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

ABE-0007436 (rhmD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0007436 showshow history
Names
rhmD rhamD JW2241 ECK2240 yfaW b2247
Product
L-rhamnonate dehydratase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 2360209 2361414 1206 402
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR013341 (IPR013341 Mandelate racemase/muconate lactonizing enzyme, N-terminal domain) Apr 2008
Automated Process Approved IPR013342 (IPR013342 Mandelate racemase/muconate lactonizing enzyme, C-terminal) Apr 2008
Automated Process Approved IPR001354 (IPR001354 (DEPRECATED) Mandelate racemase/muconate lactonizing enzyme/methylaspartate ammonia-lyase) Apr 2008
Automated Process Approved IPR029065 (IPR029065 Enolase C-terminal domain-like) Jul 2018
Automated Process Approved IPR023444 (IPR023444 L-rhamnonate dehydratase) Jul 2018
Automated Process Approved IPR036849 (IPR036849 Enolase-like, C-terminal domain superfamily) Jul 2018
Automated Process Approved PF02746 (PF02746 Mandelate racemase / muconate lactonizing enzyme, N-terminal domain) Jul 2018
Automated Process Approved PF13378 (PF13378 Enolase C-terminal domain-like) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001354
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0050032 L-rhamnonate dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR023444
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001354
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Automated Process Approved name rhmD Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym yfaW Published Annotation - Database Name: GenProtEC Jul 2002
Person Approved synonym JW2241 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym rhamD Published Annotation - PubMed ID: 18754693
Reference: Escherichia coli K-12 		Mar 2009
Person Approved synonym ECK2240 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2247 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product L-rhamnonate dehydratase Experimental - PubMed ID: 18754693
Reference: Escherichia coli K-12 		Mar 2009
Person Approved alternate product name putative racemase Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family IPR001354 (DEPRECATED) Mandelate racemase/muconate lactonizing enzyme/methylaspartate ammonia-lyase Protein Sequence Similarity - InterPro Domain: IPR001354
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR013342 Mandelate racemase/muconate lactonizing enzyme, C-terminal Protein Sequence Similarity - InterPro Domain: IPR013342
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR013341 Mandelate racemase/muconate lactonizing enzyme, N-terminal domain Protein Sequence Similarity - InterPro Domain: IPR013341
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR029065 Enolase C-terminal domain-like Protein Sequence Similarity - InterPro Domain: IPR029065
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR036849 Enolase-like, C-terminal domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036849
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF13378 Enolase C-terminal domain-like Protein Sequence Similarity - PFAM Model Name: PF13378
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF02746 Mandelate racemase / muconate lactonizing enzyme, N-terminal domain Protein Sequence Similarity - PFAM Model Name: PF02746
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR023444 L-rhamnonate dehydratase Protein Sequence Similarity - InterPro Domain: IPR023444
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Automated Process Uncurated EC number 4.2.1.90 Published Annotation - Database Name: EC2GO: GO:0050032
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
Person Uncurated comment The coordinates of yfaW have been changed from those reported in the GenBank entry (GBAN:U00096.2) to correspond to the start site predicted by EasyGene and by GeneMark.hmm using multiple models, removing 4 codons from the N-terminus. Unpublished Sequence Analysis - Author Name, Email; Comment: Eric Neeno-Eckwall, ecneenoeckwa@wisc.edu
Reference: Escherichia coli K-12 MG1655 		Feb 2009
Automated Process Approved db xref EcoGene:EG14085 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:226510960 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:945881 Published Annotation - Entrez Gene Database ID: 945881
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P77215 Published Annotation - Swiss-Prot Accession Number: P77215 Jan 2006
Automated Process Approved db xref UniProtKB/Swiss-Prot:P77215 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0007436 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 note putative racemase Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75307.2 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:0008152 metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001354
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:IPR001354
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0050032 L-rhamnonate dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR023444
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-0005799 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003554 yfaW CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003869 yfaW CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0005440 yfaW CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003884 rhmD CDS
Partial ortholog
Person Uncurated Go view Shigella dysenteriae 197 ADU-0002810 yfaW pseudogene
Person Uncurated Go view Shigella dysenteriae 197 ADU-0005705 yfaW pseudogene
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003092 rhmD CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0003812 rhmD CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0003291 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0002308 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008974 CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0002196 yfaW CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002076 CDS
Person Approved Go view Escherichia coli ATCC 8739 AEM-0006995 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078926 rhmD CDS
Person Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0002538 yfaW CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0000615 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0006726 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0005251 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0006693 CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0007769 CDS
Person Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008228 CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0005704 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0006013 CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0006946 CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0007296 CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0006901 CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0006174 CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0007468 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027221 yfaW CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0005086 rhmD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007063 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0002820 CDS
Person Approved Go view Escherichia coli K-12 DH10B AEC-0002115 yfaW CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002320 yfaW CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002635 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0002623 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0176779 CDS
Person Approved Go view Escherichia coli SMS-3-5 AFT-0002400 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133146 yfaW CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0000141 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0002536 yfaW CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0002661 yfaW CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0006596 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0002685 yfaW CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0006899 CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0007333 yfaW CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0006971 yfaW CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0006239 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0006893 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0006195 CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0004274 CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0006024 CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0006838 CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0007425 CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0000573 CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0000572 yfaW CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0000698 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0007080 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0005102 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0006597 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0006572 CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0110208 CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0082284 CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0002832 yfaW CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0097323 yfaW CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0006990 CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0006832 CDS
Person Approved Go view Shigella boydii 227 ADV-0002269 CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0005910 CDS
Person Approved Go view Shigella sonnei 046 ADD-0002527 pseudogene
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
FB22838mutantTn5 InsertionRequest the StrainABE-0007436rhmDb2247::Tn5(KAN-I-SceI) at position 668 in Minus orientation ,+ pKD46 0Blattner Laboratory
FB23409mutantTn5 InsertionRequest the StrainABE-0007436rhmDb2247::Tn5KAN-I-SceI at position 668 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 2355209 to 2366414
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0007424glpBCDSforward23542652355524Downstream
ABE-0007426glpCCDSforward23555212356711Downstream
ABE-0007429rpnECDSforward23569042357803Downstream
ABE-0285064ypaACDSforward23578162358001Downstream
ABE-0007431yfaUCDScomplement23580422358845Downstream
ABE-0007433yfaVCDScomplement23588632360152Downstream
ABE-0007436rhmDCDScomplement23602092361414Matches
ABE-0007438yfaXCDScomplement23614292362211Upstream
ABE-0007441yfaYCDScomplement23624312363633Upstream
ABE-0007445yfaZCDScomplement23637332364275Upstream
ABE-0007449nudICDSforward23645542364979Upstream
ABE-0007451aisCDScomplement23650182365620Upstream
ABE-0007456arnBCDSforward23659282367067Upstream
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.