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

ABE-0004813 (patD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0004813 showshow history
Names
patD prr JW1439 ECK1438 ydcW b1444
Product
gamma-aminobutyraldehyde dehydrogenase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 1515578 1517002 1425 475
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR015590 (IPR015590 Aldehyde dehydrogenase domain) Apr 2008
Automated Process Approved IPR017749 (IPR017749 Gamma-aminobutyraldehyde dehydrogenase) Jul 2018
Automated Process Approved IPR015657 (IPR015657 Aminobutyraldehyde dehydrogenase) Jul 2018
Automated Process Approved IPR016161 (IPR016161 Aldehyde/histidinol dehydrogenase) Jul 2018
Automated Process Approved PF00171 (PF00171 Aldehyde dehydrogenase family) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO biological process GO:0009447 putrescine catabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017749
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR015590, IPR017749, IPR016161
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO biological process GO:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR015590, IPR016161
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated 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:0051287 NAD binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017749
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0019145 aminobutyraldehyde dehydrogenase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017749
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR015590, IPR016161
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Uncurated name patD Published Annotation - PubMed ID: 22636776
Reference: Escherichia coli K-12 W3110 		Sep 2018
Person Approved synonym ECK1438 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated synonym prr Published Annotation - PubMed ID: 3897201
Reference: Escherichia coli K-12 		Apr 2009
Person Approved synonym JW1439 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ydcW Published Annotation - Swiss-Prot Accession Number: P77674 Aug 2002
Person Approved locus tag b1444 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product gamma-aminobutyraldehyde dehydrogenase Experimental - PubMed ID: 16023116
Reference: Escherichia coli K-12 MG1655 		Apr 2009
Person Uncurated alternate product name medium-chain aldehyde dehydrogenase Experimental - PubMed ID: 15381418
Reference: Escherichia coli K-12 		Apr 2009
Person Uncurated alternate product name pyrroline dehydrogenase Experimental - PubMed ID: 3897201
Reference: Escherichia coli K-12 		Apr 2009
Protein Family
Automated Process Approved protein family IPR015590 Aldehyde dehydrogenase domain Protein Sequence Similarity - InterPro Domain: IPR015590
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF00171 Aldehyde dehydrogenase family Protein Sequence Similarity - PFAM Model Name: PF00171
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR017749 Gamma-aminobutyraldehyde dehydrogenase Protein Sequence Similarity - InterPro Domain: IPR017749
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR015657 Aminobutyraldehyde dehydrogenase Protein Sequence Similarity - InterPro Domain: IPR015657
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR016161 Aldehyde/histidinol dehydrogenase Protein Sequence Similarity - InterPro Domain: IPR016161
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 1.2.1.19 Experimental - PubMed ID: 3129020
Reference: Escherichia coli K-12 		Apr 2009
Automated Process Uncurated EC number 1.-.-.- Published Annotation - Database Name: EC2GO: GO:0016491
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 EcoGene:EG13766 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P77674 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:945876 Published Annotation - Entrez Gene Database ID: 945876
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref ASAP:ABE-0004813 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1787715 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P77674 Published Annotation - Swiss-Prot Accession Number: P77674 Jan 2005
Person Approved function putative enzyme; Not classified Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note putative aldehyde dehydrogenase Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74526.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Cytoplasmic Predicted by PSORTb - PSORTb Final_Score: 9.97
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
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:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR015590, IPR016161
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO biological process GO:0009447 putrescine catabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017749
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO biological process GO:0055114 (OBSOLETE) oxidation-reduction process GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR015590, IPR017749, IPR016161
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated 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:0016491 oxidoreductase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR015590, IPR016161
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0051287 NAD binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017749
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Uncurated GO molecular function GO:0019145 aminobutyraldehyde dehydrogenase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR017749
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0001941 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002527 prr CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002589 patD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0000077 prr CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002456 patD CDS
Ortholog
Automated Process Uncurated Go view Brenneria salicis ATCC 15712 [T] AMK-0003750 CDS
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0004219 CDS
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0002165 ydcW CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0002008 ydcW CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002307 prr CDS
Automated Process Uncurated Go view Citrobacter freundii ATCC 8090 [T] AVI-0002973 prr_2 CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0007610 CDS
Person Uncurated Go view Dickeya dadantii 3937 ABF-0018623 patD CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0002687 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0002853 ydcW CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0004014 ydcW CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005450 ydcW CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001458 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0010031 ydcW CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001424 ydcW CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002900 ydcW CDS
Person Approved Go view Escherichia coli ATCC 8739 AEM-0007973 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005117 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0077986 patD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001555 ydcW CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005300 ydcW CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0006296 ydcW CDS
Person Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0001697 ydcW CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006063 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0003306 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0005428 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0009793 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007972 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0007092 ydcW CDS
Person Approved Go view Escherichia coli EC4115 (EHEC) BAS-0006889 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006968 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0011364 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0008029 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0008471 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0007060 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007164 ydcW CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008820 ydcW CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0026049 ydcW CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0008003 prr CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006205 ydcW CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0001861 CDS
Person Approved Go view Escherichia coli K-12 DH10B AEC-0001353 ydcW CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001485 ydcW CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001741 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001528 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0001677 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0175815 CDS
Person Uncurated Go view Escherichia coli SE11 AFS-0001555 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001729 ydcW CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132016 ydcW CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0002080 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001670 ydcW CDS
Person Uncurated Go view Hafnia alvei ATCC 13337 [T] AMD-0001602 ydcW CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0001929 ydcW CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0005901 CDS
Person Uncurated Go view Pectobacterium atrosepticum SCRI1043 ABL-0061795 CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0000885 CDS
Person Uncurated Go view Pectobacterium carotovorum WPP14 ADT-0000401 CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0001817 CDS
Automated Process Uncurated Go view Pectobacterium sp. PC1 AFL-0006171 CDS
Person Uncurated Go view Salmonella Agona SL483 BBX-0005738 ydcW CDS
Person Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0001434 CDS
Person Approved Go view Salmonella Choleraesuis SC-B67 ADB-0001868 ydcW CDS
Person Uncurated Go view Salmonella Dublin CT_02021853 BCB-0006015 CDS
Person Uncurated Go view Salmonella Enteritidis P125109 BCF-0004762 ydcW CDS
Person Uncurated Go view Salmonella Gallinarum 287/91 BCG-0004647 ydcW CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0004878 ydcW CDS
Person Uncurated Go view Salmonella Heidelberg SL476 BBV-0006139 ydcW CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0005078 ydcW CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0005129 ydcW CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0004589 ydcW CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0005210 ydcW CDS
Person Uncurated Go view Salmonella Newport SL254 BBQ-0006078 ydcW CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0004705 ydcW CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0001274 CDS
Person Approved Go view Salmonella Paratyphi A ATCC 9150 ADA-0001271 ydcW CDS
Person Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0001699 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0006325 ydcW CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0005295 ydcW CDS
Person Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0005799 ydcW CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0005137 ydcW CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0108065 CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0083220 CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0001936 ydcW CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0095253 ydcW CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0007759 ydcW CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0005778 ydcW CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0006967 CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0002062 ydcW CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0001997 CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0073003 CDS
Person Approved Go view Shigella flexneri 301 ABT-0088074 CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0001890 CDS
Person Approved Go view Shigella sonnei 046 ADD-0001846 ydcW CDS
Person Uncurated Go view Xenorhabdus nematophila ATCC 19061 [T] ADW-0004066 ydcW CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0013344 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0003906 ydcW 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
FB22167mutantTn5 InsertionRequest the StrainABE-0004813patDb1444::Tn5KAN-I-SceI at position 1155 in Minus orientation ,+ pKD460Blattner Laboratory
FB23099mutantTn5 InsertionRequest the StrainABE-0004813patDb1444::Tn5KAN-I-SceI at position 1155 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 1510578 to 1522002
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0004800ydcRCDSforward15100031511409Upstream
ABE-0004803ydcSCDSforward15116541512799Upstream
ABE-0004805ydcTCDSforward15128171513830Upstream
ABE-0004807ydcUCDSforward15138311514772Upstream
ABE-0004809ydcVCDSforward15147621515556Upstream
ABE-0285723matS11protein_bindforward15149541514966Upstream
ABE-0004813patDCDSforward15155781517002Matches
ABE-0285182yncLCDScomplement15170991517194Downstream
ABE-0004818ortTCDSforward15173891517562Downstream
ABE-0004821ydcYCDSforward15176481517881Downstream
ABE-0004823ydcZCDScomplement15178821518331Downstream
ABE-0004827mnaTCDScomplement15183281518846Downstream
ABE-0004834curACDSforward15190271520064Downstream
ABE-0004837mcbRCDSforward15202621520927Downstream
ABE-0004839yncDCDScomplement15209631523065Downstream
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.