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