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

ABE-0010052 (ttdB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0010052 showshow history
Names
ttdB ygjB JW3034 ECK3052 b3062
Product
L-tartrate dehydratase subunit beta
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3207371 3207976 606 202
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR004647 (IPR004647 Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain) Apr 2008
Automated Process Approved IPR036660 (IPR036660 Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain superfamily) Jul 2018
Automated Process Approved PF05683 (PF05683 Fumarase C-terminus) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0006113 fermentation Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
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 Uncurated GO molecular function GO:0016836 hydro-lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR004647, IPR036660
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016829 lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004647
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name ttdB Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym JW3034 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym ygjB Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym ECK3052 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b3062 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product L-tartrate dehydratase subunit beta Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Person Uncurated alternate product name L-tartrate dehydratase, beta subunit Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name L-tartrate dehydratase, subunit B Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family PF05683 Fumarase C-terminus Protein Sequence Similarity - PFAM Model Name: PF05683
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR004647 Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain Protein Sequence Similarity - InterPro Domain: IPR004647
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR036660 Fe-S hydro-lyase, tartrate dehydratase beta-type, catalytic domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036660
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Automated Process Uncurated EC number 4.2.1.- Published Annotation - Database Name: EC2GO: GO:0016836
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Approved EC number 4.2.1.32 Published Annotation - Swiss-Prot Accession Number: P0AC35 Feb 2006
Person Uncurated MultiFun 1.3.5 (metabolism; energy metabolism, carbon; fermentation) 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 ASAP:ABE-0010052 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P0AC35 Published Annotation - Swiss-Prot Accession Number: P0AC35 Jan 2006
Automated Process Approved db xref GeneID:947568 Published Annotation - Entrez Gene Database ID: 947568
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1789443 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P0AC35 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG11169 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Energy metabolism, carbon: Fermentation Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note L-tartrate dehydratase, subunit B; GO_process: GO:0006113 - fermentation Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC76098.1 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:0006113 fermentation Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
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 Uncurated GO molecular function GO:0016836 hydro-lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR004647, IPR036660
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0016829 lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004647
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-0004272 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003079 ttdB CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003375 ttdB CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0008875 ttdB CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0003029 ttdB CDS
Ortholog
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0002108 CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0000695 ttdB CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0004634 ttdB CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0000111 CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0002435 ttdB CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0005695 ttdB CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0003182 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0008054 ttdB CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0003146 ttdB CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001117 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006080 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005506 ttdB CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0009259 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079984 ttdB CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003525 ttdB CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0004126 ttdB CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0005593 ttdB CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0005601 ttdB CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0003575 ttdB CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007960 ttdB CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0000334 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0007714 ttdB CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0006231 ttdB CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0008489 ttdB CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0010803 ttdB CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0009210 ttdB CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0005955 ttdB CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0007015 ttdB CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005996 ttdB CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005818 ttdB CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005402 ttdB CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0006247 ttdB CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0028089 ttdB CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0007559 ttdB CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007925 ttdB CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003588 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002859 ttdB CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003131 ttdB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003297 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003471 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003529 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003405 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003353 ttdB CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0134002 ttdB CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0005904 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003507 ttdB CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0003686 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0006238 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0007712 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0003844 ttdB CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0007965 CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0010413 CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0009855 CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0007096 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0008011 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0008600 CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0008410 CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0008208 CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0007108 CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0007974 CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0005092 CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0003254 CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0003220 ttdB CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0004197 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0008135 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0008050 ttdB CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0007617 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0008531 CDS
Person Uncurated Go view Salmonella Typhi CT18 ABX-0112479 ttdB CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0084989 ttdB CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0004052 CDS
Person Uncurated Go view Salmonella Typhimurium LT2 [T] ABU-0100400 CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0005874 CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0008882 CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0008038 CDS
Person Uncurated Go view Shigella boydii 227 ADV-0003207 ttdB CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0004052 ttdB CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074495 ttdB CDS
Person Approved Go view Shigella flexneri 301 ABT-0089348 ttdB CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0003305 ttdB CDS
Person Approved Go view Shigella sonnei 046 ADD-0003492 ttdB 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
FB21016mutantTn5 InsertionRequest the StrainABE-0010052ttdBttdB::Tn5KAN-I-SceI at position 142 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 3202371 to 3212976
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0010031ccaCDSforward32018913203129Upstream
ABE-0285573repeat_regionforward32031443203268Upstream
ABE-0010034bacACDScomplement32033103204131Upstream
ABE-0010036folBCDScomplement32042213204589Upstream
ABE-0010042plsYCDSforward32046943205311Upstream
ABE-0010045ttdRCDScomplement32053243206256Upstream
ABE-0010050ttdACDSforward32064633207374Overlaps Upstream
ABE-0010052ttdBCDSforward32073713207976Matches
ABE-0010056ttdTCDSforward32080243209487Downstream
ABE-0285574repeat_regionforward32094993209518Downstream
ABE-0010058tsaDCDScomplement32095303210543Downstream
ABE-0010063rpsUCDSforward32107813210996Downstream
ABE-0010065dnaGCDSforward32111073212852Downstream
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.