bamA: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

bamA

Gene Synonym(s)

ECK0176, b0177, JW0172, up05, ecfK, yzzN, yzzY, omp85(N.m.), bamA, yaeT[1][2][3], omp85, yaeT

Product Desc.

YaeT[2]; YaeT-component of outer membrane protein assembly complex[4];

Component of Outer Membrane Protein Assembly Complex[4]

Product Synonyms(s)

conserved protein[1], B0177[2][1], YzzN[2][1], YzzY[2][1], EcfK[2][1], YaeT[2][1], BamA [3], ecfK, ECK0176, JW0172, omp85, yaeT, yzzN, yzzY, b0177

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression
Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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Notes

A consensus has been reached for renaming the genes that encode components of the outer membrane β-barrel assembly machine, (formerly known as the YaeT complex of E. coli or the Omp85 complex of N. meningitidis). The new designation for this multi-component structure is the Bam complex (for beta-barrel assembly machine).

The Bam complex in E. coli consists of BamA (YaeT), BamB (YfgL), BamC (NlpB), BamD (YfiO), and BamE (SmpA). Letters have been assigned on the basis of molecular weight, from highest to lowest [3].

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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

bamA

Mnemonic

Beta-barrel assembly machine

Synonyms

ECK0176, b0177, JW0172, up05, ecfK, yzzN, yzzY, omp85(N.m.), bamA, yaeT[1][2][3], omp85, yaeT

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Notes

A consensus has been reached for renaming the genes that encode components of the outer membrane β-barrel assembly machine, (formerly known as the YaeT complex of E. coli or the Omp85 complex of N. meningitidis). The new designation for this multi-component structure is the Bam complex (for beta-barrel assembly machine).

The Bam complex in E. coli consists of BamA (YaeT), BamB (YfgL), BamC (NlpB), BamD (YfiO), and BamE (SmpA). Letters have been assigned on the basis of molecular weight, from highest to lowest [3].

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

4.27 minutes 

MG1655: 197928..200360
<gbrowseImage> name=NC_000913:197928..200360 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 200770..203202
<gbrowseImage> name=NC_012967:200770..203202 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 197927..200359
<gbrowseImage> name=NC_012759:197927..200359 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 197928..200360
<gbrowseImage> name=NC_007779:197928..200360 source=W3110 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

Coding Start (SO:0000323)

MG1655

197988

Edman degradation

PMID:9298646


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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

yaeT6

in-frame insertion of Gln–Lys after amino acid 218 of YaeT (BamA)

Sensitivity to

Rifampicin, Erythromycin, Novobiocin, Bacitracin

[5]

Suppressor of imp4213 sensitivity to deoxycholate and chenodeoxycholate

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Notes

yaeT6 carries a 6-bp in-frame insertion (agaaac) between codons 218 and 219 of yaeT. At the protein level, the suppressor mutation results in an in-frame insertion of Gln–Lys after amino acid 218 of YaeT. The yaeT6 mutation was isolated as a suppressor of the imp4213 allele of lptD.[5]

The mutant allele bamA66 is a deletion of the R64 codon of bamA. The mutant protein is referred to as BamA(delR64). The bamA66 mutation was isolated as a suppressor that conferred increased resistance to bacitracin of a strain carrying the imp208 allele of lptD. In an lptD+ background, bamA66 displays a slight sensitivity to vancomycin and rifampin and causes a moderate reduction (20–30%) in OMP levels, but is synthetically lethal with the depletion of BamB, conditionally lethal in the absence of DegP or SurA; i.e. no growth at or above 37°C and 40°C respectively.[6]

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

JW0172

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCGATGAAAAAGTTGCTCAT

Primer 2:CCCCAGGTTTTACCGATGTTAAA

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[7]

est. P1 cotransduction: 10% [8]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[7]

est. P1 cotransduction: 25% [8]
Synonyms:zae-502::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:G6093

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12676

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944870

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002713

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2541

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000605

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

BamA

Synonyms

conserved protein[1], B0177[2][1], YzzN[2][1], YzzY[2][1], EcfK[2][1], YaeT[2][1], BamA [3], ecfK, ECK0176, JW0172, omp85, yaeT, yzzN, yzzY, b0177

Product description

YaeT[2]; YaeT-component of outer membrane protein assembly complex[4];

Component of Outer Membrane Protein Assembly Complex[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:0043165

Gram-negative-bacterium-type cell outer membrane assembly

PMID:15851030

IPI: Inferred from Physical Interaction

EcoliWiki:yfgL EcoliWiki:nlpB EcoliWiki:yfiO


P

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:0009279

cell outer membrane

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01430

C

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:15851030

IPI: Inferred from Physical Interaction

EcoliWiki:nlpB EcoliWiki:yfgL EcoliWiki:yfiO


F

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:0009279

cell outer membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0040

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

Protein

Subunits of Outer Membrane Protein Assembly Complex

Protein

skp

PMID:19402753

LCMS(ID Probability):99.5

Protein

edd

PMID:19402753

LCMS(ID Probability):99.6

Protein

gldA

PMID:19402753

LCMS(ID Probability):99.4

Protein

yegQ

PMID:19402753

MALDI(Z-score):27.086609

Protein

fur

PMID:19402753

LCMS(ID Probability):99.6

Protein

acnB

PMID:19402753

LCMS(ID Probability):99.6

Protein

gcvP

PMID:19402753

LCMS(ID Probability):99.6

Protein

gabD

PMID:19402753

LCMS(ID Probability):99.6

Protein

deoA

PMID:19402753

LCMS(ID Probability):99.6

Protein

aldA

PMID:19402753

LCMS(ID Probability):99.6

Protein

folD

PMID:19402753

LCMS(ID Probability):99.6

Protein

BamB (yfgL)

BamB directly binds BamA (YaeT). Interaction between BamA-BamB is independent of BamA-BamCDE interactions. [9],[10]

Protein

BamC (nlpB)

BamC is part of the BamCDE sub-complex that binds to BamA (YaeT). Interaction of BamCDE sub-complex with BamA is independent of BamA-BamB interaction. [9],[10]

Protein

BamD (yfiO)

BamD is part of the BamCDE sub-complex that binds to BamA (YaeT). BamD directly binds BamA. Interaction of BamCDE sub-complex with BamA is independent of BamA-BamB interaction. [9],[10]

Protein

BamE (smpA)

BamE is part of the BamCDE sub-complex that binds to BamA (YaeT). Interaction of BamCDE sub-complex with BamA is independent of BamA-BamB interaction. [10]


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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

Outer Membrane

PMID:15951436, PMID:16102012, PMID:9298646

EchoLocation:ecfK

Outer Membrane

PMID:9298646

EchoLocation:ecfK


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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

MAMKKLLIAS LLFSSATVYG AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS
NTIRALFATG NFEDVRVLRD GDTLLVQVKE RPTIASITFS GNKSVKDDML KQNLEASGVR
VGESLDRTTI ADIEKGLEDF YYSVGKYSAS VKAVVTPLPR NRVDLKLVFQ EGVSAEIQQI
NIVGNHAFTT DELISHFQLR DEVPWWNVVG DRKYQKQKLA GDLETLRSYY LDRGYARFNI
DSTQVSLTPD KKGIYVTVNI TEGDQYKLSG VEVSGNLAGH SAEIEQLTKI EPGELYNGTK
VTKMEDDIKK LLGRYGYAYP RVQSMPEIND ADKTVKLRVN VDAGNRFYVR KIRFEGNDTS
KDAVLRREMR QMEGAWLGSD LVDQGKERLN RLGFFETVDT DTQRVPGSPD QVDVVYKVKE
RNTGSFNFGI GYGTESGVSF QAGVQQDNWL GTGYAVGING TKNDYQTYAE LSVTNPYFTV
DGVSLGGRLF YNDFQADDAD LSDYTNKSYG TDVTLGFPIN EYNSLRAGLG YVHNSLSNMQ
PQVAMWRYLY SMGEHPSTSD QDNSFKTDDF TFNYGWTYNK LDRGYFPTDG SRVNLTGKVT
IPGSDNEYYK VTLDTATYVP IDDDHKWVVL GRTRWGYGDG LGGKEMPFYE NFYAGGSSTV
RGFQSNTIGP KAVYFPHQAS NYDPDYDYEC ATQDGAKDLC KSDDAVGGNA MAVASLEFIT
PTPFISDKYA NSVRTSFFWD MGTVWDTNWD SSQYSGYPDY SDPSNIRMSA GIALQWMSPL
GPLVFSYAQP FKKYDGDKAE QFQFNIGKTW
Length

810

Mol. Wt

90.553 kDa

pI

4.8 (calculated)

Extinction coefficient

141,530 - 141,780 (calc based on 47 Y, 13 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

1-20

UniProt Manual:Signal Peptides

UniProt:P0A940

Domain

448..810

PF01103 Surface antigen

PMID:19920124

Domain

24..91

PF07244 Surface antigen variable number repeat

PMID:19920124

Domain

92..172

PF07244 Surface antigen variable number repeat

PMID:19920124

Domain

175..263

PF07244 Surface antigen variable number repeat

PMID:19920124

Domain

266..344

PF07244 Surface antigen variable number repeat

PMID:19920124

Domain

347..421

PF07244 Surface antigen variable number repeat

PMID:19920124

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

Structures

<beststructure> gene=bamA 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:16128170

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944870

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000605

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A940

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6093

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12676

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944870

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002713

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2541

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 EMG2

180

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: M60

PMID: 9298646

Protein

E. coli K-12 EMG2

80

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: M61

PMID: 9298646

Protein

E. coli K-12 MG1655

3904

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

1512

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

2826

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

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)

yaeT-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE

yaeT

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_000913:197908..197948 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


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

Type Reference Notes

microarray

GEO Profiles:b0177 (EcoliWiki Page)

NCBI GEO profiles for yaeT

microarray

GenExpDB:b0177 (EcoliWiki Page)

Summary of data for yaeT 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 (197801..197953) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ11; Well:F4[11]

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Notes

Accessions Related to bamA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6093

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2541

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0177

EcoGene

EcoGene:EG12676

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002713

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000605

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

Anopheles gambiae

  • ENSANGP00000025498 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000016312 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000001270 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000001158 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-041114-30 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-041114-30 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-1732 (score: 0.845)
  • ZDB-GENE-040426-806 (score: 0.845)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000022917 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000345445 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000007689 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1915903 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000016520 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC17C96 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000146321 (score: 1.000; bootstrap: 100%)
  • NEWSINFRUP00000148770 (score: 0.763)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00003777001 (score: 1.000; bootstrap: 100%)
  • GSTENP00004537001 (score: 0.766)

From Inparanoid:20070104

Shigella flexneri

YAET

From SHIGELLACYC

E. coli O157

YAET

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)

PF01103 Surface antigen

Pfam (EcoliWiki Page)

PF07244 Surface antigen variable number repeat

Pfam (EcoliWiki Page)

PF07244 Surface antigen variable number repeat

Pfam (EcoliWiki Page)

PF07244 Surface antigen variable number repeat

Pfam (EcoliWiki Page)

PF07244 Surface antigen variable number repeat

Pfam (EcoliWiki Page)

PF07244 Surface antigen variable number repeat

EcoCyc

EcoCyc:G6093

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12676

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002713

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2541

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000605

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 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 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 3.5 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  4. 4.0 4.1 4.2 4.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  5. 5.0 5.1 Ruiz, N et al. (2006) Probing the barrier function of the outer membrane with chemical conditionality. ACS Chem. Biol. 1 385-95 PubMed
  6. Bennion, D et al. (2010) Dissection of β-barrel outer membrane protein assembly pathways through characterizing BamA POTRA 1 mutants of Escherichia coli. Mol. Microbiol. 77 1153-71 PubMed
  7. 7.0 7.1 CGSC: The Coli Genetics Stock Center
  8. 8.0 8.1 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).
  9. 9.0 9.1 9.2 Malinverni, JC et al. (2006) YfiO stabilizes the YaeT complex and is essential for outer membrane protein assembly in Escherichia coli. Mol. Microbiol. 61 151-64 PubMed
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