RegulonDB RegulonDB 10.8: Gene Form
   

holA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

leuS holA nadD lptE TSS_767 TSS_767 TSS_766 (cluster) TSS_766 (cluster) TSS_765 TSS_765 TSS_764 TSS_764 TSS_763 TSS_763 TSS_762 TSS_762 cobCp6 cobCp6 cobCp7 cobCp7

Gene      
Name: holA    Texpresso search in the literature
Synonym(s): ECK0633, EG11412, b0640
Genome position(nucleotides): 670574 <-- 671605 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.33
External database links:  
ASAP:
 ABE-0002192
CGSC:
 31431
ECHOBASE:
 EB1384
OU-MICROARRAY:
 b0640
PortEco:
 holA
STRING:
 511145.b0640
COLOMBOS: holA


Product      
Name: DNA polymerase III subunit δ
Synonym(s): HolA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 38.704
Isoelectric point: 7.0
Motif(s):
 
Type Positions Sequence
211 -> 343 HFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG
1 -> 140 MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQ
141 -> 210 TPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAA
214 -> 338 PFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLAD
21 -> 190 YLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSL

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0009360 - DNA polymerase III complex
molecular_function GO:0003677 - DNA binding
GO:0003887 - DNA-directed DNA polymerase activity
GO:0016779 - nucleotidyltransferase activity
GO:0005515 - protein binding
GO:0016740 - transferase activity
biological_process GO:0006260 - DNA replication
GO:0006261 - DNA-dependent DNA replication
GO:0071897 - DNA biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] Dong Z., et al., 1993
External database links:  
DIP:
 DIP-9931N
ECOCYC:
 EG11412-MONOMER
ECOLIWIKI:
 b0640
INTERPRO:
 IPR008921
INTERPRO:
 IPR005790
INTERPRO:
 IPR010372
INTERPRO:
 IPR027417
INTERPRO:
 IPR032780
MINT:
 MINT-1235044
MODBASE:
 P28630
PDB:
 3GLH
PDB:
 3GLG
PDB:
 3GLF
PDB:
 1XXI
PDB:
 1XXH
PDB:
 1JR3
PDB:
 1JQL
PDB:
 1JQJ
PDB:
 3GLI
PFAM:
 PF06144
PFAM:
 PF14840
PRIDE:
 P28630
PRODB:
 PRO_000022916
REFSEQ:
 NP_415173
SMR:
 P28630
UNIPROT:
 P28630


Operon      
Name: leuS-lptE-holA-nadD-cobC         
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 cobCp7 669944 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter cobCp6 670046 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_762 670902 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_763 671450 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_764 673731 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_765 673832 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_766 (cluster) 674050 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [3]
  promoter TSS_767 674222 reverse nd [RS-EPT-CBR] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] Dong Z., Onrust R., Skangalis M., O'Donnell M., 1993, DNA polymerase III accessory proteins. I. holA and holB encoding delta and delta'., J Biol Chem 268(16):11758-65

 [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

 [3] 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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