RegulonDB RegulonDB 10.9: Gene Form
   

atpD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

atpD atpG atpC TSS_4307 TSS_4307 TSS_4306 TSS_4306 TSS_4305 (cluster) TSS_4305 (cluster) TSS_4304 (cluster) TSS_4304 (cluster) TSS_4303 TSS_4303 TSS_4302 TSS_4302 TSS_4301 (cluster) TSS_4301 (cluster) TSS_4300 TSS_4300 TSS_4299 (cluster) TSS_4299 (cluster) TSS_4298 TSS_4298 TSS_4297 TSS_4297 TSS_4296 TSS_4296 TSS_4295 TSS_4295 TSS_4294 TSS_4294 atpCp1 atpCp1 TSS_4293 TSS_4293

Gene      
Name: atpD    Texpresso search in the literature
Synonym(s): ECK3725, EG10101, b3732, papB, uncD
Genome position(nucleotides): 3915993 <-- 3917375 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.74
External database links:  
ASAP:
ABE-0012208
CGSC:
30
ECHOBASE:
EB0099
ECOLIHUB:
atpD
OU-MICROARRAY:
b3732
STRING:
511145.b3732
COLOMBOS: atpD


Product      
Name: ATP synthase F1 complex subunit β
Synonym(s): ATP synthase F1 complex - beta subunit, AtpD, PapB, UncD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 50.325
Isoelectric point: 4.635
Motif(s):
 
Type Positions Sequence
2 -> 460 ATGKIVQVIGAVVDVEFPQDAVPRVYDALEVQNGNERLVLEVQQQLGGGIVRTIAMGSSDGLRRGLDVKDLEHPIEVPVGKATLGRIMNVLGEPVDMKGEIGEEERWAIHRAAPSYEELSNSQELLETGIKVIDLMCPFAKGGKVGLFGGAGVGKTVNMMELIRNIAIEHSGYSVFAGVGERTREGNDFYHEMTDSNVIDKVSLVYGQMNEPPGNRLRVALTGLTMAEKFRDEGRDVLLFVDNIYRYTLAGTEVSALLGRMPSAVGYQPTLAEEMGVLQERITSTKTGSITSVQAVYVPADDLTDPSPATTFAHLDATVVLSRQIASLGIYPAVDPLDSTSRQLDPLVVGQEHYDTARGVQSILQRYQELKDIIAILGMDELSEEDKLVVARARKIQRFLSQPFFVAEVFTGSPGKYVSLKDTIRGFKGIMEGEYDHLPEQAFYMVGSIEEAVEKAKKL
157 -> 157 T
381 -> 387 DELSEED
6 -> 72 IVQVIGAVVDVEFPQDAVPRVYDALEVQNGNERLVLEVQQQLGGGIVRTIAMGSSDGLRRGLDVKDL
130 -> 342 GIKVIDLMCPFAKGGKVGLFGGAGVGKTVNMMELIRNIAIEHSGYSVFAGVGERTREGNDFYHEMTDSNVIDKVSLVYGQMNEPPGNRLRVALTGLTMAEKFRDEGRDVLLFVDNIYRYTLAGTEVSALLGRMPSAVGYQPTLAEEMGVLQERITSTKTGSITSVQAVYVPADDLTDPSPATTFAHLDATVVLSRQIASLGIYPAVDPLDSTS

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.8 - ATP proton motive force interconversion
  4 - transport --> 4.3 - Primary Active Transporters --> 4.3.A - Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters --> 4.3.A.2 - The H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) Su
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0045261 - proton-transporting ATP synthase complex, catalytic core F(1)
molecular_function GO:0005515 - protein binding
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0046933 - proton-transporting ATP synthase activity, rotational mechanism
GO:0046961 - proton-transporting ATPase activity, rotational mechanism
biological_process GO:0006754 - ATP biosynthetic process
GO:0006811 - ion transport
GO:0015986 - ATP synthesis coupled proton transport
GO:0046034 - ATP metabolic process
GO:1902600 - proton transmembrane transport
External database links:  
DIP:
DIP-31846N
ECOCYC:
ATPD-MONOMER
ECOLIWIKI:
b3732
INTERPRO:
IPR003593
INTERPRO:
IPR036121
INTERPRO:
IPR027417
INTERPRO:
IPR000194
INTERPRO:
IPR024034
INTERPRO:
IPR004100
INTERPRO:
IPR005722
INTERPRO:
IPR020003
MINT:
P0ABB4
PDB:
5T4P
PDB:
5T4Q
PDB:
5T4O
PDB:
3OAA
PDB:
1D8S
PFAM:
PF00006
PFAM:
PF02874
PRIDE:
P0ABB4
PRODB:
PRO_000022189
PROSITE:
PS00152
REFSEQ:
NP_418188
SMART:
SM00382
SMR:
P0ABB4
SWISSMODEL:
P0ABB4
UNIPROT:
P0ABB4


Operon      
Name: atpIBEFHAGDC         
Operon arrangement:
Transcription unit        Promoter
atpBEFHAGDC
atpBEFHAGDC
atpIBEFHAGDC


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_4293 3915989 reverse nd [RS-EPT-CBR] [1]
  promoter atpCp1 3916059 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_4294 3916641 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_4295 3916759 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_4296 3916978 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_4297 3917001 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_4298 3917107 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_4299 (cluster) 3917272 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_4300 3917275 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_4301 (cluster) 3917397 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_4302 3917446 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_4303 3917736 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_4304 (cluster) 3917740 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_4305 (cluster) 3917744 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_4306 3917765 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_4307 3918078 reverse 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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