rihA:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

rihA

Gene Synonym(s)

ECK0644, b0651, JW0646, ybeK[1], ybeK

Product Desc.

G6358[2][3]

Ribonucleoside hydrolase, pyrimidine specific[4]

Product Synonyms(s)

ribonucleoside hydrolase 1[1], B0651[2][1], YbeK[2][1], RihA[2][1] , ECK0644, JW0646, ybeK, b0651

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rihA[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

rihA

Mnemonic

Ribonucleoside hydrolase

Synonyms

ECK0644, b0651, JW0646, ybeK[1], ybeK

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

14.71 minutes 

MG1655: 683635..682700
<gbrowseImage> name=NC_000913:682700..683635 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 664198..663263
<gbrowseImage> name=NC_012967:663263..664198 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 585460..586395
<gbrowseImage> name=NC_012759:585460..586395 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 684834..683899
<gbrowseImage> name=NC_007779:683899..684834 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 622967..622032
<gbrowseImage> name=NC_010473:622032..622967 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 736227..735292
<gbrowseImage> name=NC_010473:735292..736227 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔrihA (Keio:JW0646)

deletion

deletion

PMID:16738554

Shigen
CGSC8742[5]

ΔrihA784::kan

PMID:16738554

CGSC:102712


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0646

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCACTGCCAATTCTGTTAGA

Primer 2:CCAGCGTAAAATTTCAGACGATC

3A2

Kohara Phage

Genobase

PMID:3038334

crcA280::Tn10

Linked marker

CAG12077 = CGSC7347[5]

est. P1 cotransduction: 33% [6]
Synonyms:zbe-280::Tn10

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[5]

est. P1 cotransduction: 53% [6]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:G6358

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12701

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002965

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945503

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2563

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002227

Escherichia coli str. K-12 substr. MG1655

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Notes

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

RihA

Synonyms

ribonucleoside hydrolase 1[1], B0651[2][1], YbeK[2][1], RihA[2][1] , ECK0644, JW0646, ybeK, b0651

Product description

G6358[2][3]

Ribonucleoside hydrolase, pyrimidine specific[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0006206

pyrimidine base metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01431

P

Seeded from EcoCyc (v14.0)

complete

GO:0009226

nucleotide-sugar biosynthetic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0008152

metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

P

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0016798

hydrolase activity, acting on glycosyl bonds

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01431

F

Seeded from EcoCyc (v14.0)

complete

GO:0016798

hydrolase activity, acting on glycosyl bonds

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

F

Seeded from EcoCyc (v14.0)

complete

GO:0005509

calcium ion binding

PMID:16411753

IDA: Inferred from Direct Assay

F

complete

GO:0005515

protein binding

PMID:16411753

IPI: Inferred from Physical Interaction

EcoliWiki:rihA


F

complete

GO:0046133

pyrimidine ribonucleoside catabolic process

PMID:11027694

IMP: Inferred from Mutant Phenotype

P

A pyrimidine hydrolase, it catalyzes the hydrolysis of cytidine or uridine to cytosine or uracil and ribose.

complete

GO:0050263

ribosylpyrimidine nucleosidase activity

PMID:11027694

IMP: Inferred from Mutant Phenotype

F

A pyrimidine hydrolase, it catalyzes the hydrolysis of cytidine or uridine to cytosine or uracil and ribose.

complete

GO:0045437

uridine nucleosidase activity

PMID:11027694

IMP: Inferred from Mutant Phenotype

F

A pyrimidine hydrolase, it catalyzes the hydrolysis of cytidine or uridine to cytosine or uracil and ribose.

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

rhsC

PMID:16606699

Experiment(s):EBI-1137587

Protein

gfcD

PMID:16606699

Experiment(s):EBI-1137587

Protein

ydcS

PMID:16606699

Experiment(s):EBI-1137587

Protein

rhsA

PMID:16606699

Experiment(s):EBI-1137587

Protein

baeS

PMID:16606699

Experiment(s):EBI-1137587

Protein

malT

PMID:16606699

Experiment(s):EBI-1137587

Protein

arnA

PMID:16606699

Experiment(s):EBI-1137587

Protein

paaA

PMID:16606699

Experiment(s):EBI-1137587

Protein

nadE

PMID:16606699

Experiment(s):EBI-1137587

Protein

btuD

PMID:16606699

Experiment(s):EBI-1137587

Protein

mutS

PMID:16606699

Experiment(s):EBI-1137587

Protein

hemB

PMID:16606699

Experiment(s):EBI-1137587

Protein

emrA

PMID:16606699

Experiment(s):EBI-1137587

Protein

baeR

PMID:16606699

Experiment(s):EBI-1137587

Protein

nanE

PMID:16606699

Experiment(s):EBI-1137587
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MALPILLDCD PGHDDAIAIV LALASPELDV KAITSSAGNQ TPEKTLRNVL RMLTLLNRTD
IPVAGGAVKP LMRELIIADN VHGESGLDGP ALPEPTFAPQ NCTAVELMAK TLRESAEPVT
IVSTGPQTNV ALLLNSHPEL HSKIARIVIM GGAMGLGNWT PAAEFNIYVD PEAAEIVFQS
GIPVVMAGLD VTHKAQIHVE DTERFRAIGN PVSTIVAELL DFFLEYHKDE KWGFVGAPLH
DPCTIAWLLK PELFTSVERW VGVETQGKYT QGMTVVDYYY LTGNKPNATV MVDVDRQGFV
DLLADRLKFY A
Length

311

Mol. Wt

33.822 kDa

pI

4.7 (calculated)

Extinction coefficient

32,430 - 32,805 (calc based on 7 Y, 4 W, and 3 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

2..311

PF01156 Inosine-uridine preferring nucleoside hydrolase

PMID:19920124

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=rihA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128634

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945503

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002227

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P41409

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6358

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12701

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945503

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002965

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2563

Escherichia coli str. K-12 substr. MG1655

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

516

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

175

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

199

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

rihA

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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:683615..683655 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0651 (EcoliWiki Page)

NCBI GEO profiles for rihA

microarray

GenExpDB:b0651 (EcoliWiki Page)

Summary of data for rihA from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (683564..683822) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ14; Well:D11[7]

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Notes

Accessions Related to rihA Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:G6358

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2563

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0651

EcoGene

EcoGene:EG12701

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002965

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002227

Escherichia coli str. K-12 substr. MG1655

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000012099 (score: 1.000; bootstrap: 100%)
  • ENSANGP00000014129 (score: 1.000; bootstrap: 100%)
  • ENSANGP00000013256 (score: 0.206)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000034813 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G05620 (score: 1.000; bootstrap: 99%)
  • AT2G36310 (score: 0.300)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00025632 (score: 1.000; bootstrap: 100%)
  • WBGene00041901 (score: 0.151)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00017436 (score: 1.000; bootstrap: 100%)
  • WBGene00012834 (score: 0.181)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000000218 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-041010-52 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-041010-52 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0231227 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0030510 (score: 1.000; bootstrap: 100%)
  • FBgn0030511 (score: 0.198)
  • FBgn0032436 (score: 0.191)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA11456-PA (score: 1.000; bootstrap: 100%)
  • GA10803-PA (score: 0.222)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000001284 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q84MH2 (score: 1.000; bootstrap: 99%)
  • Q75GR9 (score: 1.000; bootstrap: 99%)
  • Q652Q8 (score: 1.000; bootstrap: 99%)
  • Q75GR8 (score: 0.671)
  • Q6ZJ05 (score: 0.668)
  • Q6PPF8 (score: 0.637)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YDR400W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC16836c (score: 1.000; bootstrap: 92%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000131414 (score: 1.000; bootstrap: 100%)
  • NEWSINFRUP00000163815 (score: 0.541)
  • NEWSINFRUP00000128742 (score: 0.331)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00025772001 (score: 1.000; bootstrap: 100%)
  • GSTENP00027122001 (score: 0.181)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000032489 (score: 1.000; bootstrap: 96%)

From Inparanoid:20070104

Shigella flexneri

YBEK

From SHIGELLACYC

E. coli O157

YBEK

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

Pfam (EcoliWiki Page)

PF01156 Inosine-uridine preferring nucleoside hydrolase

Superfamily (EcoliWiki Page)

SUPERFAMILY:53590

EcoCyc

EcoCyc:G6358

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12701

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002965

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2563

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002227

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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