RegulonDB RegulonDB 10.7: Gene Form
   

yciT gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yciT osmB yciZ RcsB yciTp1 yciTp1 yciTp yciTp osmBp1 osmBp1 TSS_1729 TSS_1729 osmBp2 osmBp2 TSS_1728 TSS_1728

Gene      
Name: yciT    Texpresso search in the literature
Synonym(s): ECK1279, G6638, b1284, deoT
Genome position(nucleotides): 1343597 <-- 1344346 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.8
External database links:  
ASAP:
ABE-0004312
ECHOBASE:
EB3664
OU-MICROARRAY:
b1284
PORTECO:
yciT
REGULONDB:
b1284
STRING:
511145.b1284
M3D: yciT
COLOMBOS: yciT
PortEco: b1284


Product      
Name: putative DNA-binding transcriptional regulator YciT
Synonym(s): DeoT, YciT
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 27.603
Isoelectric point: 6.402
Motif(s):
 
Type Positions Sequence
4 -> 59 RQQTILQMVIDQGQVSVTDLAKATGVSEVTIRQDLNTLEKLSYLRRAHGFAVSLDS
1 -> 56 MNSRQQTILQMVIDQGQVSVTDLAKATGVSEVTIRQDLNTLEKLSYLRRAHGFAVS
18 -> 37 VSVTDLAKATGVSEVTIRQD
69 -> 227 NYTLKRELAEFAASLVQPGETIFIENGSSNALLARTLGEQKKNVTIITVSSYIAHLLKDAPCEVILLGGVYQKKSESMVGPLTRQCIQQVHFSKAFIGIDGWQPETGFTGRDMMRTDVVNAVLEKECEAIVLTDSSKFGAVHSYSIGPVERFNRVITDS

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0006974 - cellular response to DNA damage stimulus
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
[IMP] Inferred from mutant phenotype
Reference(s): [1] Elgrably-Weiss M., et al., 2006
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
External database links:  
DIP:
DIP-11592N
ECOCYC:
G6638-MONOMER
ECOLIWIKI:
b1284
INTERPRO:
IPR018356
INTERPRO:
IPR014036
INTERPRO:
IPR001034
INTERPRO:
IPR036388
INTERPRO:
IPR037171
INTERPRO:
IPR036390
MODBASE:
P76034
PFAM:
PF00455
PFAM:
PF08220
PRIDE:
P76034
PRINTS:
PR00037
PROSITE:
PS51000
PROSITE:
PS00894
PROTEINMODELPORTAL:
P76034
REFSEQ:
NP_415800
SMART:
SM00420
SMR:
P76034
UNIPROT:
P76034


Operon      
Name: yciZT         
Operon arrangement:
Transcription unit        Promoter
yciT
yciZT


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_1728 1343368 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_1729 1343371 reverse nd [RS-EPT-CBR] [4]
  promoter yciTp1 1344544 reverse Similarity to the consensus
Read more >
[ICWHO] [5]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Elgrably-Weiss M., Schlosser-Silverman E., Rosenshine I., Altuvia S., 2006, DeoT, a DeoR-type transcriptional regulator of multiple target genes., FEMS Microbiol Lett 254(1):141-148

 [2] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [3] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [5] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78


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