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allS:On One Page

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Gene Name	allS (synonyms: ybbS, ECK0497, b0504, JW0492, glxA1)^[1]^[2]
Product(s)	YbbS product^[1]: DNA-binding transcriptional activator of the allD operon product, B0504 product, AllS product, GlxA1 product
Description	DNA-binding transcriptional regulator^[2] AllS transcriptional activator^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): allS^[2]
Regulation/Activity
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Gene

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Nomenclature

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Standard name	allS
Mnemonic
Synonyms	ybbS, ECK0497, b0504, JW0492, glxA1^[1]^[2]
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Notes

Location(s) and DNA Sequence

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Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	11.43 minutes	MG1655: 531445..530519	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 531445..530519	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

11.43 minutes

MG1655: 531445..530519
gbrowse_img.php?coord=529519..532445&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 531445..530519
gbrowse_img.php?coord=529519..532445&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
ΔallS787::kan					PMID:16738554^[4]	CGSC:106126
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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:
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Resource

Resource Type

Source

Notes/Reference

Plasmid clone

Shigen

PMID:16769691^[5]

Status:

Primer 1:

Primer 2:

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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G6274
EchoBASE (EcoliWiki Page)	EchoBASE:EB3053
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0504
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C0619
EcoGene (EcoliWiki Page)	EcoGene:EG13267
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YBBS
ASAP (EcoliWikiPage)	ASAP:ABE-0001742
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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	YbbS
Synonyms	DNA-binding transcriptional activator of the allD operon^[1], B0504^[2]^[1], AllS^[2]^[1], YbbS ^[2]^[1], GlxA1^[2]^[1]
Product description	DNA-binding transcriptional regulator^[2]; AllS transcriptional activator^[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:0003677	DNA binding	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc 12.5 ^[6]	complete
	GO:0003700	transcription factor activity	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000847	F	Seeded from EcoCyc 12.5 ^[6]	complete
	GO:0016563	transcription activator activity	PMID:12460564^[7]	IMP: Inferred from Mutant Phenotype		F	Seeded from EcoCyc 12.5 ^[6]	complete
	GO:0045893	positive regulation of transcription, DNA-dependent	PMID:12460564^[7]	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc 12.5 ^[6]	complete
	GO:0016563	transcription activator activity	PMID:12460564^[7]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc 11.1^[3].	complete
	GO:0045893	positive regulation of transcription, DNA-dependent	PMID:12460564^[7]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc 11.1^[3].	complete
	GO:0006350	transcription				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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Notes

Structure and Physical Properties

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Physical Properties

Sequence	at EcoCyc MFDPETLRTF IAVAETGSFS KAAERLCKTT ATISYRIKLL EENTGVALFF RTTRSVTLTA AGEHLLSQAR DWLSWLESMP SELQQVNDGV ERQVNIVINN LLYNPQAVAQ LLAWLNERYP FTQFHISRQI YMGVWDSLLY EGFSLAIGVT GTEALANTFS LDPLGSVQWR FVMAADHPLA NVEEPLTEAQ LRRFPAVNIE DSARTLTKRV AWRLPGQKEI IVPDMETKIA AHLAGVGIGF LPKSLCQSMI DNQQLVSRVI PTMRPPSPLS LAWRKFGSGK AVEDIVTLFT QRRPEISGFL EIFGNPRS
Mol. Wt	34.51 kDa (calc) ^[2]
pI
Extinction coefficient	45950 - 46200 (calc based on 5 Y, 7 W, and 2 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
Domain	2 - 59	HTH lysR-type	UniProt:P0ACR0
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Structure

Structures	Representative homolog: 1IZ1\|A (Cupriavidus necator) 6-69 of 308 residues (E-value: 4.1e-06) (Percent Identity: 43.75) View all other structures.
Models	View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP)
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Structures

Representative homolog:
1IZ1|A (Cupriavidus necator)
6-69 of 308 residues (E-value: 4.1e-06) (Percent Identity: 43.75)
View all other structures.

Models

View models at:

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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:G6274-MONOMER
UniProt (EcoliWiki Page)	UniProt:P0ACR0
RefSeq (EcoliWiki Page)	RefSeq:NP_415037
ModBase (EcoliWiki Page)	ModBase:P0ACR0
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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)
allS
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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=531425..531465&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:b0504 (EcoliWiki Page)	Summary of data for allS from multiple microarray studies
microarray	GEO Profiles:b0504 (EcoliWiki Page)	NCBI GEO profiles for allS
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to allS Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G6274
EchoBASE (EcoliWiki Page)	EchoBASE:EB3053
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b0504
EcoGene (EcoliWiki Page)	EcoGene:EG13267
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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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Organism	Homologs (Statistics)	Comments
Shigella flexneri	YBBS	From SHIGELLACYC
E. coli O157	YBBS	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Organism	Homologs (Statistics)	Comments
Shigella flexneri	YBBS	From SHIGELLACYC
E. coli O157	YBBS	From ECOO157CYC
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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 ^2.6 ^2.7 ^2.8 ^2.9 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 ^3.4 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 ^6.2 ^6.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^7.0 ^7.1 ^7.2 ^7.3 Rintoul MR et al. (2002) Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS. J Mol Biol 324: 599-610 PubMed EcoliWiki page

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

allS: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 allS Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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