RegulonDB RegulonDB 10.7: Gene Form
   

alpA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yfjI yfjH alpA anti-anti-terminator anti-terminator terminator yfjIp3 yfjIp3 yfjIp10 yfjIp10 yfjIp8 yfjIp8 yfjIp9 yfjIp9 yfjHp2 yfjHp2 yfjHp3 yfjHp3 TSS_2972 TSS_2972

Gene      
Name: alpA    Texpresso search in the literature
Synonym(s): ECK2620, EG12112, b2624
Genome position(nucleotides): 2758644 --> 2758856 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
46.95
External database links:  
ASAP:
ABE-0008636
CGSC:
33086
ECHOBASE:
EB2035
OU-MICROARRAY:
b2624
PORTECO:
alpA
REGULONDB:
b2624
STRING:
511145.b2624
M3D: alpA
COLOMBOS: alpA
PortEco: b2624


Product      
Name: CP4-57 prophage; DNA-binding transcriptional activator AlpA
Synonym(s): AlpA
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AlpA
Cellular location: cytosol
Molecular weight: 8.133
Isoelectric point: 10.847
Motif(s):
 
Type Positions Sequence
12 -> 31 LPAVIQKTGMARATIYDWLN
7 -> 63 VRILRLPAVIQKTGMARATIYDWLNPKSPRYDATFPKKRMLGVKSVGWIEAEIDEWL

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
biological_process GO:0042710 - biofilm formation
GO:0045893 - positive regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Trempy JE., et al., 1994
External database links:  
ECOCYC:
PD02850
ECOLIWIKI:
b2624
INTERPRO:
IPR010260
PFAM:
PF05930
PRIDE:
P33997
PRODB:
PRO_000022085
PROTEINMODELPORTAL:
P33997
REFSEQ:
NP_417113
UNIPROT:
P33997


Operon      
Name: alpA         
Operon arrangement:
Transcription unit        Promoter
 


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_2972 2758658 reverse nd [RS-EPT-CBR] [2]
  promoter yfjHp3 2758660 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yfjHp2 2758663 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yfjIp9 2758855 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yfjIp8 2758881 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yfjIp10 2758928 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yfjIp3 2758978 forward Similarity to the consensus
Read more >
[ICWHO] [3]


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] Trempy JE., Kirby JE., Gottesman S., 1994, Alp suppression of Lon: dependence on the slpA gene., J Bacteriol 176(7):2061-7

 [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.

 [3] 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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