ydcR: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

YdcR

Synonyms

fused predicted DNA-binding transcriptional regulator[1], predicted amino transferase[1], B1439[2][1], YdcR[2][1] , ECK1433, JW1434, b1439

Product description

fused predicted DNA-binding transcriptional regulator and predicted amino transferase[2][3]

Putative HTH transcriptional regulator with aminotransferase domain; MocR family[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:IPR000524

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015421

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000524

C

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:0006350

transcription

PMID:10734204[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACP5

P

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

PMID:15556475[6]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACP5

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:IPR000524

P

Seeded from EcoCyc (v14.0)

complete

GO:0008483

transaminase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0032

F

Seeded from EcoCyc (v14.0)

complete

GO:0009058

biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004839

P

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc (v14.0)

complete

GO:0016769

transferase activity, transferring nitrogenous groups

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004839

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004839

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015421

F

Seeded from EcoCyc (v14.0)

complete

GO:0030528

transcription regulator activity

PMID:10734204[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACP5

F

Seeded from EcoCyc (v14.0)

complete

GO:0030528

transcription regulator activity

PMID:15556475[6]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACP5

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

Protein

groL

PMID:16606699[7]

Experiment(s):EBI-1139849
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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 

MKKYQQLAEQ LREQIASGIW QPGDRLPSLR DQVALSGMSF MTVSHAYQLL ESQGYIIARP
QSGYYVAPQA IKMPKAPVIP VTRDEAVDIN TYIFDMLQAS RDPSVVPFAS AFPDPRLFPL
QQLNRSLAQV SKTATAMSVI ENLPPGNAEL RQAIARRYAL QGITISPDEI VITAGALEAL
NLSLQAVTEP GDWVIVENPC FYGALQALER LRLKALSVAT DVKEGIDLQA LELALQEYPV
KACWLMTNSQ NPLGFTLTPQ KKAQLVALLN QYNVTLIEDD VYSELYFGRE KPLPAKAWDR
HDGVLHCSSF SKCLVPGFRI GWVAAGKHAR KIQRLQLMST LSTSSPMQLA LVDYLSTRRY
DAHLRRLRRQ LAERKQRAWQ ALLRYLPAEV KIHHNDSGYF LWLELPEPLD AGELSLAALT
HHISIAPGKM FSTGENWSRF FRFNTAWQWG EREEQAVKQL GKLIQERL
Length

468

Mol. Wt

52.793 kDa

pI

9.1 (calculated)

Extinction coefficient

78,840 - 79,340 (calc based on 16 Y, 10 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

120..458

PF00155 Aminotransferase class I and II

PMID:19920124[8]

Domain

3..66

PF00392 Bacterial regulatory proteins, gntR family

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=ydcR 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:16129398

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946004

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004800

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77730

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6750

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13761

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946004

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003339

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3524

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 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 Pérez-Rueda, E & Collado-Vides, J (2000) The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28 1838-47 PubMed
  6. ↑ 6.0 6.1 Pérez-Rueda, E et al. (2004) Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 28 341-50 PubMed
  7. ↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 8.0 8.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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