RegulonDB RegulonDB 11.1: Gene Form
   

ybjM gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybjL ybjM grxA terminator TSS_999 TSS_999 ybjLp10 ybjLp10 ybjMp4 ybjMp4 ybjLp12 ybjLp12 TSS_998 TSS_998 ybjMp8 ybjMp8 TSS_997 (cluster) TSS_997 (cluster) TSS_996 TSS_996 TSS_995 TSS_995 TSS_994 (cluster) TSS_994 (cluster) TSS_993 TSS_993 TSS_992 TSS_992

Gene      
Name: ybjM    Texpresso search in the literature
Synonym(s): ECK0839, G6446, b0848
Genome position(nucleotides): 890089 --> 890466
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.74
External database links:  
ASAP:
 ABE-0002891
ECHOBASE:
 EB3446
ECOLIHUB:
 ybjM
OU-MICROARRAY:
 b0848
STRING:
 511145.b0848
COLOMBOS: ybjM


Product      
Name: putative inner membrane protein
Synonym(s): YbjM
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 14.203
Isoelectric point: 10.774
Motif(s):
 
Type Positions Sequence Comment
3 -> 117 HKQRWAGAICCFVLFIVVCLFLATHMKGAFRAAGHPEIGLLFFILPGAVASFFSQRREVLKPLFGAMLAAPCSMLIMRLFFSPTRSFWQELAWLLSAVFWCALGALCFLFISSLF
7 -> 27 WAGAICCFVLFIVVCLFLATH UniProt: Helical.
35 -> 55 AGHPEIGLLFFILPGAVASFF UniProt: Helical.
65 -> 85 LFGAMLAAPCSMLIMRLFFSP UniProt: Helical.
93 -> 113 LAWLLSAVFWCALGALCFLFI UniProt: Helical.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P64439
ECOCYC:
 G6446-MONOMER
ECOLIWIKI:
 b0848
INTERPRO:
 IPR020368
PFAM:
 PF11045
PRIDE:
 P64439
REFSEQ:
 NP_415369
UNIPROT:
 P64439


Operon      
Name: ybjM         
Operon arrangement:
Transcription unit        Promoter
ybjM


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_992 888924 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_993 888928 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_994 (cluster) 888947 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_995 888953 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_996 889468 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_997 (cluster) 889475 reverse nd [RS-EPT-CBR] [1]
  promoter ybjMp8 889885 forward nd [COMP-AINF] [2]
  promoter TSS_998 889888 forward nd [RS-EPT-CBR] [1]
  promoter ybjLp12 889938 reverse nd [COMP-AINF] [2]
  promoter ybjMp4 889940 forward nd [COMP-AINF] [2]
  promoter ybjLp10 889941 reverse nd [COMP-AINF] [2]
  promoter TSS_999 889945 reverse nd [RS-EPT-CBR] [1]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] 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.

 [2] 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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