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

ABE-0006680 (dacD) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0006680 showshow history
Names
dacD phsF yeeC phsE JW5329 ECK2004 b2010
Product
D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 6b)
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 2081381 2082547 1167 389
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR012338 (IPR012338 Beta-lactamase/transpeptidase-like) Apr 2008
Automated Process Approved IPR001967 (IPR001967 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal) Apr 2008
Automated Process Approved IPR012907 (IPR012907 Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal) Apr 2008
Automated Process Approved IPR015956 (IPR015956 Penicillin-binding protein, C-terminal domain superfamily) Jul 2018
Automated Process Approved PF00768 (PF00768 D-alanyl-D-alanine carboxypeptidase) Jul 2018
Automated Process Approved PF07943 (PF07943 Penicillin-binding protein 5, C-terminal domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0006508 proteolysis GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001967
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0005886 plasma membrane GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Uncurated GO molecular function GO:0004180 carboxypeptidase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR015956
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001967
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name dacD Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym JW5329 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym phsE Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved synonym phsF Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym ECK2004 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym yeeC Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved locus tag b2010 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 6b) Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated alternate product name DD-carboxypeptidase, penicillin-binding protein 6b Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name penicillin binding protein 6b Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family IPR012338 Beta-lactamase/transpeptidase-like Protein Sequence Similarity - InterPro Domain: IPR012338
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR001967 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal Protein Sequence Similarity - InterPro Domain: IPR001967
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR012907 Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal Protein Sequence Similarity - InterPro Domain: IPR012907
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR015956 Penicillin-binding protein, C-terminal domain superfamily Protein Sequence Similarity - InterPro Domain: IPR015956
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00768 D-alanyl-D-alanine carboxypeptidase Protein Sequence Similarity - PFAM Model Name: PF00768
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF07943 Penicillin-binding protein 5, C-terminal domain Protein Sequence Similarity - PFAM Model Name: PF07943
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 3.4.16.4 Published Annotation - Swiss-Prot Accession Number: P33013 Feb 2006
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 EcoGene:EG11893 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P33013 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:946518 Published Annotation - Entrez Gene Database ID: 946518
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P33013 Published Annotation - Swiss-Prot Accession Number: P33013 Jan 2005
Automated Process Approved db xref ASAP:ABE-0006680 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:87082022 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function putative enzyme; Murein sacculus, peptidoglycan Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note penicillin binding protein 6b; GO_component: GO:0009274 - peptidoglycan-based cell wall Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75071.2 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Uncurated subcellular localization Cytoplasmic Membrane Predicted by PSORTb - PSORTb Final_Score: 8.60
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
Automated Process Approved GO biological process GO:0006508 proteolysis GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001967
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO cellular component GO:0005886 plasma membrane GO Inferred from Electronic Annotation - PubMed ID: 15501914
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Automated Process Approved GO molecular function GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001967
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0004180 carboxypeptidase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR015956
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002886 dacD CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0002735 dacD CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0002543 dacD CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002613 dacD CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0002778 dacD CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0001265 CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002880 dacD CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0003556 dacD CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0003479 CDS
Automated Process Uncurated Go view Erwinia tasmaniensis Et1/99 [T] AFI-0001416 dacD CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0003534 dacD CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0004964 dacD CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0002072 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0009379 dacD CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001961 dacD CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002358 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0007275 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0008421 dacD CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0008039 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078671 dacD CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0002347 dacD CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0002675 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0010262 dacD CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0006368 dacD CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0002291 dacD CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006738 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0006029 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0006265 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0010546 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0010527 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0009682 dacD CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0007706 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0009676 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0010402 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0010349 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0009764 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0009646 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0009665 dacD CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0010471 dacD CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0026895 dacD CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0004831 dacD CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006820 dacD CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0002591 dacD CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001886 dacD CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002064 dacD CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0002483 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0002455 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0002374 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0002376 CDS
Person Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0179800 pseudogene
Automated Process Approved Go view Escherichia coli SE11 AFS-0002323 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001050 dacD CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132816 dacD CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0001997 CDS
Person Uncurated Go view Escherichia coli UTI89 (UPEC) AEA-0005477 dacD pseudogene
Automated Process Uncurated Go view Ewingella americana ATCC 33852 [T] AMA-0001591 CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0002476 dacD CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0000802 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0001827 CDS
Automated Process Uncurated Go view Pantoea agglomerans SL1-M5 ALY-0001942 dacD CDS
Automated Process Uncurated Go view Pantoea ananatis AJ13355 AOV-0001783 dacD CDS
Automated Process Uncurated Go view Pantoea ananatis B1-9 APL-0002255 CDS
Automated Process Uncurated Go view Pantoea ananatis LMG 20103 AKB-0002523 dacD CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0001623 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0010290 CDS
Automated Process Uncurated Go view Pantoea sp. aB AJV-0001354 CDS
Automated Process Uncurated Go view Pantoea stewartii DC283 ACV-0289470 dacD CDS
Automated Process Uncurated Go view Pantoea vagans C9-1 ALK-0005697 dacD CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0006354 CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0000860 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0002432 dacD CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0006665 CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0006562 dacD CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0006235 dacD CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0004356 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0006647 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0005947 CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0006392 CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0004029 CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0005775 CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0006602 CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0007670 CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0001049 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0006836 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0006288 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0006312 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0007996 CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0109570 yeeC pseudogene
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0002556 dacD CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0096610 dacD CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0007223 CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0004734 CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0005335 CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0003155 CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0002572 dacD CDS
Person Approved Go view Shigella sonnei 046 ADD-0002284 dacD CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0016210 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0003177 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 2076381 to 2087547
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0234210CP4-44prophageforward20661592079031Downstream
ABE-0285479misc_featureforward20673542079031Downstream
ABE-0006650yeeSCDSforward20763082076754Downstream
ABE-0006653yeeTCDSforward20768172077038Downstream
ABE-0006656cbeACDSforward20771122077480Downstream
ABE-0006659cbtACDSforward20775692077943Downstream
ABE-0006661yeeWpseudogeneforward20779402078260Downstream
ABE-0285240yoeDpseudogenecomplement20785492078677Downstream
ABE-0285059yoeFpseudogeneforward20787492078931Downstream
ABE-0006663tmaRCDScomplement20790322079361Downstream
ABE-0006667yeeACDScomplement20795332080591Downstream
ABE-0006670sbmCCDScomplement20807892081262Downstream
ABE-0006680dacDCDScomplement20813812082547Matches
ABE-0006686sbcBCDSforward20827562084183Upstream
ABE-0006688tsuBCDScomplement20842262084453Upstream
ABE-0006691tsuACDScomplement20844672085525Upstream
ABE-0006696plaPCDScomplement20857042087062Upstream
ABE-0285221yoeICDScomplement20870522087114Upstream
ABE-0006700yeeYCDScomplement20873292088258Upstream
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.