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Product(s) |

Expression|

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Standard Name	pgpB
Gene Synonym(s)	ECK1273, b1278, JW1270^[1], JW1270
Product Desc.	Phosphatidylglycerophosphate phosphatase, membrane bound; also has a minor undecaprenyl pyrophosphate pyrophosphatase (UppP) activity^[2]
Product Synonyms(s)	phosphatidylglycerophosphatase B^[1], B1278^[3]^[1], PgpB^[3]^[1] , ECK1273, JW1270, b1278
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pgpB^[3]
Regulation/Activity
Quick Links
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Notes

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The pgpA gene is nonessential, but is synthetically lethal with a bacA ybjG double mutant, due to its UppP activity. ybjG, pgpB, and lpxT are paralogs. Overexpression confers bacitracin resistance.^[2]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	pgpB
Mnemonic	Phosphatidylglycerophosphate phosphatase
Synonyms	ECK1273, b1278, JW1270^[1], JW1270
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	28.82 minutes	MG1655: 1337354..1338118 <gbrowseImage> name=NC_000913:1337354..1338118 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1337702..1338466 <gbrowseImage> name=NC_012967:1337702..1338466 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1228203..1228967 <gbrowseImage> name=NC_012759:1228203..1228967 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1341044..1341808 <gbrowseImage> name=NC_007779:1341044..1341808 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1426750..1427514 <gbrowseImage> name=NC_010473:1426750..1427514 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔpgpB (Keio:JW1270)	deletion	deletion			PMID:16738554	Shigen CGSC9142^[4]
ΔpgpB786::kan					PMID:16738554	CGSC:102316
pgpB	deletion		Sensitivity to	increases sensitivity to bicyclomycin	PMID:21357484		fig 2
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW1270	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGTTCGATTGCCAGACGTAC Primer 2:CCACTTTCTTGTTCTCGTTGCGC
18B6	Kohara Phage	Genobase	PMID:3038334
trpC83::Tn10	Linked marker	CAG18455 = CGSC7371^[4]	est. P1 cotransduction: 49% ^[5] Synonyms:trpB83::Tn10
zcj-233::Tn10	Linked marker	CAG12028 = CGSC7373^[4]	est. P1 cotransduction: 29% ^[5] Synonyms:zci-233::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10705	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10705	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000697	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945863	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0699	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004294	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	PgpB
Synonyms	phosphatidylglycerophosphatase B^[1], B1278^[3]^[1], PgpB^[3]^[1] , ECK1273, JW1270, b1278
Product description	Phosphatidylglycerophosphate phosphatase, membrane bound; also has a minor undecaprenyl pyrophosphate pyrophosphatase (UppP) activity^[2]
EC number (for enzymes)	3.1.3.27^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000326	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016118	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008962	phosphatidylglycerophosphatase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.1.3.27	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009279	cell outer membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0998	C	Seeded from EcoCyc (v14.0)	complete
	GO:0009395	phospholipid catabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0595	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000326	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	rrmA		PMID:16606699	Experiment(s):EBI-1139444
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source
plasma membrane	C-terminus localized in the cytoplasm with 6 predicted transmembrane domains	Daley et al. (2005) ^[6]
plasma membrane			From EcoCyc^[7]
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MRSIARRTAV GAALLLVMPV AVWISGWRWQ PGEQSWLLKA AFWVTETVTQ PWGVITHLIL FGWFLWCLRF RIKAAFVLFA ILAAAILVGQ GVKSWIKDKV QEPRPFVIWL EKTHHIPVDE FYTLKRAERG NLVKEQLAEE KNIPQYLRSH WQKETGFAFP SGHTMFAASW ALLAVGLLWP RRRTLTIAIL LVWATGVMGS RLLLGMHWPR DLVVATLISW ALVAVATWLA QRICGPLTPP AEENREIAQR EQES
Length	254
Mol. Wt	29.021 kDa
pI	10.5 (calculated)
Extinction coefficient	96,480 - 96,730 (calc based on 2 Y, 17 W, and 2 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Domain	73..234	PF01569 PAP2 superfamily		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=pgpB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16129239	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945863	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004294	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A924	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10705	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10705	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945863	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000697	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0699	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	80	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	67	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	46^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
pgpB
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:1337334..1337374 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b1278 (EcoliWiki Page)	NCBI GEO profiles for pgpB
microarray	GenExpDB:b1278 (EcoliWiki Page)	Summary of data for pgpB from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (1337095..1337369) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:G8^[8]
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Notes

Accessions Related to pgpB Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10705	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0699	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1278
EcoGene	EcoGene:EG10705	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000697	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004294	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Shigella flexneri	PGPB	From SHIGELLACYC
E. coli O157	PGPB	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF01569 PAP2 superfamily
Superfamily (EcoliWiki Page)	SUPERFAMILY:48317
EcoCyc	EcoCyc:EG10705	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10705	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000697	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0699	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004294	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

pgpB:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to pgpB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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