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

ABE-0001152 (prpD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0001152 showshow history
Names
prpD yahT acnC JW0325 ECK0331 b0334
Product
2-methylcitrate dehydratase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 351215 352666 1452 484
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR005656 (IPR005656 MmgE/PrpD) Apr 2008
Automated Process Approved IPR012705 (IPR012705 2-methylcitrate dehydratase PrpD) Apr 2008
Automated Process Approved IPR036148 (IPR036148 MmgE/PrpD superfamily) Jul 2018
Automated Process Approved PF03972 (PF03972 MmgE/PrpD N-terminal domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0019629 propionate catabolic process, 2-methylcitrate cycle GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012705
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0016829 lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005656, IPR036148
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0047547 2-methylcitrate dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012705
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0051537 2 iron, 2 sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012705
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name prpD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK0331 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym yahT Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym JW0325 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym acnC Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved locus tag b0334 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product 2-methylcitrate dehydratase Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated alternate product name 2-methyl citrate dehydratase Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family IPR012705 2-methylcitrate dehydratase PrpD Protein Sequence Similarity - InterPro Domain: IPR012705
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR005656 MmgE/PrpD Protein Sequence Similarity - InterPro Domain: IPR005656
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF03972 MmgE/PrpD N-terminal domain Protein Sequence Similarity - PFAM Model Name: PF03972
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR036148 MmgE/PrpD superfamily Protein Sequence Similarity - InterPro Domain: IPR036148
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 4.2.1.79 Published Annotation - Swiss-Prot Accession Number: P77243 Feb 2006
Automated Process Uncurated EC number 4.-.-.- Published Annotation - Database Name: EC2GO: GO:0016829
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated 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 EcoGene:EG13603 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0001152 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:945931 Published Annotation - Entrez Gene Database ID: 945931
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1786528 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P77243 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P77243 Published Annotation - Swiss-Prot Accession Number: P77243 Jan 2005
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 AAC73437.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Unknown Predicted by PSORTb - PSORTb Final_Score: 2.00
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Uncurated subsystem component of in silico model iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655 		Mar 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 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
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0019629 propionate catabolic process, 2-methylcitrate cycle GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012705
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0047547 2-methylcitrate dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012705
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0016829 lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005656, IPR036148
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0051537 2 iron, 2 sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR012705
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-0005951 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003283 prpD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003451 prpD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004163 prpD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003026 prpD CDS
Ortholog
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0001105 prpD CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0001617 prpD CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0000555 prpD CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0007481 prpD CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0000413 CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0000330 prpD CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0003972 prpD CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0009298 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0007050 prpD CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005769 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0076528 prpD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0000394 prpD CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0000483 prpD CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0007040 prpD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0008063 prpD CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0000312 prpD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0004808 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0003900 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0010577 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0008160 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0009237 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0007331 prpD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0005244 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0007958 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0008975 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0007866 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0009139 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0007581 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0007440 prpD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0008939 prpD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0024319 prpD CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0008727 prpD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0005081 prpD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0000337 prpD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0000486 prpD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0000570 prpD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0000481 prpD CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0000451 prpD CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0174546 prpD CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0000367 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0000364 prpD CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0130278 prpD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0004952 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0000366 prpD CDS
Person Uncurated Go view Photorhabdus luminescens subsp. laumondii TTO1 [T] ACD-0144895 prpD CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0004582 prpD CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0002687 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0000481 prpD CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0004680 prpD CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0001197 prpD CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0001176 prpD CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0005771 prpD CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0004830 prpD CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0004186 prpD CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0004691 prpD CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0006731 prpD CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0008850 prpD CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0004780 prpD CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0006918 prpD CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0002371 CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0002353 prpD CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0003240 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0005070 prpD CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0007043 prpD CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0004512 prpD CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0006729 prpD CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0106078 prpD CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0084209 prpD CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0000434 prpD CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0091706 prpD CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0009131 prpD CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0005468 prpD CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0006453 prpD CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0004344 prpD CDS
Person Uncurated Go view Xenorhabdus nematophila ATCC 19061 [T] ADW-0002148 prpD 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
FB20156mutantTn5 InsertionRequest the StrainABE-0001152prpDprpD::Tn5KAN-I-SceI at position 762 in Plus orientation ,+ pKD460Blattner Laboratory
FB20157mutantTn5 InsertionRequest the StrainABE-0001152prpDprpD::Tn5KAN-I-SceI at position 762 in Plus orientation ,- pKD465Blattner 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 346215 to 357666
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0001122yahNCDScomplement345666346337Upstream
ABE-0001130yahOCDSforward346484346759Upstream
ABE-0285347repeat_regionforward346824346853Upstream
ABE-0001133prpRCDScomplement346857348443Upstream
ABE-0001138prpBCDSforward348682349572Upstream
ABE-0285348repeat_regionforward349605349969Upstream
ABE-0001148prpCCDSforward350012351181Upstream
ABE-0001152prpDCDSforward351215352666Matches
ABE-0001154prpECDSforward352706354592Downstream
ABE-0285349repeat_regionforward354599354769Downstream
ABE-0001159codBCDSforward354922356181Downstream
ABE-0001161codACDSforward356171357454Downstream
ABE-0285350repeat_regionforward357484357562Downstream
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.