BGC0000413

BGC0000413: Pf-5 pyoverdine biosynthetic gene cluster from Pseudomonas protegens Pf-5

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Location: 4,702,146 - 4,877,199 nt. (total: 175,054 nt).
This entry is originally from NCBI GenBank CP000076.1.

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

other genes

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Gene details

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General

Compounds

Genes

Biosynthesis

History

NRPS/PKS domains

KnownClusterBlast

General information about the BGC

MIBiG accession	BGC0000413
Short description	Pf-5 pyoverdine biosynthetic gene cluster from Pseudomonas protegens Pf-5
Status	Quality: questionable The quality level of this entry. Status: active The status of this entry. Completeness: unknown Whether the entry covers everything needed for the pathway producing the compound(s)
Biosynthetic class(es)	NRPS (Type I)
Loci	CP000076.1 4702146 - 4877199 via
Compounds	Pf-5 pyoverdine
Species	Pseudomonas protegens Pf-5 [taxonomy]
References	[1] The pvc gene cluster of Pseudomonas aeruginosa: role in synthesis of the pyoverdine chromophore and regulation by PtxR and PvdS. Stintzi A et al., J Bacteriol (1999) PMID:10383985 [2] Ferric-pyoverdine recognition by Fpv outer membrane proteins of Pseudomonas protegens Pf-5. Hartney SL et al., J Bacteriol (2013) PMID:23222724 [3] Novel pyoverdine biosynthesis gene(s) of Pseudomonas aeruginosa PAO. Stintzi A et al., Microbiology (Reading) (1996) PMID:8704959

Chemical products information

Pf-5 pyoverdine Evidence:

Copy SMILES

C₄₈H₆₈N₁₅O₂₀

Chemical database entries
NPAtlas

List of genes involved in compound(s) production

Identifiers	Position	Product	Extra
PFL_4077 AAY93338.1	4702146 - 4702862 (-)	MgtC family protein	copy AA seq copy Nt seq
PFL_4078 AAY93339.1 mgtA_2	4703067 - 4705832 (-)	magnesium-importing ATPase	copy AA seq copy Nt seq
PFL_4079 AAY93340.1 pvdA	4706381 - 4707718 (-)	L-ornithine 5-monooxygenase PvdA	copy AA seq copy Nt seq
PFL_4080 AAY93341.2 fpvI	4707868 - 4708347 (-)	RNA polymerase sigma-70 factor, ECF subfamily, FpvI	copy AA seq copy Nt seq
PFL_4081 AAY93342.1	4708677 - 4709849 (+)	efflux transporter, RND family, MFP subunit	copy AA seq copy Nt seq
PFL_4082 AAY93343.1	4709850 - 4711823 (+)	efflux ABC transporter, ATP-binding/permease protein	copy AA seq copy Nt seq
PFL_4083 AAY93344.1	4711831 - 4713222 (+)	efflux transporter, outer membrane factor lipoprotein, NodT family	copy AA seq copy Nt seq
PFL_4084 AAY93345.1	4713323 - 4713622 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4085 AAY93346.1	4713641 - 4714078 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4086 AAY93347.2 pvdP	4714089 - 4715717 (-)	chromophore maturation protein PvdP	copy AA seq copy Nt seq
PFL_4087 AAY93348.2 pvdM	4715925 - 4717298 (+)	putative dipeptidase precursor	copy AA seq copy Nt seq
PFL_4088 AAY93349.1 pvdN	4717320 - 4718615 (+)	chromophore maturation protein PvdN	copy AA seq copy Nt seq
PFL_4089 AAY93350.1 pvdO	4718663 - 4719556 (+)	chromophore maturation protein PvdO	copy AA seq copy Nt seq
PFL_4090 AAY93351.2 pvdF	4719611 - 4720474 (-)	N(5)-hydroxyornithine transformylase PvdF	copy AA seq copy Nt seq
PFL_4091 AAY93352.1 pvdE	4720675 - 4722327 (+)	pyoverdine ABC transporter, permease/ATP-binding protein PvdE	copy AA seq copy Nt seq
PFL_4092 AAY93353.1 fpvA	4722429 - 4724897 (+)	TonB-dependent outermembrane ferripyoverdine receptor FpvA	copy AA seq copy Nt seq
PFL_4093 AAY93354.1 pvdD	4725296 - 4738528 (-)	non-ribosomal peptide synthetase PvdD	copy AA seq copy Nt seq
PFL_4094 AAY93355.1 pvdJ	4738541 - 4745122 (-)	non-ribosomal peptide synthetase PvdJ	copy AA seq copy Nt seq
PFL_4095 AAY93356.2 pvdI	4745122 - 4756269 (-)	non-ribosomal peptide synthetase PvdI	copy AA seq copy Nt seq
PFL_4096 AAY93357.2	4756482 - 4757450 (+)	siderophore-interacting protein	copy AA seq copy Nt seq
PFL_4097 AAY93358.1	4757632 - 4758363 (-)	thioesterase	copy AA seq copy Nt seq
PFL_4098 AAY93359.1	4758443 - 4759615 (-)	transporter, major facilitator family	copy AA seq copy Nt seq
PFL_4099 AAY93360.1	4759751 - 4760338 (+)	transcriptional regulator, TetR family	copy AA seq copy Nt seq
PFL_4100 AAY93361.1 gdh	4760451 - 4761251 (+)	glucose 1-dehydrogenase	copy AA seq copy Nt seq
PFL_4101 AAY93362.1	4761244 - 4763070 (+)	glycosyl hydrolase, family 15	copy AA seq copy Nt seq
PFL_4102 AAY93363.1	4763137 - 4763514 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4103 AAY93364.1	4763511 - 4763972 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4104 AAY93365.1	4764310 - 4765215 (+)	alpha/beta hydrolase family protein	copy AA seq copy Nt seq
PFL_4105 AAY93366.1	4765217 - 4765765 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4106 AAY93367.1	4765781 - 4767223 (+)	NAD dependent epimerase/dehydratase family protein	copy AA seq copy Nt seq
PFL_4107 AAY93368.1	4767238 - 4769676 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4108 AAY93369.2	4769686 - 4770669 (-)	transcriptional regulator, AraC family	copy AA seq copy Nt seq
PFL_4109 AAY93370.1 inhA	4770762 - 4771448 (+)	isonitrile hydratase InhA	copy AA seq copy Nt seq
PFL_4110 AAY93371.1	4771453 - 4771797 (-)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4111 AAY93372.1	4771822 - 4772454 (-)	translocator protein, LysE family	copy AA seq copy Nt seq
PFL_4112 AAY93373.1	4772542 - 4773867 (+)	transcriptional regulator, GntR family/aminotransferase, classes I and II family protein	copy AA seq copy Nt seq
PFL_4113 AAY93374.2 str	4774202 - 4775005 (-)	streptomycin 3''-kinase	copy AA seq copy Nt seq
PFL_4114 AAY93375.1	4775084 - 4775542 (-)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4115 AAY93376.1	4775676 - 4776998 (+)	ADP-ribosylglycohydrolase family protein	copy AA seq copy Nt seq
PFL_4116 AAY93377.1	4777036 - 4777437 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4117 AAY93378.1 peaD	4777540 - 4778658 (-)	quinohemoprotein amine dehydrogenase, beta subunit PeaD	copy AA seq copy Nt seq
PFL_4118 AAY93379.2 peaC	4778682 - 4779005 (-)	quinohemoprotein amine dehydrogenase, gamma subunit PeaC	copy AA seq copy Nt seq
PFL_4119 AAY93380.1 peaB	4779007 - 4780440 (-)	putative quinohemoprotein amine dehydrogenase modification protein PeaB	copy AA seq copy Nt seq
PFL_4120 AAY93381.1 peaA	4780520 - 4782100 (-)	quinohemoprotein amine dehydrogenase, alpha subunit PeaA	copy AA seq copy Nt seq
PFL_4121 AAY93382.1	4782408 - 4784168 (+)	KWG repeat protein	copy AA seq copy Nt seq
PFL_4122 AAY93383.1	4784270 - 4784935 (+)	HAD hydrolase, family IA, variant 3	copy AA seq copy Nt seq
PFL_4123 AAY93384.1	4785323 - 4787038 (-)	putative 2-isopropylmalate synthase	copy AA seq copy Nt seq
PFL_4124 AAY93385.2	4787314 - 4788144 (+)	transcriptional regulator, AraC family	copy AA seq copy Nt seq
PFL_4125 AAY93386.1	4788149 - 4789738 (-)	drug resistance transporter, EmrB/QacA family	copy AA seq copy Nt seq
PFL_4126 AAY93387.1	4789731 - 4790840 (-)	auxiliary transport protein, membrane fusion protein family	copy AA seq copy Nt seq
PFL_4127 AAY93388.1	4790837 - 4792315 (-)	efflux transporter, outer membrane factor lipoprotein, NodT family	copy AA seq copy Nt seq
PFL_4128 AAY93389.1	4792342 - 4792584 (-)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4129 AAY93390.1	4792570 - 4793130 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4130 AAY93391.1 peaE	4793331 - 4794821 (+)	phenylacetaldehyde dehydrogenase PeaE	copy AA seq copy Nt seq
PFL_4131 AAY93392.1	4795008 - 4796927 (+)	amidohydrolase family protein	copy AA seq copy Nt seq
PFL_4132 AAY93393.1 peaF	4797065 - 4798384 (-)	phenylethylamine degradation protein PeaF	copy AA seq copy Nt seq
PFL_4133 AAY93394.1	4798369 - 4799052 (-)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4134 AAY93395.1 peaH	4799042 - 4800760 (-)	2-phenylethylamine uptake protein PeaH	copy AA seq copy Nt seq
PFL_4135 AAY93396.1 peaR	4800760 - 4802664 (-)	sigma-54 dependent transcriptional activator PeaR	copy AA seq copy Nt seq
PFL_4136 AAY93397.1 aphA_2	4803120 - 4804145 (-)	acetylpolyamine aminohydrolase	copy AA seq copy Nt seq
PFL_4137 AAY93398.2	4804156 - 4805385 (-)	N-carbamyl-L-amino acid amidohydrolase	copy AA seq copy Nt seq
PFL_4138 AAY93399.1	4805405 - 4806718 (-)	transporter, major facilitator family	copy AA seq copy Nt seq
PFL_4139 AAY93400.1	4806897 - 4807862 (+)	transcriptional regulator, LysR family	copy AA seq copy Nt seq
PFL_4140 AAY93401.1 mrdA_1	4807864 - 4809756 (-)	penicillin-binding protein 2	copy AA seq copy Nt seq
PFL_4146 AAY93402.2	4815878 - 4816765 (+)	integral membrane protein, DUF6 family	copy AA seq copy Nt seq
PFL_4147 AAY93403.1	4816924 - 4817205 (+)	putative lipoprotein	copy AA seq copy Nt seq
PFL_4148 AAY93404.1	4817215 - 4817784 (-)	transcriptional regulator, TetR family	copy AA seq copy Nt seq
PFL_4149 AAY93405.1	4817878 - 4818618 (+)	short chain dehydrogenase/reductase family protein	copy AA seq copy Nt seq
PFL_4150 AAY93406.1	4818656 - 4819252 (+)	DsbA-like thioredoxin domain protein	copy AA seq copy Nt seq
PFL_4151 AAY93407.1	4819337 - 4821145 (-)	peptidase, M24 family	copy AA seq copy Nt seq
PFL_4152 AAY93408.1	4821201 - 4822370 (-)	aminotransferase, class V	copy AA seq copy Nt seq
PFL_4153 AAY93409.1	4822581 - 4823195 (-)	translocator protein, LysE family	copy AA seq copy Nt seq
PFL_4154 AAY93410.1	4823404 - 4823628 (-)	putative lipoprotein	copy AA seq copy Nt seq
PFL_4155 AAY93411.1 msuE	4823959 - 4824522 (+)	NADH-dependent FMN reductase	copy AA seq copy Nt seq
PFL_4156 AAY93412.1 msuD	4824532 - 4825671 (+)	methanesulfonate sulfonatase MsuD	copy AA seq copy Nt seq
PFL_4157 AAY93413.2 msuC	4825806 - 4826993 (+)	putative monooxygenase MsuC	copy AA seq copy Nt seq
PFL_4158 AAY93414.1	4827018 - 4828118 (+)	sigma-54 dependent transcriptional regulator	copy AA seq copy Nt seq
PFL_4159 AAY93415.1	4828115 - 4828480 (-)	antibiotic biosynthesis monooxygenase	copy AA seq copy Nt seq
PFL_4160 AAY93416.1 soxR	4828589 - 4829062 (+)	redox-sensitive transcriptional activator SoxR	copy AA seq copy Nt seq
PFL_4162 AAY93418.1	4831091 - 4831735 (+)	organic radical activating enzyme family protein	copy AA seq copy Nt seq
PFL_4163 AAY93419.1	4831751 - 4838068 (+)	histidine kinase	copy AA seq copy Nt seq
PFL_4164 AAY93420.1	4838065 - 4839399 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4165 AAY93421.1	4839497 - 4840267 (-)	lipoprotein, NLPA family	copy AA seq copy Nt seq
PFL_4166 AAY93422.1	4840350 - 4841015 (-)	putative ABC transporter, permease protein	copy AA seq copy Nt seq
PFL_4167 AAY93423.1	4841019 - 4842311 (-)	monooxygenase, DszC family	copy AA seq copy Nt seq
PFL_4168 AAY93424.1	4842526 - 4842993 (+)	glyoxalase family protein	copy AA seq copy Nt seq
PFL_4169 AAY93425.1	4843290 - 4844513 (+)	PepSY-associated TM helix domain protein	copy AA seq copy Nt seq
PFL_4170 AAY93426.1	4844510 - 4845052 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4171 AAY93427.1	4845049 - 4845387 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4172 AAY93428.1	4845384 - 4845956 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4173 AAY93429.2	4845992 - 4846921 (+)	cation ABC transporter, MZT family, periplasmic cation-binding protein	copy AA seq copy Nt seq
PFL_4174 AAY93430.1	4846918 - 4847661 (+)	cation ABC transporter, MZT family, ATP-binding protein	copy AA seq copy Nt seq
PFL_4175 AAY93431.1	4847661 - 4848560 (+)	cation ABC transporter, MZT family, permease protein	copy AA seq copy Nt seq
PFL_4176 AAY93432.1	4848561 - 4849544 (+)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4177 AAY93433.1	4849756 - 4850583 (+)	methyltransferase domain protein	copy AA seq copy Nt seq
PFL_4178 AAY93434.1	4850873 - 4851097 (-)	MbtH-like protein	copy AA seq copy Nt seq
PFL_4179 AAY93435.2 pvdH	4851180 - 4852592 (-)	2,4-diaminobutyrate 4-transaminase	copy AA seq copy Nt seq
PFL_4180 AAY93436.1	4852828 - 4854153 (-)	sensor histidine kinase	copy AA seq copy Nt seq
PFL_4181 AAY93437.1	4854154 - 4854831 (-)	DNA-binding response regulator	copy AA seq copy Nt seq
PFL_4182 AAY93438.1 dsbD	4854985 - 4856736 (+)	thiol:disulfide interchange protein DsbD	copy AA seq copy Nt seq
PFL_4183 AAY93439.1	4856736 - 4857599 (+)	antioxidant, AhpC family	copy AA seq copy Nt seq
PFL_4184 AAY93440.1 dsbG	4857575 - 4858342 (+)	thiol:disulfide interchange protein DsbG	copy AA seq copy Nt seq
PFL_4185 AAY93441.1	4858556 - 4859368 (-)	alpha/beta hydrolase family protein	copy AA seq copy Nt seq
PFL_4186 AAY93442.1	4859477 - 4860100 (-)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4187 AAY93443.1	4860392 - 4861441 (-)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4188 AAY93444.1	4861561 - 4862811 (-)	conserved hypothetical protein	copy AA seq copy Nt seq
PFL_4189 AAY93445.1 pvdL	4862826 - 4875854 (-)	non-ribosomal peptide synthetase PvdL	copy AA seq copy Nt seq
PFL_4190 AAY93446.1 pvdS	4876228 - 4876776 (+)	RNA polymerase sigma-70 factor, ECF subfamily, PvdS	copy AA seq copy Nt seq
PFL_4191 AAY93447.1 pvdY	4876810 - 4877199 (-)	pyoverdine biosynthesis protein	copy AA seq copy Nt seq

Biosynthesis information

Biosynthetic modules

Name

Unk01

Type

nrps-type1

Genes

pvdD

Substrates

alanine (evidence: Structure-based inference [2])

Integrated Monomers

Domains

adenylation

Name

Unk02

Type

nrps-type1

Genes

pvdD

Substrates

N5-formyl-N5-hydroxyornithine (evidence: Structure-based inference, Homology)

Integrated Monomers

Domains

adenylation

Name

Unk03

Type

nrps-type1

Genes

pvdD

Substrates

lysine (evidence: Structure-based inference [2])

Integrated Monomers

Domains

adenylation

Name

Unk04

Type

nrps-type1

Genes

pvdJ

Substrates

threonine (evidence: Structure-based inference [2])

Integrated Monomers

Domains

adenylation

Name

Unk05

Type

nrps-type1

Genes

pvdJ

Substrates

alanine (evidence: Structure-based inference [2])

Integrated Monomers

Domains

adenylation

Name

Unk06

Type

nrps-type1

Genes

pvdI

Substrates

aspartic acid (evidence: Structure-based inference, Homology)

Integrated Monomers

Domains

adenylation

Name

Unk07

Type

nrps-type1

Genes

pvdI

Substrates

N5-formyl-N5-hydroxyornithine (evidence: Structure-based inference, Homology)

Integrated Monomers

Domains

adenylation

Name

Unk08

Type

nrps-type1

Genes

pvdI

Substrates

lysine (evidence: Structure-based inference [2])

Integrated Monomers

Domains

adenylation

Name

Unk09

Type

nrps-type1

Genes

pvdL

Substrates

glutamic acid (evidence: Structure-based inference [2])

Integrated Monomers

Domains

adenylation

Name

Unk10

Type

nrps-type1

Genes

pvdL

Substrates

tyrosine (evidence: Structure-based inference [2])

Integrated Monomers

Domains

adenylation

Name

Unk11

Type

nrps-type1

Genes

pvdL

Substrates

2,4-diaminobutyric acid (evidence: Structure-based inference [2])

Integrated Monomers

Domains

adenylation

Annotation changelog

Entry version: 4

Date

Changes

Submitters

Reviewers

2022-10-07

Update chemical activity to schema version 2.11

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

2022-10-07

Changed chemical structures for compounds: Pf-5 pyoverdine.

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

2022-10-07

Renamed compounds: pyoverdin to Pf-5 pyoverdine.

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

2022-10-07

Updated NPAtlas ID for compounds: Pf-5 pyoverdine.

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

Entry version: 3

Date

Changes

Submitters

Reviewers

2022-09-15

Updated bioactivity data

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

2022-09-15

Added NRP substrate specificities

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

Entry version: 2

Date

Changes

Submitters

Reviewers

2019-10-16

Migrated from v1.4

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

2019-10-16

Updated compound(s) information (NPAtlas curation)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

Entry version: 1

Date

Changes

Submitters

Reviewers

2015-06-12

Submitted

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

Detailed domain annotation

Selected features only

Show module domains

Similar known gene clusters from MIBiG 4.0