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alsR:On One Page

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Gene Name	alsR (synonyms: rpiR, ECK4082, b4089, JW4050, yjcY)^[1]^[2]
Product(s)	RpiR product, RpiR product^[1]^[2]: B4089 product, AlsR product, YjcY product
Description	AlsR transcriptional repressor^[2]^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): alsRBACE^[2]
Regulation/Activity
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Gene

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Nomenclature

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Standard name	alsR
Mnemonic
Synonyms	rpiR, ECK4082, b4089, JW4050, yjcY^[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	92.9 minutes, 92.9 minutes	MG1655: 4311014..4310124	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 4317669..4316779	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

92.9 minutes, 92.9 minutes

MG1655: 4311014..4310124
gbrowse_img.php?coord=4309124..4312014&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 4317669..4316779
gbrowse_img.php?coord=4315779..4318669&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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Alleles and Phenotypes

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Allele	Reference	Availability
rpiR2		CGSC:73760
ΔrpiR784::kan	PMID:16738554^[4]	CGSC:102772
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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:G7821
EchoBASE (EcoliWiki Page)	EchoBASE:EB2353
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4089
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C5095
EcoGene (EcoliWiki Page)	EcoGene:EG12459
ASAP (EcoliWikiPage)	ASAP:ABE-0013400
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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	RpiR product
Synonyms	AlsR product^[2]^[1], B4089 product^[2]^[1], YjcY product^[2]^[1]
Product description	Txnl repressor for als operon and rpiB^[6]
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:0003700	transcription factor activity	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000281	F	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0005529	sugar binding	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001347	F	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0003677	DNA binding	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0005975	carbohydrate metabolic process	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001347	P	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0006350	transcription	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0006355	regulation of transcription, DNA-dependent	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR000281 SP_KW:KW-0805	P	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0006350	transcription	PMID:8576032^[8]	IEP: Inferred from Expression Pattern		P	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0006350	transcription	PMID:9401019^[9]	IEP: Inferred from Expression Pattern		P	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0016564	transcription repressor activity	PMID:8576032^[8]	IEP: Inferred from Expression Pattern		F	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0016564	transcription repressor activity	PMID:9401019^[9]	IEP: Inferred from Expression Pattern		F	Seeded from EcoCyc 12.5 ^[7]	complete
	GO:0009052	pentose-phosphate shunt, non-oxidative branch				P	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0005737	cytoplasm				C	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0016052	carbohydrate catabolic process				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 MASSIQGQEN VMSQSEFDSA LPNGIGLAPY LRMKQEGMTE NESRIVEWLL KPGNLSCAPA IKDVAEALAV SEAMIVKVSK LLGFSGFRNL RSALEDYFSQ SEQVLPSELA FDEAPQDVVN KVFNITLRTI MEGQSIVNVD EIHRAARFFY QARQRDLYGA GGSNAICADV QHKFLRIGVR CQAYPDAHIM MMSASLLQEG DVVLVVTHSG RTSDVKAAVE LAKKNGAKII CITHSYHSPI AKLADYIICS PAPETPLLGR NASARILQLT LLDAFFVSVA QLNIEQANIN MQKTGAIVDF FSPGALK
Mol. Wt	32.36 kDa (calc) ^[2]
pI
Extinction coefficient	15930 - 16555 (calc based on 7 Y, 1 W, and 5 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
Domain	14 - 90	HTH rpiR-type	UniProt:P0ACS7
Domain	135 - 296	SIS	UniProt:P0ACS7
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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

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:MONOMER0-2482
PFAM (EcoliWiki Page)	PFAM:PF01418
UniProt (EcoliWiki Page)	UniProt:P0ACS7
RefSeq (EcoliWiki Page)	RefSeq:NP_418513
ModBase (EcoliWiki Page)	ModBase:P0ACS7
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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)
alsRBACE
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Figure courtesy of RegulonDB

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

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=4310994..4311034&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:b4089 (EcoliWiki Page)	Summary of data for alsR from multiple microarray studies
microarray	GEO Profiles:b4089 (EcoliWiki Page)	NCBI GEO profiles for alsR
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (4310535..4310946) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ02; Well:B3^[10]
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Notes

Accessions Related to alsR Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G7821
EchoBASE (EcoliWiki Page)	EchoBASE:EB2353
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b4089
EcoGene (EcoliWiki Page)	EcoGene:EG12459
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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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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF01418
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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 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 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
↑
↑ ^7.0 ^7.1 ^7.2 ^7.3 ^7.4 ^7.5 ^7.6 ^7.7 ^7.8 ^7.9 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^8.0 ^8.1 Sorensen KI & Hove-Jensen B (1996) Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression. J Bacteriol 178: 1003-11 PubMed EcoliWiki page
↑ ^9.0 ^9.1 Kim C et al. (1997) The D-allose operon of Escherichia coli K-12. J Bacteriol 179: 7631-7 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/alsR:On_One_Page"

alsR:On One Page

From EcoliWiki

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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 alsR Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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