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

ABE-0000633 (ldcC) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0000633 showshow history
Names
ldcC LDC2 ldcH ldc JW0181 ECK0185 b0186
Product
lysine decarboxylase 2
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 209679 211820 2142 714
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Automated Process Approved IPR000310 (IPR000310 Orn/Lys/Arg decarboxylase, major domain) Apr 2008
Automated Process Approved IPR008286 (IPR008286 Orn/Lys/Arg decarboxylase, C-terminal) Apr 2008
Automated Process Approved IPR005308 (IPR005308 Orn/Lys/Arg decarboxylase, N-terminal) Apr 2008
Automated Process Approved IPR015424 (IPR015424 Pyridoxal phosphate-dependent transferase) Apr 2008
Automated Process Approved IPR015422 (IPR015422 Pyridoxal phosphate-dependent transferase, small domain) Apr 2008
Automated Process Approved IPR011193 (IPR011193 Ornithine/lysine/arginine decarboxylase) Apr 2008
Automated Process Approved IPR015421 (IPR015421 Pyridoxal phosphate-dependent transferase, major domain) Apr 2008
Automated Process Approved IPR036633 (IPR036633 Orn/Lys/Arg decarboxylase, C-terminal domain superfamily) Jul 2018
Automated Process Approved PF03709 (PF03709 Orn/Lys/Arg decarboxylase, N-terminal domain) Jul 2018
Automated Process Approved PF01276 (PF01276 Orn/Lys/Arg decarboxylase, major domain) Jul 2018
Automated Process Approved PF03711 (PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Approved GO biological process GO:0006520 cellular amino acid metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011193
Reference: Escherichia coli K-12 MG1655
Apr 2008
Person Uncurated GO biological process GO:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Person Uncurated GO biological process GO:0006096 glycolytic 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 - Database Name:Identifier: INTERPRO:IPR011193
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved GO molecular function GO:0030170 pyridoxal phosphate binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR015422
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved GO molecular function GO:0016831 carboxy-lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005308
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000310
Reference: Escherichia coli K-12 MG1655
Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name ldcC Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655
Oct 1998
Person Approved synonym ECK0185 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW0181 Published Annotation - PubMed ID: 16397293 Jan 2006
Automated Process Approved synonym ldc Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Approved synonym LDC2 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Approved synonym ldcH Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Person Approved locus tag b0186 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product lysine decarboxylase 2 Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12
Oct 2021
Person Approved alternate product name lysine decarboxylase 2, constitutive Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655
Jan 2006
Protein Family
Automated Process Approved protein family IPR008286 Orn/Lys/Arg decarboxylase, C-terminal Protein Sequence Similarity - InterPro Domain: IPR008286
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved protein family IPR000310 Orn/Lys/Arg decarboxylase, major domain Protein Sequence Similarity - InterPro Domain: IPR000310
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved protein family IPR005308 Orn/Lys/Arg decarboxylase, N-terminal Protein Sequence Similarity - InterPro Domain: IPR005308
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved protein family IPR015422 Pyridoxal phosphate-dependent transferase, small domain Protein Sequence Similarity - InterPro Domain: IPR015422
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved protein family IPR015424 Pyridoxal phosphate-dependent transferase Protein Sequence Similarity - InterPro Domain: IPR015424
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved protein family PF03709 Orn/Lys/Arg decarboxylase, N-terminal domain Protein Sequence Similarity - PFAM Model Name: PF03709
Reference: Escherichia coli K-12 MG1655
Jul 2018
Automated Process Approved protein family IPR036633 Orn/Lys/Arg decarboxylase, C-terminal domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036633
Reference: Escherichia coli K-12 MG1655
Jul 2018
Automated Process Approved protein family IPR011193 Ornithine/lysine/arginine decarboxylase Protein Sequence Similarity - InterPro Domain: IPR011193
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved protein family PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain Protein Sequence Similarity - PFAM Model Name: PF03711
Reference: Escherichia coli K-12 MG1655
Jul 2018
Automated Process Approved protein family IPR015421 Pyridoxal phosphate-dependent transferase, major domain Protein Sequence Similarity - InterPro Domain: IPR015421
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved protein family PF01276 Orn/Lys/Arg decarboxylase, major domain Protein Sequence Similarity - PFAM Model Name: PF01276
Reference: Escherichia coli K-12 MG1655
Jul 2018
Other
Person Approved EC number 4.1.1.18 Published Annotation - Swiss-Prot Accession Number: P52095 Feb 2006
Automated Process Uncurated EC number 4.1.1.- Published Annotation - Database Name: EC2GO: GO:0016831
Reference: Escherichia coli K-12 MG1655
Jul 2018
Person Uncurated MultiFun 1.1.1 (metabolism; carbon utilization; carbon compounds) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.3.1 (metabolism; energy metabolism, carbon; glycolysis) 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
Person Approved db xref UniProtKB:P52095 Published Annotation - Swiss-Prot Accession Number: P52095 Jan 2005
Automated Process Approved db xref GeneID:944887 Published Annotation - Entrez Gene Database ID: 944887
Reference: Escherichia coli K-12 MG1655
Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P52095 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Approved db xref ASAP:ABE-0000633 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Approved db xref GI:1786384 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Approved db xref EcoGene:EG13219 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Person Approved function enzyme; Energy metabolism, carbon: Pyruvate dehydrogenase Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655
Oct 1998
Person Uncurated molecular interaction Interacts with the product of cadA ASAP:13526:(interacting residues not known); by MALDI-TOF and LC-MS Experimental - PubMed ID: 15690043
Reference: Escherichia coli K-12 W3110
Mar 2005
Automated Process Approved note GO_process: GO:0006096 - glycolysis; GO_process: GO:0016052 - carbohydrate catabolic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655
Oct 2013
Automated Process Approved protein id AAC73297.1 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 iMC1010 Experimental - PubMed ID: 15129285
Reference: Escherichia coli K-12 MG1655
Mar 2009
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 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:0016052 carbohydrate catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0006520 cellular amino acid metabolic process GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR011193
Reference: Escherichia coli K-12 MG1655
Apr 2008
Person Uncurated GO biological process GO:0006096 glycolytic 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 - Database Name:Identifier: INTERPRO:IPR011193
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved GO molecular function GO:0030170 pyridoxal phosphate binding GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR015422
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved GO molecular function GO:0016831 carboxy-lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR005308
Reference: Escherichia coli K-12 MG1655
Apr 2008
Automated Process Approved GO molecular function GO:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000310
Reference: Escherichia coli K-12 MG1655
Apr 2008
Comparative to toptop
Author Approval Details Genome Feature Name Type
Homolog
Person Uncurated Go view Escherichia coli CFT073 (UPEC) ABR-0081346 cadA CDS
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0004167 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0000054 ldcC CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0000074 ldcC CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0000043 ldcC CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0000007 ldcC CDS
Ortholog
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0001042 ldcC_1 CDS
Automated Process Uncurated Go view Citrobacter freundii ATCC 8090 [T] AVI-0001452 ldcC_2 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0000195 CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0000181 ldcC CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0004112 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0009535 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0076289 ldcC CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0000191 ldcC CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0000241 CDS
Automated Process Uncurated Go view Escherichia coli E2348/69 (EPEC) BCI-0000197 ldcC CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0004639 ldcC CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0005036 ldcC1 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0024102 ldcC CDS
Automated Process Uncurated Go view Escherichia coli F11 (UPEC) ADQ-0007869 ldcC CDS
Automated Process Approved Go view Escherichia coli HS ADR-0004871 ldcC1 CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0000494 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0000225 ldcC CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0000186 ldcC CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0000172 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0000156 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0000292 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0000219 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0174401 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0000186 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0000198 ldcC1 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0130067 ldcC CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0000202 ldcC CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0000262 ldcC CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0000242 ldcC CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0105840 ldcC CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0081947 ldcC CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0091336 ldcC CDS
Person Uncurated Go view Shigella boydii 227 ADV-0005096 ldcC pseudogene
Automated Process Approved Go view Shigella boydii BS512 ADJ-0005577 ldcC1 CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0005595 ldcC pseudogene
Person Approved Go view Shigella flexneri 2457T ABQ-0071117 ldcC CDS
Person Uncurated Go view Shigella flexneri 301 ABT-0086537 ldcC CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0000173 ldcC CDS
Person Approved Go view Shigella sonnei 046 ADD-0000214 ldcC 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 204679 to 216820
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0000622rnhBCDSforward204493205089Upstream
ABE-0000624dnaECDSforward205126208608Upstream
ABE-0000630accACDSforward208621209580Upstream
ABE-0000633ldcCCDSforward209679211820Matches
ABE-0000635yaeRCDSforward211877212266Downstream
ABE-0000638tilSCDSforward212331213629Downstream
ABE-0285334repeat_regionforward213632213668Downstream
ABE-0000641rofCDScomplement213678213932Downstream
ABE-0047214yaePCDScomplement213925214125Downstream
ABE-0000648yaeQCDSforward214291214836Downstream
ABE-0000650arfBCDSforward214833215255Downstream
ABE-0000652nlpECDSforward215269215979Downstream
ABE-0285335repeat_regionforward216027216137Downstream
ABE-0000655yaeFCDScomplement216179217003Downstream
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.