HHsearch alignment for GI: 254780636 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=99.52 E-value=2.6e-14 Score=102.46 Aligned_cols=134 Identities=19% Similarity=0.212 Sum_probs=102.3
Q ss_pred HHHHHHCCCCCEEE-------------CCCCHHHHHHHHHHHCCCC---CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC
Q ss_conf 76777323640230-------------1000016888654200000---0045789886521100000088777654200
Q gi|254780636|r 66 LVGMLVDEKREKIF-------------HYGRFDIAVLFYTFGVRVR---PVFCTKIASRLTRTYTNQHGLKDNLKELLGI 129 (207)
Q Consensus 66 L~~ll~d~~i~KV~-------------Hn~~~D~~~L~~~~gi~~~---~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~ 129 (207)
T Consensus 444 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~K~~~~~L~~~-g~~~~~~~~~~D~~laaYll~~~~~~~~l~~~~~~y~~~ 522 (1005)
T TIGR00593 444 FAEWLLKETIKKALEELLVSASKVKVAHDAKFLMHLLKRK-GIELIEIGVIFDTMLAAYLLDPAQVSKDLDTLAKRYLVE 522 (1005)
T ss_pred HHHHHHHCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHCCC
T ss_conf 8998740001455521002341012288999999999743-773344211454899999843035640278999871343
Q ss_pred CCCCC----C--EEC--CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-------------------HCCCHHHHHH
Q ss_conf 24675----2--003--6565443236899998645999999999999999-------------------7491899999
Q gi|254780636|r 130 NISKA----Q--QSS--DWSADDLSDEQLQYAASDVVHLHALRLQFTEKLQ-------------------RLGRSDLATS 182 (207)
Q Consensus 130 ~ldK~----~--q~S--dW~~rpLs~~Qi~YAA~Dv~~l~~L~~~l~~~L~-------------------~~~~~~~~~~ 182 (207)
T Consensus 523 ~~~~d~~~~~~~~~~~~~~a~~~-~~~~~~~~~~~~~~~~~L~~~l~~~L~~eDaDitfrlyhylklrle~~~~~~L~~e 601 (1005)
T TIGR00593 523 ELILDDDRKEEGIKKLAKFADPD-LEEAIEYLARKAAATARLAEELLKELDAEDADITFRLYHYLKLRLEENKLLSLYEE 601 (1005)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHHHHHHHH
T ss_conf 46778731345544334441121-77889999999999999999988873113220466777788865163889999988
Q ss_pred -HHHHHHHHHHHHHCCCCCCC
Q ss_conf -99640068999866798888
Q gi|254780636|r 183 -CCNFLMDRAELDLLGWENVD 202 (207)
Q Consensus 183 -e~~~l~~~~~me~~g~~~~~ 202 (207)
T Consensus 602 iE~Pl~~VL~~ME~~Gi~-~D 621 (1005)
T TIGR00593 602 IELPLSKVLAEMEKTGIK-VD 621 (1005)
T ss_pred HCCCHHHHHHHHHHHHHH-HH
T ss_conf 420078999998776678-70