Escherichia coli K-12 MG1655
About ASAP Data Release Policy University of Wisconsin—Madison
Home    Overview    Annotations    BLAST    Downloads    Comparative Genomics    Experiments    Strains    Help (this script)    User: guest  / Log On   
Working With: Genome: Escherichia coli K-12 MG1655 Version: v3

ABE-0006759 (rfbC) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0006759 showshow history
Names
rfbC JW2023 ECK2032 rmlC rfbD b2038
Product
dTDP-4-deoxyrhamnose-3,5-epimerase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 2109581 2110138 558 186
Sequence

Get full DNA or protein sequence

View sequence with flanking regions: bases upstream and bases downstream

Context

Browse sequence in GaPP

You last hovered over feature (none)
Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR000888 (IPR000888 dTDP-4-dehydrorhamnose 3,5-epimerase-related) Apr 2008
Automated Process Approved IPR011051 (IPR011051 RmlC-like cupin domain superfamily) Apr 2008
Automated Process Approved IPR014710 (IPR014710 RmlC-like jelly roll fold) Apr 2008
Automated Process Approved PF00908 (PF00908 dTDP-4-dehydrorhamnose 3,5-epimerase) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0009226 nucleotide-sugar biosynthetic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO biological process GO:0019305 dTDP-rhamnose biosynthetic process Experimental - PubMed ID: 10217500
Reference: Escherichia coli 		Mar 2005
Automated Process Approved GO biological process GO:0009103 lipopolysaccharide biosynthetic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Approved GO biological process GO:0009243 O antigen biosynthetic process Experimental - PubMed ID: 10217500
Reference: Escherichia coli 		Mar 2005
Person Uncurated GO biological process GO:0009103 lipopolysaccharide biosynthetic process Experimental - PubMed ID: 10217500
Reference: Escherichia coli 		Mar 2005
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
Person Approved GO cellular component GO:0005737 cytoplasm Experimental - PubMed ID: 10455186 Mar 2005
Automated Process Approved GO molecular function GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Approved GO molecular function GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity Experimental - PubMed ID: 10217500
Reference: Escherichia coli 		Mar 2005
Person Uncurated GO molecular function GO:0042803 protein homodimerization activity Protein Sequence Similarity - ASAP FeatureID: 96700
Reference: Salmonella Typhimurium LT2 		Mar 2005
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name rfbC Experimental - PubMed ID: 7517390
Reference: Escherichia coli 		Feb 2005
Person Approved synonym rmlC Published Sequence Analysis - PubMed ID: 9004408 Jan 2005
Person Approved synonym JW2023 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK2032 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym rfbD Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved locus tag b2038 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product dTDP-4-deoxyrhamnose-3,5-epimerase Published Annotation - PubMed ID: 16397293 Jan 2006
Protein Family
Automated Process Approved protein family IPR011051 RmlC-like cupin domain superfamily Protein Sequence Similarity - InterPro Domain: IPR011051
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF00908 dTDP-4-dehydrorhamnose 3,5-epimerase Protein Sequence Similarity - PFAM Model Name: PF00908
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR000888 dTDP-4-dehydrorhamnose 3,5-epimerase-related Protein Sequence Similarity - InterPro Domain: IPR000888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR014710 RmlC-like jelly roll fold Protein Sequence Similarity - InterPro Domain: IPR014710
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 5.1.3.13 Experimental - PubMed ID: 10217500
Reference: Escherichia coli 		Mar 2005
Person Approved MultiFun 7.1 (location of gene products; cytoplasm) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Approved MultiFun 6.3 (cell structure; surface antigens (ECA, O antigen of LPS)) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 6.1 (cell structure; membrane) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Approved MultiFun 1.6.3.1 (metabolism; macromolecules (cellular constituent) biosynthesis; lipopolysaccharide; O antigen) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.7.10 (metabolism; central intermediary metabolism; sugar nucleotide biosynthesis, conversions) 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
Person Approved comment The rfbC gene product does not form a complex with the product of the rfbD gene (ASAP:6764), as was previously postulated. Experimental - PubMed ID: 10217500
Reference: Escherichia coli 		Mar 2005
Person Approved comment Note that the gene order rfbBCAD was used in some of the earlier papers, but it was agreed that gene names would correspond with order rfbBDAC, reversing the assignment of rfbC and rfbD, given in those papers. Published Annotation - Web Resource URL: http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/38129 Feb 2005
Automated Process Approved db xref GI:1788350 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0006759 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG11979 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P37745 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated db xref NCBI_gi:508240 Published Annotation - GenPept Accession Number: 508240 Feb 2005
Person Approved db xref UniProtKB:P37745 Published Annotation - Swiss-Prot Accession Number: P37745 Jan 2005
Person Uncurated db xref NCBI_gi:510251 Published Annotation - GenPept Accession Number: 510251 Feb 2005
Automated Process Approved db xref GeneID:947482 Published Annotation - Entrez Gene Database ID: 947482
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved function enzyme; Central intermediary metabolism: Sugar-nucleotide biosynthesis, conversions Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved molecular interaction Interacts with the product of groL ASAP:13568:(interacting residues not known); by MALDI-TOF Experimental - PubMed ID: 15690043
Reference: Escherichia coli K-12 W3110 		Mar 2005
Automated Process Approved note dTDP-6-deoxy-D-glucose-3,5 epimerase; GO_component: GO:0005737 - cytoplasm; GO_function: GO:0042803 - protein homodimerization activity; GO_process: GO:0009226 - nucleotide-sugar biosynthetic process; GO_process: GO:0009243 - O antigen biosynthetic process; GO_process: GO:0009103 - lipopolysaccharide biosynthetic process; GO_process: GO:0019305 - dTDP-rhamnose biosynthetic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75099.1 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: 8.96
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:0019305 dTDP-rhamnose biosynthetic process Experimental - PubMed ID: 10217500
Reference: Escherichia coli 		Mar 2005
Person Uncurated GO biological process GO:0009103 lipopolysaccharide biosynthetic process Experimental - PubMed ID: 10217500
Reference: Escherichia coli 		Mar 2005
Person Approved GO biological process GO:0009243 O antigen biosynthetic process Experimental - PubMed ID: 10217500
Reference: Escherichia coli 		Mar 2005
Automated Process Approved GO biological process GO:0009103 lipopolysaccharide biosynthetic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0009226 nucleotide-sugar biosynthetic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Approved GO cellular component GO:0005737 cytoplasm Experimental - PubMed ID: 10455186 Mar 2005
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 Approved GO molecular function GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO molecular function GO:0042803 protein homodimerization activity Protein Sequence Similarity - ASAP FeatureID: 96700
Reference: Salmonella Typhimurium LT2 		Mar 2005
Person Approved GO molecular function GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity Experimental - PubMed ID: 10217500
Reference: Escherichia coli 		Mar 2005
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0002219 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003716 rfbC CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003503 rfbC CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0004059 rfbC CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0004168 rfbC CDS
Ortholog
Automated Process Uncurated Go view Brenneria salicis ATCC 15712 [T] AMK-0003619 CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0001239 rfbC CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0007807 CDS
Person Uncurated Go view Dickeya dadantii 3937 ABF-0020461 rfbC CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0000691 CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0001983 rmlC CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0008011 CDS
Automated Process Uncurated Go view Escherichia coli E24377A (ETEC) ADO-0006766 rfbC CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001914 rfbC CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002095 rfbC CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0008273 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0001858 CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0001587 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0010320 CDS
Automated Process Uncurated Go view Pantoea vagans C9-1 ALK-0005728 rfbC CDS
Person Uncurated Go view Pectobacterium atrosepticum SCRI1043 ABL-0061697 rfbC CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0000817 rfbC CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0004173 rfbC CDS
Person Uncurated Go view Pseudomonas syringae pv. tomato DC3000 ADG-0001105 rfbC-1 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0006388 rfbC CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0006701 rfbC CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0006672 rfbC CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0006344 rfbC CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0006682 rfbC CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0005982 rfbC CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0004067 rfbC CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0005814 rfbC CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0000775 CDS
Person Approved Go view Salmonella Paratyphi A ATCC 9150 ADA-0000772 rfbC CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0000943 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0006871 rfbC CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0006322 rfbC CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0006406 rfbC CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0005629 rfbC CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0109670 rfbC CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0082491 rfbC CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0002592 rfbC CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0096700 rfbC CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0004704 rfbC CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0005370 rfbC CDS
Person Uncurated Go view Shewanella oneidensis MR-1 ACY-0266783 rfbC CDS
Person Uncurated Go view Shigella boydii 227 ADV-0000943 rfbC CDS
Automated Process Uncurated Go view Shigella boydii BS512 ADJ-0006596 rfbC CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0002544 rfbC CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0073338 rfbC CDS
Person Approved Go view Shigella flexneri 301 ABT-0088386 rfbC CDS
Automated Process Uncurated Go view Shigella flexneri 8401 BAG-0002249 rfbC 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)
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 2104581 to 2115138
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0006749wbbJCDScomplement21044942105084Downstream
ABE-0006751wbbICDScomplement21050652106057Downstream
ABE-0006753wbbHCDScomplement21060602107226Downstream
ABE-0006755glfCDScomplement21072262108329Downstream
ABE-0006757rfbXCDScomplement21083372109584Overlaps Downstream
ABE-0006759rfbCCDScomplement21095812110138Matches
ABE-0006762rfbACDScomplement21101382111019Overlaps Upstream
ABE-0006764rfbDCDScomplement21110772111976Upstream
ABE-0006766rfbBCDScomplement21119762113061Upstream
ABE-0006771galFCDScomplement21134342114327Upstream
ABE-0006774wcaMCDScomplement21145022115896Upstream
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.