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

ABE-0012442 (dapF) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0012442 showshow history
Names
dapF JW5592 ECK3804 b3809
Product
diaminopimelate epimerase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 3994762 3995586 825 275
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Person Approved ADX-0001452
EnteroFam0012442: Trusted threshold=805.3; Members of this family are defined by searches with an hmm constructed from an alignment of putative orthologous proteins from eight genomes (E. coli MG1655, E. coli EDL933, S. enterica Typhimurium LT2, S. enterica Typhi CT18, Y. pestis CO92, Y. pseudotuberculosis 32953, E. chrysanthemi 3937 and E. carotovora atroseptica SCRI1043). 		Jan 2006
Automated Process Approved IPR001653 (IPR001653 Diaminopimelate epimerase, DapF) Apr 2008
Automated Process Approved PF01678 (PF01678 Diaminopimelate epimerase) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Approved GO biological process GO:0009089 lysine biosynthetic process via diaminopimelate Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0009089 lysine biosynthetic process via diaminopimelate GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001653
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 molecular function GO:0008837 diaminopimelate epimerase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001653
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Automated Process Approved name dapF Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 MG1655 		Sep 2007
Person Approved synonym JW5592 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK3804 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b3809 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product diaminopimelate epimerase Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved alternate product name diaminopimelate epimerase Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Jan 2006
Protein Family
Person Approved EnteroFam EnteroFam0012442: Trusted threshold=805.3; Members of this family are defined by searches with an hmm constructed from an alignment of putative orthologous proteins from eight genomes (E. coli MG1655, E. coli EDL933, S. enterica Typhimurium LT2, S. enterica Typhi CT18, Y. pestis CO92, Y. pseudotuberculosis 32953, E. chrysanthemi 3937 and E. carotovora atroseptica SCRI1043). Protein Sequence Similarity - ASAP FeatureID: ADX-0001452
Reference: EnteroFams 		Jan 2006
Automated Process Approved protein family PF01678 Diaminopimelate epimerase Protein Sequence Similarity - PFAM Model Name: PF01678
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR001653 Diaminopimelate epimerase, DapF Protein Sequence Similarity - InterPro Domain: IPR001653
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Other
Person Approved EC number 5.1.1.7 Published Annotation - Swiss-Prot Accession Number: P0A6K1 Feb 2006
Person Uncurated MultiFun 1.5.1.7 (metabolism; building block biosynthesis; amino acids; lysine, diaminopimelate) 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 ASAP:ABE-0012442 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref EcoGene:EG10209 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P0A6K1 Published Annotation - Swiss-Prot Accession Number: P0A6K1 Jan 2006
Automated Process Approved db xref GI:87082334 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:948364 Published Annotation - Entrez Gene Database ID: 948364
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref UniProtKB/Swiss-Prot:P0A6K1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved function enzyme; Amino acid biosynthesis: Lysine Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Automated Process Approved note GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009089 - lysine biosynthetic process via diaminopimelate Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC76812.2 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: 9.97
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
Person Approved GO biological process GO:0009089 lysine biosynthetic process via diaminopimelate Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Automated Process Approved GO biological process GO:0009089 lysine biosynthetic process via diaminopimelate GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001653
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 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 molecular function GO:0008837 diaminopimelate epimerase activity GO Inferred from Electronic Annotation - Database Name:Identifier: INTERPRO:IPR001653
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Person Approved Go view EnteroFams ADX-0001452 dapF CDS
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0000806 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0000161 dapF CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0000153 dapF CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0000389 dapF CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0000428 dapF CDS
Ortholog
Automated Process Uncurated Go view Brenneria salicis ATCC 15712 [T] AMK-0002397 CDS
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0002374 CDS
Person Uncurated Go view Buchnera aphidicola APS ABZ-0129859 dapF CDS
Person Uncurated Go view Buchnera aphidicola Bp ABW-0105259 dapF CDS
Person Uncurated Go view Buchnera aphidicola Sg [T] ABV-0104706 dapF CDS
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0000214 dapF CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0004008 dapF CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0004464 dapF CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0000460 dapF CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0004600 CDS
Person Approved Go view Dickeya dadantii 3937 ABF-0015010 dapF CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0003981 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0000095 dapF CDS
Automated Process Uncurated Go view Erwinia amylovora ATCC 49946 ACW-0296584 dapF CDS
Automated Process Uncurated Go view Erwinia amylovora ATCC BAA-2158 APN-0000261 dapF CDS
Automated Process Uncurated Go view Erwinia tasmaniensis Et1/99 [T] AFI-0000241 dapF CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0001704 dapF CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0007893 dapF CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0004045 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0007236 dapF CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0003848 dapF CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0000377 dapF CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0010418 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0008929 dapF CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0006228 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0080926 dapF CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0004225 dapF CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0004839 dapF CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0006274 dapF CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0009604 dapF CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0004372 dapF CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0008761 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0002621 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0008577 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0007090 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007281 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0008487 dapF CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0010081 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0008244 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0007893 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0005679 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0007520 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0009485 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0008835 dapF CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0006960 dapF CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0028948 dapF CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0009557 dapF CDS
Automated Process Approved Go view Escherichia coli HS ADR-0008720 dapF CDS
Automated Process Uncurated Go view Escherichia coli J96 (UPEC) CQK-0004353 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003536 dapF CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0003542 dapF CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0004491 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004488 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0004317 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0004378 dapF CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0178502 dapF CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0004178 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0004171 dapF CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0134829 dapF CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0004784 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004381 dapF CDS
Automated Process Uncurated Go view Ewingella americana ATCC 33852 [T] AMA-0003838 dapF CDS
Person Uncurated Go view Hafnia alvei ATCC 13337 [T] AMD-0000944 dapF CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0004356 dapF CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0002244 dapF CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0004620 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0003275 CDS
Automated Process Uncurated Go view Pantoea agglomerans SL1-M5 ALY-0000154 dapF CDS
Automated Process Uncurated Go view Pantoea ananatis AJ13355 AOV-0003406 dapF CDS
Automated Process Uncurated Go view Pantoea ananatis B1-9 APL-0000573 CDS
Automated Process Uncurated Go view Pantoea ananatis LMG 20103 AKB-0000172 dapF CDS
Automated Process Approved Go view Pantoea ananatis PA13 APK-0004214 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0007925 CDS
Automated Process Uncurated Go view Pantoea sp. aB AJV-0003602 CDS
Automated Process Approved Go view Pantoea stewartii DC283 ACV-0288627 dapF CDS
Automated Process Uncurated Go view Pantoea vagans C9-1 ALK-0007162 dapF CDS
Person Approved Go view Pectobacterium atrosepticum SCRI1043 ABL-0064509 dapF CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0002475 dapF CDS
Person Uncurated Go view Pectobacterium carotovorum WPP14 ADT-0003214 dapF CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0003413 dapF CDS
Automated Process Uncurated Go view Pectobacterium sp. PC1 AFL-0009252 CDS
Person Uncurated Go view Photorhabdus luminescens subsp. laumondii TTO1 [T] ACD-0147374 dapF CDS
Person Uncurated Go view Pseudomonas syringae pv. tomato DC3000 ADG-0000225 dapF CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0008341 dapF CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0003889 CDS
Person Approved Go view Salmonella Choleraesuis SC-B67 ADB-0004508 dapF CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0008577 dapF CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0012369 dapF CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0010670 dapF CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0007607 dapF CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0008631 dapF CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0008229 dapF CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0007542 dapF CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0008156 dapF CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0007729 dapF CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0008579 dapF CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0008844 dapF CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0003827 CDS
Person Approved Go view Salmonella Paratyphi A ATCC 9150 ADA-0003786 dapF CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0004919 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0008756 dapF CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0008884 dapF CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0008224 dapF CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0007618 dapF CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0112641 dapF CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0085072 dapF CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0004754 dapF CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0102158 dapF CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0005219 dapF CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0008826 dapF CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0007987 dapF CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0000771 dapF CDS
Person Uncurated Go view Shewanella oneidensis MR-1 ACY-0267956 dapF CDS
Person Approved Go view Shigella boydii 227 ADV-0004163 dapF CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0009686 dapF CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0006779 dapF CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0004445 dapF CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0075122 dapF CDS
Person Approved Go view Shigella flexneri 301 ABT-0090104 dapF CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0003920 dapF CDS
Person Approved Go view Shigella sonnei 046 ADD-0004336 dapF CDS
Person Uncurated Go view Sodalis glossinidius morsitans AEB-0002428 CDS
Person Uncurated Go view Vibrio cholerae N16961 ADH-0000133 VC0126 CDS
Person Uncurated Go view Wigglesworthia brevipalpis ACB-0135769 dapF CDS
Person Approved Go view Wigglesworthia morsitans AEQ-0000434 dapF CDS
Person Uncurated Go view Xenorhabdus nematophila ATCC 19061 [T] ADW-0000640 dapF CDS
Automated Process Uncurated Go view Yersinia bercovieri ATCC 43970 [T] AEK-0001929 CDS
Automated Process Uncurated Go view Yersinia enterocolitica 8081 BAH-0000602 dapF CDS
Automated Process Uncurated Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0002509 dapF CDS
Automated Process Uncurated Go view Yersinia intermedia ATCC 29909 [T] AEH-0001708 dapF CDS
Automated Process Uncurated Go view Yersinia mollaretii ATCC 43969 [T] AEJ-0003859 CDS
Person Approved Go view Yersinia pestis 91001 (biovar Microtus) ACQ-0241945 dapF CDS
Automated Process Uncurated Go view Yersinia pestis Angola (biovar Pestoides) ADI-0004646 dapF CDS
Automated Process Uncurated Go view Yersinia pestis Antiqua (biovar Antiqua) BAE-0000227 dapF CDS
Automated Process Uncurated Go view Yersinia pestis B42003004 (biovar Antiqua) BAL-0007639 dapF CDS
Automated Process Uncurated Go view Yersinia pestis CA88-4125 (biovar Orientalis) BAF-0003534 dapF CDS
Person Approved Go view Yersinia pestis CO92 (biovar Orientalis) ABY-0128243 dapF CDS
Automated Process Uncurated Go view Yersinia pestis E1979001 (biovar Antiqua) BAM-0008093 dapF CDS
Automated Process Uncurated Go view Yersinia pestis F1991016 (biovar Orientalis) BAQ-0006481 dapF CDS
Automated Process Uncurated Go view Yersinia pestis FV-1 (biovar Orientalis) BAK-0002803 CDS
Automated Process Uncurated Go view Yersinia pestis IP275 (biovar Orientalis) BAC-0008477 dapF CDS
Automated Process Uncurated Go view Yersinia pestis K1973002 (biovar Mediaevalis) BAO-0007471 dapF CDS
Person Approved Go view Yersinia pestis KIM (biovar Mediaevalis) ABI-0029991 dapF CDS
Automated Process Uncurated Go view Yersinia pestis MG05-1020 (biovar Orientalis) BAP-0006927 dapF CDS
Automated Process Uncurated Go view Yersinia pestis Nepal516 (biovar Antiqua) BAD-0000157 dapF CDS
Automated Process Uncurated Go view Yersinia pestis Pestoides F (biovar Pestoides) BAI-0004149 CDS
Automated Process Uncurated Go view Yersinia pestis UG05-0454 (biovar Antiqua) BAN-0008147 dapF CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis IP31758 ADS-0004140 dapF CDS
Person Approved Go view Yersinia pseudotuberculosis IP32953 ACZ-0000208 dapF CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis PB1/+ AFV-0000242 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis YPIII AFW-0004760 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0000304 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0000682 dapF 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 3989762 to 4000586
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0012425hemDCDScomplement39890883989828Upstream
ABE-0012427hemCCDScomplement39898253990766Upstream
ABE-0012432cyaACDSforward39911533993699Upstream
ABE-0012435cyaYCDScomplement39937393994059Upstream
ABE-0285079yifLCDSforward39945223994725Upstream
ABE-0012442dapFCDSforward39947623995586Matches
ABE-0012444yigACDSforward39955833996290Overlaps Downstream
ABE-0012448xerCCDSforward39962873997183Downstream
ABE-0012450yigBCDSforward39971833997899Downstream
ABE-0012455uvrDCDSforward39979834000145Downstream
ABE-0285640repeat_regionforward40001504000252Downstream
ABE-0174110yigECDScomplement40002924001056Downstream
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.