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

ABE-0000109 (rihC) - Escherichia coli K-12 MG1655 - Feature Annotation

ASAP ID
ABE-0000109 showshow history
Names
rihC JW0028 ECK0031 yaaF b0030
Product
ribonucleoside hydrolase 3
Type
CDS
Location
# Contig Strand Left Right Length (b.p.) Length (a.a.)
1 Chromosome forward 27293 28207 915 305
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 IPR001910 (IPR001910 Inosine/uridine-preferring nucleoside hydrolase domain) Apr 2008
Automated Process Approved IPR023186 (IPR023186 Inosine/uridine-preferring nucleoside hydrolase) Jul 2018
Automated Process Approved IPR036452 (IPR036452 Ribonucleoside hydrolase-like) Jul 2018
Automated Process Approved PF01156 (PF01156 Inosine-uridine preferring nucleoside hydrolase) Jul 2018
Gene Ontology to toptop
Author Approval Type Annotation Evidence Annotated
Person Uncurated GO biological process GO:0009226 nucleotide-sugar biosynthetic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Annotations to toptop
Author Approval Type Annotation Evidence Annotated
Nomenclature
Person Approved name rihC Experimental - PubMed ID: 11027694
Reference: Escherichia coli 		Aug 2002
Person Approved synonym ECK0031 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved synonym yaaF Published Annotation - GenBank Accession Number: U00096
Reference: Escherichia coli MG1655 		Oct 1998
Person Approved synonym JW0028 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Approved locus tag b0030 Unique Identifier - Origin: Guy Plunkett III, guy@genome.wisc.edu May 2004
Product
Person Approved product ribonucleoside hydrolase 3 Published Annotation - PubMed ID: 16397293 Jan 2006
Person Uncurated alternate product name ribonucleoside hydrolase 3 Published Annotation - Database Name: GenProtEC Jan 2006
Person Uncurated alternate product name nucleoside hydrolase Experimental - PubMed ID: 11027694
Reference: Escherichia coli 		Jan 2006
Protein Family
Automated Process Approved protein family IPR001910 Inosine/uridine-preferring nucleoside hydrolase domain Protein Sequence Similarity - InterPro Domain: IPR001910
Reference: Escherichia coli K-12 MG1655 		Apr 2008
Automated Process Approved protein family IPR023186 Inosine/uridine-preferring nucleoside hydrolase Protein Sequence Similarity - InterPro Domain: IPR023186
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family PF01156 Inosine-uridine preferring nucleoside hydrolase Protein Sequence Similarity - PFAM Model Name: PF01156
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Automated Process Approved protein family IPR036452 Ribonucleoside hydrolase-like Protein Sequence Similarity - InterPro Domain: IPR036452
Reference: Escherichia coli K-12 MG1655 		Jul 2018
Other
Person Uncurated EC number 3.2.-.- Protein Sequence Similarity - InterPro Domain: IPR001910
Reference: Escherichia coli K-12 MG1655 		Dec 2008
Person Uncurated MultiFun 1.7.10 (metabolism; central intermediary metabolism; sugar nucleotide biosynthesis, conversions) 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 EcoGene:EG11082 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref UniProtKB/Swiss-Prot:P22564 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved db xref UniProtKB:P22564 Published Annotation - Swiss-Prot Accession Number: P22564 Jan 2005
Automated Process Approved db xref ASAP:ABE-0000109 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved db xref GeneID:944796 Published Annotation - Entrez Gene Database ID: 944796
Reference: Escherichia coli K-12 MG1655 		Jun 2009
Automated Process Approved db xref GI:1786213 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved note GO_process: GO:0009226 - nucleotide-sugar biosynthetic process Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Automated Process Approved protein id AAC73141.1 Published Annotation - GenBank Accession Number: U00096.3
Reference: Escherichia coli K-12 MG1655 		Oct 2013
Person Approved regulation expression regulated by dsrA; expression is reduced in strain overexpressing dsrA Experimental - PubMed ID: 15342588
Reference: Escherichia coli K-12 M182 		Oct 2005
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 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:0009226 nucleotide-sugar biosynthetic process Ontology Mapping - Source and Dest Ontology: MultiFun to GO Mar 2004
Comparative to toptop
Author Approval Details Genome Feature Name Type
Member
Automated Process Uncurated Go view OrthoMCL (14 enterobacteria) AMM-0003995 CDS
Automated Process Uncurated Go view OrthoMCL (205 gammaproteobacteria) APP-0002985 rihC CDS
Automated Process Uncurated Go view OrthoMCL (307 Enterobacteriaceae) ATM-0003097 rihC CDS
Automated Process Uncurated Go view OrthoMCL (42 Serratia) BEZ-0008695 rihC CDS
Automated Process Uncurated Go view OrthoMCL (UW draft) CQJ-0002988 rihC CDS
Ortholog
Automated Process Uncurated Go view Buttiauxella agrestis ATCC 33320 [T] APC-0003698 rihC CDS
Automated Process Uncurated Go view Citrobacter amalonaticus ATCC 25405 [T] AUW-0000877 rihC CDS
Automated Process Uncurated Go view Citrobacter freundii ATCC 8090 [T] AVI-0001286 rihC CDS
Automated Process Uncurated Go view Dickeya chrysanthemi Ech1591 AFK-0005031 CDS
Person Approved Go view Dickeya dadantii 3937 ABF-0016735 rihC CDS
Automated Process Uncurated Go view Dickeya parazeae Ech586 AGC-0003676 CDS
Automated Process Uncurated Go view Escherichia albertii TW07627 AFX-0000829 CDS
Automated Process Uncurated Go view Escherichia coli 101-1 (EAEC) BAB-0009045 rihC CDS
Automated Process Approved Go view Escherichia coli 536 (UPEC) AEF-0000029 CDS
Automated Process Uncurated Go view Escherichia coli 53638 (EIEC) ADP-0006550 CDS
Automated Process Uncurated Go view Escherichia coli APEC O1 (APEC) AEG-0000025 rihC CDS
Automated Process Approved Go view Escherichia coli ATCC 11775 [T] AMC-0004280 CDS
Person Uncurated Go view Escherichia coli ATCC 8739 AEM-0009718 rihC pseudogene
Automated Process Uncurated Go view Escherichia coli B171 (EPEC) ADN-0009672 rihC CDS
Automated Process Uncurated Go view Escherichia coli B7A (ETEC) ADK-0009373 RihC CDS
Person Approved Go view Escherichia coli CFT073 (UPEC) ABR-0081812 rihC pseudogene
Automated Process Uncurated Go view Escherichia coli DEC7E (UM-IGS draft) CFX-0000021 rihC CDS
Automated Process Uncurated Go view Escherichia coli DEC9A (UM-IGS draft) CFY-0000069 CDS
Automated Process Uncurated Go view Escherichia coli E110019 (EPEC) ADM-0009665 rihC CDS
Automated Process Uncurated Go view Escherichia coli E22 (EPEC) ADL-0010177 rihC CDS
Automated Process Approved Go view Escherichia coli E2348/69 (EPEC) BCI-0000033 rihC CDS
Automated Process Approved Go view Escherichia coli E24377A (ETEC) ADO-0004481 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC4024 (EHEC) BBI-0002965 CDS
Automated Process Uncurated Go view Escherichia coli EC4042 (EHEC) BBA-0009270 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC4045 (EHEC) BBB-0007782 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC4076 (EHEC) BAZ-0008287 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC4113 (EHEC) BAY-0009816 rihC CDS
Automated Process Approved Go view Escherichia coli EC4115 (EHEC) BAS-0004872 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC4196 (EHEC) BAX-0009520 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC4206 (EHEC) BAW-0008592 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC4401 (EHEC) BAV-0008788 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC4486 (EHEC) BAU-0006143 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC4501 (EHEC) BAT-0008373 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC508 (EHEC) BBJ-0009616 rihC CDS
Automated Process Uncurated Go view Escherichia coli EC869 (EHEC) BBC-0005417 rihC CDS
Person Approved Go view Escherichia coli EDL933 (EHEC) ABH-0023942 rihC CDS
Automated Process Approved Go view Escherichia coli F11 (UPEC) ADQ-0009388 rihC CDS
Automated Process Approved Go view Escherichia coli HS ADR-0004713 rihC CDS
Person Uncurated Go view Escherichia coli K-12 DH10B AEC-0000100 rihC CDS
Person Approved Go view Escherichia coli K-12 W3110 ADY-0000032 rihC CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR68 CGA-0000339 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR71 CGB-0000321 CDS
Automated Process Uncurated Go view Escherichia coli MOD1-ECOR8 CFZ-0000211 CDS
Automated Process Approved Go view Escherichia coli SE11 AFS-0000029 CDS
Automated Process Approved Go view Escherichia coli SMS-3-5 AFT-0000029 rihC CDS
Person Approved Go view Escherichia coli Sakai (EHEC) ACA-0129912 rihC CDS
Automated Process Uncurated Go view Escherichia coli TW14588 (EHEC) BBK-0001451 CDS
Automated Process Approved Go view Escherichia coli UTI89 (UPEC) AEA-0000033 rihC CDS
Person Uncurated Go view Klebsiella pneumoniae subsp. pneumoniae MGH 78578 AEP-0000026 rihC CDS
Automated Process Uncurated Go view Salmonella Agona SL483 BBX-0004240 CDS
Automated Process Uncurated Go view Salmonella Arizonae CDC 346-86 BCD-0003094 CDS
Person Approved Go view Salmonella Choleraesuis SC-B67 ADB-0000052 rihC CDS
Automated Process Uncurated Go view Salmonella Dublin CT_02021853 BCB-0004336 CDS
Automated Process Uncurated Go view Salmonella Enteritidis P125109 BCF-0000169 rihC CDS
Automated Process Uncurated Go view Salmonella Gallinarum 287/91 BCG-0000165 rihC CDS
Automated Process Uncurated Go view Salmonella Hadar RI_05P066 BBT-0006780 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL476 BBV-0004424 CDS
Automated Process Uncurated Go view Salmonella Heidelberg SL486 BBW-0007264 CDS
Automated Process Uncurated Go view Salmonella Javiana GA_MM04042433 BCA-0004388 CDS
Automated Process Uncurated Go view Salmonella Kentucky CDC 191 BBZ-0004871 CDS
Automated Process Uncurated Go view Salmonella Kentucky CVM29188 BBP-0008481 CDS
Automated Process Uncurated Go view Salmonella Newport SL254 BBQ-0004430 CDS
Automated Process Uncurated Go view Salmonella Newport SL317 BBR-0006004 CDS
Automated Process Uncurated Go view Salmonella Paratyphi A AKU_12601 BCH-0000054 CDS
Person Approved Go view Salmonella Paratyphi A ATCC 9150 ADA-0000053 rihC CDS
Automated Process Uncurated Go view Salmonella Paratyphi B SPB7 BCC-0000064 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA23 BBN-0004732 CDS
Automated Process Uncurated Go view Salmonella Saintpaul SARA29 BBM-0006071 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund CVM19633 BBO-0004152 CDS
Automated Process Uncurated Go view Salmonella Schwarzengrund SL480 BBY-0004295 CDS
Person Approved Go view Salmonella Typhi CT18 ABX-0105390 rihC CDS
Person Approved Go view Salmonella Typhi Ty2 ABS-0081764 rihC CDS
Automated Process Uncurated Go view Salmonella Typhimurium 14028S AJR-0000062 rihC CDS
Person Approved Go view Salmonella Typhimurium LT2 [T] ABU-0090786 rihC CDS
Automated Process Uncurated Go view Salmonella Virchow SL491 BBS-0004457 CDS
Automated Process Uncurated Go view Salmonella Weltevreden SL484 BBU-0007254 CDS
Automated Process Uncurated Go view Salmonella enterica CVM23701 BBL-0004348 CDS
Person Approved Go view Shigella boydii 227 ADV-0000033 yaaF CDS
Automated Process Approved Go view Shigella boydii BS512 ADJ-0005430 rihC CDS
Automated Process Uncurated Go view Shigella dysenteriae 1012 BAA-0007379 rihC CDS
Person Approved Go view Shigella dysenteriae 197 ADU-0000058 yaaF CDS
Person Approved Go view Shigella flexneri 2457T ABQ-0070953 rihC CDS
Person Approved Go view Shigella flexneri 301 ABT-0086392 rihC CDS
Automated Process Approved Go view Shigella flexneri 8401 BAG-0000026 yaaF CDS
Person Approved Go view Shigella sonnei 046 ADD-0000039 rihC CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 43003 APO-0002146 CDS
Automated Process Uncurated Go view Yokenella regensburgei ATCC 49455 [T] AMG-0000172 CDS
Molecular Interactions to toptop
Author Approval Feature Name Technique Evidence Comment Annotated
Person Approved ABE-0000109 rihC lambda repressor assay Doodle - bnumber: b0030 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)
Strains to toptop

Strains with mutations in this feature.

Strain NameStrain TypeStrain InformationStrain RequestFeatureIDNameMutation DetailsExperiments Using StrainSubmitter
FB20001mutantTn5 InsertionRequest the StrainABE-0000109rihCyaaF::Tn5KAN-I-SceI at position 349 in Minus orientation ,- pKD465Blattner Laboratory
FB20002mutantTn5 InsertionRequest the StrainABE-0000109rihCyaaF::Tn5KAN-I-SceI at position 349 in Minus orientation ,+ pKD460Blattner 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 22293 to 33207
FeatureIDNameFeature TypeStrandLeft EndRight EndRelationship
ABE-0000001sourceforward14641652Contains
ABE-0000091ribFCDSforward2140722348Upstream
ABE-0000094ileSCDSforward2239125207Upstream
ABE-0000096lspACDSforward2520725701Upstream
ABE-0285321repeat_regionforward2571025795Upstream
ABE-0000101fkpBCDSforward2582626275Upstream
ABE-0000103ispHCDSforward2627727227Upstream
ABE-0000109rihCCDSforward2729328207Matches
ABE-0000112dapBCDSforward2837429195Downstream
ABE-0000118carACDSforward2965130799Downstream
ABE-0000121carBCDSforward3081734038Downstream
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.