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

ABE-0010284 (garD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0010284 showshow history
Names
garD JW3097 ECK3116 yhaG b3128
Product
galactarate dehydratase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3275282 3276853 1572 524
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR007392 (IPR007392 D-galactarate/Altronate dehydratase, C-terminal) Apr 2008
Automated Process Approved IPR013974 (IPR013974 SAF domain) Apr 2008
Automated Process Approved IPR010916 (IPR010916 TonB box, conserved site) Apr 2008
Automated Process Approved IPR017654 (IPR017654 Galactarate dehydratase GarD-like) Jul 2018
Automated Process Approved PF04295 (PF04295 D-galactarate dehydratase / Altronate hydrolase, C terminus) Jul 2018
Automated Process Approved PF08666 (PF08666 SAF domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO biological process GO:0046392 galactarate catabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017654
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Approved GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Uncurated GO molecular function GO:0008867 galactarate dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017654
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0016829 lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR007392
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016836 hydro-lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR007392
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name garD Published Annotation - Database Name: GenProtEC Jul 2002
Person Approved synonym JW3097 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK3116 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym yhaG Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved locus tag b3128 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product galactarate dehydratase Experimental - PubMed ID: 31811683
Reference: Escherichia coli K-12 		Feb 2021
Person Approved alternate product name (D)-galactarate dehydrogenase Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family PF04295 D-galactarate dehydratase / Altronate hydrolase, C terminus Protein Sequence Similarity - PFAM Model Name: PF04295
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR007392 D-galactarate/Altronate dehydratase, C-terminal Protein Sequence Similarity - InterPro Domain: IPR007392
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR017654 Galactarate dehydratase GarD-like Protein Sequence Similarity - InterPro Domain: IPR017654
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR013974 SAF domain Protein Sequence Similarity - InterPro Domain: IPR013974
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF08666 SAF domain Protein Sequence Similarity - PFAM Model Name: PF08666
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR010916 TonB box, conserved site Protein Sequence Similarity - InterPro Domain: IPR010916
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Automated Process Uncurated EC number 4.-.-.- Published Annotation - Database Name: EC2GO: GO:0016829
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Approved EC number 4.2.1.42 Published Annotation - Swiss-Prot Accession Number: P39829 Feb 2006
Person Approved MultiFun 1.1.1 (metabolism; carbon utilization; carbon compounds) 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-0010284 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P39829 Published Annotation - Swiss-Prot Accession Number: P39829 Jan 2005
Automated Process Approved db xref GeneID:947641 Published Annotation - Entrez Gene Database ID: 947641
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1789516 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P39829 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG12522 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved function 1.1.1 metabolism; carbon utilization; carbon compounds Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved note GO_process: GO:0016052 - carbohydrate catabolic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC76162.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved subcellular localization Cytoplasmic Predicted by PSORTb - PSORTb Final_Score: 8.96
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Approved 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 iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655 		Mar 2009
Person Approved subsystem component of in silico model iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655 		Feb 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 Uncurated GO biological process GO:0046392 galactarate catabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017654
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Approved GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Uncurated GO molecular function GO:0008867 galactarate dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017654
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0016829 lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR007392
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016836 hydro-lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR007392
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-0002339 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002741 garD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002625 garD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004268 garD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002527 garD CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0000580 garD CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0000625 garD CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0004780 garD CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0005336 CDS
Person Approved Go view Dickeya dadantii 3937 ABF-0014845 garD CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0003423 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0004493 garD CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0002311 garD CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0008061 garD CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0003248 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0007979 garD CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0003199 garD CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001059 garD CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006002 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0007289 garD CDS
Person Uncurated Go view Escherichia coli B7A (ETEC) ADK-0009723 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0080055 garD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003598 garD CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0004222 garD CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005490 garD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0005674 garD CDS
Automated Process Uncurated Go view Escherichia coli E2348/69 (EPEC) BCI-0003638 garD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0008040 garD CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0002804 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007782 garD CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006298 garD CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007829 garD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0007401 garD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0009278 garD CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0005886 garD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0007083 garD CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0006064 garD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0008968 garD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0007661 garD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005470 garD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0006315 garD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0028153 garD CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0007264 garD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0008003 garD CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002918 garD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003196 garD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003774 garD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003697 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003402 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003475 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003423 garD CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0134065 garD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0005972 CDS
Automated Process Uncurated Go view Escherichia coli UTI89 (UPEC) AEA-0003568 garD CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0003587 garD CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0001854 garD CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0005335 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0002378 CDS
Automated Process Uncurated Go view Pantoea agglomerans SL1-M5 ALY-0002599 CDS
Automated Process Uncurated Go view Pantoea ananatis AJ13355 AOV-0002412 garD CDS
Automated Process Uncurated Go view Pantoea ananatis B1-9 APL-0001592 CDS
Automated Process Uncurated Go view Pantoea ananatis LMG 20103 AKB-0003178 garD CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0000976 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0010843 CDS
Automated Process Uncurated Go view Pantoea sp. aB AJV-0000833 CDS
Automated Process Uncurated Go view Pantoea stewartii DC283 ACV-0291111 garD CDS
Automated Process Uncurated Go view Pantoea vagans C9-1 ALK-0006229 yhaG CDS
Person Uncurated Go view Pectobacterium atrosepticum SCRI1043 ABL-0063892 garD CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0002053 garD CDS
Person Uncurated Go view Pectobacterium carotovorum WPP14 ADT-0000921 garD CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0004017 garD CDS
Automated Process Uncurated Go view Pectobacterium sp. PC1 AFL-0008564 CDS
Person Uncurated Go view Pseudomonas syringae pv. tomato DC3000 ADG-0004623 garD CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0007609 garD CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0004579 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0003735 pseudogene
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0010075 garD CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0009531 garD CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0007205 garD CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0007909 garD CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0006828 garD CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0005823 garD CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0006291 garD CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0007003 garD CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0007870 garD CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0005199 garD CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0003118 garD misc_feature
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0004075 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0008025 garD CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0007304 garD CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0007515 garD CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0007187 garD CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0112242 garD CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0084890 garD CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0003941 garD CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0100104 garD CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0005976 garD CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0006056 garD CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0004609 garD CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0006401 garD CDS
Person Uncurated Go view Shigella flexneri 2457T ABQ-0074575 yhaG CDS
Person Uncurated Go view Shigella flexneri 301 ABT-0089405 yhaG CDS
Person Approved Go view Shigella sonnei 046 ADD-0003587 garD CDS
Automated Process Uncurated Go view Yersinia bercovieri ATCC 43970 [T] AEK-0001970 CDS
Automated Process Uncurated Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0002853 uxaA_1 CDS
Automated Process Uncurated Go view Yersinia intermedia ATCC 29909 [T] AEH-0003021 uxaA_1 CDS
Automated Process Uncurated Go view Yersinia mollaretii ATCC 43969 [T] AEJ-0003029 CDS
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
FB21858mutantTn5 InsertionRequest the StrainABE-0010284garDyhaG::Tn5KAN-I-SceI at position 844 in Minus orientation ,+ pKD460Blattner Laboratory
FB23002mutantTn5 InsertionRequest the StrainABE-0010284garDyhaG::Tn5KAN-I-SceI at position 844 in Minus orientation ,- pKD465Tim Durfee (durf@genome.wisc.edu)
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 3270282 to 3281853
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0010269rnpBncRNAcomplement32702163270592Upstream
ABE-0010271garKCDScomplement32706253271770Upstream
ABE-0010273garRCDScomplement32718673272751Upstream
ABE-0010276garLCDScomplement32727873273557Upstream
ABE-0010279garPCDScomplement32735733274907Upstream
ABE-0010284garDCDSforward32752823276853Matches
ABE-0010287prlFCDSforward32770023277337Downstream
ABE-0010289yhaVCDSforward32773373277801Downstream
ABE-0285586repeat_regionforward32778193277847Downstream
ABE-0010291agaRCDScomplement32778563278665Downstream
ABE-0010295kbaZCDSforward32789143280194Downstream
ABE-0010297agaVCDSforward32802173280690Downstream
ABE-0010299agaWpseudogeneforward32807013281076Downstream
ABE-0285164agaW_1CDSpforward32807013281102Downstream
ABE-0010302agaApseudogeneforward32810713281625Downstream
ABE-0285587repeat_regionforward32817023281783Downstream
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.