ugpA:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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Standard Name

ugpA

Gene Synonym(s)

ECK3436, b3452, JW3417, psiB, psiC, ugp[1]

Product Desc.

UgpA[2][3];

Component of glycerol-3-P ABC transporter[2][3]

sn-Glycerol-3-phosphate transport system, integral membrane protein[4]

Product Synonyms(s)

glycerol-3-phosphate transporter subunit[1], membrane component of ABC superfamily[1], B3452[2][1], Ugp[2][1], PsiC[2][1], PsiB[2][1], UgpA[2][1] , ECK3436, JW3417, psiB, psiC, b3452

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ugpBAECQ[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Pho regulon.[4]



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

ugpA

Mnemonic

Uptake glycerol phosphate

Synonyms

ECK3436, b3452, JW3417, psiB, psiC, ugp[1]

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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

77.33 minutes, 77.33 minutes 

MG1655: 3588934..3588047
<gbrowseImage> name=NC_000913:3588047..3588934 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3521587..3520700
<gbrowseImage> name=NC_012967:3520700..3521587 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3476541..3477428
<gbrowseImage> name=NC_012759:3476541..3477428 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4049504..4050391
<gbrowseImage> name=NC_007779:4049504..4050391 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3686679..3685792
<gbrowseImage> name=NC_010473:3685792..3686679 source=DH10B preset=GeneLocation </gbrowseImage>

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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

ΔugpA (Keio:JW3417)

deletion

deletion

PMID:16738554

Shigen
CGSC10541[5]

ugpA::Tn5KAN-I-SceI (FB21216)

Insertion at nt 437 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21216

contains pKD46

ΔugpA782::kan

PMID:16738554

CGSC:103280


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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

JW3417

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCATCATCCCGTCCGGTGTT

Primer 2:CCTTGGTAACGCACCTTGCTTTC

1B6

Kohara Phage

Genobase

PMID:3038334

5B10

Kohara Phage

Genobase

PMID:3038334

10F5

Kohara Phage

Genobase

PMID:3038334

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[5]

est. P1 cotransduction: 39% [6]
Synonyms:zhg-3086::Tn10, zhh-21::Tn10

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: 90% [6]
Synonyms:zhf-50::Tn10, zhf-5::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:EG11046

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11046

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001035

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947957

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1039

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011272

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

UgpA

Synonyms

glycerol-3-phosphate transporter subunit[1], membrane component of ABC superfamily[1], B3452[2][1], Ugp[2][1], PsiC[2][1], PsiB[2][1], UgpA[2][1] , ECK3436, JW3417, psiB, psiC, b3452

Product description

UgpA[2][3];

Component of glycerol-3-P ABC transporter[2][3]

sn-Glycerol-3-phosphate transport system, integral membrane protein[4]

EC number (for enzymes)


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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

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

Subunits of glycerol-3-P ABC transporter

could be indirect

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.5

Protein

ompA

PMID:19402753

LCMS(ID Probability):99.6

Protein

ompC

PMID:19402753

LCMS(ID Probability):99.6

Protein

atpD

PMID:19402753

LCMS(ID Probability):99.6

Protein

atpA

PMID:19402753

LCMS(ID Probability):99.6

Protein

ompX

PMID:19402753

LCMS(ID Probability):99.6

Protein

atpC

PMID:19402753

LCMS(ID Probability):99.6

Protein

ybiO

PMID:19402753

LCMS(ID Probability):99.6

Protein

ugpC

PMID:19402753

LCMS(ID Probability):99.6

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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 Notes

plasma membrane

C-terminus localized in the cytoplasm with 6 predicted transmembrane domains

Daley et al. (2005) [7]

plasma membrane

From EcoCyc[3]


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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

MSSSRPVFRS RWLPYLLVAP QLIITVIFFI WPAGEALWYS LQSVDPFGFS SQFVGLDNFV
TLFHDSYYLD SFWTTIKFST FVTVSGLLVS LFFAALVEYI VRGSRFYQTL MLLPYAVAPA
VAAVLWIFLF NPGRGLITHF LAEFGYDWNH AQNSGQAMFL VVFASVWKQI SYNFLFFYAA
LQSIPRSLIE AAAIDGAGPI RRFFKIALPL IAPVSFFLLV VNLVYAFFDT FPVIDAATSG
GPVQATTTLI YKIYREGFTG LDLASSAAQS VVLMFLVIVL TVVQFRYVES KVRYQ
Length

295

Mol. Wt

33.264 kDa

pI

9.2 (calculated)

Extinction coefficient

60,850 (calc based on 15 Y, 7 W, and 0 C residues)


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

86..294

PF00528 Binding-protein-dependent transport system inner membrane component

PMID:19920124

<motif_map/>

tmhmm.php?gene=ugpA&show=pic&.jpg
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=ugpA 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:16131324

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947957

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011272

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P10905

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11046

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11046

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947957

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001035

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1039

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

10a

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

27

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

0a

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

Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

ugpBAECQ

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_000913:3588914..3588954 source=MG1655 flip=1 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


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b3452 (EcoliWiki Page)

NCBI GEO profiles for ugpA

microarray

GenExpDB:b3452 (EcoliWiki Page)

Summary of data for ugpA from multiple microarray studies


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 (3588443..3588689) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ14; Well:D4[8]

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Notes

Accessions Related to ugpA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11046

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1039

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3452

EcoGene

EcoGene:EG11046

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001035

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011272

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Xenopus tropicalis

  • ENSXETP00000041318 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

UGPA

From SHIGELLACYC

E. coli O157

UGPA

From ECOO157CYC


Do-It-Yourself Web Tools

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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)

PF00528 Binding-protein-dependent transport system inner membrane component

EcoCyc

EcoCyc:EG11046

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11046

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001035

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1039

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011272

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 3.2 3.3 3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. 6.0 6.1 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).
  7. Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  8. Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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