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alaS:On One Page

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Gene Name	alaS (synonyms: ECK2692, b2697, JW2667, act, ala-act, lovB, ala-a)^[1]
Product(s)	AlaS product^[1]: alanyl-tRNA synthetase product, Act product, B2697 product, LovB product, ala-act product
Description	alanyl-tRNA synthetase^[2] AlaS transcriptional repressor; alanyl-tRNA synthetase^[3] Component of alanyl-tRNA synthetase^[2]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): alaS^[2]
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	alaS
Mnemonic
Synonyms	ECK2692, b2697, JW2667, act, ala-act, lovB, ala-a^[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	60.72 minutes	MG1655: 2820033..2817403	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 2820667..2818037	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

60.72 minutes

MG1655: 2820033..2817403
gbrowse_img.php?coord=2816403..2821033&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 2820667..2818037
gbrowse_img.php?coord=2817037..2821667&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: Description	Reference	Availability	Comments
ΔalaS (Keio:JW2667)	deletion	deletion		PMID:16738554^[4]	Shigen CGSC10104^[5]	Strain contains duplication detected by PCRPMID:18652654^[6]
alaS5(ts)			temperature sensitive		CGSC:9418
alaS4(ts)			temperature sensitive		CGSC:9420
alaS6(ts)			temperature sensitive		CGSC:9435
alaS3(ts)			temperature sensitive		CGSC:27060
ΔalaS772::kan				PMID:16738554^[4]	CGSC:99960
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW2667	Plasmid clone	Shigen	PMID:16769691^[7] Status:Clone OK Primer 1:GCCAGCAAGAGCACCGCTGAGAT Primer 2:CCTTGCAATTTCGCGCTGACCCA
pheA18::Tn10	Linked marker	CAG12158 = CGSC7421^[5]	est. P1 cotransduction: % ^[8]
srlD3131::Tn10	Linked marker	CAG18642 = CGSC7423^[5]	est. P1 cotransduction: 76% ^[8] Synonyms:zfh-3131::Tn10, zfi-3131::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG10034
EchoBASE (EcoliWiki Page)	EchoBASE:EB0033
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2697
EcoGene (EcoliWiki Page)	EcoGene:EG10034
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:ALAS
CGSC (EcoliWiki Page)	CGSC:1039
ASAP (EcoliWikiPage)	ASAP:ABE-0008869
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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	AlaS
Synonyms	alanyl-tRNA synthetase^[1], Act^[2]^[1], B2697^[2]^[1], LovB^[2]^[1], AlaS^[2]^[1], ala-act^[2]^[1]
Product description	alanyl-tRNA synthetase^[2]; AlaS transcriptional repressor; alanyl-tRNA synthetase^[3]; Component of ; alanyl-tRNA synthetase^[2]; AlaS transcriptional repressor; alanyl-tRNA synthetase^[3]
EC number (for enzymes)	6.1.1.7^[1]
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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:0005524	ATP binding	GO_REF:0000002 GO_REF:0000004 GO_REF:0000020	IEA: Inferred from Electronic Annotation	InterPro:IPR002318 SP_KW:KW-0067 HAMAP:MF_00036	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0004813	alanine-tRNA ligase activity	GO_REF:0000002 GO_REF:0000003 GO_REF:0000020	IEA: Inferred from Electronic Annotation	InterPro:IPR002318 EC:6.1.1.7 HAMAP:MF_00036	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0004812	aminoacyl-tRNA ligase activity	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0030	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0003676	nucleic acid binding	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003156	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0000166	nucleotide binding	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR002318 SP_KW:KW-0547	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0046872	metal ion binding	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0005737	cytoplasm	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR002318 SP_KW:KW-0963	C	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0006412	translation	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR002318 SP_KW:KW-0648	P	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0006419	alanyl-tRNA aminoacylation	GO_REF:0000002 GO_REF:0000020	IEA: Inferred from Electronic Annotation	InterPro:IPR002318 HAMAP:MF_00036	P	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0008270	zinc ion binding	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0016874	ligase activity	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0436	F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0004813	alanine-tRNA ligase activity	PMID:7005211^[10]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0005624	membrane fraction	PMID:16858726^[11]	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0006419	alanyl-tRNA aminoacylation	PMID:7005211^[10]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0008270	zinc ion binding	PMID:1712632^[12]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0016566	specific transcriptional repressor activity	PMID:6264314^[13]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0045892	negative regulation of transcription, DNA-dependent	PMID:6264314^[13]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc 12.5 ^[9]	complete
	GO:0006418	tRNA aminoacylation for protein translation				P	Seeded from Riley et al 2006 ^[1].	required fields missing
	GO:0045892	negative regulation of transcription, DNA-dependent	PMID:6264314^[13]	IDA		P	Seeded from EcoCyc 11.1^[3].	required fields missing
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Interactions

Partner Type	Partner	Notes	References
Protein	Subunits of alanyl-tRNA synthetase	could be indirect
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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 MSKSTAEIRQ AFLDFFHSKG HQVVASSSLV PHNDPTLLFT NAGMNQFKDV FLGLDKRNYS RATTSQRCVR AGGKHNDLEN VGYTARHHTF FEMLGNFSFG DYFKHDAIQF AWELLTSEKW FALPKERLWV TVYESDDEAY EIWEKEVGIP RERIIRIGDN KGAPYASDNF WQMGDTGPCG PCTEIFYDHG DHIWGGPPGS PEEDGDRYIE IWNIVFMQFN RQADGTMEPL PKPSVDTGMG LERIAAVLQH VNSNYDIDLF RTLIQAVAKV TGATDLSNKS LRVIADHIRS CAFLIADGVM PSNENRGYVL RRIIRRAVRH GNMLGAKETF FYKLVGPLID VMGSAGEDLK RQQAQVEQVL KTEEEQFART LERGLALLDE ELAKLSGDTL DGETAFRLYD TYGFPVDLTA DVCRERNIKV DEAGFEAAME EQRRRAREAS GFGADYNAMI RVDSASEFKG YDHLELNGKV TALFVDGKAV DAINAGQEAV VVLDQTPFYA ESGGQVGDKG ELKGANFSFA VEDTQKYGQA IGHIGKLAAG SLKVGDAVQA DVDEARRARI RLNHSATHLM HAALRQVLGT HVSQKGSLVN DKVLRFDFSH NEAMKPEEIR AVEDLVNTQI RRNLPIETNI MDLEAAKAKG AMALFGEKYD ERVRVLSMGD FSTELCGGTH ASRTGDIGLF RIISESGTAA GVRRIEAVTG EGAIATVHAD SDRLSEVAHL LKGDSNNLAD KVRSVLERTR QLEKELQQLK EQAAAQESAN LSSKAIDVNG VKLLVSELSG VEPKMLRTMV DDLKNQLGST IIVLATVVEG KVSLIAGVSK DVTDRVKAGE LIGMVAQQVG GKGGGRPDMA QAGGTDAAAL PAALASVKGW VSAKLQ
Mol. Wt	96.03 kDa (calc) ^[2]
pI
Extinction coefficient	70820 - 71570 (calc based on 18 Y, 8 W, and 6 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
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Structure

Structures	Representative homolog: 1V7O\|A (Pyrococcus horikoshii) 9-132 of 876 residues (E-value: 1.2e-07) (Percent Identity: 31.75) 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:
1V7O|A (Pyrococcus horikoshii)
9-132 of 876 residues (E-value: 1.2e-07) (Percent Identity: 31.75)
View all other structures.

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:ALAS-MONOMER
SwissModel (EcoliWiki Page)	SwissModel:P00957
UniProt (EcoliWiki Page)	UniProt:P00957
PFAM (EcoliWiki Page)	PFAM:PF01411
RefSeq (EcoliWiki Page)	RefSeq:NP_417177
ModBase (EcoliWiki Page)	ModBase:P00957
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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)
alaS
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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=2820013..2820053&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:b2697 (EcoliWiki Page)	Summary of data for alaS from multiple microarray studies
microarray	GEO Profiles:b2697 (EcoliWiki Page)	NCBI GEO profiles for alaS
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (2819936..2820163) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ10; Well:B11^[14]
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Notes

Accessions Related to alaS Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG10034
EchoBASE (EcoliWiki Page)	EchoBASE:EB0033
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b2697
EcoGene (EcoliWiki Page)	EcoGene:EG10034
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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
Anopheles gambiae	ENSANGP00000013174 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000003987 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G22800 (score: 1.000; bootstrap: 89%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000026393 (score: 1.000; bootstrap: 100%) ENSBTAP00000018232 (score: 0.129)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00033089 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00000197 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000029841 (score: 1.000; bootstrap: 100%) ENSCAFP00000002926 (score: 0.166)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000015190 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-030131-3663 (score: 1.000; bootstrap: 100%) ZDB-GENE-050913-159 (score: 0.320)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0214894 (score: 1.000; bootstrap: 49%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0027094 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA12250-PA (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000003043 (score: 1.000; bootstrap: 100%) ENSGALP00000016505 (score: 0.233)	From Inparanoid:20070104
Homo sapiens	ENSP00000261772 (score: 1.000; bootstrap: 100%) ENSP00000244571 (score: 0.177)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000018898 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000018141 (score: 1.000; bootstrap: 100%) ENSMODP00000023615 (score: 0.163)	From Inparanoid:20070104
Mus musculus	MGI:2384560 (score: 1.000; bootstrap: 100%) MGI:2681839 (score: 0.179)	From Inparanoid:20070104
Oryza gramene	Q94GG8 (score: 1.000; bootstrap: 74%) Q7XGA3 (score: 1.000; bootstrap: 77%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000014170 (score: 1.000; bootstrap: 100%) ENSPTRP00000031143 (score: 0.176)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000025051 (score: 1.000; bootstrap: 100%) ENSRNOP00000037568 (score: 0.174)	From Inparanoid:20070104
Saccharomyces cerevisiae	YOR335C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC23C119 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000160311 (score: 1.000; bootstrap: 74%) NEWSINFRUP00000144283 (score: 0.092)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00006546001 (score: 1.000; bootstrap: 100%) GSTENP00008928001 (score: 0.052)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000016680 (score: 1.000; bootstrap: 55%)	From Inparanoid:20070104
Shigella flexneri	ALAS	From SHIGELLACYC
E. coli O157	ALAS	From ECOO157CYC
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Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF01411
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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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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
↑ ^4.0 ^4.1 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
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ Plaimas K et al. (2008) Machine learning based analyses on metabolic networks supports high-throughput knockout screens. BMC Syst Biol 2: 67 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
↑ ^8.0 ^8.1 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).
↑ ^9.00 ^9.01 ^9.02 ^9.03 ^9.04 ^9.05 ^9.06 ^9.07 ^9.08 ^9.09 ^9.10 ^9.11 ^9.12 ^9.13 ^9.14 ^9.15 ^9.16 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^10.0 ^10.1 Putney SD et al. (1981) Purification and properties of alanine tRNA synthetase from Escherichia coli A tetramer of identical subunits. J Biol Chem 256: 198-204 PubMed EcoliWiki page
↑ Lasserre JP et al. (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27: 3306-21 PubMed EcoliWiki page
↑ Miller WT et al. (1991) Evidence for a "cysteine-histidine box" metal-binding site in an Escherichia coli aminoacyl-tRNA synthetase. Biochemistry 30: 6970-6 PubMed EcoliWiki page
↑ ^13.0 ^13.1 ^13.2 Putney SD & Schimmel P (1981) An aminoacyl tRNA synthetase binds to a specific DNA sequence and regulates its gene transcription. Nature 291: 632-5 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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alaS:On One Page

From EcoliWiki

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

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Alleles and Phenotypes

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Genetic Resources

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Accessions in Other Databases

Notes

Links

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Product(s)

Nomenclature

Notes

Function

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Localization

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Structure and Physical Properties

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Gene Product Resources

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Accessions in Other Databases

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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 alaS Expression

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Evolution

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