>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 = 74.6 bits (184), Expect = 8e-14
 Identities = 52/200 (26%), Positives = 85/200 (42%), Gaps = 38/200 (19%)

Query: 263 SILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSG 322
            I  H  +  L +   LN+L S+    L  +         GR+  +    GA  +GR S 
Sbjct: 25  YIEEHPAVRLLLEYRKLNKLISTFGEKLPKHIHPV----TGRIHPSFNQIGA-ASGRMS- 78

Query: 323 CVFQP--QNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVAD 380
           C   P  Q +PR+                               R C +A  G KL++AD
Sbjct: 79  C-SNPNLQQIPREREF----------------------------RRCFVAPEGNKLIIAD 109

Query: 381 LAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALG 440
            + IE R+ A I+G++  I A+  GED++  T +     PI++++KE+R + K +   L 
Sbjct: 110 YSQIELRIAAEISGDERMISAYQKGEDLHRLTASLITGKPIEEITKEERQLAKAVNFGLI 169

Query: 441 YQGGAKVFKTMASHC-GLDL 459
           Y   AK  +  A    G+++
Sbjct: 170 YGMSAKGLREYARTNYGVEM 189