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Gene |

Product(s) |

Expression|

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Standard Name	bamC
Gene Synonym(s)	ECK2473, b2477, JW2462, dapX, bamC , nlpB^[1]^[2], nlpB
Product Desc.	lipoprotein-34^[3]; NlpB-lipoprotein component of outer membrane protein assembly complex^[4]; Component of Outer Membrane Protein Assembly Complex^[4]
Product Synonyms(s)	lipoprotein^[1], B2477^[3]^[1], DapX^[3]^[1], NlpB^[3]^[1], lipoprotein-34^[4]^[1]; BamC ^[2] , dapX, ECK2473, JW2462, nlpB, b2477
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	bamC
Mnemonic	Beta-barrel assembly machine
Synonyms	ECK2473, b2477, JW2462, dapX, bamC , nlpB^[1]^[2], nlpB
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</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].

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	55.95 minutes	MG1655: 2596887..2595853 <gbrowseImage> name=NC_000913:2595853..2596887 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2481658..2482692 <gbrowseImage> name=NC_012759:2481658..2482692 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2597521..2596487 <gbrowseImage> name=NC_007779:2596487..2597521 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)	Reference	Availability	Comments
ΔnlpB (Keio:JW2462)	deletion	deletion	PMID:16738554	Shigen CGSC9964^[5]
nlpB::Tn5KAN-2 (FB21135)	Insertion at nt 123 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20820	does not contain pKD46
nlpB::Tn5KAN-2 (FB21135)	Insertion at nt 123 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20821	contains pKD46
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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
JW2462	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTTACTCTGTTCAAAAGTC Primer 2:CCtTTGCTAAACGCAGCCTGGAA
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 93% ^[6]
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 2% ^[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:EG10658	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10658	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000651	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946954	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0652	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008161	Escherichia coli str. K-12 substr. MG1655
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Notes

NlpB is not essential and demonstrates very subtle outer membrane defects. nlpB- cells affect the stability of the multiprotein YaeT (Bam) complex in vitro ^[7],^[8].

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	NlpB
Synonyms	lipoprotein^[1], B2477^[3]^[1], DapX^[3]^[1], NlpB^[3]^[1], lipoprotein-34^[4]^[1]; BamC ^[2] , dapX, ECK2473, JW2462, nlpB, b2477
Product description	lipoprotein-34^[3]; NlpB-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:yaeT 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:0043165	Gram-negative-bacterium-type cell outer membrane assembly	PMID:15851030	IGI: Inferred from Genetic Interaction	EcoliWiki:yaeT EcoliWiki:yfgL 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: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	rfaS		PMID:16606699	Experiment(s):EBI-1142993
Protein	phnN		PMID:16606699	Experiment(s):EBI-1142993
Protein	serB		PMID:16606699	Experiment(s):EBI-1142993
Protein	nadE		PMID:16606699	Experiment(s):EBI-1142993
Protein	BamA (yaeT)	BamC (NlpB) is part of the BamCDE subcomplex. The BamCDE subcomplex interacts with BamA (YaeT) ^[7],^[8].
Protein	BamD (yfiO)	BamD (YfiO) is part of the BamCDE subcomplex. BamD interacts with BamA (YaeT) directly. This interaction is stabilized by BamC (NlpB) and BamE (SmpA) ^[7],^[8].
Protein	BamE (smpA)	BamE (SmpA) is part of the BamCDE subcomplex. ^[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:10806384	EchoLocation:nlpB
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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 MMAYSVQKSR LAKVAGVSLV LLLAACSSDS RYKRQVSGDE AYLEAAPLAE LHAPAGMILP VTSGDYAIPV TNGSGAVGKA LDIRPPAQPL ALVSGARTQF TGDTASLLVE NGRGNTLWPQ VVSVLQAKNY TITQRDDAGQ TLTTDWVQWN RLDEDEQYRG RYQISVKPQG YQQAVTVKLL NLEQAGKPVA DAASMQRYST EMMNVISAGL DKSATDAANA AQNRASTTMD VQSAADDTGL PMLVVRGPFN VVWQRLPAAL EKVGMKVTDS TRSQGNMAVT YKPLSDSDWQ ELGASDPGLA SGDYKLQVGD LDNRSSLQFI DPKGHTLTQS QNDALVAVFQ AAFSK
Length	345
Mol. Wt	36.973 kDa
pI	4.4 (calculated)
Extinction coefficient	43,890 - 44,015 (calc based on 11 Y, 5 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	1-24	UniProt Manual:Signal Peptides	UniProt:P0A903
Domain	40..343	PF06804 NlpB/DapX lipoprotein		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=bamC 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.

</protect>

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:90111442	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946954	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008161	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A903	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10658	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10658	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946954	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000651	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0652	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 MG1655	2653	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	1103	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	1379	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

Cellular Levels

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Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MC4100	8.68E+02	molecules/cell	Medium: combined data from rich and minimal media	37
Protein	E. coli K-12 MC4100	8.68E+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	2653	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	1103	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	1379	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)
nlpB
dapA-nlpB
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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_000913:2596867..2596907 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:b2477 (EcoliWiki Page)	NCBI GEO profiles for nlpB
microarray	GenExpDB:b2477 (EcoliWiki Page)	Summary of data for nlpB 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 bamC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10658	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0652	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2477
EcoGene	EcoGene:EG10658	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000651	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008161	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	NLPB	From SHIGELLACYC
E. coli O157	NLPB	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)	PF06804 NlpB/DapX lipoprotein
EcoCyc	EcoCyc:EG10658	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10658	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000651	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0652	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008161	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 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 ^3.6 ^3.7 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 ^4.4 ^4.5 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).
↑ ^7.0 ^7.1 ^7.2 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
↑ ^8.0 ^8.1 ^8.2 ^8.3 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

bamC: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

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 bamC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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