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

ABE-0004002 (ldcA) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0004002 showshow history
Names
ldcA ycgQ JW1181 ECK1180 b1192
Product
L,D-carboxypeptidase A
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 1242166 1243080 915 305
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR003507 (IPR003507 Peptidase family S66) Apr 2008
Automated Process Approved IPR029062 (IPR029062 Class I glutamine amidotransferase-like) Jul 2018
Automated Process Approved IPR027461 (IPR027461 LD-carboxypeptidase A, C-terminal domain superfamily) Jul 2018
Automated Process Approved PF02016 (PF02016 LD-carboxypeptidase N-terminal domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0000270 peptidoglycan metabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated 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 ldcA Experimental - PubMed ID: 10428950
Reference: Escherichia coli 		Aug 2002
Automated Process Approved synonym ycgQ Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym JW1181 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK1180 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b1192 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product L,D-carboxypeptidase A Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved alternate product name murein tetrapeptide carboxypeptidase; LD-carboxypeptidase A Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated alternate product name L, D-carboxypeptidase A (in murein recycling) Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name L,D-carboxypeptidase Experimental - PubMed ID: 10428950
Reference: Escherichia coli 		Jan 2006
Protein Family
Automated Process Approved protein family IPR027461 LD-carboxypeptidase A, C-terminal domain superfamily Protein Sequence Similarity - InterPro Domain: IPR027461
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR003507 Peptidase family S66 Protein Sequence Similarity - InterPro Domain: IPR003507
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR029062 Class I glutamine amidotransferase-like Protein Sequence Similarity - InterPro Domain: IPR029062
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF02016 LD-carboxypeptidase N-terminal domain Protein Sequence Similarity - PFAM Model Name: PF02016
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 3.4.17.13 Published Annotation - Swiss-Prot Accession Number: P76008 Feb 2006
Person Uncurated MultiFun 1.7.34 (metabolism; central intermediary metabolism; peptidoglycan (murein) turnover, recycling) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 7.1 (location of gene products; cytoplasm) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 6.2 (cell structure; peptidoglycan (murein)) 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 UniProtKB/Swiss-Prot:P76008 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P76008 Published Annotation - Swiss-Prot Accession Number: P76008 Jan 2006
Automated Process Approved db xref GeneID:945756 Published Annotation - Entrez Gene Database ID: 945756
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1787441 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0004002 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG13898 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved function enzyme; Murein sacculus, peptidoglycan Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved note GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0000270 - peptidoglycan metabolic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC74276.1 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 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:0000270 peptidoglycan metabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO cellular component GO:0005737 cytoplasm Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0003329 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002416 ldcA CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002495 ldcA CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0007543 ldcA CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002390 ldcA CDS
Ortholog
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0001566 CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002556 ldcA CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0003219 ldcA CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0003165 CDS
Automated Process Uncurated Go view Erwinia amylovora ATCC 49946 ACW-0300899 ldcA CDS
Automated Process Uncurated Go view Erwinia amylovora ATCC BAA-2158 APN-0001704 ycgQ CDS
Automated Process Uncurated Go view Erwinia tasmaniensis Et1/99 [T] AFI-0002001 ldcA CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0003800 ldcA CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0006054 ldcA CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0001245 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0009785 ldcA CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001137 ldcA CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0003157 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0008238 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0005088 ldcA CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0008947 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0077752 ldcA CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0001327 ldcA CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0001640 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0009882 ldcA CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0010564 ldcA CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0001394 ldcA CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0005779 ldcA CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0004058 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0010391 ldcA CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0009426 ldcA CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0009083 ldcA CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0008848 ldcA CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0006519 ldcA CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0010366 ldcA CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0008503 ldcA CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0010498 ldcA CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0009936 ldcA CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0009788 ldcA CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0007995 ldcA CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0025743 ldcA CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0005842 ldcA CDS
Automated Process Approved Go view Escherichia coli HS ADR-0005972 ldcA CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0001501 ldcA CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001118 ldcA CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0001208 ldcA CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001571 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0001482 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001430 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0001449 ldcA CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0175528 ldcA CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0001267 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001955 ldcA CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0131638 ldcA CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0002432 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0001382 ldcA CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0002312 ldcA CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0000408 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0000869 CDS
Automated Process Uncurated Go view Pantoea agglomerans SL1-M5 ALY-0004218 CDS
Automated Process Uncurated Go view Pantoea ananatis AJ13355 AOV-0000908 ldcA CDS
Automated Process Uncurated Go view Pantoea ananatis B1-9 APL-0003266 CDS
Automated Process Uncurated Go view Pantoea ananatis LMG 20103 AKB-0001603 ldcA CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0002656 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0009297 CDS
Automated Process Uncurated Go view Pantoea sp. aB AJV-0003282 CDS
Automated Process Uncurated Go view Pantoea stewartii DC283 ACV-0287338 ldcA CDS
Automated Process Uncurated Go view Pantoea vagans C9-1 ALK-0004759 ycgQ CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0005509 CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0001186 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0002103 ycgQ CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0005790 CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0004036 ycgQ CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0003997 ycgQ CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0004652 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0006360 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0005300 CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0005354 CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0008124 CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0005438 CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0006303 CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0004480 CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0001075 CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0001073 ycgQ CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0001429 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0006552 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0008632 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0006026 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0007101 CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0108878 CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0082791 CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0002178 ldcA CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0095856 ldcA CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0007527 CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0006867 CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0007414 CDS
Person Approved Go view Shigella boydii 227 ADV-0002086 CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0006753 ldcA CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0007827 ldcA CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0001403 CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0072323 CDS
Person Uncurated Go view Shigella flexneri 301 ABT-0087522 CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0001275 CDS
Person Approved Go view Shigella sonnei 046 ADD-0001275 ldcA CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0012428 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0004125 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
FB22897mutantTn5 InsertionRequest the StrainABE-0004002ldcAb1192::Tn5(KAN-I-SceI) at position 211 in Plus orientation ,+ pKD46 0Blattner 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 1237166 to 1248080
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0003990ycgBCDScomplement12357091237241Downstream
ABE-0003995dadACDSforward12375711238869Downstream
ABE-0003997dadXCDSforward12388791239949Downstream
ABE-0285760mobile_elementforward12401881240289Downstream
ABE-0285759ymgMCDSforward12402601240463Downstream
ABE-0003999cvrACDScomplement12403351242071Downstream
ABE-0004002ldcACDScomplement12421661243080Matches
ABE-0004006emtACDSforward12431801243791Upstream
ABE-0004009ycgRCDScomplement12437931244527Upstream
ABE-0004014ymgECDSforward12447281244982Upstream
ABE-0004019ycgYCDSforward12451601245600Upstream
ABE-0004021treACDScomplement12456791247376Upstream
ABE-0285435repeat_regionforward12476581247688Upstream
ABE-0004024dhaMCDScomplement12476961249114Upstream
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.