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