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