ybhD: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

YbhD

Synonyms

predicted DNA-binding transcriptional regulator[1], B0768[2][1], YbhD[2][1] , ECK0757, JW5896, b0768

Product description

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

Putative LysR-family transcriptional regulator, function unknown[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

GO:0030528

transcription regulator activity

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P03030

F

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
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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 

MQLKFLTASH PKSSLPFSGV IMKHELSSMK AFVILAESSS FNNAAKLLNI TQPALTRRIK
KMEEDLHVQL FERTTRKVTL TKAGKRLLPE ARELIKKFDE TLFNIRDMNA YHRGMVTLAC
IPTAVFYFLP LAIGKFNELY PNIKVRILEQ GTNNCMESVL CNESDFGINM NNVTNSSIDF
TPLVNEPFVL ACRRDHPLAK KQLVEWQELV GYKMIGVRSS SGNRLLIEQQ LADKPWKLDW
FYEVRHLSTS LGLVEAGLGI SALPGLAMPH APYSSIIGIP LVEPVIRRTL GIIRRKDAVL
SPAAERFFAL LINLWTDDKD NLWTNIVERQ RHALQEIG
Length

338

Mol. Wt

38.33 kDa

pI

9.6 (calculated)

Extinction coefficient

36,440 - 36,940 (calc based on 6 Y, 5 W, and 4 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

88..295

PF03466 LysR substrate binding domain

PMID:19920124[6]

Domain

5..64

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=ybhD 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:145698233

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944869

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002613

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P52696

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6398

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13230

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944869

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002998

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3019

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. ↑ Pérez-Rueda, E et al. (2004) Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 28 341-50 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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