yhbY: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

yhbY

Gene Synonym(s)

ECK3169, b3180, JW3147[1], JW3147

Product Desc.

predicted RNA-binding protein[2][3]

RNA binding protein, associated with pre-50S ribosomal subunits; functions in ribosome assembly[4]

Product Synonyms(s)

predicted RNA-binding protein[1], B3180[2][1], YhbY[2][1] , ECK3169, JW3147, b3180

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yhbY[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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Similar to IF3 C-terminal RNA binding fold. AFMB Structural Genomics target No. 131 (http://afmb.cnrs-mrs.fr/article171.html). UPF0044 family. Single CRM domain protein.[4]



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

yhbY

Mnemonic

Systematic nomenclature

Synonyms

ECK3169, b3180, JW3147[1], JW3147

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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

71.68 minutes 

MG1655: 3325812..3326105
<gbrowseImage> name=NC_000913:3325812..3326105 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3263024..3263317
<gbrowseImage> name=NC_012967:3263024..3263317 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3212960..3213253
<gbrowseImage> name=NC_012759:3212960..3213253 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3327645..3327938
<gbrowseImage> name=NC_007779:3327645..3327938 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3423557..3423850
<gbrowseImage> name=NC_010473:3423557..3423850 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

ΔyhbY (Keio:JW3147)

deletion

deletion

PMID:16738554

Shigen
CGSC10391[5]

ΔyhbY787::kan

PMID:16738554

CGSC:105120


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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

JW3147

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAATCTGAGTACTAAACAAAA

Primer 2:CCGCGTGGCAGCGAGATTTTACG

18H7

Kohara Phage

Genobase

PMID:3038334

14F11

Kohara Phage

Genobase

PMID:3038334

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

est. P1 cotransduction: % [6]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: 83% [6]
Synonyms:zgj-203::Tn10, zha-203::Tn10

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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:EG12794

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12794

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002385

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947688

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2646

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010452

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

YhbY

Synonyms

predicted RNA-binding protein[1], B3180[2][1], YhbY[2][1] , ECK3169, JW3147, b3180

Product description

predicted RNA-binding protein[2][3]

RNA binding protein, associated with pre-50S ribosomal subunits; functions in ribosome assembly[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:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001890

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017924

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

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

rplB

PMID:15690043

Experiment(s):EBI-881886

Protein

rplC

PMID:15690043

Experiment(s):EBI-881886

Protein

rplD

PMID:15690043

Experiment(s):EBI-881886

Protein

rplK

PMID:15690043

Experiment(s):EBI-881886

Protein

rplM

PMID:15690043

Experiment(s):EBI-881886

Protein

rpsB

PMID:15690043

Experiment(s):EBI-881886

Protein

rpsG

PMID:15690043

Experiment(s):EBI-881886

Protein

rluC

PMID:15690043

Experiment(s):EBI-881886

Protein

rluB

PMID:15690043

Experiment(s):EBI-881886, EBI-889536

Protein

yfiF

PMID:15690043

Experiment(s):EBI-881886

Protein

rplT

PMID:15690043

Experiment(s):EBI-889393

Protein

rplU

PMID:15690043

Experiment(s):EBI-889393

Protein

zntA

PMID:15690043

Experiment(s):EBI-889393

Protein

rplO

PMID:16606699

Experiment(s):EBI-1145047

Protein

lsrG

PMID:16606699

Experiment(s):EBI-1145047

Protein

nadE

PMID:16606699

Experiment(s):EBI-1145047

Protein

rplB

PMID:16606699

Experiment(s):EBI-1145047

Protein

ydfR

PMID:16606699

Experiment(s):EBI-1145047

Protein

rplQ

PMID:16606699

Experiment(s):EBI-1145047

Protein

groS

PMID:19402753

MALDI(Z-score):28.324956

Protein

rplK

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):13.034070

Protein

tufB

PMID:19402753

MALDI(Z-score):20.303129

Protein

adhE

PMID:19402753

MALDI(Z-score):28.152109

Protein

rplE

PMID:19402753

MALDI(Z-score):23.439949

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.0

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.2

Protein

ffh

PMID:19402753

MALDI(Z-score):28.658739

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplF

PMID:19402753

MALDI(Z-score):26.302971

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplR

PMID:19402753

LCMS(ID Probability):99.2

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):3.041265

Protein

rpsD

PMID:19402753

MALDI(Z-score):18.219385

Protein

rpsA

PMID:19402753

MALDI(Z-score):28.320974

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753

MALDI(Z-score):28.314038

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):22.983698

Protein

rluC

PMID:19402753

MALDI(Z-score):37.777698

Protein

rplD

PMID:19402753

LCMS(ID Probability):96.7 MALDI(Z-score):31.631039

Protein

yfiF

PMID:19402753

MALDI(Z-score):37.160918

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

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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 

MNLSTKQKQH LKGLAHPLKP VVLLGSNGLT EGVLAEIEQA LEHHELIKVK IATEDRETKT
LIVEAIVRET GACNVQVIGK TLVLYRPTKE RKISLPR
Length

97

Mol. Wt

10.783 kDa

pI

9.8 (calculated)

Extinction coefficient

1,490 - 1,615 (calc based on 1 Y, 0 W, and 1 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

3..86

PF01985 CRS1 / YhbY (CRM) domain

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=yhbY 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:16131070

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947688

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010452

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AGK4

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12794

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12794

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947688

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002385

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2646

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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 MC4100

1.04E+03

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

136.661+/-0.649

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.27632+/-0.02551

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.674061433

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

17221

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

2765

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

8448

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)

yhbY

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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_000913:3325792..3325832 source=MG1655 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:b3180 (EcoliWiki Page)

NCBI GEO profiles for yhbY

microarray

GenExpDB:b3180 (EcoliWiki Page)

Summary of data for yhbY 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
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Notes

Accessions Related to yhbY Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12794

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2646

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3180

EcoGene

EcoGene:EG12794

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002385

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010452

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Arabidopsis thaliana

  • AT4G39040 (score: 1.000; bootstrap: 100%)
  • AT2G21350 (score: 0.201)

From Inparanoid:20070104

Shigella flexneri

YHBY

From SHIGELLACYC

E. coli O157

YHBY

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:75471

Pfam (EcoliWiki Page)

PF01985 CRS1 / YhbY (CRM) domain

EcoCyc

EcoCyc:EG12794

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12794

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002385

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2646

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010452

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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 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 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 4.2 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).

Categories

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