yhbY:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

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[5]

Experiment(s):EBI-881886

Protein

rplC

PMID:15690043[5]

Experiment(s):EBI-881886

Protein

rplD

PMID:15690043[5]

Experiment(s):EBI-881886

Protein

rplK

PMID:15690043[5]

Experiment(s):EBI-881886

Protein

rplM

PMID:15690043[5]

Experiment(s):EBI-881886

Protein

rpsB

PMID:15690043[5]

Experiment(s):EBI-881886

Protein

rpsG

PMID:15690043[5]

Experiment(s):EBI-881886

Protein

rluC

PMID:15690043[5]

Experiment(s):EBI-881886

Protein

rluB

PMID:15690043[5]

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

Protein

yfiF

PMID:15690043[5]

Experiment(s):EBI-881886

Protein

rplT

PMID:15690043[5]

Experiment(s):EBI-889393

Protein

rplU

PMID:15690043[5]

Experiment(s):EBI-889393

Protein

zntA

PMID:15690043[5]

Experiment(s):EBI-889393

Protein

rplO

PMID:16606699[6]

Experiment(s):EBI-1145047

Protein

lsrG

PMID:16606699[6]

Experiment(s):EBI-1145047

Protein

nadE

PMID:16606699[6]

Experiment(s):EBI-1145047

Protein

rplB

PMID:16606699[6]

Experiment(s):EBI-1145047

Protein

ydfR

PMID:16606699[6]

Experiment(s):EBI-1145047

Protein

rplQ

PMID:16606699[6]

Experiment(s):EBI-1145047

Protein

groS

PMID:19402753[7]

MALDI(Z-score):28.324956

Protein

rplK

PMID:19402753[7]

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

Protein

tufB

PMID:19402753[7]

MALDI(Z-score):20.303129

Protein

adhE

PMID:19402753[7]

MALDI(Z-score):28.152109

Protein

rplE

PMID:19402753[7]

MALDI(Z-score):23.439949

Protein

rplT

PMID:19402753[7]

LCMS(ID Probability):99.0

Protein

rpsJ

PMID:19402753[7]

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

Protein

rpsP

PMID:19402753[7]

LCMS(ID Probability):99.2

Protein

ffh

PMID:19402753[7]

MALDI(Z-score):28.658739

Protein

rpsF

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rplF

PMID:19402753[7]

MALDI(Z-score):26.302971

Protein

rpsT

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rplR

PMID:19402753[7]

LCMS(ID Probability):99.2

Protein

rplU

PMID:19402753[7]

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

Protein

rpsD

PMID:19402753[7]

MALDI(Z-score):18.219385

Protein

rpsA

PMID:19402753[7]

MALDI(Z-score):28.320974

Protein

rpsN

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753[7]

MALDI(Z-score):28.314038

Protein

rplM

PMID:19402753[7]

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

Protein

rluC

PMID:19402753[7]

MALDI(Z-score):37.777698

Protein

rplD

PMID:19402753[7]

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

Protein

yfiF

PMID:19402753[7]

MALDI(Z-score):37.160918

Protein

rplL

PMID:19402753[7]

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[8]

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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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References

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

  1. ↑ 1.0 1.1 1.2 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 5.12 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 7.15 7.16 7.17 7.18 7.19 7.20 7.21 7.22 7.23 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  8. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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