RegulonDB RegulonDB 10.9: Gene Form
   

ycfT gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mfd lolC ycfT lolD terminator TSS_1450 TSS_1450 lolCp5 lolCp5 lolCp6 lolCp6 TSS_1449 TSS_1449 ycfTp11 ycfTp11 ycfTp9 ycfTp9 mfdp1 mfdp1 TSS_1447 TSS_1447 mfdp2 mfdp2 TSS_1445 TSS_1445 TSS_1444 (cluster) TSS_1444 (cluster) TSS_1443 TSS_1443

Gene      
Name: ycfT    Texpresso search in the literature
Synonym(s): ECK1101, G6572, b1115
Genome position(nucleotides): 1174092 <-- 1175165 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
49.53
External database links:  
ASAP:
ABE-0003767
ECHOBASE:
EB3212
ECOLIHUB:
ycfT
OU-MICROARRAY:
b1115
STRING:
511145.b1115
COLOMBOS: ycfT


Product      
Name: inner membrane protein YcfT
Synonym(s): YcfT
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 40.834
Isoelectric point: 9.604
Motif(s):
 
Type Positions Sequence
136 -> 156 GMITASTSLWYLYALIVYFVV
232 -> 252 VGAWLFTISLLLSLVSIVVIM
87 -> 107 IWNIFWVLALWGVVQWLALSA
311 -> 331 TLLLVYPFVSLFICTVAGLLV
13 -> 33 GLCICLVVIYHSVITFYPHLT

 

Classification:
Multifun Terms (GenProtEC)  
  4 - transport --> 4.9.B - Putative uncharacterized transport protein
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0016747 - transferase activity, transferring acyl groups other than amino-acyl groups
Note(s): Note(s): ...[more].
Evidence: [AIFS] Automated inference of function from sequence
Reference(s): [1] Paradis-Bleau C., et al., 2014
[2] Rapp M., et al., 2004
External database links:  
ECOCYC:
G6572-MONOMER
ECOLIWIKI:
b1115
INTERPRO:
IPR002656
PFAM:
PF01757
PRIDE:
P75955
REFSEQ:
NP_415633
UNIPROT:
P75955


Operon      
Name: ycfT         
Operon arrangement:
Transcription unit        Promoter
ycfT


RNA cis-regulatory element    
Attenuation: Translational


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_1443 1171800 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1444 (cluster) 1173832 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [3]
  promoter TSS_1445 1173978 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1447 1174023 reverse nd [RS-EPT-CBR] [3]
  promoter ycfTp9 1175325 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ycfTp11 1175329 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_1449 1175350 forward nd [RS-EPT-CBR] [3]
  promoter lolCp6 1175374 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter lolCp5 1175399 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_1450 1176220 forward nd [RS-EPT-CBR] [3]


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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [2] Rapp M., Drew D., Daley DO., Nilsson J., Carvalho T., Melen K., De Gier JW., Von Heijne G., 2004, Experimentally based topology models for E. coli inner membrane proteins., Protein Sci 13(4):937-45

 [3] 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.

 [4] 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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