RPSBLAST alignment for GI: 254780277 and conserved domain: cd08642

>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 = 63.0 bits (154), Expect = 4e-10
 Identities = 90/360 (25%), Positives = 143/360 (39%), Gaps = 83/360 (23%)

Query: 622 NLSSPKQLGDILFTK-LKFPSGAKTKTGQWKTTAQDLEQINCGDNPIIKNILEWRQ-LSK 679
           N +SP QL D L  +  +  S  K      K     L +   GD   +K +LE RQ LSK
Sbjct: 28  NPNSPAQLKDWLNEQGGEVDSLLK------KDVVALLLKTAPGD---VKRVLELRQELSK 78

Query: 680 IKSTYADSLPNHINKRTQRVH---TFYSLASTMTGRLASLEPNLQNIP------------ 724
                 +++   +     RV     FY  A+  TGR A     +QN+P            
Sbjct: 79  TSVKKYEAMERAVCS-DGRVRGLLQFYG-ANR-TGRWAGRLVQVQNLPRNYLKDLDLARE 135

Query: 725 ----------------IKTDLGQKIRRAFISPPTKKLISADYSQIELRILAHIAKITPLY 768
                           +   L Q IR AFI     + I +D+S IE R++A +A      
Sbjct: 136 LVKSGDFDALELLYGSVPDVLSQLIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRL 195

Query: 769 QVFENSLDIHRMVAAEIFGVNIEKVSP--QMRRHAKTINFSIIYGISPFRL----ATQLR 822
            VF     I+   A+++FGV +EK+     +R+  K    ++ YG S   L    A ++ 
Sbjct: 196 DVFATHGKIYEASASQMFGVPVEKIGKNSHLRQKGKVAELALGYGGSVGALKAMGALEMG 255

Query: 823 IPRSEAADYIKRYFHRFPGIHEY---IEKT-KNFVRQNGYVETIFGRRIHYDEINSPKSS 878
           +   E    +  + +  P I +    ++K  K  V++   V+               K  
Sbjct: 256 LTEDELPGIVDAWRNANPNIVKLWWDVDKAAKKAVKERKTVKL------------GGK-L 302

Query: 879 IRNINERAAINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEIT 938
           + NI         +Q  A D    AM+ + K+  D      +++ +HDE+V EVPE E +
Sbjct: 303 VENI---------VQAIARDCLAEAMLRLEKAGYD------IVMHVHDEVVIEVPEGEGS 347