HHsearch alignment for GI: 254780553 and conserved domain: TIGR00593

>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion. Accurate replication is thus one of the most important events in the cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=94.75  E-value=0.044  Score=34.53  Aligned_cols=107  Identities=13%  Similarity=0.218  Sum_probs=68.3

Q ss_pred             CEEEEEECCHHHHHHCCCCCC-EEEEEEEEE------EC----CCCEEEEEEECHHHHHHHHHHH--------HHHHCCC
Q ss_conf             832389708688985024798-499999999------73----8841899970677999999985--------0100051
Q gi|254780553|r   23 GVCYIIYCPIRTLSCLGKIGD-FCTLFVETH------MR----QDQIRLFGFLSDLDRQWFMLLQ--------SVQGVGA   83 (207)
Q Consensus        23 GvGY~i~vs~~~~~~l~~~g~-~v~l~~~~~------vr----Ed~~~LyGF~~~~Er~~F~~Li--------~V~GIGp   83 (207)
T Consensus       124 ~~G~~V~I~sgDrD~lQLvs~e~V~V~~~~~~~g~~~~~~~t~e~V~eKyGv~P~Q~~D~~-AL~GD~SDNiPGV~GIGe  202 (1005)
T TIGR00593       124 KEGYEVRIISGDRDLLQLVSDENVKVLIPERKKGKTEFTEITPEYVVEKYGVTPSQLVDLK-ALVGDSSDNIPGVKGIGE  202 (1005)
T ss_pred             HCCCEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCEECCHHHHHHHCCCCHHHHHHHH-HCCCCCCCCCCCCCCCCC
T ss_conf             4685489983784621121786148864354567543101177898754186745788762-046888878599897376


Q ss_pred             HHHHHHHCCC-CHHHHHHHHHCCCHHHHHHCCCCCH-HHHHHHHHHHHH
Q ss_conf             0112443157-8999999985156687510457116-799999999742
Q gi|254780553|r   84 RVAMGVLSRI-TATELVESIILQNSKVIAQIPGISM-KIASRIMTELKG  130 (207)
Q Consensus        84 K~AL~iLs~l-~~~~l~~aI~~~D~~~L~~vpGIGk-KtA~rIi~ELk~  130 (207)
T Consensus       203 KTA~kLL~~fgsLe~iy~~~ylkealr~~~~~~~k~~~~~~~L~~~~e~  251 (1005)
T TIGR00593       203 KTAAKLLQEFGSLENIYENTYLKEALRLDNLDQIKSEKLREKLIAHKED  251 (1005)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             5689999872108999988778888747758622865788999987753