yciT:Gene Product(s)

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

Nomenclature

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Standard name

YciT

Synonyms

predicted DNA-binding transcriptional regulator[1], B1284[2][1], YciT[2][1], DeoT[2][1] , deoT, ECK1279, JW1276, b1284

Product description

DNA-binding transcriptional regulator[2][3]

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. 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:IPR001034

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018356

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001034

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018356

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:15556475[4]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACK5

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:IPR001034

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:IPR018356

P

Seeded from EcoCyc (v14.0)

complete

GO:0016564

transcription repressor activity

PMID:15556475[4]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACK5

F

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:11967071[5]

IEP: Inferred from Expression Pattern

P

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

fabI

PMID:16606699[6]

Experiment(s):EBI-1139466

Protein

groL

PMID:16606699[6]

Experiment(s):EBI-1139466

Protein

nadE

PMID:16606699[6]

Experiment(s):EBI-1139466
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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 

MNSRQQTILQ MVIDQGQVSV TDLAKATGVS EVTIRQDLNT LEKLSYLRRA HGFAVSLDSD
DVETRMMSNY TLKRELAEFA ASLVQPGETI FIENGSSNAL LARTLGEQKK NVTIITVSSY
IAHLLKDAPC EVILLGGVYQ KKSESMVGPL TRQCIQQVHF SKAFIGIDGW QPETGFTGRD
MMRTDVVNAV LEKECEAIVL TDSSKFGAVH SYSIGPVERF NRVITDSKIR ASDLMHLEHS
KLTIHVVDI
Length

249

Mol. Wt

27.602 kDa

pI

6.4 (calculated)

Extinction coefficient

12,950 - 13,325 (calc based on 5 Y, 1 W, and 3 C residues)

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See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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

70..226

PF00455 Bacterial regulatory proteins, deoR family

PMID:19920124[7]

Domain

4..60

PF08220 DeoR-like helix-turn-helix domain

PMID:19920124[7]

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

<motif_map/>

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

Structures

<beststructure> gene=yciT taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

<protect>

</protect>

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:16129245

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945869

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004312

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76034

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6638

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13905

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945869

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003233

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3664

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 2.3 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. ↑ 4.0 4.1 Pérez-Rueda, E et al. (2004) Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 28 341-50 PubMed
  5. ↑ Khil, PP & Camerini-Otero, RD (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 44 89-105 PubMed
  6. ↑ 6.0 6.1 6.2 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ 7.0 7.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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