RegulonDB RegulonDB 10.8: Gene Form
   

ydgH gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pntA ydgI ydgH terminator anti-terminator ydgHp5 ydgHp5 TSS_1893 TSS_1893 TSS_1892 TSS_1892 TSS_1891 TSS_1891 TSS_1890 TSS_1890 pntAp pntAp TSS_1889 TSS_1889 TSS_1888 TSS_1888 pntBp6 pntBp6

Gene      
Name: ydgH    Texpresso search in the literature
Synonym(s): ECK1599, G6860, b1604
Genome position(nucleotides): 1678427 --> 1679371 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.11
External database links:  
ASAP:
ABE-0005359
ECHOBASE:
EB3688
OU-MICROARRAY:
b1604
PortEco:
ydgH
STRING:
511145.b1604
COLOMBOS: ydgH


Product      
Name: DUF1471 domain-containing protein YdgH
Synonym(s): YdgH
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 33.903
Isoelectric point: 9.765
Motif(s):
 
Type Positions Sequence
35 -> 90 KPFDRVVVTGRFNAIGEAVKAVSRRADKEGAASFYVVDTSDFGNSGNWRVVADLYK
1 -> 19 MKLKNTLLASALLSAMAFS
259 -> 314 MVPFDSIKFSGNYGNMTEVSYQVAKRAAKKGAKYYHITRQWQERGNNLTVSADLYK
20 -> 314 VNAATELTPEQAAAVKPFDRVVVTGRFNAIGEAVKAVSRRADKEGAASFYVVDTSDFGNSGNWRVVADLYKADAEKAEETSNRVINGVVELPKDQAVLIEPFDTVTVQGFYRSQPEVNDAITKAAKAKGAYSFYIVRQIDANQGGNQRITAFIYKKDAKKRIVQSPDVIPADSEAGRAALAAGGEAAKKVEIPGVATTASPSSEVGRFFETQSSKGGRYTVTLPDGTKVEELNKATAAMMVPFDSIKFSGNYGNMTEVSYQVAKRAAKKGAKYYHITRQWQERGNNLTVSADLYK
119 -> 174 EPFDTVTVQGFYRSQPEVNDAITKAAKAKGAYSFYIVRQIDANQGGNQRITAFIYK

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11716N
ECOCYC:
G6860-MONOMER
ECOLIWIKI:
b1604
INTERPRO:
IPR025539
INTERPRO:
IPR010854
INTERPRO:
IPR025543
INTERPRO:
IPR036275
PFAM:
PF07338
PRIDE:
P76177
REFSEQ:
NP_416121
SMR:
P76177
UNIPROT:
P76177


Operon      
Name: ydgH         
Operon arrangement:
Transcription unit        Promoter
 


RNA cis-regulatory element    
Attenuation: Transcriptional


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 pntBp6 1676548 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_1888 1676849 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1889 1677293 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1890 1678014 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1891 1678308 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1892 1678368 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1893 1678370 forward nd [RS-EPT-CBR] [2]
  promoter ydgHp5 1678377 forward Similarity to the consensus
Read more >
[ICWHO] [1]


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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