HHsearch alignment for GI: 254780936 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=93.90  E-value=0.57  Score=26.50  Aligned_cols=142  Identities=21%  Similarity=0.281  Sum_probs=73.8

Q ss_pred             EEEEHHHH----HHHHHH----C----CCCCC----H-HHHHHHHHHCCE-EEEEEEEECCCC---------------CC
Q ss_conf             99807899----999985----0----87679----8-999999851792-999999730688---------------73
Q gi|254780936|r   10 LFIDGANL----YASSKA----L----GFDID----Y-RKLLKAFRSRAI-VIRAYYYTTVVG---------------DP   56 (182)
Q Consensus        10 IfID~~Nl----~~~~~~----~----~~~~d----~-~~L~~~l~~~~~-l~~~~~y~~~~~---------------~~   56 (182)
T Consensus         2 ~LiDG~~lafRayfAl~~~~~~L~~~~G~~t~A~yGF~~~L~~~l~~~~Pm~~~~~aFD~~~~TFR~e~Y~~YKa~R~~t   81 (1005)
T TIGR00593         2 LLIDGHSLAFRAYFALPNNKKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPMTYVAVAFDSGTKTFRHEAYEEYKANRAKT   81 (1005)
T ss_pred             EEEEHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHHCHHHCCCCCCC
T ss_conf             23403479999988622114666667887116778889999999974189516998876888851666253315788888


Q ss_pred             HHHHHHHHH-HHHHHHHCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHH-CCCCEEEEECCCHHHHHHHHHHHH
Q ss_conf             146777579-998897559569753458953788865435653299999999942-115889998386658999999998
Q gi|254780936|r   57 EQQFSPLHP-LLDWLHYNGFQVVAKVAKEFTENCGRKRVKSSMDVELAVDAFEQS-EGLEHLVIFSGDGCFTTLVAALQR  134 (182)
Q Consensus        57 ~~~~~~~~~-~~~~l~~~g~~v~~~~~~~~~~~~~~~~~kk~~Dv~laiD~~~~a-~~~d~~iLvSGD~Df~pli~~lr~  134 (182)
T Consensus        82 P~el~~Qi~~i~e~l~algi~~~e~~GY-----------E--ADD~IaTLA~~a~~~G~~-V~I~sgDrD~lQLvs~e--  145 (1005)
T TIGR00593        82 PEELIEQIPLIKELLEALGIPILEVEGY-----------E--ADDVIATLAKQAEKEGYE-VRIISGDRDLLQLVSDE--  145 (1005)
T ss_pred             CHHHHHHHHHHHHHHHHCCCEEEECCCC-----------C--HHHHHHHHHHHHHHCCCE-EEEEECCCCCCCCCCCC--
T ss_conf             8746876899999999719818822887-----------1--012899988877546854-89983784621121786--


Q ss_pred             CCCEEEEEEEECCCCCCCHHHHHHHCCCCEEHHHHHHHHCCCCC
Q ss_conf             49889999831577654708999852111518997876225831
Q gi|254780936|r  135 KVKKVTIVSTVLSDPSMASDQLRRQADYFMDLAYLKNEIARDPD  178 (182)
Q Consensus       135 ~Gk~V~v~~~~~~~~~~~S~~L~~~ad~fi~l~~l~~~i~r~~~  178 (182)
T Consensus       146 ---~V~V~~~~-~~~g~~~~~-------~~t~e~V~eKyGv~P~  178 (1005)
T TIGR00593       146 ---NVKVLIPE-RKKGKTEFT-------EITPEYVVEKYGVTPS  178 (1005)
T ss_pred             ---CEEEEECC-CCCCCCCCE-------ECCHHHHHHHCCCCHH
T ss_conf             ---14886435-456754310-------1177898754186745