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

ABE-0002362 (speF) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0002362 showshow history
Names
speF JW0680 ECK0681 b0693
Product
ornithine decarboxylase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome complement 718262 720460 2199 733
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 IPR011006 (IPR011006 CheY-like superfamily) 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 IPR027568 (IPR027568 Ornithine decarboxylase SpeF) Jul 2018
Automated Process Approved IPR036633 (IPR036633 Orn/Lys/Arg decarboxylase, C-terminal domain superfamily) Jul 2018
Automated Process Approved PF01276 (PF01276 Orn/Lys/Arg decarboxylase, major domain) Jul 2018
Automated Process Approved PF03709 (PF03709 Orn/Lys/Arg decarboxylase, N-terminal 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:0006596 polyamine biosynthetic 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 Uncurated GO molecular function GO:0004586 ornithine decarboxylase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR027568
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000310
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
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name speF Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK0681 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW0680 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b0693 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product ornithine decarboxylase Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 		Oct 2021
Person Approved alternate product name ornithine decarboxylase isozyme, inducible Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
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 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 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 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 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 IPR011006 CheY-like superfamily Protein Sequence Similarity - InterPro Domain: IPR011006
Reference: Escherichia coli K-12 MG1655 		Apr 2008
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 IPR027568 Ornithine decarboxylase SpeF Protein Sequence Similarity - InterPro Domain: IPR027568
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 PF01276 Orn/Lys/Arg decarboxylase, major domain Protein Sequence Similarity - PFAM Model Name: PF01276
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain Protein Sequence Similarity - PFAM Model Name: PF03711
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 4.1.1.17 Published Annotation - Swiss-Prot Accession Number: P24169 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 1.7.14 (metabolism; central intermediary metabolism; polyamine biosynthesis) 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:P24169 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GI:1786909 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P24169 Published Annotation - Swiss-Prot Accession Number: P24169 Jan 2005
Automated Process Approved db xref EcoGene:EG10964 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:945297 Published Annotation - Entrez Gene Database ID: 945297
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref ASAP:ABE-0002362 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Central intermediary metabolism: Polyamine biosynthesis Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note GO_process: GO:0006596 - polyamine biosynthetic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC73787.1 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 iAF1260 Experimental - PubMed ID: 17593909
Reference: Escherichia coli K-12 MG1655 		Jan 2009
Person Uncurated subsystem component of in silico model iJR904 Experimental - PubMed ID: 12952533
Reference: Escherichia coli K-12 MG1655 		Feb 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: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:0006596 polyamine biosynthetic 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:0003824 catalytic activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR000310
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Uncurated GO molecular function GO:0004586 ornithine decarboxylase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR027568
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0000060 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0000039 speF CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0000040 speF CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0000051 speF CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0000033 speF CDS
Ortholog
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0001504 speC_2 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0000718 CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0000618 speF CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0003664 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0008896 CDS
Person Uncurated Go view Escherichia coli B7A (ETEC) ADK-0007475 speF pseudogene
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0076861 speF CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0000743 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0000850 CDS
Automated Process Uncurated Go view Escherichia coli E2348/69 (EPEC) BCI-0000613 speF CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0005165 speF CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0005625 speF CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0024673 speF CDS
Automated Process Uncurated Go view Escherichia coli F11 (UPEC) ADQ-0009330 speF CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0000981 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0000674 speF CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0000699 speF CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0000933 speF CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0000781 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0000776 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0174868 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0000769 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0000714 speF CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0130622 speF CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0000697 speF CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0000859 speF CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0002040 speF CDS
Person Uncurated Go view Salmonella Typhi CT18 ABX-0285118 speF pseudogene
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0285091 speF pseudogene
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0092657 speF CDS
Person Uncurated Go view Shigella boydii 227 ADV-0000597 speF CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0285595 speF pseudogene
Person Uncurated Go view Shigella flexneri 301 ABT-0286348 speF pseudogene
Person Approved Go view Shigella sonnei 046 ADD-0000692 speF CDS
Person Uncurated Go view Vibrio cholerae N16961 ADH-0003956 VCA1063 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 713262 to 725460
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0002343seqACDSforward712987713532Downstream
ABE-0002345pgmCDSforward713558715198Downstream
ABE-0285392repeat_regionforward715264715361Downstream
ABE-0002350ybfPCDSforward715412715906Downstream
ABE-0002352ybfG_2CDSpcomplement715947716357Downstream
ABE-0285121ybfGpseudogenecomplement715947716597Downstream
ABE-0002355ybfG_1CDSpcomplement716388716597Downstream
ABE-0285170ybfIpseudogenecomplement716721716864Downstream
ABE-0002360potECDScomplement716946718265Overlaps Downstream
ABE-0002362speFCDScomplement718262720460Matches
ABE-0285828speFLCDScomplement720718720822Upstream
ABE-0002366kdpECDScomplement721056721733Upstream
ABE-0002368kdpDCDScomplement721730724414Upstream
ABE-0002374kdpCCDScomplement724407724979Upstream
ABE-0002376kdpBCDScomplement724988727036Upstream
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.