bamD:On One Page

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

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Standard Name

bamD

Gene Synonym(s)

ECK2593, b2595, JW2577, ecfD, bamD, yfiO[1][2], yfiO

Product Desc.

YfiO[3]; YfiO-lipoprotein component of outer membrane protein assembly complex[4];

Component of Outer Membrane Protein Assembly Complex[4]

Product Synonyms(s)

predicted lipoprotein[1], B2595[3][1], EcfD[3][1], YfiO[3][1], BamD [2], ecfD, ECK2593, JW2577, yfiO, b2595

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 [2].

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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

bamD

Mnemonic

Beta-barrel assembly machine

Synonyms

ECK2593, b2595, JW2577, ecfD, bamD, yfiO[1][2], yfiO

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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 [2].

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

58.93 minutes 

MG1655: 2734168..2734905
<gbrowseImage> name=NC_000913:2734168..2734905 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2619980..2620717
<gbrowseImage> name=NC_012759:2619980..2620717 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2734802..2735539
<gbrowseImage> name=NC_007779:2734802..2735539 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
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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

yfiO4

C-terminal truncation of 57 nucleotides

C-terminal truncation of 19 amino acids (-MNAQAEKVAKIIAANSSNT), followed by non-native 10 amino acid tail resulting from drug cassette insertion (+ICLLYTSQPV).

Partial loss-of-function mutation. Results in lower levels of outer membrane beta-barrel proteins and outer membrane sensitivity.

[5],[6]

Protein encoded by yfiO4 destabilizes BamCDE sub-complex [5], and results in unstable protein at 37 degrees during stationary phase [6]

yfiO5

C-terminal truncation of 54 nucleotides

C-terminal truncation of 18 amino acids (-NAQAEKVAKIIAANSSNT), followed by non-native 1 amino acid tail resulting from drug cassette insertion (+V)

Partial loss-of-function mutation. Results in lower levels of outer membrane beta-barrel proteins and outer membrane sensitivity.

[5],[6]

Protein encoded by yfiO5 destabilizes BamCDE sub-complex [5], and results in unstable protein at 37 degrees during stationary phase [6]. yfiO5 outer membrane sensitivity more severe than yfiO4.

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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

JW2577

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACGCGCATGAAATATCTGGT

Primer 2:CCTGTATTGCTGCTGTTTGCGGC

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[7]

est. P1 cotransduction: 40% [8]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[7]

est. P1 cotransduction: 90% [8]

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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:G7352

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14222

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003921

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947086

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3974

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008536

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

YfiO

Synonyms

predicted lipoprotein[1], B2595[3][1], EcfD[3][1], YfiO[3][1], BamD [2], ecfD, ECK2593, JW2577, yfiO, b2595

Product description

YfiO[3]; YfiO-lipoprotein 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: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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0998

C

Seeded from EcoCyc (v14.0)

complete

GO:0043165

Gram-negative-bacterium-type cell outer membrane assembly

PMID:15851030

IGI: Inferred from Genetic Interaction

EcoliWiki:nlpB EcoliWiki:yaeT EcoliWiki:yfgL


P

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

GO:0005515

protein binding

PMID:15851030

IPI: Inferred from Physical Interaction

EcoliWiki:nlpB EcoliWiki:yaeT EcoliWiki:yfgL


F

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

Subunits of Outer Membrane Protein Assembly Complex

Protein

BamA (yaeT)

BamD (YfiO) directly binds BamA. BamD is part of the BamCDE subcomplex [5],[6].

Protein

BamC (nlpB)

BamC is part of the BamCDE sub-complex that binds to BamA (YaeT) [5],[6].

Protein

BamE (smpA)

BamE is part of the BamCDE sub-complex that binds to BamA (YaeT) [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

outer membrane

Outer membrane

PMID:16372265

EchoLocation:ecfD


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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 

MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN
RYPFGPYSQQ VQLDLIYAYY KNADLPLAQA AIDRFIRLNP THPNIDYVMY MRGLTNMALD
DSALQGFFGV DRSDRDPQHA RAAFSDFSKL VRGYPNSQYT TDATKRLVFL KDRLAKYEYS
VAEYYTERGA WVAVVNRVEG MLRDYPDTQA TRDALPLMEN AYRQMQMNAQ AEKVAKIIAA
NSSNT
Length

245

Mol. Wt

27.829 kDa

pI

6.3 (calculated)

Extinction coefficient

36,330 - 36,455 (calc based on 17 Y, 2 W, and 1 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

motif

1-19

UniProt Manual:Signal Peptides

UniProt:P0AC02


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

Structures

<beststructure> gene=bamD 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:16130516

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947086

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008536

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AC02

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7352

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14222

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947086

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003921

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3974

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 MC4100

8.59E+02

molecules/cell

  • Medium: combined data from rich and minimal media

37

Protein

E. coli K-12 MC4100

8.59E+02

molecules/cell

  • Medium: combined data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

6620

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

2233

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

2761

molecules/cell/generation

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

Ribosome Profiling

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)

yfiO

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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_000913:2734148..2734188 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:b2595 (EcoliWiki Page)

NCBI GEO profiles for yfiO

microarray

GenExpDB:b2595 (EcoliWiki Page)

Summary of data for yfiO 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 (2733956..2734194) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ08; Well:G10[9]

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Notes

Accessions Related to bamD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7352

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3974

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2595

EcoGene

EcoGene:EG14222

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003921

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008536

Escherichia coli str. K-12 substr. MG1655

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Evolution

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Homologs in Other Organisms

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Organism Homologs (Statistics) Comments

Xenopus tropicalis

  • ENSXETP00000023513 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

S2828

From SHIGELLACYC

E. coli O157

Z3889

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
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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 2.4 2.5 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 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 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 5.2 5.3 5.4 5.5 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
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 Sklar, JG et al. (2007) Lipoprotein SmpA is a component of the YaeT complex that assembles outer membrane proteins in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 104 6400-5 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. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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