0.40	ribosomal	labyrinthopeptin A2, labyrinthopeptin A1, labyrinthopeptin A3	Actinomadura namibiensis
BGC0000592.5	0.40	ribosomal	microviridin B	Microcystis aeruginosa NIES-298
BGC0000496.5	0.40	ribosomal	AmfS	Streptomyces griseus subsp. griseus NBRC 13350

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:

EC604_RS07905: PT_FPPS_like

Domain 1 (533 - 755): Prenyltransferase; Farnesyl diphosphate synthase like

Subtype: unknown

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

Transcription Factor Binding Sites

Binding sites found:

CRP

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

Confidence: strong

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 21.85 out of 25.88

Confidence: medium

AbrC3

Description: Antibiotic production activator
Species: Streptomyces coelicolor
Score: 17.05 out of 18.16

Confidence: strong

Additional weak hits (7):

CopR

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

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.53 out of 31.73

Confidence: weak

HypR

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

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.59 out of 28.14

Confidence: weak

MatP

Description: Cell cycle regulator
Species: Escherichia coli str. K-12 substr. MG1655
Score: 22.38 out of 25.75

Confidence: weak

BldD

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

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 20.28 out of 25.88

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
AbrC3	Antibiotic production activator
CRP	Cyclic AMP receptor protein
PsrA	Oleic acid responsive regulator

NZ_RIAS01000003.1 - Region 3 - RRE-containing

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Location: 428,626 - 450,158 nt. (total: 21,533 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

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

Translocases: transport

EC604_RS08630: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.49	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002667.2	0.44	ribosomal	estericin A	Clostridium estertheticum
BGC0000599.5	0.43	ribosomal	thuricin CD α, thuricin CD β	Bacillus thuringiensis
BGC0000600.3	0.42	ribosomal	thurincin H	Bacillus thuringiensis
BGC0001787.3	0.42	ribosomal	suicin 3908	Streptococcus suis
BGC0002700.2	0.42	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0001555.4	0.41	ribosomal	colicin V	Escherichia coli chi7122
BGC0000551.5	0.41	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000616.4	0.40	ribosomal	amylocyclicin	Bacillus velezensis FZB42
BGC0001210.5	0.40	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.49	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002667.2	0.44	ribosomal	estericin A	Clostridium estertheticum
BGC0000599.5	0.43	ribosomal	thuricin CD α, thuricin CD β	Bacillus thuringiensis
BGC0000600.3	0.42	ribosomal	thurincin H	Bacillus thuringiensis
BGC0001787.3	0.42	ribosomal	suicin 3908	Streptococcus suis
BGC0002700.2	0.42	ribosomal	bacinapeptin	Bacillus nakamurai
BGC0001555.4	0.41	ribosomal	colicin V	Escherichia coli chi7122
BGC0000551.5	0.41	ribosomal	SapB	Streptomyces coelicolor A3(2)
BGC0000616.4	0.40	ribosomal	amylocyclicin	Bacillus velezensis FZB42
BGC0001210.5	0.40	ribosomal	pseudomycoicidin	Bacillus pseudomycoides DSM 12442

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

ToxT

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

Confidence: strong

ToxT

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

Confidence: strong

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.58 out of 26.06

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.24 out of 26.06

Confidence: medium

ArgR

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

Confidence: medium

Additional weak hits (4):

HipB

Description: Bacterial antitoxin HipB
Species: Escherichia coli BL21(DE3)
Score: 25.17 out of 33.73

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.75 out of 26.06

Confidence: weak

MogR

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

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 24.42 out of 33.14

Confidence: weak

RREFinder

TFBS Finder

RRE predictions

: RRE type: Other_Sactipeptide_rSAM_RRE; Location: 22 - 139; Score: 34.4

TFBS definitions

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

NZ_RIAS01000005.1 - Region 1 - NRPS-like

Download region GenBank file

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Location: 242,291 - 285,995 nt. (total: 43,705 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

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TFBS Finder

NRPS/PKS modules

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 methyltransferase

EC604_RS11955: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

EC604_RS11985: methyltransferase

smcogs: SMCOG1089: methyltransferase

Ligases: ligase

EC604_RS11940: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

Translocases: transport

EC604_RS12000: MMPL domain-containing transport protein

smcogs: SMCOG1035: MMPL domain-containing transport protein

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.60	NRPS	peramine	Epichloe festucae
BGC0002135.2	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0001249.5	0.59	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002276.2	0.59	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000357.5	0.59	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0002286.3	0.59	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.59	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.59	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.61	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002164.2	0.60	NRPS	peramine	Epichloe festucae
BGC0002135.2	0.60	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001166.5	0.60	NRPS	HC-toxin	Alternaria jesenskae
BGC0001249.5	0.59	NRPS	dimethylcoprogen	Alternaria alternata
BGC0002276.2	0.59	NRPS	choline	Aspergillus nidulans FGSC A4
BGC0000357.5	0.59	NRPS	cyclo-(D-Phe-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Trp-D-Val-L-Val), cyclo-(D-Phe-L-Phe-D-Val-L-Ile), cyclo-(D-Phe-L-Phe-D-Ile-L-Val), cyclo-(D-Tyr-L-Trp-D-Val-L-Ile), cyclo-(D-Tyr-L-Trp-D-Ile-L-Val), cyclo-(D-Tyr-L-Phe-D-Val-L-Ile), cyclo-(D-Tyr-L-Phe-D-Ile-L-Val)	Penicillium rubens Wisconsin 54-1255
BGC0002286.3	0.59	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0000307.4	0.59	NRPS	AbT1	Aureobasidium pullulans
BGC0001240.4	0.59	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 22.30 out of 27.78

Confidence: medium

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 25.37 out of 28.14

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.72 out of 28.19

Confidence: medium

AbrC3

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

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: 18.57 out of 18.57

Confidence: strong

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 17.58 out of 20.97

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 22.93 out of 27.55

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.06 out of 26.06

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 23.30 out of 26.06

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.22 out of 26.06

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 20.87 out of 28.19

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 21.23 out of 28.19

Confidence: medium

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.80 out of 20.01

Confidence: medium

ZuR variant 1

Description: Zinc-responsive repressor
Species: Streptomyces coelicolor
Score: 22.73 out of 28.19

Confidence: medium

Additional weak hits (10):

ArcA

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

Confidence: weak

PerR

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

Confidence: weak

PerR

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

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

LexA variant 3

Description: Repressor of DNA damage response
Species: Escherichia coli str. K-12 substr. MG1655
Score: 23.06 out of 32.93

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 21.41 out of 28.14

Confidence: weak

MogR

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

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.09 out of 26.06

Confidence: weak

MogR

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

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 25.93 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 1, location 242290 - 285995:

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

Polymer prediction:: (X)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

EC604_RS11940: X

AMP-binding (225..634): 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:: LVVAFDASVWDGTITVAGEVNVYGPTECTVATTT
Nearest Stachelhaus code(s):: bMe-Phe DAWTTAVAAK (65% 8Å match)
Stachelhaus code match:: 90% (moderate)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AbrC3	Antibiotic production activator
ArgR	Regulator of arginine biosynthesis genes
CcpA	Catabolite control protein A
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
GnfM	Regulator of nitrogen-fixation genes
MogR	Repressor of flagellar motility genes
PerR	Peroxide regulator
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_RIAS01000006.1 - Region 1 - NRPS,transAT-PKS

Download region GenBank file

Download region SVG

Location: 71,593 - 138,252 nt. (total: 66,660 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

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 methyltransferase

EC604_RS13070: methyltransferase

smcogs: SMCOG1248: methyltransferase

EC604_RS13135: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: deacetylase hydrolase

EC604_RS13065: metallo-beta-lactamase family protein

smcogs: SMCOG1170: metallo-beta-lactamase family protein

EC604_RS13090: acetylornithine deacetylase

smcogs: SMCOG1247: acetylornithine deacetylase

Lyases: lyase

EC604_RS13150: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

EC604_RS30265: argininosuccinate lyase/adenylosuccinate lyase

smcogs: SMCOG1063: argininosuccinate lyase/adenylosuccinate lyase

Ligases: ligase synthase

EC604_RS13110: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS13125: condensation domain-containing protein

smcogs: SMCOG1127: condensation domain-containing protein

EC604_RS13130: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

EC604_RS30270: cysteine synthase

smcogs: SMCOG1081: cysteine synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	0.86	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.81	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.81	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.80	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002286.3	0.79	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.76	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.74	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001758.4	0.73	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0000342.4	0.70	NRPS	enniatin	Fusarium equiseti
BGC0001166.5	0.70	NRPS	HC-toxin	Alternaria jesenskae

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001132.4	0.74	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0001128.4	0.72	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	0.72	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001825.4	0.72	NRPS	xenematide	Xenorhabdus nematophila AN6/1
BGC0002286.3	0.72	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0002135.2	0.70	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	0.70	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001758.4	0.69	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0000342.4	0.68	NRPS	enniatin	Fusarium equiseti
BGC0001166.5	0.68	NRPS	HC-toxin	Alternaria jesenskae

Similar known clusters from MIBiG 4.0

Similar subclusters

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

ToxT

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

Confidence: strong

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.93 out of 30.25

Confidence: medium

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 21.43 out of 24.78

Confidence: medium

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 22.86 out of 26.12

Confidence: medium

AfsR

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

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.01 out of 26.06

Confidence: medium

ZuR variant 1

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

Confidence: medium

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.19 out of 25.31

Confidence: medium

Additional weak hits (10):

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 20.70 out of 27.55

Confidence: weak

CopR

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

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 24.85 out of 36.54

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.91 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

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 24.97 out of 31.73

Confidence: weak

LuxO

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

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.79 out of 30.25

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 20.49 out of 29.51

Confidence: weak

HypR

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

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 71592 - 138252:

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

Polymer prediction:: (fatty_acid - mal) + (X - Gly) + (Gly - Asp)

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

EC604_RS13110: Gly - Asp

Search NORINE for peptide: strict or relaxed

AMP-binding (228..621): 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:: FSMTFDISVLELQALCGGEWNMYGPTETTIWSAI
Nearest Stachelhaus code(s):: Gly DILQLGMIWK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1276..1683): Asp

nrpys: Asp

SVM prediction details:

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

Stachelhaus prediction details:

Stachelhaus sequence:: YGTSADLGNTMHKIVLGGEINHYGPTETTIGVAT
Nearest Stachelhaus code(s):: Asp DLTKVGHIGK (76% 8Å match)
Stachelhaus code match:: 100% (strong)

EC604_RS13125: X - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (449..865): X

nrpys: Dpr, Dab

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:: HAKAFDISVWQAEMISTGEVNTYGATECSDDTSH
Nearest Stachelhaus code(s):: Dpr DIWELTADDK (79% 8Å match); Dab DIWELTADDK (68% 8Å match)
Stachelhaus code match:: 80% (moderate)

AMP-binding (1525..1918): 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:: FSMTFDISVLELQALCGGEWNMYGPTETTIWSAI
Nearest Stachelhaus code(s):: Gly DILQLGMIWK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

EC604_RS13130: fatty_acid

CAL_domain (169..479): fatty_acid

minowa: fatty_acid

Prediction, score:

fatty_acid: 132.6
NH2: 20.4
shikimic_acid: 0.0
Acetyl-CoA: 0.0
AHBA: 0.0

EC604_RS13135: mal

PKS_AT (5..283): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 79.2%; inactive: 66.7%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 63.2
inactive: 35.0
Methylmalonyl-CoA: 27.6
Methoxymalonyl-CoA: 25.3
Propionyl-CoA: 17.3
fatty_acid: 10.2
trans-1,2-CPDA: 0.0
Isobutyryl-CoA: 0.0
Ethylmalonyl-CoA: 0.0
CHC-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
AfsR	Pleiotropic regulatory for antibiotic production
CatR	H2O2-responsive repressor
ColR	Phenol-responsive regulator
LexA variant 2	Repressor of DNA damage response
LuxO	Repressor of luminescence
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_RIAS01000007.1 - Region 1 - NRPS,T1PKS,transAT-PKS

Download region GenBank file

Download region SVG

Location: 72,623 - 204,156 nt. (total: 131,534 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))
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

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

EC604_RS14575: 3-hydroxybutyryl-CoA dehydrogenase

smcogs: SMCOG1095: 3-hydroxybutyryl-CoA dehydrogenase

EC604_RS14590: acyl-CoA dehydrogenase

smcogs: SMCOG1006: acyl-CoA dehydrogenase

Transferases: acylase methyltransferase

EC604_RS14495: methyltransferase

smcogs: SMCOG1089: methyltransferase

EC604_RS14650: malonyl CoA-acyl carrier protein transacylase

smcogs: SMCOG1021: malonyl CoA-acyl carrier protein transacylase

Hydrolases: esterase hydrolase phosphatase

EC604_RS14565: thioesterase

smcogs: SMCOG1004: thioesterase

EC604_RS14580: FkbH like protein

smcogs: SMCOG1256: FkbH like protein

EC604_RS14595: beta-lactamase

smcogs: SMCOG1053: beta-lactamase

Ligases: ligase synthase

EC604_RS14535: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS14560: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS14600: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS14630: AMP-dependent synthetase and ligase

smcogs: SMCOG1002: AMP-dependent synthetase and ligase

EC604_RS14635: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

EC604_RS14655: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

EC604_RS14670: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

EC604_RS14675: Beta-ketoacyl synthase

smcogs: SMCOG1093: Beta-ketoacyl synthase

EC604_RS14680: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

EC604_RS14685: Beta-ketoacyl synthase

smcogs: SMCOG1022: Beta-ketoacyl synthase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002135.2	1.32	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001135.5	1.30	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0001128.4	1.22	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001261.3	1.22	NRPS	AM-toxin	Alternaria alternata
BGC0001132.4	1.20	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	1.20	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001833.4	1.19	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001166.5	1.15	NRPS	HC-toxin	Alternaria jesenskae
BGC0001758.4	1.14	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001240.4	1.10	NRPS	serinocyclin A, serinocyclin B	Metarhizium robertsii

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001135.5	0.75	NRPS	bicornutin A1, bicornutin A2	Xenorhabdus budapestensis
BGC0002135.2	0.75	NRPS	bovienimide A	Xenorhabdus bovienii SS-2004
BGC0001758.4	0.74	NRPS	rhizomide A, rhizomide B, rhizomide C	Paraburkholderia rhizoxinica HKI 454
BGC0001128.4	0.74	NRPS	gamexpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001132.4	0.73	NRPS	xenotetrapeptide	Xenorhabdus nematophila ATCC 19061
BGC0002286.3	0.73	NRPS	ririwpeptide A, ririwpeptide B, ririwpeptide C	Photorhabdus laumondii subsp. laumondii TTO1
BGC0001249.5	0.73	NRPS	dimethylcoprogen	Alternaria alternata
BGC0001833.4	0.73	NRPS	icosalide A, icosalide B	Burkholderia gladioli
BGC0001261.3	0.72	NRPS	AM-toxin	Alternaria alternata
BGC0001641.4	0.71	NRPS	kolossin	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:

ToxT

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

Confidence: strong

ToxT

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

Confidence: strong

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: 19.84 out of 23.79

Confidence: medium

GnfM

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

Confidence: medium

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.52 out of 27.55

Confidence: medium

CcpA

Description: Catabolite control protein A
Species: Streptococcus & Clostridium sp.
Score: 19.14 out of 20.97

Confidence: strong

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.35 out of 26.06

Confidence: medium

ZuR variant 1

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

Confidence: medium

Additional weak hits (15):

LuxO

Description: Repressor of luminescence
Species: Vibrio campbellii ATCC BAA-1116
Score: 21.11 out of 26.12

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 22.93 out of 31.73

Confidence: weak

HexR

Description: Glucose-responsive regulator
Species: Shewanella oneidensis MR-1
Score: 23.62 out of 31.73

Confidence: weak

FuR variant 1

Description: Ferric Uptake Regulator
Species: Bacillus, Pseudomonas, Yersinia sp.
Score: 21.65 out of 29.38

Confidence: weak

ColR

Description: Phenol-responsive regulator
Species: Pseudomonas putida KT2440
Score: 22.20 out of 30.25

Confidence: weak

PsrA

Description: Oleic acid responsive regulator
Species: Pseudomonas sp.
Score: 19.99 out of 25.88

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 20.91 out of 29.51

Confidence: weak

DosR

Description: Hypoxia stress response regulator
Species: Mycobacterium tuberculosis H37Rv
Score: 22.59 out of 29.51

Confidence: weak

HgtR

Description: Hydrogen-dependent regulator
Species: Geobacter sulfurreducens PCA
Score: 25.33 out of 36.54

Confidence: weak

LexA variant 2

Description: Repressor of DNA damage response
Species: Bacillus subtilis subsp. subtilis str. 168
Score: 19.79 out of 24.78

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.84 out of 26.06

Confidence: weak

PerR

Description: Peroxide regulator
Species: Bacillus & Staphylococcus sp.
Score: 22.83 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

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 21.66 out of 26.06

Confidence: weak

ZuR variant 2

Description: Zinc-responsive repressor
Species: Pseudomonas protegens Pf-5
Score: 23.37 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 1, location 72622 - 204156:

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

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

Direct lookup in NORINE database: strict or relaxed

Link to NORINE database query form

NRPS/PKS substrate predictions

EC604_RS14535: Thr - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (889..1294): 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:: LNIHFDFSVWEGNQIFGGEVNMYGITETTVHVSY
Nearest Stachelhaus code(s):: Thr DFWNIGMVHK (94% 8Å match)
Stachelhaus code match:: 100% (strong)

AMP-binding (1942..2332): 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:: LSITFDIFVIELQMLIGGEYNMYGPTETTVWSTM
Nearest Stachelhaus code(s):: Gly DILQLGMVWK (74% 8Å match)
Stachelhaus code match:: 90% (moderate)

EC604_RS14560: Asn

Search NORINE for peptide: strict or relaxed

AMP-binding (459..850): 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:: YWATFDLTITSVKIVVGGEYNEYGPTEAVVGCMI
Nearest Stachelhaus code(s):: Asn DLTKVGEVGK (85% 8Å match)
Stachelhaus code match:: 100% (strong)

EC604_RS14600: X - Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (470..868): 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:: RWMTYDSAVWQWDFIVGGETNLYGPTEASIGCVF
Nearest Stachelhaus code(s):: Orn DVWNIGLIHK (56% 8Å match)
Stachelhaus code match:: 70% (weak)

AMP-binding (1513..1897): 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:: LAITFDIFVLEIQSLIGGEFNMYGPTETTVWSTV
Nearest Stachelhaus code(s):: Gly DILQLGMVWK (74% 8Å match)
Stachelhaus code match:: 100% (strong)

EC604_RS14630: X

AMP-binding (257..651): 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:: TWFYSDPSVEDANFLSGGEYNNYGPTEAAIDCLS
Nearest Stachelhaus code(s):: ohmeTyr DPWGLGLIDK (59% 8Å match); OH-Orn DMENLGLINK (50% 8Å match); ohdmTyr DPWGLGLIDK (47% 8Å match)
Stachelhaus code match:: 70% (weak)

EC604_RS14635: mal - Leu

Search NORINE for peptide: strict or relaxed

PKS_AT (533..827): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 75.0%; inactive: 62.5%; 2-Rhyd-Malonyl-CoA: 58.3%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 121.0
inactive: 87.2
Methoxymalonyl-CoA: 60.4
Methylmalonyl-CoA: 40.7
Propionyl-CoA: 18.9
Isobutyryl-CoA: 15.0
CHC-CoA: 9.8
trans-1,2-CPDA: 0.0
fatty_acid: 0.0
Ethylmalonyl-CoA: 0.0
Benzoyl-CoA: 0.0
Acetyl-CoA: 0.0
3-Methylbutyryl-CoA: 0.0
2-Methylbutyryl-CoA: 0.0

AMP-binding (1965..2349): Leu

nrpys: Leu

SVM prediction details:

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

Stachelhaus prediction details:

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

EC604_RS14645: X - Gly

Search NORINE for peptide: strict or relaxed

A-OX (295..1059): X

No predictions made

AMP-binding (1676..2072): 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:: FGITFDIFVLELQLLIGGEYNMYGPTETTVWSLL
Nearest Stachelhaus code(s):: Gly DILQLGMVWK (76% 8Å match)
Stachelhaus code match:: 100% (strong)

EC604_RS14650: mal

PKS_AT (6..287): mal

ATSignature: Malonyl-CoA

Top 3 matches:: Malonyl-CoA: 79.2%; inactive: 66.7%; 2-Methylbutyryl-CoA: 54.2%

minowa: Malonyl-CoA

Prediction, score:

Malonyl-CoA: 131.7
Methylmalonyl-CoA: 55.5
Methoxymalonyl-CoA: 48.2
inactive: 45.9
Propionyl-CoA: 43.9
2-Methylbutyryl-CoA: 25.6
CHC-CoA: 25.0
Ethylmalonyl-CoA: 24.0
Isobutyryl-CoA: 17.0
Acetyl-CoA: 16.7
trans-1,2-CPDA: 12.0
fatty_acid: 11.6
Benzoyl-CoA: 10.9
3-Methylbutyryl-CoA: 0.0

EC604_RS14665: X

A-OX (266..1029): X

No predictions made

EC604_RS14675: Gly

Search NORINE for peptide: strict or relaxed

AMP-binding (2004..2396): 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:: FGMTFDISFLELQMLIGGEYNMYGPTETTIWSTM
Nearest Stachelhaus code(s):: Gly DILQLGMIWK (82% 8Å match)
Stachelhaus code match:: 100% (strong)

Link to PARAS substrate predictor

TFBS definitions

Regulator	Description
CcpA	Catabolite control protein A
GnfM	Regulator of nitrogen-fixation genes
IolR	Regulator of the inositol catabolism
MogR	Repressor of flagellar motility genes
ToxT	Regulator of MSHA biosynthesis
ZuR variant 1	Zinc-responsive repressor

NZ_RIAS01000007.1 - Region 2 - ranthipeptide

Download region GenBank file

Download region SVG

Location: 229,203 - 250,829 nt. (total: 21,627 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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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

Transferases: acetyltransferase glycosyltransferase

EC604_RS14805: GCN5-related N-acetyltransferase

smcogs: SMCOG1111: GCN5-related N-acetyltransferase

EC604_RS14835: glycosyl transferase group 1

smcogs: SMCOG1045: glycosyl transferase group 1

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.50	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002583.2	0.46	ribosomal	tryglysin B	Streptococcus mutans UA159
BGC0001552.3	0.44	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000734.3	0.44	saccharide	capsular polysaccharide	Pasteurella multocida
BGC0001550.3	0.44	ribosomal	citrulassin D	Streptomyces katrae
BGC0001634.3	0.43	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0002289.2	0.43	ribosomal	Leepeptin	Streptomyces leeuwenhoekii
BGC0001496.3	0.42	ribosomal	actinokineosin	Actinokineospora spheciospongiae
BGC0002064.2	0.42	ribosomal	felipeptin A2, felipeptin A1	Amycolatopsis sp. YIM 10
BGC0000551.5	0.41	ribosomal	SapB	Streptomyces coelicolor A3(2)

Reference	Similarity score	Type	Compound(s)	Organism
BGC0002306.2	0.50	ribosomal	freyrasin	Paenibacillus polymyxa ATCC 842
BGC0002583.2	0.46	ribosomal	tryglysin B	Streptococcus mutans UA159
BGC0001552.3	0.44	ribosomal	citrulassin F	Streptomyces avermitilis MA-4680 = NBRC 14893
BGC0000734.3	0.44	saccharide	capsular polysaccharide	Pasteurella multocida
BGC0001550.3	0.44	ribosomal	citrulassin D	Streptomyces katrae
BGC0001634.3	0.43	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0002289.2	0.43	ribosomal	Leepeptin	Streptomyces leeuwenhoekii
BGC0001496.3	0.42	ribosomal	actinokineosin	Actinokineospora spheciospongiae
BGC0002064.2	0.42	ribosomal	felipeptin A2, felipeptin A1	Amycolatopsis sp. YIM 10
BGC0000551.5	0.41	ribosomal	SapB	Streptomyces coelicolor A3(2)

Similar known clusters from MIBiG 4.0

No significant matches found.

Similar subclusters

No significant matches found.

Transcription Factor Binding Sites

Binding sites found:

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: 21.65 out of 27.78

Confidence: medium

ArgR

Description: Regulator of arginine biosynthesis genes
Species: Streptomyces coelicolor
Score: 18.06 out of 20.01

Confidence: medium

Additional weak hits (1):

HipB

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

Confidence: weak

RREFinder

TFBS Finder

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 5 - 87; Score: 26.5

TFBS definitions

Regulator	Description
ArgR	Regulator of arginine biosynthesis genes
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
ToxT	Regulator of MSHA biosynthesis

NZ_RIAS01000008.1 - Region 1 - lassopeptide

Download region GenBank file

Download region SVG

Location: 31,192 - 55,173 nt. (total: 23,982 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

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

Lasso peptides

TFBS Finder

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Hydrolases: deacetylase hydrolase

EC604_RS15330: polysaccharide deacetylase

smcogs: SMCOG1235: polysaccharide deacetylase

EC604_RS15375: asparagine synthase (glutamine-hydrolyzing)

smcogs: SMCOG1177: asparagine synthase (glutamine-hydrolyzing)

Lyases: cyclase

EC604_RS15400: diguanylate cyclase

smcogs: SMCOG1025: diguanylate cyclase

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001356.4	0.68	ribosomal	paeninodin	Paenibacillus dendritiformis C454
BGC0002151.2	0.53	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0002312.2	0.53	ribosomal	ubonodin	Burkholderia ubonensis
BGC0002150.2	0.53	ribosomal	triculamin	Streptomyces triculaminicus
BGC0001634.3	0.53	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0000575.5	0.52	ribosomal	lariatin	Rhodococcus jostii
BGC0001889.2	0.51	ribosomal	fusilassin	Thermobifida fusca YX
BGC0001496.3	0.47	ribosomal	actinokineosin	Actinokineospora spheciospongiae
BGC0001639.3	0.46	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0000578.3	0.43	ribosomal	SRO15-2005	Streptomyces filamentosus NRRL 15998

Reference	Similarity score	Type	Compound(s)	Organism
BGC0001356.4	0.68	ribosomal	paeninodin	Paenibacillus dendritiformis C454
BGC0002151.2	0.53	ribosomal	alboverticillin	Streptomyces griseocarneus
BGC0002312.2	0.53	ribosomal	ubonodin	Burkholderia ubonensis
BGC0002150.2	0.53	ribosomal	triculamin	Streptomyces triculaminicus
BGC0001634.3	0.53	ribosomal	keywimysin	Streptomyces sp. NRRL F-5702
BGC0000575.5	0.52	ribosomal	lariatin	Rhodococcus jostii
BGC0001889.2	0.51	ribosomal	fusilassin	Thermobifida fusca YX
BGC0001496.3	0.47	ribosomal	actinokineosin	Actinokineospora spheciospongiae
BGC0001639.3	0.46	ribosomal	klebsidin	Klebsiella pneumoniae
BGC0000578.3	0.43	ribosomal	SRO15-2005	Streptomyces filamentosus NRRL 15998

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:

GnfM

Description: Regulator of nitrogen-fixation genes
Species: Geobacter sulfurreducens PCA
Score: 21.63 out of 27.55

Confidence: medium

AfsQ1

Description: Two-component system AfsQ1-Q2, activator of antibiotic production
Species: Streptomyces coelicolor
Score: 18.42 out of 19.52

Confidence: strong

CatR

Description: H2O2-responsive repressor
Species: Streptomyces coelicolor
Score: 21.97 out of 25.31

Confidence: strong

Additional weak hits (2):

ANR

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

Confidence: weak

NrtR

Description: NAD synthesis repressor
Species: Streptomyces coelicolor
Score: 22.39 out of 35.63

Confidence: weak

Lasso peptides

RREFinder

TFBS Finder

Core peptide predictions

No core peptides found.

RRE predictions

: RRE type: Stand_Alone_Lasso_RRE; Location: 11 - 95; Score: 97.2

TFBS definitions

Regulator	Description
AfsQ1	Two-component system AfsQ1-Q2, activator of antibiotic production
CatR	H2O2-responsive repressor
GnfM	Regulator of nitrogen-fixation genes

NZ_RIAS01000009.1 - Region 1 - terpene

Download region GenBank file

Download region SVG

Location: 68,633 - 89,505 nt. (total: 20,873 nt) Show pHMM detection rules used

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

Legend:

core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

resistance

binding site

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Gene details

Select a gene to view the details available for it

Gene overview

Tailoring

MIBiG comparison

KnownClusterBlast

SubClusterBlast

Terpene

TFBS Finder

Gene/CDS overview

Filter:

Automatically zoom to filtered/selected features

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

Tailoring functions

Oxidoreductases: dehydrogenase

EC604_RS16915: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

EC604_RS16920: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

EC604_RS16945: dehydrogenase

smcogs: SMCOG1222: dehydrogenase

Ligases: synthase

EC604_RS16940: polyprenol-monophosphomannose synthase ppm1

smcogs: SMCOG1123: polyprenol-monophosphomannose synthase ppm1

Similar gene clusters

Analysis type:

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000645.3	0.57	terpene	carotenoid	Halobacillus halophilus DSM 2266
BGC0000656.5	0.47	terpene	zeaxanthin	Xanthobacter autotrophicus Py2
BGC0000640.3	0.45	terpene	carotenoid	Enterobacteriaceae bacterium DC404
BGC0000642.3	0.43	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0000635.3	0.42	terpene	carotenoid	Paracoccus sp. N81106
BGC0000646.5	0.42	terpene	β-carotein	uncultured bacterium
BGC0000664.5	0.42	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000638.3	0.41	terpene	carotenoid	Pantoea ananatis
BGC0000634.3	0.40	terpene	carotenoid	Brevundimonas sp. SD212
BGC0000639.3	0.40	terpene	carotenoid	Enterobacteriaceae bacterium DC260

Reference	Similarity score	Type	Compound(s)	Organism
BGC0000645.3	0.57	terpene	carotenoid	Halobacillus halophilus DSM 2266
BGC0000656.5	0.47	terpene	zeaxanthin	Xanthobacter autotrophicus Py2
BGC0000640.3	0.45	terpene	carotenoid	Enterobacteriaceae bacterium DC404
BGC0000642.3	0.43	terpene	carotenoid	Enterobacteriaceae bacterium DC413
BGC0000635.3	0.42	terpene	carotenoid	Paracoccus sp. N81106
BGC0000646.5	0.42	terpene	β-carotein	uncultured bacterium
BGC0000664.5	0.42	terpene	isorenieratene	Streptomyces griseus subsp. griseus NBRC 13350
BGC0000638.3	0.41	terpene	carotenoid	Pantoea ananatis
BGC0000634.3	0.40	terpene	carotenoid	Brevundimonas sp. SD212
BGC0000639.3	0.40	terpene	carotenoid	Enterobacteriaceae bacterium DC260

Similar known clusters from MIBiG 4.0

Similar subclusters

No significant matches found.

Detailed terpene predictions

Product predictions:

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

Genes with terpene domains:

EC604_RS16925: PT_phytoene_like

Domain 1 (7 - 271): Prenyltransferase; Phytoene synthase like

Subtype: unknown

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

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

RutR

Description: Regulator of the pyrimidine and purine metabolism
Species: Escherichia coli str. K-12 substr. MG1655
Score: 21.71 out of 26.85

Confidence: medium

MexT

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

Confidence: strong

ArcA

Description: Repressor of carbon oxidation
Species: Escherichia coli str. K-12 substr. MG1655
Score: 19.26 out of 21.55

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.93 out of 26.06

Confidence: medium

CodY

Description: Regulator of stationary phase and virulence in Gram-positive bacteria
Species: Bacillus, Lactococcus & Streptococcus sp.
Score: 20.76 out of 27.78

Confidence: medium

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 22.10 out of 26.06

Confidence: medium

CRP

Description: Cyclic AMP receptor protein
Species: Escherichia coli str. K-12 substr. MG1655
Score: 16.91 out of 19.26

Confidence: medium

Additional weak hits (3):

CopR

Description: Copper-responsive regulator
Species: Lactococcus lactis subsp. lactis Il1403
Score: 21.62 out of 30.97

Confidence: weak

MogR

Description: Repressor of flagellar motility genes
Species: Listeria monocytogenes EGD-e
Score: 20.16 out of 26.06

Confidence: weak

HipB

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

Confidence: weak

Terpene

TFBS Finder

Glossary

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

TFBS definitions

Regulator	Description
ArcA	Repressor of carbon oxidation
CRP	Cyclic AMP receptor protein
CodY	Regulator of stationary phase and virulence in Gram-positive bacteria
MexT	Global virulence regulator
MogR	Repressor of flagellar motility genes
RutR	Regulator of the pyrimidine and purine metabolism
ToxT	Regulator of MSHA biosynthesis