HHsearch alignment for GI: 254780127 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=98.27 E-value=1.1e-06 Score=62.31 Aligned_cols=125 Identities=14% Similarity=0.122 Sum_probs=86.1
Q ss_pred EEEECCCCCEEEEEEECC-C---HHHHHHHH-CCCCC---CCCCH-HHHHCCCCCCCCHHH-HHCCCCCHHHHHHCCCHH
Q ss_conf 997335485058866228-7---67866540-44410---00015-776087511057022-100642100133078877
Q gi|254780127|r 377 VVADLAGIEARVLAWIAG-E---DWKIKAFA-NGEDI---YVTTY-AKAFNTPIDKVSKEQ-RAIGKVMELALGYQGGAK 446 (675)
Q Consensus 377 v~aDySqiElRvlA~ls~-d---~~li~~f~-~g~D~---h~~tA-~~~~~~~~~~v~~~~-R~~aK~~~~gl~YG~G~~ 446 (675)
T Consensus 789 iLAHlS~De~Li~AF~~~~DIH~~TA~~~Fgv~~~~vtp~~RR~AK~vNFGivY----GmSafgLA~~L~---------- 854 (1005)
T TIGR00593 789 ILAHLSQDENLIEAFKNGEDIHTQTASRLFGVEEEDVTPNMRRIAKAVNFGIVY----GMSAFGLARELG---------- 854 (1005)
T ss_pred HHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCCHHHCCHHHHCCCCEEEEHHHH----CCCHHHHHHHHC----------
T ss_conf 998640786799997548871388999972989774496460474144301321----012057777508----------
Q ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 89887887088864036666656667654788999999999875111010310889788999999867307899999999
Q gi|254780127|r 447 VFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTE 526 (675)
Q Consensus 447 ~l~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ea~~~~~~~~~~~p~i~~~~~~~~~ 526 (675)
T Consensus 855 ------------Is~~EA~~fIe~YF~~yPgv~~Y~~~~~~~ar~~GYV~Tl~gR---------RRY~~~i~s~n~~~R~ 913 (1005)
T TIGR00593 855 ------------ISRKEAKEFIERYFERYPGVKEYLENTVEEARKKGYVTTLLGR---------RRYIPDINSRNRNLRE 913 (1005)
T ss_pred ------------CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCEEEECCC---------EECCCCCCHHHHHHHH
T ss_conf ------------8888999999999763413899999999999736855630465---------6115763223577799
Q ss_pred HHHHHHHCCC
Q ss_conf 9999963372
Q gi|254780127|r 527 GFACVVQEGG 536 (675)
Q Consensus 527 ~~~~~~~~~~ 536 (675)
T Consensus 914 ~AER~A~NaP 923 (1005)
T TIGR00593 914 AAERMAINAP 923 (1005)
T ss_pred HHHHHHHCCC
T ss_conf 9999873675