ybdO: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

YbdO

Synonyms

predicted DNA-binding transcriptional regulator[1], B0603[2][1], YbdO[2][1] , ECK0597, JW0596, b0603

Product description

predicted DNA-binding transcriptional regulator LYSR-type[2][3]

Required for swarming phenotype, function unknown; probable LysR-family transcriptional regulator[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:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000847

F

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000847

P

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

ymfM

PMID:16606699[5]

Experiment(s):EBI-1137360

Protein

groL

PMID:16606699[5]

Experiment(s):EBI-1137360
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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 

MANLYDLKKF DLNLLVIFEC IYQHLSISKA AESLYITPSA VSQSLQRLRA QFNDPLFIRS
GKGIAPTTTG LNLHHHLEKN LRGLEQTINI VNKSELKKNF IIYGPQLISC SNNSMLIRCL
RQDSSVEIEC HDILMSAENA EELLVHRKAD LVITQMPVIS RSVICMPLHT IRNTLICSNR
HPRITDNSTY EQIMAEEFTQ LISKSAGVDD IQMEIDERFM NRKISFRGSS LLTIINSIAV
TDLLGIVPYE LYNSYRDFLN LKEIKLEHPL PSIKLYISYN KSSLNNLVFS RFIDRLNESF
Length

300

Mol. Wt

34.398 kDa

pI

7.5 (calculated)

Extinction coefficient

14,900 - 15,650 (calc based on 10 Y, 0 W, and 6 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

116..300

PF03466 LysR substrate binding domain

PMID:19920124[6]

Domain

12..71

PF00126 Bacterial regulatory helix-turn-helix protein, lysR family

PMID:19920124[6]

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

Structures

<beststructure> gene=ybdO 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:16128586

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945216

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002077

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77746

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6332

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13534

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945216

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002939

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3305

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. ↑ 5.0 5.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ 6.0 6.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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