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Standard Name	bamB
Gene Synonym(s)	ECK2508, b2512, JW2496, bamB , yfgL^[1]^[2], yfgL
Product Desc.	YfgL^[3]; YfgL-lipoprotein component of outer membrane protein assembly complex^[4]; Component of Outer Membrane Protein Assembly Complex^[4]
Product Synonyms(s)	protein assembly complex, lipoprotein component^[1], B2512^[3]^[1], YfgL^[3]^[1], BamB ^[2] , ECK2508, JW2496, yfgL, b2512
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

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	bamB
Mnemonic	Beta-barrel assembly machine
Synonyms	ECK2508, b2512, JW2496, bamB , yfgL^[1]^[2], yfgL
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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	56.8 minutes	MG1655: 2636674..2635496 <gbrowseImage> name=NC_000913:2635496..2636674 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2559471..2558293 <gbrowseImage> name=NC_012967:2558293..2559471 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2521301..2522479 <gbrowseImage> name=NC_012759:2521301..2522479 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2637308..2636130 <gbrowseImage> name=NC_007779:2636130..2637308 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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: Description	Reference	Availability
ΔyfgL (Keio:JW2496)	deletion	deletion		PMID:16738554	Shigen CGSC9989^[5]
yfgL S172C		S172C	Can be cross-linked using cysteine-specific crosslinkers to YaeT (BamA).	PMID:18165306
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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
JW2496	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAATTGCGTAAATTACTGCT Primer 2:CCACGTGTAATAGAGTACACGGT
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 16% ^[6]
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 35% ^[6] Synonyms:zff-208::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:G7320	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14208	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003892	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946982	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3960	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008272	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	YfgL
Synonyms	protein assembly complex, lipoprotein component^[1], B2512^[3]^[1], YfgL^[3]^[1], BamB ^[2] , ECK2508, JW2496, yfgL, b2512
Product description	YfgL^[3]; YfgL-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. 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:0005515	protein binding	PMID:15851030	IPI: Inferred from Physical Interaction	EcoliWiki:yfiO EcoliWiki:nlpB EcoliWiki:yaeT	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:0043165	Gram-negative-bacterium-type cell outer membrane assembly	PMID:15851030	IPI: Inferred from Physical Interaction	EcoliWiki:nlpB EcoliWiki:yaeT EcoliWiki:yfiO	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:0005515	protein binding	PMID:18165306	IPI: Inferred from Physical Interaction		F	YfgL residue S172 specifically makes direct contact with YaeT (BamA) (Figure 4).	Missing: with/from
	GO:0031225	anchored to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9901	C	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	Subunits of Outer Membrane Protein Assembly Complex
Protein	lldD		PMID:16606699	Experiment(s):EBI-1143074
Protein	BamA (yaeT)	BamB (YfgL) directly binds BamA (YaeT). Interaction between BamA-BamB is independent of BamA-BamCDE interactions. ^[7],^[8]
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See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki. </protect>

Notes

Localization

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

Compartment	Evidence	Reference/Source
outer membrane
Outer membrane	PMID:15174130	EchoLocation:yfgL
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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 MQLRKLLLPG LLSVTLLSGC SLFNSEEDVV KMSPLPTVEN QFTPTTAWST SVGSGIGNFY SNLHPALADN VVYAADRAGL VKALNADDGK EIWSVSLAEK DGWFSKEPAL LSGGVTVSGG HVYIGSEKAQ VYALNTSDGT VAWQTKVAGE ALSRPVVSDG LVLIHTSNGQ LQALNEADGA VKWTVNLDMP SLSLRGESAP TTAFGAAVVG GDNGRVSAVL MEQGQMIWQQ RISQATGSTE IDRLSDVDTT PVVVNGVVFA LAYNGNLTAL DLRSGQIMWK RELGSVNDFI VDGNRIYLVD QNDRVMALTI DGGVTLWTQS DLLHRLLTSP VLYNGNLVVG DSEGYLHWIN VEDGRFVAQQ KVDSSGFQTE PVAADGKLLI QAKDGTVYSI TR
Length	392
Mol. Wt	41.886 kDa
pI	4.6 (calculated)
Extinction coefficient	62,910 - 63,035 (calc based on 9 Y, 9 W, and 1 C residues)
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See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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:P77774
Domain	70..107	PF01011 PQQ enzyme repeat		PMID:19920124
Domain	120..157	PF01011 PQQ enzyme repeat		PMID:19920124
Domain	256..292	PF01011 PQQ enzyme repeat		PMID:19920124
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See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

<motif_map/>

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

Structures

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

Models

View models at:

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

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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:16130437	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946982	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008272	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77774	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7320	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14208	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946982	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003892	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3960	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	Reference(s)
Protein	E. coli K-12 MC4100	6.64E+02	molecules/cell	Medium: combined data from rich and minimal media	37
Protein	E. coli K-12 MC4100	6.64E+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	3080	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	1064	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	1541	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)
yfgL-der
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Figure courtesy of RegulonDB

</protect>

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_000913:2636654..2636694 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b2512 (EcoliWiki Page)	NCBI GEO profiles for yfgL
microarray	GenExpDB:b2512 (EcoliWiki Page)	Summary of data for yfgL 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
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Notes

Accessions Related to bamB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7320	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3960	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2512
EcoGene	EcoGene:EG14208	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003892	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008272	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	S2730	From SHIGELLACYC
E. coli O157	Z3775	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)	PF01011 PQQ enzyme repeat
Pfam (EcoliWiki Page)	PF01011 PQQ enzyme repeat
Pfam (EcoliWiki Page)	PF01011 PQQ enzyme repeat
Superfamily (EcoliWiki Page)	SUPERFAMILY:50998
EcoCyc	EcoCyc:G7320	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14208	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003892	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3960	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008272	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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^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.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ 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
↑ 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

bamB: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 bamB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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