>gnl|CDD|176479 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. Length = 378

 Score =  178 bits (455), Expect = 3e-45
 Identities = 73/195 (37%), Positives = 104/195 (53%), Gaps = 16/195 (8%)

Query: 268 SNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQP 327
                  K ++  R   S +++ K   +  AV SDGR+RG LQFYGA+RTGRW+G + Q 
Sbjct: 60  KTAPGDVKRVLELRQELSKTSVKKYEAMERAVCSDGRVRGLLQFYGANRTGRWAGRLVQV 119

Query: 328 QNLPRQERSEEILTQTIQALNRG---------ETIADPLGLASDCVRSCIIASNGKKLVV 378
           QNLPR    +  L    + +  G          ++ D L   S  +R+  I S G + +V
Sbjct: 120 QNLPRNYLKD--LDLARELVKSGDFDALELLYGSVPDVL---SQLIRTAFIPSEGHRFIV 174

Query: 379 ADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSK--EQRAIGKVME 436
           +D + IEARV+AW+AGE W++  FA    IY  + ++ F  P++K+ K    R  GKV E
Sbjct: 175 SDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASASQMFGVPVEKIGKNSHLRQKGKVAE 234

Query: 437 LALGYQGGAKVFKTM 451
           LALGY G     K M
Sbjct: 235 LALGYGGSVGALKAM 249