>gnl|CDD|176480 cd08643, DNA_pol_A_pol_I_B, Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase 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 = 429

 Score =  102 bits (256), Expect = 5e-22
 Identities = 84/386 (21%), Positives = 147/386 (38%), Gaps = 55/386 (14%)

Query: 621 FNLSSPKQLGDILFTKLKFPSGAKTKTGQWKTTAQDLEQINCGDNPIIKNILEWRQLSKI 680
           FN SS K +   L  K  +     T++G+ K     L ++   D P  K + E+  + K 
Sbjct: 65  FNPSSRKHIAKRLKAKYGWEPQEFTESGEPKVDEDVLSKL---DYPEAKLLAEYLLVQKR 121

Query: 681 KSTYADSLPN---HINKRTQRVHTFYSLASTMTGRLASLEPNLQNIP-IKTDLGQKIRRA 736
               AD   N    +     R+H   +    +TGR     PN+  +P + +  G++ R  
Sbjct: 122 LGQLADG-NNAWLKLVHEDGRIHGAVNTNGAVTGRATHFSPNMAQVPAVGSPYGKECREL 180

Query: 737 FISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVNIEKVSPQ 796
           F  PP   L+ AD S +ELR LAH          ++      +++  +I   N + +   
Sbjct: 181 FGVPPGWSLVGADASGLELRCLAH------YLARYDGGAYTRKVLGGDIHWANAQAMGLL 234

Query: 797 MRRHAKTINFSIIYGISPFRLATQLRIPRSEAADYI------------------------ 832
            R  AKT  ++ +YG    +L   +      A +                          
Sbjct: 235 SRDGAKTFIYAFLYGAGDEKLGQIVGDDLRTAKNLNAEWPQTKKGTIKKIADKAKGRVVR 294

Query: 833 KRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPI 892
             +    P + + I+K K   ++ G++  + GRRI           +R  +  AA+N  +
Sbjct: 295 ANFLKGLPALGKLIKKVKEAAKKRGHLVGLDGRRIR----------VR--SAHAALNTLL 342

Query: 893 QGSAADITRRAMISVHKSLEDHKLAT----KMLLQIHDELVFEVPEEEITTASQIIVHSM 948
           Q + A + ++ ++ +   L           +    +HDE+  E  +       +I V + 
Sbjct: 343 QSAGAILMKKWLVLLDDELTAKGGVWGGDFEYCAWVHDEVQIECRKGIAEEVGKIAVEAA 402

Query: 949 EKACLPKINLRVPLKVNIKVSNNWQE 974
           EKA     N R PL     +  NW E
Sbjct: 403 EKAGE-HFNFRCPLAGEFDIGRNWAE 427