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

ABE-0006766 (rfbB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0006766 showshow history
Names
rfbB JW2026 ECK2035 rmlB som b2041
Product
dTDP-glucose 4,6 dehydratase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 2111976 2113061 1086 362
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR005888 (IPR005888 dTDP-glucose 4,6-dehydratase) Apr 2008
Automated Process Approved IPR001509 (IPR001509 NAD-dependent epimerase/dehydratase) Apr 2008
Automated Process Approved IPR016040 (IPR016040 NAD(P)-binding domain) Jul 2018
Automated Process Approved IPR036291 (IPR036291 NAD(P)-binding domain superfamily) Jul 2018
Automated Process Approved PF16363 (PF16363 GDP-mannose 4,6 dehydratase) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Approved GO biological process GO:0009243 O antigen biosynthetic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0009225 nucleotide-sugar metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO biological process GO:0044237 cellular metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001509
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Approved 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:0009435 NAD biosynthetic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Approved GO cellular component GO:0005737 cytoplasm Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0050662 (OBSOLETE) coenzyme binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001509
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:IPR001509
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0008460 dTDP-glucose 4,6-dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name rfbB Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym rmlB Published Sequence Analysis - PubMed ID: 9004408 Jan 2005
Person Approved synonym JW2026 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK2035 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym som Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved locus tag b2041 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product dTDP-glucose 4,6 dehydratase Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Person Approved alternate product name dTDP-glucose 4,6 dehydratase Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Person Uncurated alternate product name dTDP-glucose 4,6 dehydratase, NAD(P)-binding Published Annotation - Database Name: GenProtEC Jan 2006
Protein Family
Automated Process Approved protein family IPR005888 dTDP-glucose 4,6-dehydratase Protein Sequence Similarity - InterPro Domain: IPR005888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR036291 NAD(P)-binding domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036291
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF16363 GDP-mannose 4,6 dehydratase Protein Sequence Similarity - PFAM Model Name: PF16363
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR016040 NAD(P)-binding domain Protein Sequence Similarity - InterPro Domain: IPR016040
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR001509 NAD-dependent epimerase/dehydratase Protein Sequence Similarity - InterPro Domain: IPR001509
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 4.2.1.46 Published Annotation - Swiss-Prot Accession Number: P37759 Feb 2006
Person Approved MultiFun 1.7.10 (metabolism; central intermediary metabolism; sugar nucleotide biosynthesis, conversions) 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 1.5.3.7 (metabolism; building block biosynthesis; cofactor, small molecule carrier; nicotinamide adenine dinucleotide) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Approved MultiFun 7.1 (location of gene products; cytoplasm) 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 6.3 (cell structure; surface antigens (ECA, O antigen of LPS)) 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:EG12412 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated db xref NCBI_gi:2665489 Published Annotation - GenPept Accession Number: 2665489 Feb 2005
Person Approved db xref UniProtKB:P37759 Published Annotation - Swiss-Prot Accession Number: P37759 Jan 2005
Automated Process Approved db xref UniProtKB/Swiss-Prot:P37759 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:945276 Published Annotation - Entrez Gene Database ID: 945276
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref ASAP:ABE-0006766 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1788353 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Central intermediary metabolism: Sugar-nucleotide biosynthesis, conversions Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note dTDP-glucose 4,6 dehydratase; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0005737 - cytoplasm; GO_function: GO:0042280 - cell surface antigen activity, host-interacting; GO_process: GO:0009243 - O antigen biosynthetic process; GO_process: GO:0009226 - nucleotide-sugar biosynthetic process; GO_process: GO:0009435 - NAD biosynthetic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75102.1 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
Automated Process Approved GO biological process GO:0044237 cellular metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001509
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Approved GO biological process GO:0009243 O antigen biosynthetic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO biological process GO:0009435 NAD biosynthetic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0009225 nucleotide-sugar metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Approved 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 Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO molecular function GO:0008460 dTDP-glucose 4,6-dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005888
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0050662 (OBSOLETE) coenzyme binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001509
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:IPR001509
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-0006766 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0000051 rffG CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0000051 rffG CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0000068 rffG CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0000072 rffG CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0002807 rfbB CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0001237 rfbB CDS
Automated Process Uncurated Go view Citrobacter freundii ATCC 8090 [T] AVI-0003593 rfbB CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0003496 rfbB CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0004993 rfbB CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001986 rfbB CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002330 rfbB CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007245 rmlB CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0008008 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0002706 CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0006400 rfbB CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006769 rfbB2 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0002620 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001917 rfbB CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002098 rfbB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0002521 rfbB CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0002319 rfbB CDS
Automated Process Uncurated Go view Ewingella americana ATCC 33852 [T] AMA-0001383 rfbB CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0000827 rfbB CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0001861 CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0001584 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0010323 CDS
Automated Process Uncurated Go view Pantoea stewartii DC283 ACV-0289520 rfbB CDS
Automated Process Uncurated Go view Pantoea vagans C9-1 ALK-0005731 rfbB CDS
Person Uncurated Go view Pseudomonas syringae pv. tomato DC3000 ADG-0001109 rfbB-1 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0006391 rfbB CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0006704 rfbB CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0006679 rfbB CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0006350 rfbB CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0004317 rfbB CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0006685 rfbB CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0005985 rfbB CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0006431 rfbB CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0004070 rfbB CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0005817 rfbB CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0006642 rfbB CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0007630 rfbB CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0000772 CDS
Person Approved Go view Salmonella Paratyphi A ATCC 9150 ADA-0000769 rfbB CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0000940 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0006874 rfbB CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0006325 rfbB CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0006409 rfbB CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0109675 rfbB CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0082488 rfbB CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0002595 rfbB CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0096708 rfbB CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0004701 rfbB CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0005373 rfbB CDS
Person Uncurated Go view Shewanella oneidensis MR-1 ACY-0266811 rfbB CDS
Person Uncurated Go view Shigella boydii 227 ADV-0000946 rfbB CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0006593 rfbB2 CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0002541 rfbB CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0073341 rfbB CDS
Person Approved Go view Shigella flexneri 301 ABT-0088389 rfbB CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0002252 rfbB CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0016346 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0003150 rfbB 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
FB20591mutantTn5 InsertionRequest the StrainABE-0006766rfbBrfbB::Tn5KAN-2 at position 344 in Plus orientation ,- pKD460Blattner Laboratory
FB20592mutantTn5 InsertionRequest the StrainABE-0006766rfbBrfbB::Tn5KAN-2 at position 344 in Plus 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 2106976 to 2118061
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0006753wbbHCDScomplement21060602107226Downstream
ABE-0006755glfCDScomplement21072262108329Downstream
ABE-0006757rfbXCDScomplement21083372109584Downstream
ABE-0006759rfbCCDScomplement21095812110138Downstream
ABE-0006762rfbACDScomplement21101382111019Downstream
ABE-0006764rfbDCDScomplement21110772111976Overlaps Downstream
ABE-0006766rfbBCDScomplement21119762113061Matches
ABE-0006771galFCDScomplement21134342114327Upstream
ABE-0006774wcaMCDScomplement21145022115896Upstream
ABE-0006777wcaLCDScomplement21159072117127Upstream
ABE-0006780wcaKCDScomplement21171242118404Upstream
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.