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

ABE-0009172 (sdaB) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0009172 showshow history
Names
sdaB JW2768 ECK2792 b2797
Product
L-serine deaminase II
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 2929576 2930943 1368 456
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 IPR004644 (IPR004644 Iron-sulphur-dependent L-serine dehydratase single chain form) Apr 2008
Automated Process Approved IPR005130 (IPR005130 Serine dehydratase-like, alpha subunit) Apr 2008
Automated Process Approved IPR005131 (IPR005131 Serine dehydratase beta chain) Apr 2008
Automated Process Approved IPR029009 (IPR029009 Allosteric substrate binding domain superfamily) Jul 2018
Automated Process Approved PF03315 (PF03315 Serine dehydratase beta chain) Jul 2018
Automated Process Approved PF03313 (PF03313 Serine dehydratase alpha chain) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0019395 fatty acid oxidation Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0006094 gluconeogenesis GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004644
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0009063 cellular amino acid catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO molecular function GO:0051539 4 iron, 4 sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005131
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0003941 L-serine ammonia-lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004644
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name sdaB Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym ECK2792 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym JW2768 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b2797 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product L-serine deaminase II Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated alternate product name L-serine deaminase 2 Published Annotation - Database Name: GenProtEC Jan 2006
Person Approved alternate product name L-serine dehydratase (deaminase), L-SD2 Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Automated Process Approved protein family IPR029009 Allosteric substrate binding domain superfamily Protein Sequence Similarity - InterPro Domain: IPR029009
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR004644 Iron-sulphur-dependent L-serine dehydratase single chain form Protein Sequence Similarity - InterPro Domain: IPR004644
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR005130 Serine dehydratase-like, alpha subunit Protein Sequence Similarity - InterPro Domain: IPR005130
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR005131 Serine dehydratase beta chain Protein Sequence Similarity - InterPro Domain: IPR005131
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family PF03315 Serine dehydratase beta chain Protein Sequence Similarity - PFAM Model Name: PF03315
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF03313 Serine dehydratase alpha chain Protein Sequence Similarity - PFAM Model Name: PF03313
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Approved EC number 4.3.1.17 Published Annotation - Swiss-Prot Accession Number: P30744 Feb 2006
Person Uncurated MultiFun 1.1.3 (metabolism; carbon utilization; amino acids) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.7.30 (metabolism; central intermediary metabolism; threonine catabolism) Published Annotation - MultiFun Database Name: MultiFun Feb 2002
Person Uncurated MultiFun 1.1.2 (metabolism; carbon utilization; fatty acids) 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:1789161 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P30744 Published Annotation - Swiss-Prot Accession Number: P30744 Jan 2005
Automated Process Approved db xref UniProtKB/Swiss-Prot:P30744 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0009172 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG11623 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:947262 Published Annotation - Entrez Gene Database ID: 947262
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Person Approved function enzyme; Degradation of small molecules: Amino acids Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note L-serine dehydratase (deaminase), L-SD2; GO_process: GO:0019395 - fatty acid oxidation; GO_process: GO:0009063 - cellular amino acid catabolic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC75839.1 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:0009063 cellular amino acid catabolic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0006094 gluconeogenesis GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004644
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Person Uncurated GO biological process GO:0019395 fatty acid oxidation Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Uncurated GO molecular function GO:0051539 4 iron, 4 sulfur cluster binding GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR005131
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved GO molecular function GO:0003941 L-serine ammonia-lyase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR004644
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-0000013 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0000013 tdcG CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0000011 tdcG CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0000004 tdcG CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0000005 tdcG CDS
Ortholog
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0003618 sdaB CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0004350 sdaB CDS
Person Approved Go view Dickeya dadantii 3937 ABF-0017173 sdaB CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0002794 sdaB CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0001492 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0006413 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0079520 sdaB CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0003197 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0003710 CDS
Automated Process Uncurated Go view Escherichia coli E2348/69 (EPEC) BCI-0003258 sdaB CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0007538 sdaB CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0008897 sdaB CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0027786 sdaB CDS
Automated Process Uncurated Go view Escherichia coli F11 (UPEC) ADQ-0006123 sdaB CDS
Automated Process Approved Go view Escherichia coli HS ADR-0007617 sdaB CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0003255 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0002620 sdaB CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0002866 sdaB CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0003489 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0003635 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0003356 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0003115 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0177365 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0003114 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0002935 sdaB CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0133694 sdaB CDS
Person Approved Go view Escherichia coli UTI89 (UPEC) AEA-0003177 sdaB CDS
Person Uncurated Go view Pectobacterium atrosepticum SCRI1043 ABL-0063447 sdaB CDS
Person Uncurated Go view Pectobacterium carotovorum WPP14 ADT-0001977 sdaB CDS
Person Uncurated Go view Salmonella Choleraesuis SC-B67 ADB-0003403 sdaB CDS
Person Uncurated Go view Salmonella Paratyphi A ATCC 9150 ADA-0002834 sdaB CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0111669 sdaB CDS
Person Uncurated Go view Salmonella Typhi Ty2 ABS-0084597 sdaB CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0099273 sdaB CDS
Person Approved Go view Shigella boydii 227 ADV-0002953 sdaB CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0008486 sdaB CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0003446 sdaB CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0074181 sdaB CDS
Person Approved Go view Shigella flexneri 301 ABT-0089062 sdaB CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0003070 sdaB CDS
Person Approved Go view Shigella sonnei 046 ADD-0003230 sdaB CDS
Person Uncurated Go view Trabulsiella guamensis ATCC 49490 [T] APH-0002729 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
FB20931mutantTn5 InsertionRequest the StrainABE-0009172sdaBsdaB::Tn5KAN-I-SceI at position 894 in Plus orientation ,+ pKD460Blattner Laboratory
FB20932mutantTn5 InsertionRequest the StrainABE-0009172sdaBsdaB::Tn5KAN-I-SceI at position 894 in Plus orientation ,- pKD465Blattner 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 2924576 to 2935943
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0009154sydCDScomplement29247352925280Upstream
ABE-0009162queFCDSforward29253482926196Upstream
ABE-0009166ppnNCDSforward29263082927672Upstream
ABE-0009169sdaCCDSforward29282292929518Upstream
ABE-0009172sdaBCDSforward29295762930943Matches
ABE-0009174ygdGCDSforward29310552931810Downstream
ABE-0285548repeat_regionforward29318172931846Downstream
ABE-0009177fucOCDScomplement29318652933013Downstream
ABE-0009179fucACDScomplement29330412933688Downstream
ABE-0009187fucPCDSforward29342352935551Downstream
ABE-0009189fucICDSforward29355842937359Downstream
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.