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

ABE-0009486 (lysS) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0009486 showshow history
Names
lysS JW2858 ECK2885 herC asuD b2890
Product
lysine-tRNA ligase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 3033657 3035174 1518 506
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR012340 (IPR012340 Nucleic acid-binding, OB-fold) Apr 2008
Automated Process Approved IPR002313 (IPR002313 Lysine-tRNA ligase, class II) Apr 2008
Automated Process Approved IPR004365 (IPR004365 OB-fold nucleic acid binding domain, AA-tRNA synthetase-type) Apr 2008
Automated Process Approved IPR004364 (IPR004364 Aminoacyl-tRNA synthetase, class II (D/K/N)) Apr 2008
Automated Process Approved IPR006195 (IPR006195 Aminoacyl-tRNA synthetase, class II) Apr 2008
Automated Process Approved PF01336 (PF01336 OB-fold nucleic acid binding domain) Jul 2018
Automated Process Approved PF00152 (PF00152 tRNA synthetases class II (D, K and N)) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Approved GO biological process GO:0006418 tRNA aminoacylation for protein translation Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0006418 tRNA aminoacylation for protein translation GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004364
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO biological process GO:0006430 lysyl-tRNA aminoacylation GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002313
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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 Approved GO cellular component GO:0005737 cytoplasm GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004364
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO cellular component GO:0005737 cytoplasm Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO molecular function GO:0000166 nucleotide binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR004364
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0004812 aminoacyl-tRNA ligase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004364
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0005524 ATP binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002313
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0004824 lysine-tRNA ligase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002313
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0003676 nucleic acid binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004365
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name lysS Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym asuD Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved synonym herC Published Sequence Analysis - PubMed ID: 9729611 Aug 2003
Person Approved synonym JW2858 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK2885 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2890 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product lysine-tRNA ligase Published Annotation - EcoCyc Accession Number: EG10552
Reference: Escherichia coli K-12 MG1655 		Oct 2021
Person Uncurated alternate product name lysine tRNA synthetase, constitutive Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name lysine tRNA synthetase, constitutive; suppressor of ColE1 mutation in primer RNA Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family IPR012340 Nucleic acid-binding, OB-fold Protein Sequence Similarity - InterPro Domain: IPR012340
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF01336 OB-fold nucleic acid binding domain Protein Sequence Similarity - PFAM Model Name: PF01336
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF00152 tRNA synthetases class II (D, K and N) Protein Sequence Similarity - PFAM Model Name: PF00152
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR004364 Aminoacyl-tRNA synthetase, class II (D/K/N) Protein Sequence Similarity - InterPro Domain: IPR004364
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR006195 Aminoacyl-tRNA synthetase, class II Protein Sequence Similarity - InterPro Domain: IPR006195
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR002313 Lysine-tRNA ligase, class II Protein Sequence Similarity - InterPro Domain: IPR002313
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR004365 OB-fold nucleic acid binding domain, AA-tRNA synthetase-type Protein Sequence Similarity - InterPro Domain: IPR004365
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 6.1.1.6 Published Annotation - Swiss-Prot Accession Number: P0A8N3 Feb 2006
Automated Process Uncurated EC number 6.1.1.- Published Annotation - Database Name: EC2GO: GO:0004812
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Person Uncurated MultiFun 2.3.1 (information transfer; protein related; amino acid -activation) 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
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:1789256 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG10552 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P0A8N3 Published Annotation - Swiss-Prot Accession Number: P0A8N3 Jan 2006
Automated Process Approved db xref GeneID:947372 Published Annotation - Entrez Gene Database ID: 947372
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P0A8N3 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0009486 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Aminoacyl tRNA synthetases, tRNA modification Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Uncurated molecular interaction Interacts with the product of lysU ASAP:13520:(interacting residues not known); by MALDI-TOF and LC-MS Experimental - PubMed ID: 15690043
Reference: Escherichia coli K-12 W3110 		Mar 2005
Person Uncurated molecular interaction Interacts with the product of tdcD ASAP:10245:(interacting residues not known); by MALDI-TOF Experimental - PubMed ID: 15690043
Reference: Escherichia coli K-12 W3110 		Mar 2005
Automated Process Approved note lysine tRNA synthetase, constitutive; suppressor of ColE1 mutation in primer RNA; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0006418 - tRNA aminoacylation for protein translation Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75928.1 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: 10.00
Reference: Escherichia coli K-12 MG1655 		Feb 2008
Person Uncurated subsystem component of in silico model the E-matrix Experimental - PubMed ID: 19282977
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 Approved GO biological process GO:0006418 tRNA aminoacylation for protein translation Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0006418 tRNA aminoacylation for protein translation GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004364
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO biological process GO:0006430 lysyl-tRNA aminoacylation GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002313
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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
Person Uncurated 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 - Database Name:Identifier: INTERPRO:IPR004364
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0005524 ATP binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002313
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0000166 nucleotide binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR004364
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0004812 aminoacyl-tRNA ligase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004364
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0003676 nucleic acid binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004365
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved GO molecular function GO:0004824 lysine-tRNA ligase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR002313
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-0000118 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0000044 lysS CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0000049 lysS CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0000148 lysS CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0000046 lysS CDS
Ortholog
Person Uncurated Go view Buchnera aphidicola APS ABZ-0129707 lysS CDS
Person Uncurated Go view Buchnera aphidicola Bp ABW-0105115 lysS CDS
Person Uncurated Go view Buchnera aphidicola Sg [T] ABV-0104551 lysS CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003770 lysS CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0004489 lysS CDS
Person Uncurated Go view Dickeya dadantii 3937 ABF-0018048 lysS CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0002913 CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0002890 lysS CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001388 lysS CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006300 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079630 lysS CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003315 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003825 CDS
Automated Process Uncurated Go view Escherichia coli E2348/69 (EPEC) BCI-0003346 lysS CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007652 lysS1 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0009016 lysS CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027900 lysS CDS
Automated Process Uncurated Go view Escherichia coli F11 (UPEC) ADQ-0008398 lysS CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007728 lysS2 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003371 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002706 lysS CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002961 lysS CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003384 lysS CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003525 lysS CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003252 lysS CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003216 lysS CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0177471 lysS CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003214 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0003021 lysS CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133804 lysS CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003284 lysS CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0000933 CDS
Person Uncurated Go view Photorhabdus luminescens subsp. laumondii TTO1 [T] ACD-0144915 lysS CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0003485 lysS CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0002907 lysS CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0111832 lysS CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0084676 lysS CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0099473 lysS CDS
Person Approved Go view Shigella boydii 227 ADV-0003396 lysS CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0008722 lysS CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0003636 lysS CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074251 lysS CDS
Person Approved Go view Shigella flexneri 301 ABT-0089129 lysS CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0003135 lysS CDS
Person Approved Go view Shigella sonnei 046 ADD-0003326 lysS CDS
Person Uncurated Go view Wigglesworthia morsitans AEQ-0000621 lysS CDS
Person Uncurated Go view Yersinia pestis 91001 (biovar Microtus) ACQ-0242946 lysS CDS
Person Uncurated Go view Yersinia pestis Antiqua (biovar Antiqua) BAE-0000472 lysS CDS
Person Uncurated Go view Yersinia pestis CO92 (biovar Orientalis) ABY-0118218 lysS CDS
Person Uncurated Go view Yersinia pestis KIM (biovar Mediaevalis) ABI-0033039 lysS CDS
Person Uncurated Go view Yersinia pestis Nepal516 (biovar Antiqua) BAD-0003715 lysS CDS
Person Uncurated Go view Yersinia pseudotuberculosis IP32953 ACZ-0003270 lysS 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 3028657 to 3040174
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0009471ygfSCDScomplement30285243029012Downstream
ABE-0009473ygfTCDScomplement30290123030931Downstream
ABE-0009478uacTCDSforward30313673032815Downstream
ABE-0285227yqfGCDSforward30328173032942Downstream
ABE-0285740yqfHCDScomplement30329393033010Downstream
ABE-0009484idiCDSforward30330653033613Downstream
ABE-0009486lysSCDScomplement30336573035174Matches
ABE-0009488prfBCDScomplement30351843036206(Interval #2) Upstream
ABE-0009488prfBCDScomplement30362083036282(Interval #1) Upstream
ABE-0009492recJCDScomplement30363733038106Upstream
ABE-0009494dsbCCDScomplement30381123038822Upstream
ABE-0009500xerDCDScomplement30388473039743Upstream
ABE-0009503fldBCDSforward30398553040376Upstream
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.