RegulonDB RegulonDB 10.8: Gene Form
   

ypjD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ffh yfjD ypjD terminator anti-terminator anti-anti-terminator terminator TSS_2962 TSS_2962 TSS_2961 TSS_2961 TSS_2960 (cluster) TSS_2960 (cluster) TSS_2959 TSS_2959 ypjDp5 ypjDp5 ffhp ffhp ypjDp4 ypjDp4 TSS_2957 TSS_2957 TSS_2956 TSS_2956

Gene      
Name: ypjD    Texpresso search in the literature
Synonym(s): ECK2608, G7355, b2611
Genome position(nucleotides): 2747962 --> 2748753 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.65
External database links:  
ASAP:
ABE-0008591
ECHOBASE:
EB3978
OU-MICROARRAY:
b2611
PortEco:
ypjD
STRING:
511145.b2611
COLOMBOS: ypjD


Product      
Name: cytochrome c assembly family protein
Synonym(s): YpjD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 29.262
Isoelectric point: 9.311
Motif(s):
 
Type Positions Sequence
37 -> 261 SAVIALVCHAIALEARILPDGDSGQNLSLLNVGSLVSLMICTVMTIVASRNRGWLLLPIVYAFALINLALATFMPNEYITHLEATPGMLVHIGLSLFSYATLIIAALYALQLAWIDYQLKNKKLAFNQEMPPLMSIERKMFHITQIGVVLLTLTLCTGLFYMHNLFSMENIDKAVLSIVAWFVYIVLLWGHYHEGWRGRRVVWFNVAGAVILTLAYFGSRIVQQL
182 -> 201 IGVVLLTLTLCTGLFYMHNL
90 -> 109 WLLLPIVYAFALINLALATF
4 -> 23 FALLALVAYSVSLALIVPGL
124 -> 146 MLVHIGLSLFSYATLIIAALYAL

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0020037 - heme binding
biological_process GO:0017004 - cytochrome complex assembly
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
G7355-MONOMER
ECOLIWIKI:
b2611
INTERPRO:
IPR002541
PFAM:
PF01578
PRIDE:
P64432
REFSEQ:
NP_417102
UNIPROT:
P64432


Operon      
Name: ypjD         
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 TSS_2956 2746694 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2957 2747250 reverse nd [RS-EPT-CBR] [1]
  promoter ypjDp4 2747846 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter ypjDp5 2747930 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_2959 2747931 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2960 (cluster) 2748357 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_2961 2748644 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2962 2749213 forward nd [RS-EPT-CBR] [1]


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] 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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