RegulonDB RegulonDB 11.0: Gene Form
   

yhgF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yhgF greB feoA Fur FNR NagC OmpR IHF TSS_4006 TSS_4006 feoAp feoAp TSS_4005 (cluster) TSS_4005 (cluster) TSS_4004 TSS_4004 yhgFp2 yhgFp2

Gene      
Name: yhgF    Texpresso search in the literature
Synonym(s): ECK3394, G7746, b3407
Genome position(nucleotides): 3537385 --> 3539706
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
56.85
External database links:  
ASAP:
ABE-0011120
ECHOBASE:
EB2768
ECOLIHUB:
yhgF
OU-MICROARRAY:
b3407
STRING:
511145.b3407
COLOMBOS: yhgF


Product      
Name: putative RNA-binding protein YhgF
Synonym(s): YhgF
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 85.12
Isoelectric point: 6.237
Motif(s):
 
Type Positions Sequence Comment
10 -> 193 IAGEIQARPEQVDAAVRLLDEGNTVPFIARYRKEITGGLDDTQLRNLETRLSYLRELEERRQAILKSISEQGKLTDDLAKAINATLSKTELEDLYLPYKPKRRTRGQIAIEAGLEPLADLLWSDPSHTPEVAAAQYVYADKGVADTKAALDGARYILMERFAEDAALLAKVRDYLWKNAHLVST
328 -> 451 ATMGLDPGLRTGVKVAVVDATGKLVATDTIYPHTGQAAKAAMTVAALCEKHNVELVAIGNGTASRETERFYLDVQKQFPKVTAQKVIVSEAGASVYSASELAAQEFPDLDVSLRGAVSIARRLQ
491 -> 555 VNAVGVDLNTASVPLLTRVAGLTRMMAQNIVAWRDENGQFQNRQQLLKVSRLGPKAFEQCAGFLR
561 -> 630 NPLDASTVHPEAYPVVERILAATQQALKDLMGNSSELRNLKASDFTDEKFGVPTVTDIIKELEKPGRDPR
649 -> 720 QPGMILEGAVTNVTNFGAFVDIGVHQDGLVHISSLSNKFVEDPHTVVKAGDIVKVKVLEVDLQRKRIALTMR

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0003735 - structural constituent of ribosome
GO:0003723 - RNA binding
GO:0003729 - mRNA binding
biological_process GO:0006139 - nucleobase-containing compound metabolic process
GO:0006412 - translation
GO:0010212 - response to ionizing radiation
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
P46837
DIP:
DIP-12337N
ECOCYC:
G7746-MONOMER
ECOLIWIKI:
b3407
INTERPRO:
IPR041692
INTERPRO:
IPR044146
INTERPRO:
IPR037027
INTERPRO:
IPR032639
INTERPRO:
IPR023323
INTERPRO:
IPR023319
INTERPRO:
IPR022967
INTERPRO:
IPR018974
INTERPRO:
IPR012340
INTERPRO:
IPR012337
INTERPRO:
IPR010994
INTERPRO:
IPR006641
INTERPRO:
IPR003029
MODBASE:
P46837
PFAM:
PF09371
PFAM:
PF00575
PFAM:
PF12836
PFAM:
PF16921
PFAM:
PF17674
PRIDE:
P46837
PROSITE:
PS50126
REFSEQ:
NP_417866
SMART:
SM00316
SMART:
SM00732
SMR:
P46837
SWISSMODEL:
P46837
UNIPROT:
P46837


Operon      
Name: yhgF         
Operon arrangement:
Transcription unit        Promoter
yhgF


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 yhgFp2 3537176 forward nd [ICWHO] [1]
  promoter TSS_4004 3537268 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4005 (cluster) 3537353 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4006 3540058 forward nd [RS-EPT-CBR] [2]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] 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

 [2] 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.


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