gfcB: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

gfcB

Gene Synonym(s)

ymcC, ECK0977, b0986, JW0969[1][2][3], JW0969

Product Desc.

predicted outer membrane lipoprotein[3][2]

Lipoprotein required for formation of the O-antigen capsule; silenced by IS1D insertion in promoter region[4]

Product Synonyms(s)

predicted outer membrane lipoprotein[1], YmcC[3][1], B0986[3][1], GfcB[3][1] , ECK0977, JW0969, ymcC, b0986

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ymcA[3]

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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Function characterized in enteropathogenic E. coli (EPEC). Part of the gfcABCDE-etp-etk operon. gfcB and yjbF are paralogs. First 15 aa are a type II signal peptide.[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

gfcB

Mnemonic

Group 4 Capsule

Synonyms

ymcC, ECK0977, b0986, JW0969[1][2][3], JW0969

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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

22.59 minutes 

MG1655: 1048555..1047911
<gbrowseImage> name=NC_000913:1047911..1048555 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1065779..1066423
<gbrowseImage> name=NC_012967:1065779..1066423 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 950879..951523
<gbrowseImage> name=NC_012759:950879..951523 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1049754..1049110
<gbrowseImage> name=NC_007779:1049110..1049754 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1102483..1101839
<gbrowseImage> name=NC_010473:1101839..1102483 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

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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

4H11

Kohara Phage

Genobase

PMID:3038334

2F1

Kohara Phage

Genobase

PMID:3038334

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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:G6507

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13731

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003107

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949118

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3495

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003323

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

GfcB

Synonyms

predicted outer membrane lipoprotein[1], YmcC[3][1], B0986[3][1], GfcB[3][1] , ECK0977, JW0969, ymcC, b0986

Product description

predicted outer membrane lipoprotein[3][2]

Lipoprotein required for formation of the O-antigen capsule; silenced by IS1D insertion in promoter region[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

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: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:0031225

anchored to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9901

C

Seeded from EcoCyc (v14.0)

complete

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

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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

Outer membrane

PMID:15174130

EchoLocation:ymcC


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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

MRPLILSIFA LFLAGCTHSQ QSMVDTFRAS LFDNQDITVA DQQIQALPYS TMYLRLNEGQ
RIFVVLGYIE QEQSKWLSQD NAMLVTHNGR LLKTVKLNNN LLEVTNSGQD PLRNALAIKD
GSRWTRDILW SEDNHFRSAT LSSTFSFAGL ETLNIAGRNV LCNVWQEEVT STRPEKQWQN
TFWVDSATGQ VRQSRQMLGA GVIPVEMTFL KPAP
Length

214

Mol. Wt

24.267 kDa

pI

6.7 (calculated)

Extinction coefficient

37,470 - 37,720 (calc based on 3 Y, 6 W, and 2 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

motif

1-15

UniProt Manual:Signal Peptides

UniProt:P75884

Domain

13..210

PF11102 Protein of unknown function (DUF2886)

PMID:19920124

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

Structures

<beststructure> gene=gfcB 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:16128952

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949118

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003323

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75884

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6507

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13731

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949118

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003107

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3495

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

1a

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

0a

molecules/cell/generation

  • Medium: MOPS Minimal
  • 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

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

Transcription unit(s)

ymcA

File:.jpg

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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_000913:1048535..1048575 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:b0986 (EcoliWiki Page)

NCBI GEO profiles for gfcB

microarray

GenExpDB:b0986 (EcoliWiki Page)

Summary of data for gfcB 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 (1048455..1048724) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ15; Well:B2[5]

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Notes

Accessions Related to gfcB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6507

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3495

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0986

EcoGene

EcoGene:EG13731

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003107

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003323

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

Shigella flexneri

YMCC

From SHIGELLACYC

E. coli O157

YMCC

From ECOO157CYC

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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database Accession Notes

Pfam (EcoliWiki Page)

PF11102 Protein of unknown function (DUF2886)


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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. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.0 2.1 2.2 2.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 EcoCyc (release 10.6; 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. 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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