RegulonDB RegulonDB 11.1: Gene Form
   

yddM gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

adhP fdnI C0362 yddM fdnH TSS_1831 TSS_1831

Gene      
Name: yddM    Texpresso search in the literature
Synonym(s): ECK1471, G6774, b1477
Genome position(nucleotides): 1552398 <-- 1552682
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.23
External database links:  
ASAP:
 ABE-0004925
ECHOBASE:
 EB3546
ECOLIHUB:
 yddM
OU-MICROARRAY:
 b1477
STRING:
 511145.b1477
COLOMBOS: yddM


Product      
Name: DNA-binding transcriptional regulator YddM
Synonym(s): YddM
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 10.401
Isoelectric point: 9.37
Motif(s):
 
Type Positions Sequence Comment
13 -> 67 IQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMW UniProt: HTH cro/C1-type.
14 -> 65 QESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ
24 -> 43 LREFARAMEIAPSTASRLLT UniProt: H-T-H motif.

 
Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [EXP-IPI] Inferred from physical interaction
Reference(s): [1] Gao Y., et al., 2018
External database links:  
ALPHAFOLD:
 P67699
ECOCYC:
 G6774-MONOMER
ECOLIWIKI:
 b1477
INTERPRO:
 IPR010982
INTERPRO:
 IPR013430
INTERPRO:
 IPR001387
PANTHER:
 PTHR36924
PFAM:
 PF01381
PRIDE:
 P67699
PROSITE:
 PS50943
REFSEQ:
 NP_415994
SMART:
 SM00530
SMR:
 P67699
UNIPROT:
 P67699


Operon      
Name: yddM         
Operon arrangement:
Transcription unit        Promoter
yddM


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_1831 1552712 reverse nd [RS-EPT-CBR] [2]


Evidence    

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


Reference(s)    

 [1] Gao Y., Yurkovich JT., Seo SW., Kabimoldayev I., Drager A., Chen K., Sastry AV., Fang X., Mih N., Yang L., Eichner J., Cho BK., Kim D., Palsson BO., 2018, Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655., Nucleic Acids Res 46(20):10682-10696

 [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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