>gnl|CDD|176476 cd08639, DNA_pol_A_Aquificae_like, Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences. 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 for phylogenetic anaylsis of bacteria. Species of the phylum Aquificae grow in extreme thermophilic environments. The Aquificae are non-spore-forming, Gram-negative rods and strictly thermophilic. Phylum Aquificae Pol A is different from E. coli Pol I by three signature sequences consisting of a 2 amino acids (aa) insert, a 5-6 aa insert and a 6 aa deletion. These signature sequences may provide a molecular marker for the family Aquificaceae and related species. Length = 324

 Score =  237 bits (607), Expect = 1e-62
 Identities = 112/340 (32%), Positives = 190/340 (55%), Gaps = 37/340 (10%)

Query: 649 QWKTTAQDLEQ--------INCGDNPIIKNILEWRQLSKIKSTYADSLPNHINKRTQRVH 700
           +WK   ++LE+        +   ++P ++ +LE+R+L+K+ ST+ + LP HI+  T R+H
Sbjct: 5   RWKELEKELERERQEAAKELYIEEHPAVRLLLEYRKLNKLISTFGEKLPKHIHPVTGRIH 64

Query: 701 TFYSLASTMTGRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISADYSQIELRILAH 760
             ++     +GR++   PNLQ IP + +     RR F++P   KLI ADYSQIELRI A 
Sbjct: 65  PSFNQIGAASGRMSCSNPNLQQIPREREF----RRCFVAPEGNKLIIADYSQIELRIAAE 120

Query: 761 IAKITPLYQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQ 820
           I+    +   ++   D+HR+ A+ I G  IE+++ + R+ AK +NF +IYG+S   L   
Sbjct: 121 ISGDERMISAYQKGEDLHRLTASLITGKPIEEITKEERQLAKAVNFGLIYGMSAKGLREY 180

Query: 821 LR----IPRS--EAADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVE--TIFGRRIHYDEI 872
            R    +  S  EA  + + +F  + GI     +  + ++  G +E  T+ GRR  ++  
Sbjct: 181 ARTNYGVEMSLEEAEKFRESFFFFYKGIL----RWHHRLKAKGPIEVRTLLGRRRVFEYF 236

Query: 873 NSPKSSIRNINERAAINAPIQGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEV 932
              +          A+N PIQG+ ADI + A+  +   L+D  L  K++L +HDE+V EV
Sbjct: 237 TFTE----------ALNYPIQGTGADILKLALALLVDRLKD--LDAKIVLCVHDEIVLEV 284

Query: 933 PEEEITTASQIIVHSMEKACLPKINLRVPLKVNIKVSNNW 972
           PE+E   A +I+  SME+A    +  +VP++V + +S++W
Sbjct: 285 PEDEAEEAKKILESSMEEAGKRILK-KVPVEVEVSISDSW 323