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-0002124 (citD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0002124 showshow history
Names
citD ybdX JW0609 ECK0610 b0617
Product
citrate lyase acyl carrier component
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 650487 650783 297 99
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 IPR006495 (IPR006495 Citrate lyase acyl carrier protein CitD) Apr 2008
Automated Process Approved IPR023439 (IPR023439 Malonate decarboxylase/citrate lyase acyl carrier protein) Jul 2018
Automated Process Approved PF06857 (PF06857 Malonate decarboxylase delta subunit (MdcD)) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0042967 (OBSOLETE) acyl-carrier-protein biosynthetic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved 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 Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name citD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK0610 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW0609 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym ybdX Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved locus tag b0617 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product citrate lyase acyl carrier component Protein Sequence Similarity - InterPro Domain: IPR006495
Reference: Escherichia coli K-12 MG1655 		Sep 2021
Person Uncurated alternate product name citrate lyase gamma chain, acyl carrier protein Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name citrate lyase acyl carrier protein (gamma chain) Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Person Uncurated alternate product name citrate lyase, acyl carrier (gamma) subunit Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Sep 2021
Protein Family
Automated Process Approved protein family IPR006495 Citrate lyase acyl carrier protein CitD Protein Sequence Similarity - InterPro Domain: IPR006495
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF06857 Malonate decarboxylase delta subunit (MdcD) Protein Sequence Similarity - PFAM Model Name: PF06857
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR023439 Malonate decarboxylase/citrate lyase acyl carrier protein Protein Sequence Similarity - InterPro Domain: IPR023439
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Uncurated MultiFun 7.1 (location of gene products; cytoplasm) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.6.15.4 (metabolism; macromolecules (cellular constituent) biosynthesis; large molecule carriers; acyl carrier protein) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
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 GI:1786834 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P69330 Published Annotation - Swiss-Prot Accession Number: P69330 Jan 2006
Automated Process Approved db xref UniProtKB/Swiss-Prot:P69330 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0002124 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:945415 Published Annotation - Entrez Gene Database ID: 945415
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref EcoGene:EG13543 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Central intermediary metabolism: Pool, multipurpose conversions Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note citrate lyase acyl carrier protein (gamma chain); GO_component: GO:0005737 - cytoplasm; GO_process: GO:0042967 - acyl-carrier-protein biosynthetic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC73718.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved subcellular localization Cytoplasmic Predicted by PSORTb - PSORTb Final_Score: 9.26
Reference: Escherichia coli K-12 MG1655 		Feb 2008
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 iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655 		Mar 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:0042967 (OBSOLETE) acyl-carrier-protein 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 cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0000176 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002064 citD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002145 citD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0002725 citD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0001242 citD CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0001214 citD CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0001439 citD CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0001970 citD CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0007155 CDS
Person Approved Go view Dickeya dadantii 3937 ABF-0047009 citD_2 CDS
Person Approved Go view Dickeya dadantii 3937 ABF-0047074 citD_1 CDS
Person Approved Go view Enterobacter sp. 638 AEL-0004102 citD CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0000330 citD CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0006470 citD CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0000652 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0005905 citD CDS
Person Approved Go view Escherichia coli APEC O1 (APEC) AEG-0005577 citD CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0003728 citD CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0008978 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0007511 citD CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0007602 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0081778 citD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0000669 citD CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0000775 citD CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0007489 citD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0007010 citD CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0000542 citD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0005086 citD CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0001709 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0010878 citD CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0008458 citD CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0005722 citD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0005890 citD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0005545 citD CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0007320 citD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0009276 citD CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0006666 citD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0009645 citD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0005829 citD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0005927 citD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0006768 citD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0024605 citD CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0007420 citD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0005349 citD CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0000915 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0000611 citD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0000624 citD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0000886 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0000806 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0000771 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0000701 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0174799 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0000695 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0000635 citD CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0130550 citD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0005300 CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0000623 citD CDS
Person Uncurated Go view Hafnia alvei ATCC 13337 [T] AMD-0001089 citD CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0007004 CDS
Person Approved Go view Pectobacterium atrosepticum SCRI1043 ABL-0062837 citD CDS
Person Uncurated Go view Pectobacterium brasiliensis 1692 AED-0001600 citD CDS
Person Approved Go view Pectobacterium carotovorum WPP14 ADT-0000675 citD CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0001970 citD CDS
Automated Process Uncurated Go view Pectobacterium sp. PC1 AFL-0006578 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0004841 citD CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0002429 CDS
Person Approved Go view Salmonella Choleraesuis SC-B67 ADB-0000774 citD CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0004997 citD CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0001990 citD CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0001935 citD CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0005453 citD CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0005101 citD CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0004458 citD CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0007892 citD CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0006074 citD CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0004243 citD CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0005047 citD CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0007234 citD CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0002126 CDS
Person Approved Go view Salmonella Paratyphi A ATCC 9150 ADA-0002111 citD CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0002950 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0005337 citD CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0006139 citD CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0004872 citD CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0005954 citD CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0106600 citD CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0083958 citD CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0000725 citD CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0092438 citD CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0008853 citD CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0005210 citD CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0005013 citD CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0002613 citD CDS
Person Approved Go view Serratia proteamaculans 568 AEN-0009846 citD CDS
Person Approved Go view Shigella boydii 227 ADV-0000523 citD CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0005928 citD CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0005115 citD CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0071527 citD CDS
Person Approved Go view Shigella flexneri 301 ABT-0086882 citD CDS
Person Approved Go view Shigella flexneri 8401 BAG-0000603 citD CDS
Person Approved Go view Shigella sonnei 046 ADD-0000613 citD CDS
Person Approved Go view Vibrio cholerae N16961 ADH-0000861 VC0797 CDS
Person Approved Go view Yersinia bercovieri ATCC 43970 [T] AEK-0003260 citD CDS
Person Approved Go view Yersinia enterocolitica 8081 BAH-0007628 citD CDS
Person Approved Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0003612 citD CDS
Person Approved Go view Yersinia intermedia ATCC 29909 [T] AEH-0002993 citD CDS
Person Approved Go view Yersinia mollaretii ATCC 43969 [T] AEJ-0003420 citD 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
FB22812mutantTn5 InsertionRequest the StrainABE-0002124citDcitD::Tn5(KAN-I-SceI) at position 194 in Minus orientation ,+ pKD46 0Blattner Laboratory
FB23064mutantTn5 InsertionRequest the StrainABE-0002124citDcitD::Tn5KAN-I-SceI at position 194 in Minus orientation ,- pKD465Tim Durfee (durf@genome.wisc.edu)
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 645487 to 655783
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0002110citTCDScomplement645117646580Downstream
ABE-0002114citGCDScomplement646631647509Downstream
ABE-0002116citXCDScomplement647484648035Downstream
ABE-0002119citFCDScomplement648039649571Downstream
ABE-0002122citECDScomplement649582650490Overlaps Downstream
ABE-0002124citDCDScomplement650487650783Matches
ABE-0002126citCCDScomplement650798651856Upstream
ABE-0002129dpiBCDSforward652235653893Upstream
ABE-0002131dpiACDSforward653862654542Upstream
ABE-0285382repeat_regionforward654552654574Upstream
ABE-0002133dcuCCDScomplement654583655968Upstream
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.