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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	gadA
Gene Synonym(s)	ECK3502, b3517, JW3485, gadS^[1], gadS
Product Desc.	glutamate decarboxylase A subunit^[2]^[3]; Component of glutamate decarboxylase A^[2]^[3]
Product Synonyms(s)	glutamate decarboxylase A, PLP-dependent^[1], B3517^[2]^[1], GadS^[2]^[1], GadA^[2]^[1] , ECK3502, gadS, JW3485, b3517
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): gadAX^[2]
Regulation/Activity
Quick Links
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Notes

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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	gadA
Mnemonic	Glutamic acid decarboxylase
Synonyms	ECK3502, b3517, JW3485, gadS^[1], gadS
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Notes

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	78.98 minutes	MG1655: 3665603..3664203 <gbrowseImage> name=NC_000913:3664203..3665603 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3597071..3595671 <gbrowseImage> name=NC_012967:3595671..3597071 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3552697..3554097 <gbrowseImage> name=NC_012759:3552697..3554097 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3972835..3974235 <gbrowseImage> name=NC_007779:3972835..3974235 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3763348..3761948 <gbrowseImage> name=NC_010473:3761948..3763348 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	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
Coding Start (SO:0000323)	MG1655	3664203	Edman degradation	PMID:1740158 PMID:7764225 PMID:8455549 PMID:10094700
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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
ΔgadA (Keio:JW3485)	deletion	deletion	PMID:16738554	Shigen CGSC10581^[4]
gadA::Tn5KAN-I-SceI (FB21251)	Insertion at nt 989 in Minus orientation		PMID:15262929	E. coli Genome Project:FB21251	does not contain pKD46
gadA::Tn5KAN-I-SceI (FB21252)	Insertion at nt 989 in Minus orientation		PMID:15262929	E. coli Genome Project:FB21252	contains pKD46
ΔgadA772::kan			PMID:16738554	CGSC:101068
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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
JW3485	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGACCAGAAGCTGTTAACGGA Primer 2:CCGGTGTGTTTAAAGCTGTTCTG
9G3	Kohara Phage	Genobase	PMID:3038334
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[4]	est. P1 cotransduction: 1% ^[5] Synonyms:zhf-50::Tn10, zhf-5::Tn10
zic-4901::Tn10	Linked marker	CAG18492 = CGSC7457^[4]	est. P1 cotransduction: % ^[5]
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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:EG50009	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG50009	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002568	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948027	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4302	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011490	Escherichia coli str. K-12 substr. MG1655
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Notes

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	GadA
Synonyms	glutamate decarboxylase A, PLP-dependent^[1], B3517^[2]^[1], GadS^[2]^[1], GadA^[2]^[1] , ECK3502, gadS, JW3485, b3517
Product description	glutamate decarboxylase A subunit^[2]^[3]; Component of glutamate decarboxylase A^[2]^[3]
EC number (for enzymes)	4.1.1.15^[1]
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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.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0004351	glutamate decarboxylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010107	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004351	glutamate decarboxylase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.1.15	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0006536	glutamate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010107	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0019752	carboxylic acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002129	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002129	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010107	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	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 glutamate decarboxylase A	could be indirect
Protein	ssb		PMID:15690043	Experiment(s):EBI-893820
Protein	groL		PMID:16606699	Experiment(s):EBI-1146061
Protein	dnaK		PMID:16606699	Experiment(s):EBI-1146061
Protein	torA		PMID:16606699	Experiment(s):EBI-1146061
Protein	gadB		PMID:16606699	Experiment(s):EBI-1146061, EBI-1139975
Protein	ssb		PMID:19402753	LCMS(ID Probability):99.6
Protein	gadB		PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):25.596239
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Notes

Localization

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Compartment	Description	Evidence	Reference/Source	Notes
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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 MDQKLLTDFR SELLDSRFGA KAISTIAESK RFPLHEMRDD VAFQIINDEL YLDGNARQNL ATFCQTWDDE NVHKLMDLSI NKNWIDKEEY PQSAAIDLRC VNMVADLWHA PAPKNGQAVG TNTIGSSEAC MLGGMAMKWR WRKRMEAAGK PTDKPNLVCG PVQICWHKFA RYWDVELREI PMRPGQLFMD PKRMIEACDE NTIGVVPTFG VTYTGNYEFP QPLHDALDKF QADTGIDIDM HIDAASGGFL APFVAPDIVW DFRLPRVKSI SASGHKFGLA PLGCGWVIWR DEEALPQELV FNVDYLGGQI GTFAINFSRP AGQVIAQYYE FLRLGREGYT KVQNASYQVA AYLADEIAKL GPYEFICTGR PDEGIPAVCF KLKDGEDPGY TLYDLSERLR LRGWQVPAFT LGGEATDIVV MRIMCRRGFE MDFAELLLED YKASLKYLSD HPKLQGIAQQ NSFKHT
Length	466
Mol. Wt	52.686 kDa
pI	5.1 (calculated)
Extinction coefficient	84,340 - 85,590 (calc based on 16 Y, 11 W, and 10 C residues)
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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
Domain	33..383	PF00282 Pyridoxal-dependent decarboxylase conserved domain		PMID:19920124
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<motif_map/>

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

Structures

<beststructure> gene=gadA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
Purification protocol		PMID:8954890
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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:16131389	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948027	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011490	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P69908	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG50009	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG50009	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948027	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002568	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4302	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	Notes	Reference(s)
Protein	E. coli K-12 MC4100	4.98E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	674.735+/-8.282	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.34219+/-0.01093	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.111785714	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	16^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	2691	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	11^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
gadAX
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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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<protect><gbrowseImage> name=NC_000913:3665583..3665623 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

</protect>

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:b3517 (EcoliWiki Page)	NCBI GEO profiles for gadA
microarray	GenExpDB:b3517 (EcoliWiki Page)	Summary of data for gadA 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 gadA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG50009	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4302	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3517
EcoGene	EcoGene:EG50009	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002568	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011490	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
Anopheles gambiae	ENSANGP00000012191 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT2G02010 (score: 0.635) AT3G17760 (score: 1.000; bootstrap: 100%) AT5G17330 (score: 0.603) AT2G02000 (score: 0.593) AT1G65960 (score: 0.260)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000013166 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00038467 (score: 1.000; bootstrap: 100%) WBGene00031909 (score: 0.294) WBGene00042089 (score: 0.092)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00004981 (score: 0.298) WBGene00006418 (score: 1.000; bootstrap: 100%) WBGene00022427 (score: 0.231)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000020786 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000002369 (score: 1.000; bootstrap: 100%) ENSCINP00000011354 (score: 0.173)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231446 (score: 1.000; bootstrap: 100%) DDB0231439 (score: 0.516)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0010591 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA21426-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000007235 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000299297 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000012828 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000010934 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1261415 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q8LLP2 (score: 0.980) Q6ASV4 (score: 1.000; bootstrap: 100%) Q84U04 (score: 0.773) Q6YSB2 (score: 0.684) Q7XV14 (score: 0.668) Q9AQU4 (score: 0.662) Q7XZU7 (score: 0.603) Q7XV18 (score: 0.542) Q9AR41 (score: 0.540) Q5F1L4 (score: 0.330) Q5EXM3 (score: 0.160)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000004500 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000000686 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YMR250W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000131149 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00024535001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000017960 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	GADA	From SHIGELLACYC
E. coli O157	GADA	From ECOO157CYC
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Notes

Families

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

Database	Accession	Notes
Panther (EcoliWiki Page)	PTHR11999:SF1
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
Pfam (EcoliWiki Page)	PF00282 Pyridoxal-dependent decarboxylase conserved domain
EcoCyc	EcoCyc:EG50009	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG50009	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002568	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4302	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011490	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 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 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).

gadA: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

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to gadA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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