Escherichia coli K-12 MG1655
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Working With: Genome: Escherichia coli K-12 MG1655 Version: v3

ABE-0004976 (gadB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0004976 showshow history
Names
gadB JW1488 ECK1487 b1493
Product
glutamate decarboxylase B
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 1570645 1572045 1401 467
Sequence

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View sequence with flanking regions: bases upstream and bases downstream

Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR002129 (IPR002129 Pyridoxal phosphate-dependent decarboxylase) Apr 2008
Automated Process Approved IPR010107 (IPR010107 Glutamate decarboxylase) Apr 2008
Automated Process Approved IPR015424 (IPR015424 Pyridoxal phosphate-dependent transferase) Apr 2008
Automated Process Approved IPR015421 (IPR015421 Pyridoxal phosphate-dependent transferase, major domain) Apr 2008
Automated Process Approved PF00282 (PF00282 Pyridoxal-dependent decarboxylase conserved domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0009063 cellular amino acid catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0006536 glutamate metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010107
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO biological process GO:0019752 carboxylic acid metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002129
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0006520 cellular amino acid metabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO cellular component GO:0030288 outer membrane-bounded periplasmic space GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Uncurated GO cellular component GO:0005737 cytoplasm Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR015421
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0030170 pyridoxal phosphate binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010107
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0004351 glutamate decarboxylase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010107
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016831 carboxy-lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002129
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name gadB Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK1487 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW1488 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1493 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product glutamate decarboxylase B Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Person Approved alternate product name glutamate decarboxylase isozyme Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Person Uncurated alternate product name glutamate decarboxylase, PLP-dependent, isozyme beta Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family IPR015421 Pyridoxal phosphate-dependent transferase, major domain Protein Sequence Similarity - InterPro Domain: IPR015421
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR015424 Pyridoxal phosphate-dependent transferase Protein Sequence Similarity - InterPro Domain: IPR015424
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR002129 Pyridoxal phosphate-dependent decarboxylase Protein Sequence Similarity - InterPro Domain: IPR002129
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR010107 Glutamate decarboxylase Protein Sequence Similarity - InterPro Domain: IPR010107
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF00282 Pyridoxal-dependent decarboxylase conserved domain Protein Sequence Similarity - PFAM Model Name: PF00282
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 4.1.1.15 Published Annotation - Swiss-Prot Accession Number: P69910 Feb 2006
Automated Process Uncurated EC number 4.1.1.- Published Annotation - Database Name: EC2GO: GO:0016831
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated MultiFun 1.7.13 (metabolism; central intermediary metabolism; amino acid conversion) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 7.1 (location of gene products; cytoplasm) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.1.3 (metabolism; carbon utilization; amino acids) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Automated Process Approved codon start 1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0004976 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG11490 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P69910 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:946058 Published Annotation - Entrez Gene Database ID: 946058
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1787769 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P69910 Published Annotation - Swiss-Prot Accession Number: P69910 Jan 2006
Person Approved function enzyme; Central intermediary metabolism: Pool, multipurpose conversions Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Uncurated molecular interaction Interacts with the product of dnaK ASAP:52:(interacting residues not known); by MALDI-TOF Experimental - PubMed ID: 15690043
Reference: Escherichia coli K-12 W3110 		Mar 2005
Person Uncurated molecular interaction Interacts with the product of gadA ASAP:11490:(interacting residues not known); by MALDI-TOF Experimental - PubMed ID: 15690043
Reference: Escherichia coli K-12 W3110 		Mar 2005
Automated Process Approved note glutamate decarboxylase isozyme; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009063 - cellular amino acid catabolic process; GO_process: GO:0006520 - cellular amino acid metabolic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74566.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated regulation expression regulated by acetate; expression is induced by acetate Experimental - PubMed ID: 11244055
Reference: Escherichia coli ATCC43888 (EHEC) 		Nov 2005
Person Uncurated regulation expression regulated by dsrA; expression is increased in strain overexpressing dsrA Experimental - PubMed ID: 15342588
Reference: Escherichia coli K-12 M182 		Oct 2005
Automated Process Uncurated subcellular localization Periplasmic Predicted by PSORTb - PSORTb Final_Score: 9.64
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Uncurated subsystem component of in silico model iAF1260 Experimental - PubMed ID: 17593909
Reference: Escherichia coli K-12 MG1655 		Jan 2009
Person Uncurated subsystem component of in silico model iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655 		Feb 2009
Person Uncurated subsystem component of in silico model iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655 		Mar 2009
Automated Process Approved transl table 11 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Gene Ontology
Automated Process Approved GO biological process GO:0006536 glutamate metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010107
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO biological process GO:0019752 carboxylic acid metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002129
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0006520 cellular amino acid metabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO biological process GO:0009063 cellular amino acid catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO cellular component GO:0030288 outer membrane-bounded periplasmic space GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Uncurated GO cellular component GO:0005737 cytoplasm Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0016831 carboxy-lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002129
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0030170 pyridoxal phosphate binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010107
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0004351 glutamate decarboxylase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR010107
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR015421
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0005590 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002287 gadB CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002668 gadB CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0006236 gadB CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0000068 gadB CDS
Paralog
Person Approved Go view Escherichia coli K-12 MG1655 ABE-0011490 gadA CDS
Ortholog
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001501 CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0001459 gadA CDS
Automated Process Uncurated Go view Escherichia coli ATCC 11775 [T] AMC-0000025 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007914 CDS
Person Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005059 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078038 gadB CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001666 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0001923 CDS
Automated Process Uncurated Go view Escherichia coli E2348/69 (EPEC) BCI-0001733 gadB CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006121 gadB CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0006946 gadA CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0025989 gadB CDS
Automated Process Uncurated Go view Escherichia coli F11 (UPEC) ADQ-0007959 gadB CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006254 gadB CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001402 gadB CDS
Automated Process Approved Go view Escherichia coli K-12 W3110 ADY-0001534 gadB CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0001724 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0175859 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001612 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001679 gadA CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132068 gadB CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001714 gadB CDS
Automated Process Approved Go view Shigella boydii 227 ADV-0001726 gadB CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0007165 gadB CDS
Automated Process Approved Go view Shigella dysenteriae 197 ADU-0001859 gadB CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0072962 gadB CDS
Person Approved Go view Shigella flexneri 301 ABT-0088038 gadB CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0001845 gadB CDS
Automated Process Approved Go view Shigella sonnei 046 ADD-0001775 gadB CDS
Molecular Interactions to toptop
Author Approval Feature Name Technique Evidence Comment Annotated
Person Approved ABE-0004976 gadB lambda repressor assay Doodle - bnumber: b1493 Oct 2003
Experimental to toptop
SelectSetNameSetDetailsNotes
stringent responsetranscriptional profile of the stringent responseNone
Recombinant heat-shock dataexpression data for recombinant strain under heat shockThese data are from the Harcum laboratory. (Jeremy Glasner)
Suppressor tRNA expressionexperiment comparing transcript levels in cells with and without suppressor tRNA expressionThese data were reported in the paper: Herring and Blattner. 2004. Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR. J. Bacteriol. 186(20):6714-20. Link to Abstract (Jeremy Glasner)
Recombinant E. coli expressionexperiment comparing expression of wild-type E. coli with the same strain harboring a plasmid that expresses protein when induced with IPTG These data were reported in the paper: F. T. Haddadin, S. W. Harcum (2005) Transcriptome profiles for high-cell-density recombinant and wild-type Escherichia coli, Biotechnology and Bioengineering, 90:127-153. Link to Abstract (Jeremy Glasner)
Aerobic shiftAerobic shiftThese data were reported in the paper: Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. 2004. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004 May 6;429(6987):92-6. Link to Abstract (Jeremy Glasner)
CalibratorCalibrated microarray experiments (50 hybridizations)This data was used in the paper: Allen et al., J. Bacteriol. 185(21):6392-9 (Jeremy Glasner)
AffyData1Affymetrix Experiments (data from 41 chip hybridizations)This data was used in the paper: Allen et al., J. Bacteriol. 185(21):6392-9 (Jeremy Glasner)
Strains to toptop

Strains with mutations in this feature.

Strain NameStrain TypeStrain InformationStrain RequestFeatureIDNameMutation DetailsExperiments Using StrainSubmitter
FB20337mutantTn5 InsertionRequest the StrainABE-0004976gadBgadB::Tn5KAN-2 at position 820 in Minus orientation ,- pKD460Blattner Laboratory
FB20338mutantTn5 InsertionRequest the StrainABE-0004976gadBgadB::Tn5KAN-2 at position 820 in Minus orientation ,+ pKD460Blattner Laboratory
Context Table to toptop

Listed below are features that lie nearby this feature. Features encoded in multiple intervals may appear more than once in the table. Features that span the origin will have a left endpoint greater than the right endpoint.

Features overlapping the region 1565645 to 1577045
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0004963dosPCDScomplement15633341565733Downstream
ABE-0004965dosCCDScomplement15657581567140Downstream
ABE-0285781yddYCDScomplement15671781567219Downstream
ABE-0004970digHCDScomplement15675041568823Downstream
ABE-0004973gadCCDScomplement15689541570489Downstream
ABE-0004976gadBCDScomplement15706451572045Matches
ABE-0004979pqqLCDScomplement15724071575202Upstream
ABE-0004982yddBCDScomplement15752471577619Upstream
Release Notes to toptop
All MG1655 annotations and sequence data are publicly available, and investigators can use these data in publications without contacting the genome curators. This version of the sequence was the source of GenBank record U00096.3. Ongoing annotation updates to that GenBank record are being generated from a collaboration that includes ASAP, EcoGene, the Coli Genetic Stock Center, EcoliHub, EcoCyc, RegulonDB and UniProtKB/Swiss-Prot.