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abrB:On One Page

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Gene Name	abrB (synonyms: ECK0704, b0715, JW5097, ybgN)^[1]
Product(s)	AbrB product^[1]: predicted regulator product, B0715 product, YbgN product
Description	predicted regulator^[2]^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): abrB^[2]
Regulation/Activity
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Gene

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Nomenclature

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Standard name	abrB
Mnemonic
Synonyms	ECK0704, b0715, JW5097, ybgN^[1]
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Notes

Location(s) and DNA Sequence

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Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	16.08 minutes	MG1655: 746992..745946	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 748191..747145	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

16.08 minutes

MG1655: 746992..745946
gbrowse_img.php?coord=744946..747992&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 748191..747145
gbrowse_img.php?coord=746145..749191&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

GBrowse(W3110)

FASTA Dump

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Notes

Sequence Features

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Feature type	Location	Description
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Notes

Alleles and Phenotypes

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Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔabrB (Keio:JW5097)	deletion	deletion			PMID:16738554^[4]	Shigen
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
	Plasmid clone	Shigen	PMID:16769691^[5] Status: Primer 1: Primer 2:
asnB3057::Tn10	Linked marker	CAG18433 = CGSC7349^[6]	est. P1 cotransduction: 13% ^[7] Synonyms:zbf-3057::Tn10 The Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
nadA57::Tn10	Linked marker	CAG12147 = CGSC7351^[6]	est. P1 cotransduction: 26% ^[7]
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G6384
EchoBASE (EcoliWiki Page)	EchoBASE:EB3094
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0715
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C0794
EcoGene (EcoliWiki Page)	EcoGene:EG13310
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:ABRB
ASAP (EcoliWikiPage)	ASAP:ABE-0002435
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Links

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Name	URL	Comments
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Product(s)

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Nomenclature

Standard name	AbrB
Synonyms	predicted regulator^[1], B0715^[2]^[1], YbgN^[2]^[1], AbrB^[2]^[1]
Product description	predicted regulator^[2]^[3]
EC number (for enzymes)
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Notes

Function

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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(s)	Evidence Code	with/from	Aspect	Notes	Status
	GO:0016020	membrane	GO_REF:0000004 GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0397 SP_KW:KW-0472	C	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016021	integral to membrane	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006810	transport				P	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0006355	regulation of transcription, DNA-dependent				P	Seeded from EcoCyc 11.1^[3].	required fields missing
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Interactions

Partner Type	Partner	Notes	References
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Notes

Localization

Compartment	Description	Evidence	Notes
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Structure and Physical Properties

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Physical Properties

Sequence	at EcoCyc MLYRYTKEKI MRERRMPVLQ WGMLCVLSLL LSIGFLAVHL PAALLLGPMI AGIIFSMRGI TLQLPRSAFL AAQAILGCMI AQNLTGSILT TLAVNWPIVL AILLVTLLSS AIVGWLLVRY SSLPGNTGAW GSSPGGAAAM VAMAQDYGAD IRLVAFMQYL RVLFVAGAAV LVTRMMLGDN AEAVNQHIVW FPPVSINLLL TILLAVVAGT VGCLLRLPSG TMLIPMLAGA VLQSGQLITI ELPEWLLAMA YMAIGWRIGL GFDKQILLRA LRPLPQILLS IFALLAICAG MAWGLTRFMH IDFMTAYLAT SPGGLDTVAV IAAGSNADMA LIMAMQTLRL FSILLTGPAI ARFISTYAPK RSA
Mol. Wt	36.88 kDa (calc) ^[2]
pI
Extinction coefficient	55920 - 56420 (calc based on 8 Y, 8 W, and 4 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
Domain	21 - 38	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[9]' />
Domain	43 - 62	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[9]' />
Domain	69 - 91	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[9]' />
Domain	96 - 118	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[9]' />
Domain	159 - 178	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[9]' />
Domain	193 - 215	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[9]' />
Domain	277 - 299	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[9]' />
Domain	332 - 354	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[9]' />
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Click the image to view raw output from TMHMM.

Structure

Structures	No results found.
Models	View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP)
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Structures

No results found.

Models

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G6384-MONOMER
UniProt (EcoliWiki Page)	UniProt:P75747
PFAM (EcoliWiki Page)	PFAM:PF05145
RefSeq (EcoliWiki Page)	RefSeq:NP_415243
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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.

Transcription and Transcriptional Regulation

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Transcription unit(s)
abrB
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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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gbrowse_img.php?coord=746972..747012&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled+flip&width=400&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression

Allele Name	Mutation	Phenotype	Reference
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Expression Studies

Type	Reference	Notes
microarray	GenExpDB:b0715 (EcoliWiki Page)	Summary of data for abrB from multiple microarray studies
microarray	GEO Profiles:b0715 (EcoliWiki Page)	NCBI GEO profiles for abrB
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (746967..747202) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ07; Well:B10^[10]
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Notes

Accessions Related to abrB Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G6384
EchoBASE (EcoliWiki Page)	EchoBASE:EB3094
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b0715
EcoGene (EcoliWiki Page)	EcoGene:EG13310
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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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Organism	Homologs (Statistics)	Comments
Xenopus tropicalis	ENSXETP00000041900 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	ABRB	From SHIGELLACYC
E. coli O157	ABRB	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF05145
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Links

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Name	URL	Comments
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References

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↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 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 ^2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Baba T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008 PubMed EcoliWiki page
↑ Kitagawa M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res 12: 291-9 PubMed EcoliWiki page
↑ ^6.0 ^6.1 CGSC: The Coli Genetics Stock Center
↑ ^7.0 ^7.1 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).
↑ ^8.0 ^8.1 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^9.0 ^9.1 ^9.2 ^9.3 ^9.4 ^9.5 ^9.6 ^9.7 Krogh A et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-80 PubMed EcoliWiki page
↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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Retrieved from "http://ecoliwiki.net/colipedia/index.php/abrB:On_One_Page"

abrB:On One Page

From EcoliWiki

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Expression

Overview

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to abrB Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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