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

ABE-0013644 (nnr) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0013644 showshow history
Names
nnr yjeF JW4125 ECK4163 b4167
Product
NAD(P)HX epimerase/NAD(P)HX dehydratase
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 4394066 4395613 1548 516
Sequence

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Context

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Protein Families to toptop
Author Approval Family Annotated
Person Approved ADX-0001607
EnteroFam0013644: Trusted threshold=1160.5; 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 IPR004443 (IPR004443 YjeF N-terminal domain) Apr 2008
Automated Process Approved IPR006035 (IPR006035 Ureohydrolase) Apr 2008
Automated Process Approved IPR000631 (IPR000631 ATP-dependent (S)-NAD(P)H-hydrate dehydratase) Apr 2008
Automated Process Approved IPR036652 (IPR036652 YjeF N-terminal domain superfamily) Jul 2018
Automated Process Approved IPR029056 (IPR029056 Ribokinase-like) Jul 2018
Automated Process Approved PF01256 (PF01256 Carbohydrate kinase) Jul 2018
Automated Process Approved PF03853 (PF03853 YjeF-related protein N-terminus) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Automated Process Uncurated GO molecular function GO:0052855 ADP-dependent NAD(P)H-hydrate dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR000631
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Uncurated name nnr Published Annotation - PubMed ID: 21994945
Reference: Escherichia coli K-12 		Jul 2018
Automated Process Approved synonym yjeF Published Annotation - PubMed ID: 16397293
Reference: Escherichia coli K-12 MG1655 		Sep 2007
Person Approved synonym JW4125 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym ECK4163 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b4167 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Uncurated product NAD(P)HX epimerase/NAD(P)HX dehydratase Experimental - PubMed ID: 21994945
Reference: Escherichia coli K-12 		Jul 2018
Automated Process Approved alternate product name bifunctional NAD(P)H-hydrate repair enzyme; C-terminal domain ADP-dependent (S)-NAD(P)H-hydrate dehydratase and N-terminal domain NAD(P)H-hydrate epimerase Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved alternate product name predicted carbohydrate kinase Published Annotation - PubMed ID: 16397293 Jan 2006
Protein Family
Person Approved EnteroFam EnteroFam0013644: Trusted threshold=1160.5; 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-0001607
Reference: EnteroFams 		Jan 2006
Automated Process Approved protein family IPR029056 Ribokinase-like Protein Sequence Similarity - InterPro Domain: IPR029056
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF03853 YjeF-related protein N-terminus Protein Sequence Similarity - PFAM Model Name: PF03853
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR004443 YjeF N-terminal domain Protein Sequence Similarity - InterPro Domain: IPR004443
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR006035 Ureohydrolase Protein Sequence Similarity - InterPro Domain: IPR006035
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR000631 ATP-dependent (S)-NAD(P)H-hydrate dehydratase Protein Sequence Similarity - InterPro Domain: IPR000631
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR036652 YjeF N-terminal domain superfamily Protein Sequence Similarity - InterPro Domain: IPR036652
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF01256 Carbohydrate kinase Protein Sequence Similarity - PFAM Model Name: PF01256
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Uncurated EC number 3.5.3.- Protein Sequence Similarity - InterPro Domain: IPR006035
Reference: Escherichia coli K-12 MG1655 		Dec 2008
Automated Process Uncurated EC number 4.2.1.- Published Annotation - Database Name: EC2GO: GO:0052855
Reference: Escherichia coli K-12 MG1655 		Jul 2018
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 EcoGene:EG11758 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P31806 Published Annotation - Swiss-Prot Accession Number: P31806 Jan 2005
Automated Process Approved db xref GeneID:948685 Published Annotation - Entrez Gene Database ID: 948685
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1790609 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P31806 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref ASAP:ABE-0013644 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved function enzyme; Not classified Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Uncurated molecular interaction Interacts with the product of yabB ASAP:302:(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 protein id AAC77124.1 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 the E-matrix Experimental - PubMed ID: 19282977
Reference: Escherichia coli K-12 MG1655 		Mar 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 Uncurated GO molecular function GO:0052855 ADP-dependent NAD(P)H-hydrate dehydratase activity GO Inferred from Electronic Annotation - Database Name:Identifier: InterPro2GO: IPR000631
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Person Approved Go view EnteroFams ADX-0001607 nnr CDS
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0001621 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0001753 yjeF CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0001731 nnr CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0001810 yjeF CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0001677 nnr CDS
Ortholog
Automated Process Uncurated Go view Brenneria sp. EniD312 AKG-0003634 CDS
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0000468 yjeF CDS
Automated Process Uncurated Go view Cedecea davisae ATCC 33431 [T] ALZ-0003736 CDS
Automated Process Approved Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0004026 nnr CDS
Automated Process Approved Go view Citrobacter freundii ATCC 8090 [T] AVI-0001011 nnr CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0004955 CDS
Person Approved Go view Dickeya dadantii 3937 ABF-0015214 nnr CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0003743 CDS
Automated Process Uncurated Go view Enterobacter cloacae subsp. cloacae ATCC 13047 [T] (AToL DRAFT) AMB-0000804 CDS
Automated Process Uncurated Go view Erwinia amylovora ATCC 49946 ACW-0297349 CDS
Automated Process Uncurated Go view Erwinia amylovora ATCC BAA-2158 APN-0003381 yjeF CDS
Automated Process Uncurated Go view Erwinia tasmaniensis Et1/99 [T] AFI-0003073 yjeF CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0001094 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0008882 CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0004464 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0006791 CDS
Automated Process Approved Go view Escherichia coli APEC O1 (APEC) AEG-0004310 yjeF CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0004566 CDS
Automated Process Approved Go view Escherichia coli ATCC 8739 AEM-0009977 CDS
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0006142 CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0005693 CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0081465 yjeF CDS
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0004842 CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0005513 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0009556 CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0009947 CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0004791 yjeF CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0009161 CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0003231 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0009008 CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0007522 CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0007167 CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0009592 CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0010513 CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0006759 CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0008326 CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0005878 CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0009532 CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0005148 CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0029345 yjeF CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0009862 nnr CDS
Automated Process Approved Go view Escherichia coli HS ADR-0009097 CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0003850 yjeF CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0004259 yjeF CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0004891 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0004889 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0004704 CDS
Automated Process Uncurated Go view Escherichia coli Nissle 1917 AML-0004832 CDS
Automated Process Uncurated Go view Escherichia coli RS218 (NMEC) ACK-0178997 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0004568 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0004630 CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0135259 yjeF CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0001180 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0004776 yjeF CDS
Automated Process Uncurated Go view Ewingella americana ATCC 33852 [T] AMA-0003977 CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0004615 yjeF CDS
Automated Process Uncurated Go view Leclercia adecarboxylata ATCC 23216 [T] AME-0002786 CDS
Automated Process Uncurated Go view Musicola paradisiaca Ech703 AGA-0004968 CDS
Automated Process Uncurated Go view Pantoea agglomerans IG1 APM-0002685 CDS
Automated Process Uncurated Go view Pantoea agglomerans SL1-M5 ALY-0003057 CDS
Automated Process Uncurated Go view Pantoea ananatis AJ13355 AOV-0002825 yjeF CDS
Automated Process Uncurated Go view Pantoea ananatis B1-9 APL-0001167 CDS
Automated Process Uncurated Go view Pantoea ananatis LMG 20103 AKB-0003642 yjeF CDS
Automated Process Uncurated Go view Pantoea ananatis PA13 APK-0000514 CDS
Automated Process Uncurated Go view Pantoea sp. At-9b AGM-0011293 CDS
Automated Process Uncurated Go view Pantoea stewartii DC283 ACV-0288582 yjeF CDS
Automated Process Uncurated Go view Pantoea vagans C9-1 ALK-0006556 yjeF CDS
Person Approved Go view Pectobacterium atrosepticum SCRI1043 ABL-0064255 yjeF CDS
Automated Process Uncurated Go view Pectobacterium brasiliensis 1692 AED-0003263 CDS
Person Approved Go view Pectobacterium carotovorum WPP14 ADT-0003168 CDS
Automated Process Uncurated Go view Pectobacterium parmentieri WPP163 AFJ-0003834 yjeF CDS
Automated Process Uncurated Go view Pectobacterium sp. PC1 AFL-0008948 CDS
Person Uncurated Go view Pseudomonas aeruginosa PA7 AES-0005678 CDS
Person Uncurated Go view Pseudomonas aeruginosa PAO1 AEW-0005025 CDS
Person Uncurated Go view Pseudomonas aeruginosa UCBPP-PA14 AEX-0005339 CDS
Person Uncurated Go view Pseudomonas fluorescens PfO-1 AEZ-0000654 CDS
Person Uncurated Go view Pseudomonas mendocina ymp AFA-0000780 CDS
Person Uncurated Go view Pseudomonas savastanoi NCPPB 3335 AER-0003305 CDS
Person Uncurated Go view Pseudomonas stutzeri A1501 AFF-0003708 CDS
Person Uncurated Go view Pseudomonas syringae pv. phaseolicola 1448A AFH-0000570 CDS
Person Uncurated Go view Pseudomonas syringae pv. syringae B728a AFG-0001322 CDS
Person Approved Go view Pseudomonas syringae pv. tomato DC3000 ADG-0005025 CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0008794 CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0003430 CDS
Person Approved Go view Salmonella Choleraesuis SC-B67 ADB-0004998 yjeF CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0008992 CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0013658 yjeF CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0007737 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0009128 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0008442 CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0004100 CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0005851 CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0008180 CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0009062 CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0006318 CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0004207 CDS
Person Approved Go view Salmonella Paratyphi A ATCC 9150 ADA-0004168 yjeF CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0005514 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0004414 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0009144 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0008686 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0008876 CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0114863 yjeF CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0086133 yjeF CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0005244 yjeF CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0103405 yjeF CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0004782 CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0009207 CDS
Automated Process Uncurated Go view Serratia marcescens subsp. marcescens ATCC 13880 [T] AMF-0000595 CDS
Person Uncurated Go view Shewanella oneidensis MR-1 ACY-0264153 yjeF CDS
Person Approved Go view Shigella boydii 227 ADV-0004671 yjeF CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0010117 CDS
Person Uncurated Go view Shigella dysenteriae 197 ADU-0004997 yjeF pseudogene
Person Approved Go view Shigella flexneri 2457T ABQ-0075930 yjeF CDS
Person Approved Go view Shigella flexneri 301 ABT-0090535 yjeF CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0004597 yjeF CDS
Person Approved Go view Shigella sonnei 046 ADD-0004727 yjeF CDS
Person Uncurated Go view Vibrio cholerae N16961 ADH-0003080 VCA0191 CDS
Automated Process Uncurated Go view Yersinia bercovieri ATCC 43970 [T] AEK-0001995 CDS
Automated Process Uncurated Go view Yersinia enterocolitica 8081 BAH-0001167 CDS
Automated Process Uncurated Go view Yersinia frederiksenii ATCC 33641 [T] AEI-0002076 nnr CDS
Automated Process Uncurated Go view Yersinia intermedia ATCC 29909 [T] AEH-0003710 yjeF CDS
Automated Process Uncurated Go view Yersinia mollaretii ATCC 43969 [T] AEJ-0002448 CDS
Person Approved Go view Yersinia pestis 91001 (biovar Microtus) ACQ-0235428 yjeF CDS
Automated Process Uncurated Go view Yersinia pestis Angola (biovar Pestoides) ADI-0004809 CDS
Automated Process Uncurated Go view Yersinia pestis Antiqua (biovar Antiqua) BAE-0004673 yjeF CDS
Automated Process Uncurated Go view Yersinia pestis B42003004 (biovar Antiqua) BAL-0008118 CDS
Automated Process Uncurated Go view Yersinia pestis CA88-4125 (biovar Orientalis) BAF-0002943 CDS
Person Approved Go view Yersinia pestis CO92 (biovar Orientalis) ABY-0116568 yjeF CDS
Automated Process Uncurated Go view Yersinia pestis E1979001 (biovar Antiqua) BAM-0008350 CDS
Automated Process Uncurated Go view Yersinia pestis F1991016 (biovar Orientalis) BAQ-0006914 CDS
Automated Process Uncurated Go view Yersinia pestis IP275 (biovar Orientalis) BAC-0005662 CDS
Automated Process Uncurated Go view Yersinia pestis K1973002 (biovar Mediaevalis) BAO-0004055 CDS
Person Approved Go view Yersinia pestis KIM (biovar Mediaevalis) ABI-0030253 yjeF CDS
Automated Process Uncurated Go view Yersinia pestis MG05-1020 (biovar Orientalis) BAP-0004759 CDS
Automated Process Uncurated Go view Yersinia pestis Nepal516 (biovar Antiqua) BAD-0003973 yjeF CDS
Automated Process Uncurated Go view Yersinia pestis Pestoides F (biovar Pestoides) BAI-0004335 CDS
Automated Process Uncurated Go view Yersinia pestis UG05-0454 (biovar Antiqua) BAN-0006884 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis IP31758 ADS-0007681 CDS
Person Approved Go view Yersinia pseudotuberculosis IP32953 ACZ-0000455 yjeF CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis PB1/+ AFV-0000526 CDS
Automated Process Uncurated Go view Yersinia pseudotuberculosis YPIII AFW-0004514 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0000992 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0000477 CDS
Molecular Interactions to toptop
Author Approval Feature Name Technique Evidence Comment Annotated
Person Approved ABE-0013644 nnr lambda repressor assay Doodle - bnumber: b4167 Oct 2003
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 4389066 to 4400613
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0013621mscMCDScomplement43860474389370Upstream
ABE-0013623psdCDScomplement43893924390360Upstream
ABE-0013626rsgACDScomplement43904574391509Upstream
ABE-0013631ornCDSforward43916044392149Upstream
ABE-0013635glyVtRNAforward43923604392435Upstream
ABE-0013637glyXtRNAforward43924724392547Upstream
ABE-0013639glyYtRNAforward43925834392658Upstream
ABE-0285214yjeVCDSforward43928924392945Upstream
ABE-0013641queGCDScomplement43929284394067Overlaps Upstream
ABE-0013644nnrCDSforward43940664395613Matches
ABE-0013649tsaECDSforward43955854396046Overlaps Downstream
ABE-0013653amiBCDSforward43960654397402Downstream
ABE-0013655mutLCDSforward43974124399259Downstream
ABE-0013657miaACDSforward43992524400202Downstream
ABE-0013659hfqCDSforward44002884400596Downstream
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.