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

ABE-0006607 (ldtA) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0006607 showshow history
Names
ldtA yzzT yeeG srfK JW1968 ECK1985 erfK b1990
Product
L,D-transpeptidase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 2062391 2063323 933 311
Sequence

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View sequence with flanking regions: bases upstream and bases downstream

Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR005490 (IPR005490 L,D-transpeptidase catalytic domain) Apr 2008
Automated Process Approved IPR038063 (IPR038063 L,D-transpeptidase catalytic domain-like) Jul 2018
Automated Process Approved PF03734 (PF03734 L,D-transpeptidase catalytic domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO molecular function GO:0016740 transferase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005490
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Uncurated name ldtA Published Annotation - PubMed ID: 23832002
Reference: Escherichia coli K-12 BW25113 		Aug 2018
Automated Process Approved synonym srfK Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved synonym yzzT Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved synonym JW1968 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK1985 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym erfK Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved synonym yeeG Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved locus tag b1990 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product L,D-transpeptidase Experimental - PubMed ID: 17369299
Reference: Escherichia coli K-12 BW25113 		Aug 2018
Automated Process Approved alternate product name L,D-transpeptidase linking Lpp to murein Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated alternate product name conserved hypothetical protein Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name conserved protein with NAD(P)-binding Rossmann-fold domain Published Annotation - PubMed ID: 16397293 Jan 2006
Protein Family
Automated Process Approved protein family IPR005490 L,D-transpeptidase catalytic domain Protein Sequence Similarity - InterPro Domain: IPR005490
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR038063 L,D-transpeptidase catalytic domain-like Protein Sequence Similarity - InterPro Domain: IPR038063
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF03734 L,D-transpeptidase catalytic domain Protein Sequence Similarity - PFAM Model Name: PF03734
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Automated Process Uncurated EC number 2.-.-.- Published Annotation - Database Name: EC2GO: GO:0016740
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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:P39176 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1788299 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:945273 Published Annotation - Entrez Gene Database ID: 945273
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved db xref UniProtKB:P39176 Published Annotation - Swiss-Prot Accession Number: P39176 Jan 2005
Automated Process Approved db xref ASAP:ABE-0006607 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG12682 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 protein id AAC75051.1 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: 2.50
Reference: Escherichia coli K-12 MG1655 		Feb 2008
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 Uncurated GO molecular function GO:0016740 transferase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005490
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 (14 enterobacteria) AMM-0005351 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0003173 erfK CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003353 ldtA CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002935 ldtA CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0002691 erfK CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0001288 CDS
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0002831 erfK CDS
Automated Process Uncurated Go view Citrobacter freundii ATCC 8090 [T] AVI-0003507 erfK CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0003470 CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0003567 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0002006 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0009429 CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0001925 erfK CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0002396 CDS
Automated Process Uncurated Go view Escherichia coli ATCC 8739 AEM-0007284 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0008432 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0008047 ErfK CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0078607 ldtA CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0002282 erfK CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0010420 CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0002261 erfK CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0006709 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0005998 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0006235 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0010517 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0010597 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0007675 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0010431 CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0009733 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0026875 erfK CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0004775 erfK CDS
Automated Process Approved Go view Escherichia coli HS ADR-0006788 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0002489 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0001866 erfK CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002042 erfK CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0001983 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0002395 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0001892 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0002321 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0176456 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0002314 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0001133 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0132785 erfK CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0004684 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0002235 erfK CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0002443 erfK CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0000794 CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0003741 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0006306 CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0000909 CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0002384 erfK CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0006617 CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0006422 erfK CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0006103 erfK CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0004404 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0006599 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0005899 CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0006344 CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0003980 CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0005726 CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0006554 CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0007719 CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0000857 CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0000856 erfK CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0001099 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0006788 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0008268 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0006264 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0007948 CDS
Person Uncurated Go view Salmonella Typhi CT18 ABX-0109449 erfK CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0082572 erfK CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0002507 erfK CDS
Person Uncurated Go view Salmonella Typhimurium LT2 [T] ABU-0096473 erfK CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0007271 CDS
Person Approved Go view Shigella boydii 227 ADV-0001336 erfK CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0006364 CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0003779 CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0002584 erfK CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0073279 erfK CDS
Person Approved Go view Shigella flexneri 301 ABT-0088345 erfK CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0002212 erfK CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0016168 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0003190 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
FB20559mutantTn5 InsertionRequest the StrainABE-0006607ldtAerfK::Tn5KAN-2 at position 290 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 2057391 to 2068323
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0006582yeeNCDSforward20568582057574Downstream
ABE-0006584asnWtRNAcomplement20580272058102Downstream
ABE-0006586yeeOCDScomplement20582032059657Downstream
ABE-0006588asnUtRNAforward20598512059926Downstream
ABE-0006590cblCDScomplement20599642060914Downstream
ABE-0006594nacCDScomplement20610162061933Downstream
ABE-0006605asnVtRNAforward20622602062335Downstream
ABE-0006607ldtACDScomplement20623912063323Matches
ABE-0006611cobTCDScomplement20633882064467Upstream
ABE-0006613cobSCDScomplement20644792065222Upstream
ABE-0006616cobUCDScomplement20652192065764Upstream
ABE-0285237yeeHpseudogenecomplement20660652066154(Interval #2) Upstream
ABE-0006617is_elementforward20661592067353Upstream
ABE-0234210CP4-44prophageforward20661592079031Upstream
ABE-0285478mobile_elementcomplement20661592067353Upstream
ABE-0006619insH6CDScomplement20663052067285Upstream
ABE-0285237yeeHpseudogenecomplement20673542067455(Interval #1) Upstream
ABE-0285479misc_featureforward20673542079031Upstream
ABE-0285238yoeGpseudogenecomplement20674562067892Upstream
ABE-0285239yoeHpseudogenecomplement20682522068419Upstream
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.