>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 =  180 bits (458), Expect = 2e-45
 Identities = 87/264 (32%), Positives = 129/264 (48%), Gaps = 30/264 (11%)

Query: 203 LAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRV 262
           L +      D  + +L +E + LT GL  +     +LK WL  + G     L +     V
Sbjct: 1   LVNAAIACDDQYKEELLEEAKELT-GL-DNPNSPAQLKDWLNEQGGEVDSLLKKDV---V 55

Query: 263 LSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGC 322
               K       +V   R   S+++V K   +  A+ SDGR+RG LQF GA+RTGRW+G 
Sbjct: 56  ALLLKTAPGDVKRVLELRQELSKTSVKKYEAMERAVCSDGRVRGLLQFYGANRTGRWAGR 115

Query: 323 VFPPQNLPR-------------PSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVI 369
           +   QNLPR              S   + L+ +   +P           ++S  +R+  I
Sbjct: 116 LVQVQNLPRNYLKDLDLARELVKSGDFDALELLYGSVP----------DVLSQLIRTAFI 165

Query: 370 ASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQ- 428
            SEG + +V+D + IEARV+AW+AGEQW+L  F T   +Y  + ++ F V   ++ K+  
Sbjct: 166 PSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASASQMFGVPVEKIGKNSH 225

Query: 429 -RAIGKVMELALGYQGGAKAFQKM 451
            R  GKV ELALGY G   A + M
Sbjct: 226 LRQKGKVAELALGYGGSVGALKAM 249