>gnl|CDD|176473 cd06444, DNA_pol_A, Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication. DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into 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), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. 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 = 347

 Score = 80.2 bits (198), Expect = 2e-15
 Identities = 67/351 (19%), Positives = 103/351 (29%), Gaps = 97/351 (27%)

Query: 294 TLSEAVSSDGRLRGTLQFY-GASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGET 352
              +    DGR     ++  G + TGRW+      Q +PR++     L + I    R   
Sbjct: 48  PWLDQWVRDGRFHP--EYVPGGTVTGRWASRGGNAQQIPRRDP----LGRDI----RQAF 97

Query: 353 IADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTT 412
           +ADP                G  LVVAD + +E RVLA ++G++   +AF  G D+Y  T
Sbjct: 98  VADP----------------GWTLVVADASQLELRVLAALSGDEALAEAFGRGGDLYTAT 141

Query: 413 YAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTF 472
            +  F  P+      +R   K+  L   Y                     S  + +    
Sbjct: 142 ASAMFGVPVG---GGERQHAKIANLGAMYGAT---------------SGISARLLAQLRR 183

Query: 473 EDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVV 532
              ++A +       ++P F         A E V+ A R   +G                
Sbjct: 184 ISTKEAAALIELFFSRFPAF-------PKAMEYVEDAARRGERG---------------G 221

Query: 533 QEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERT 592
                +  R      R                 RR                         
Sbjct: 222 YVRTLLGRRSPPPDIRWTEVVSDPAAASRARRVRR------------------------A 257

Query: 593 YGGKLTENIVQAISRDILCEGMKN------ATKNGYDIVLTVHDEIVSETP 637
            G      +VQ  + D     M               +V  VHDE+V   P
Sbjct: 258 AGRFARNFVVQGTAADWAKLAMVALRRRLEELALDARLVFFVHDEVVLHCP 308