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

ABE-0007431 (yfaU) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0007431 showshow history
Names
yfaU rhmA JW2239 ECK2238 b2245
Product
2-keto-3-deoxy-L-rhamnonate aldolase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 2358042 2358845 804 268
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 IPR005000 (IPR005000 HpcH/HpaI aldolase/citrate lyase domain) Apr 2008
Automated Process Approved IPR015813 (IPR015813 Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily) Jul 2018
Automated Process Approved PF03328 (PF03328 HpcH/HpaI aldolase/citrate lyase family) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0006725 cellular aromatic compound metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005000
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005000, IPR015813
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016830 carbon-carbon lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005000
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name yfaU Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK2238 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW2239 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym rhmA Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved locus tag b2245 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product 2-keto-3-deoxy-L-rhamnonate aldolase Experimental - PubMed ID: 18754683
Reference: Escherichia coli K-12 		Mar 2009
Person Uncurated alternate product name putative 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family IPR005000 HpcH/HpaI aldolase/citrate lyase domain Protein Sequence Similarity - InterPro Domain: IPR005000
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR015813 Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily Protein Sequence Similarity - InterPro Domain: IPR015813
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF03328 HpcH/HpaI aldolase/citrate lyase family Protein Sequence Similarity - PFAM Model Name: PF03328
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Uncurated EC number 4.1.-.- Protein Sequence Similarity - InterPro Domain: IPR005000
Reference: Escherichia coli K-12 MG1655 		Dec 2008
Person Uncurated MultiFun 1.7.1 (metabolism; central intermediary metabolism; unassigned reversible reactions) 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:EG14083 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P76469 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1788578 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:948054 Published Annotation - Entrez Gene Database ID: 948054
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P76469 Published Annotation - Swiss-Prot Accession Number: P76469 Jan 2006
Automated Process Approved db xref ASAP:ABE-0007431 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved function enzyme; Sugar metabolism Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75305.1 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
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:0006725 cellular aromatic compound metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005000
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0016830 carbon-carbon lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005000
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005000, IPR015813
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-0004669 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0001774 yfaU CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002219 yfaU CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0002562 yfaU CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003137 yfaU CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003090 rhmA CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0003810 rhmA CDS
Automated Process Approved Go view Escherichia albertii TW07627 AFX-0003293 CDS
Automated Process Approved Go view Escherichia coli 101-1 (EAEC) BAB-0005210 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0002306 CDS
Automated Process Approved Go view Escherichia coli 53638 (EIEC) ADP-0008976 CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0002194 yfaU CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002078 CDS
Person Approved Go view Escherichia coli ATCC 8739 AEM-0006997 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078924 yfaU CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0002536 yfaU CDS
Person Uncurated Go view Escherichia coli E24377A (ETEC) ADO-0006978 yfaU pseudogene
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0000610 CDS
Person Uncurated Go view Escherichia coli EC4115 (EHEC) BAS-0008223 yfaU pseudogene
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027219 yfaU pseudogene
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0005084 rhmA CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007061 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0002818 CDS
Person Approved Go view Escherichia coli K-12 DH10B AEC-0002113 yfaU CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002318 yfaU CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002633 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0002621 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0176777 CDS
Person Uncurated Go view Escherichia coli SE11 AFS-0002548 yfaU pseudogene
Person Approved Go view Escherichia coli SMS-3-5 AFT-0002398 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133140 yfaU pseudogene
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0000146 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0002534 yfaU CDS
Person Approved Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0002659 yfaU CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0008289 CDS
Person Uncurated Go view Photorhabdus luminescens subsp. laumondii TTO1 [T] ACD-0139011 hpaI CDS
Automated Process Approved Go view Salmonella Agona SL483 BBX-0006594 CDS
Person Approved Go view Salmonella Choleraesuis SC-B67 ADB-0002683 yfaU CDS
Automated Process Approved Go view Salmonella Dublin CT_02021853 BCB-0006897 CDS
Automated Process Approved Go view Salmonella Enteritidis P125109 BCF-0007329 CDS
Automated Process Approved Go view Salmonella Gallinarum 287/91 BCG-0006965 CDS
Automated Process Approved Go view Salmonella Hadar RI_05P066 BBT-0006241 CDS
Automated Process Approved Go view Salmonella Heidelberg SL476 BBV-0006891 CDS
Automated Process Approved Go view Salmonella Heidelberg SL486 BBW-0006193 CDS
Automated Process Approved Go view Salmonella Kentucky CDC 191 BBZ-0004272 CDS
Automated Process Approved Go view Salmonella Kentucky CVM29188 BBP-0006022 CDS
Automated Process Approved Go view Salmonella Newport SL254 BBQ-0006836 CDS
Automated Process Approved Go view Salmonella Newport SL317 BBR-0007427 CDS
Automated Process Approved Go view Salmonella Paratyphi A AKU_12601 BCH-0000575 CDS
Person Approved Go view Salmonella Paratyphi A ATCC 9150 ADA-0000574 CDS
Automated Process Approved Go view Salmonella Paratyphi B SPB7 BCC-0000700 CDS
Automated Process Approved Go view Salmonella Saintpaul SARA23 BBN-0007078 CDS
Automated Process Approved Go view Salmonella Saintpaul SARA29 BBM-0005105 CDS
Automated Process Approved Go view Salmonella Schwarzengrund CVM19633 BBO-0006595 CDS
Automated Process Approved Go view Salmonella Schwarzengrund SL480 BBY-0006570 CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0110204 CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0082286 CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0002830 CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0097318 CDS
Automated Process Approved Go view Salmonella Virchow SL491 BBS-0006992 CDS
Automated Process Approved Go view Salmonella enterica CVM23701 BBL-0006830 CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0000367 hpaI CDS
Person Approved Go view Shigella boydii 227 ADV-0002271 CDS
Person Uncurated Go view Shigella boydii BS512 ADJ-0008037 yfaU pseudogene
Automated Process Approved Go view Shigella dysenteriae 1012 BAA-0005908 CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0002806 CDS
Person Uncurated Go view Shigella flexneri 2457T ABQ-0073599 yfaU pseudogene
Person Uncurated Go view Shigella flexneri 301 ABT-0088590 yfaU pseudogene
Person Uncurated Go view Shigella flexneri 8401 BAG-0002485 yfaU pseudogene
Person Approved Go view Shigella sonnei 046 ADD-0002525 yfaU CDS
Person Uncurated Go view Xenorhabdus nematophila ATCC 19061 [T] ADW-0001384 yfaU CDS
Automated Process Uncurated Go view Yersinia pestis Angola (biovar Pestoides) ADI-0005756 hpaI CDS
Automated Process Uncurated Go view Yersinia pestis B42003004 (biovar Antiqua) BAL-0004232 hpaI CDS
Automated Process Uncurated Go view Yersinia pestis E1979001 (biovar Antiqua) BAM-0007204 hpaI CDS
Automated Process Uncurated Go view Yersinia pestis F1991016 (biovar Orientalis) BAQ-0008332 hpaI CDS
Automated Process Uncurated Go view Yersinia pestis IP275 (biovar Orientalis) BAC-0008034 hpaI CDS
Automated Process Uncurated Go view Yersinia pestis K1973002 (biovar Mediaevalis) BAO-0007094 hpaI CDS
Automated Process Uncurated Go view Yersinia pestis MG05-1020 (biovar Orientalis) BAP-0006241 hpaI CDS
Automated Process Uncurated Go view Yersinia pestis UG05-0454 (biovar Antiqua) BAN-0008461 hpaI CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis IP31758 ADS-0006339 hpaI CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis PB1/+ AFV-0002094 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis YPIII AFW-0002911 CDS
Molecular Interactions to toptop
Author Approval Feature Name Technique Evidence Comment Annotated
Person Approved ABE-0007431 yfaU lambda repressor assay Doodle - bnumber: b2245 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
FB22599mutantTn5 InsertionRequest the StrainABE-0007431yfaUb2245::Tn5KAN-I-SceI at position 386 in Minus orientation ,+ pKD460Blattner Laboratory
FB23407mutantTn5 InsertionRequest the StrainABE-0007431yfaUb2245::Tn5KAN-I-SceI at position 386 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 2353042 to 2363845
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0007422glpACDSforward23526472354275Downstream
ABE-0007424glpBCDSforward23542652355524Downstream
ABE-0007426glpCCDSforward23555212356711Downstream
ABE-0007429rpnECDSforward23569042357803Downstream
ABE-0285064ypaACDSforward23578162358001Downstream
ABE-0007431yfaUCDScomplement23580422358845Matches
ABE-0007433yfaVCDScomplement23588632360152Upstream
ABE-0007436rhmDCDScomplement23602092361414Upstream
ABE-0007438yfaXCDScomplement23614292362211Upstream
ABE-0007441yfaYCDScomplement23624312363633Upstream
ABE-0007445yfaZCDScomplement23637332364275Upstream
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.