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Expression|

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Standard Name	gabT
Gene Synonym(s)	ECK2656, b2662, JW2637^[1], JW2637
Product Desc.	4-aminobutyrate aminotransferase^[2]^[3]; Component of 4-aminobutyrate transaminase^[2]^[3] 4-aminobutyrate aminotransferase^[4]
Product Synonyms(s)	4-aminobutyrate aminotransferase, PLP-dependent^[1], B2662^[2]^[1], GabT^[2]^[1] , ECK2656, JW2637, b2662
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): gabDTP^[2], csiD-ygaF-gabDTP^[2], csiD
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	gabT
Mnemonic	Gamma-AminoButyrate
Synonyms	ECK2656, b2662, JW2637^[1], JW2637
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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	60.15 minutes	MG1655: 2790757..2792037 <gbrowseImage> name=NC_000913:2790757..2792037 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2687415..2688695 <gbrowseImage> name=NC_012967:2687415..2688695 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2676569..2677849 <gbrowseImage> name=NC_012759:2676569..2677849 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2791391..2792671 <gbrowseImage> name=NC_007779:2791391..2792671 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2882522..2883802 <gbrowseImage> name=NC_010473:2882522..2883802 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	2790757	Edman degradation	PMID:2178550
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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
ΔgabT (Keio:JW2637)	deletion	deletion	PMID:16738554	Shigen
gabT::Tn5KAN-I-SceI (FB20873)	Insertion at nt 538 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20873	contains pKD46
gabT::Tn5KAN-I-SceI (FB20874)	Insertion at nt 538 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20874	does not contain pKD46
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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
JW2637	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAACAGCAATAAAGAGTTAAT Primer 2:CCtTGCTTCGCCTCATCAAAACA
12G12	Kohara Phage	Genobase	PMID:3038334
10H9	Kohara Phage	Genobase	PMID:3038334
pheA18::Tn10	Linked marker	CAG12158 = CGSC7421^[5]	est. P1 cotransduction: 8% ^[6]
srlD3131::Tn10	Linked marker	CAG18642 = CGSC7423^[5]	est. P1 cotransduction: 24% ^[6] Synonyms:zfh-3131::Tn10, zfi-3131::Tn10
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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:EG10361	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10361	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000354	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948067	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0356	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008760	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	GabT
Synonyms	4-aminobutyrate aminotransferase, PLP-dependent^[1], B2662^[2]^[1], GabT^[2]^[1] , ECK2656, JW2637, b2662
Product description	4-aminobutyrate aminotransferase^[2]^[3]; Component of 4-aminobutyrate transaminase^[2]^[3] 4-aminobutyrate aminotransferase^[4]
EC number (for enzymes)	2.6.1.19^[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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0003867	4-aminobutyrate transaminase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004632	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003867	4-aminobutyrate transaminase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.6.1.19	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005814	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
	GO:0047298	(S)-3-amino-2-methylpropionate transaminase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.6.1.22	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 4-aminobutyrate transaminase	could be indirect
Protein	nadE		PMID:16606699	Experiment(s):EBI-1143600
Protein	rstB		PMID:16606699	Experiment(s):EBI-1143600
Protein	metE		PMID:16606699	Experiment(s):EBI-1143600
Protein	yihL		PMID:16606699	Experiment(s):EBI-1143600
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

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 MNSNKELMQR RSQAIPRGVG QIHPIFADRA ENCRVWDVEG REYLDFAGGI AVLNTGHLHP KVVAAVEAQL KKLSHTCFQV LAYEPYLELC EIMNQKVPGD FAKKTLLVTT GSEAVENAVK IARAATKRSG TIAFSGAYHG RTHYTLALTG KVNPYSAGMG LMPGHVYRAL YPCPLHGISE DDAIASIHRI FKNDAAPEDI AAIVIEPVQG EGGFYASSPA FMQRLRALCD EHGIMLIADE VQSGAGRTGT LFAMEQMGVA PDLTTFAKSI AGGFPLAGVT GRAEVMDAVA PGGLGGTYAG NPIACVAALE VLKVFEQENL LQKANDLGQK LKDGLLAIAE KHPEIGDVRG LGAMIAIELF EDGDHNKPDA KLTAEIVARA RDKGLILLSC GPYYNVLRIL VPLTIEDAQI RQGLEIISQC FDEAKQ
Length	426
Mol. Wt	45.775 kDa
pI	5.7 (calculated)
Extinction coefficient	23,380 - 24,380 (calc based on 12 Y, 1 W, and 8 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	26..361	PF00202 Aminotransferase class-III		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=gabT 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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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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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:16130576	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948067	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008760	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P22256	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10361	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10361	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948067	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000354	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0356	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	1.32E+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	E. coli K-12 MG1655	49	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	369	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	16^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)
gabDTP
csiD-ygaF-gabDTP
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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_000913:2790737..2790777 source=MG1655 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

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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:b2662 (EcoliWiki Page)	NCBI GEO profiles for gabT
microarray	GenExpDB:b2662 (EcoliWiki Page)	Summary of data for gabT 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 gabT Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10361	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0356	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2662
EcoGene	EcoGene:EG10361	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000354	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008760	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	ENSANGP00000027287 (score: 1.000; bootstrap: 98%) ENSANGP00000015566 (score: 0.137)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00037892 (score: 1.000; bootstrap: 97%) WBGene00033756 (score: 0.075)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00020139 (score: 1.000; bootstrap: 95%) WBGene00020382 (score: 0.073)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000027717 (score: 1.000; bootstrap: 95%) ENSCAFP00000016665 (score: 0.116) ENSCAFP00000000346 (score: 0.099)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050913-100 (score: 1.000; bootstrap: 98%) ZDB-CDNA-050612-172 (score: 1.000; bootstrap: 98%) ZDB-CDNA-040425-2065 (score: 0.117) ZDB-GENE-040426-1133 (score: 0.117) ZDB-CDNA-051127-18 (score: 0.101) ZDB-GENE-051127-33 (score: 0.101)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0037186 (score: 1.000; bootstrap: 95%) FBgn0036381 (score: 0.115)	From Inparanoid:20070104
Drosophila pseudoobscura	GA10859-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000008293 (score: 1.000; bootstrap: 46%)	From Inparanoid:20070104
Mus musculus	MGI:2146052 (score: 1.000; bootstrap: 99%) MGI:1919010 (score: 0.072)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC10397c (score: 1.000; bootstrap: 55%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000160485 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000164668 (score: 0.102) NEWSINFRUP00000155980 (score: 0.100)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00014411001 (score: 1.000; bootstrap: 99%) GSTENP00019899001 (score: 0.111)	From Inparanoid:20070104
Shigella flexneri	GABT	From SHIGELLACYC
E. coli O157	GABT	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00202 Aminotransferase class-III
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
EcoCyc	EcoCyc:EG10361	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10361	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000354	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0356	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008760	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 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).

gabT:On One Page

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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 gabT Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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