HHsearch alignment for GI: 254781193 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=100.00  E-value=0  Score=875.36  Aligned_cols=492  Identities=22%  Similarity=0.262  Sum_probs=408.4

Q ss_pred             HHCCCCCEEEEEEHHHHHHHHHHHCCCCCC-CCCEEEHHHHHHHHCCCC---CHHHHHHHCCCCC-CHHH-HHHHHHHHH
Q ss_conf             863889819997307749999986089988-420331688999867899---9689899829981-1004-379999862
Q gi|254781193|r   60 ALENTDVTIVAHNSYFERTVLKACFNLDIP-IHRWICTLVLARSNGLPS---ALKAVGEALKLSS-QKME-EGKELIARF  133 (675)
Q Consensus        60 ~L~~~~~~kV~HNa~FD~~~L~~~~Gi~i~-~~~~~DTmi~A~~l~~~~---sL~~la~~l~l~~-~k~~-~~k~l~~~~  133 (675)
T Consensus       460 ~~~~a~~~~~~~~~K~~~~~L~~~-g~~~~~~~~~~D~~laaYll~~~~~~~~l~~~~~~y~~~~~~~d~~~~~~~~~--  536 (1005)
T TIGR00593       460 LLVSASKVKVAHDAKFLMHLLKRK-GIELIEIGVIFDTMLAAYLLDPAQVSKDLDTLAKRYLVEELILDDDRKEEGIK--  536 (1005)
T ss_pred             HCCCCCCCCCHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHH--
T ss_conf             002341012288999999999743-77334421145489999984303564027899987134346778731345544--


Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHH-----------------------------CCCC
Q ss_conf             02112343323467858532899999989989999999963010400-----------------------------0151
Q gi|254781193|r  134 CKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSS-----------------------------KEQE  184 (675)
Q Consensus       134 ~k~~~~~~~~~~~~~~~~~~~~~~~~Ya~~Dv~~t~~L~~~l~~~~~-----------------------------~E~~  184 (675)
T Consensus       537 -----------~~~~~a~~~~~~~~~~~~~~~~~~~~L~~~l~~~L~~eDaDitfrlyhylklrle~~~~~~L~~eiE~P  605 (1005)
T TIGR00593       537 -----------KLAKFADPDLEEAIEYLARKAAATARLAEELLKELDAEDADITFRLYHYLKLRLEENKLLSLYEEIELP  605 (1005)
T ss_pred             -----------HHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHCCC
T ss_conf             -----------334441121778899999999999999999888731132204667777888651638899999884200


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCC---C-CCCHH
Q ss_conf             3366665311562137999999999999999999999998728854767887999887777558888889---8-85338
Q gi|254781193|r  185 LWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDL---T-ETTCQ  260 (675)
Q Consensus       185 ~~~~~~~me~~Gi~vD~e~l~~l~~~~~~~~~~l~~~i~~~~~~~~~n~~S~~ql~~~L~~~lg~~~~~~---~-k~t~~  260 (675)
T Consensus       606 l~~VL~~ME~~Gi~~D~~~L~~L~~e~~~~l~~lE~~Iy~~-aG~~FNinSPKQL~~vLF~KL~Lp~~kK~KtG~YSTd~  684 (1005)
T TIGR00593       606 LSKVLAEMEKTGIKVDKDYLQELSKEFGEELLDLEEEIYEL-AGEEFNINSPKQLGEVLFEKLGLPVGKKTKTGSYSTDA  684 (1005)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCEECH
T ss_conf             78999998776678708999999999999999999999987-49520688733555886998478820034678621338


Q ss_pred             HHHHHHHCCCCH-HHHHH-HHHHHHHHHHHHHHHHHHHHCCCC-CCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             998721304823-89999-999997655101335788740868-967677884000132211247888444888886511
Q gi|254781193|r  261 RVLSSNKKLTPQ-AIQVF-NNRMRASRSAVLKLNTLVEAMNSD-GRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHE  337 (675)
Q Consensus       261 ~~L~~~~~~~~~-~~~~l-~~r~~~~k~~~~~~~~~~~~~~~d-gRih~~~~~~gat~TGR~S~~~pNlQnlPr~~~~~~  337 (675)
T Consensus       685 ~vLe~L~~~h~~~i~~~Ll~yR-~L~KLksTY~d~Ll~~v~~~TgRiHT~F~Qt~-TaTGRLSS~~PNLQNIPiR~~~Gr  762 (1005)
T TIGR00593       685 DVLEKLAEKHPIHIALILLEYR-QLTKLKSTYVDGLLELVNPDTGRIHTTFNQTG-TATGRLSSSNPNLQNIPIRSEEGR  762 (1005)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHH-HHHHHHHCCHHHHHHHHHHCCCCEEHHHHHHH-HHCCCCCCCCCCCCCCCCCCCCHH
T ss_conf             8999887428883689998766-66543101201338984000282731314545-635620047888544332272001


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCHHHHHEEEECC-CCCEEEEEECCCCCHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHH
Q ss_conf             3455431012333345544321003333012668-987899983453723333231146201134541133101014764
Q gi|254781193|r  338 ELDQIITHLPTSITSDPDPLQIISDCVRSCVIAS-EGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARS  416 (675)
Q Consensus       338 ~~~~~~~~~~~~~~~~~~~~~~~~~~iR~~f~a~-~G~~lv~aDySqiElRvlA~ls~d~~l~~af~~g~D~h~~tA~~~  416 (675)
T Consensus       763 ~-------------------------IR~AFva~~~g~~L~~ADYSQIELRiLAHlS~De~Li~AF~~~~DIH~~TA~~~  817 (1005)
T TIGR00593       763 K-------------------------IRKAFVAESKGWLLISADYSQIELRILAHLSQDENLIEAFKNGEDIHTQTASRL  817 (1005)
T ss_pred             H-------------------------HHHCCCCCCCCCEEEECCCCHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf             3-------------------------322002468860688526337999999864078679999754887138899997


Q ss_pred             CCCCHHHHCCHHHHHCCCCEEEEECCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             48795670620111016520210028888889987987088831134556555455556788889999887643100010
Q gi|254781193|r  417 FNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIED  496 (675)
Q Consensus       417 ~g~~~~~~~~~~R~~aK~~~~g~~YG~G~~~l~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  496 (675)
T Consensus       818 Fgv~~~~vtp~~RR~AK~vNFGivYGmSafgLA~--------------------------------------------~L  853 (1005)
T TIGR00593       818 FGVEEEDVTPNMRRIAKAVNFGIVYGMSAFGLAR--------------------------------------------EL  853 (1005)
T ss_pred             HCCCHHHCCHHHHCCCCEEEEHHHHCCCHHHHHH--------------------------------------------HH
T ss_conf             2989774496460474144301321012057777--------------------------------------------50


Q ss_pred             CCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCC
Q ss_conf             22078889999999987887899999999999999754917962154211332223445640232476631016786621
Q gi|254781193|r  497 LFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNN  576 (675)
Q Consensus       497 ~~~~~ea~~~~~~~r~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~GR~~~~~~~~~~  576 (675)
T Consensus       854 ~Is~~EA~~fIe~YF~~yPgv~~Y~~---~~~~~ar~~GYV~T-----------------------l~gRRRY~~~i~s~  907 (1005)
T TIGR00593       854 GISRKEAKEFIERYFERYPGVKEYLE---NTVEEARKKGYVTT-----------------------LLGRRRYIPDINSR  907 (1005)
T ss_pred             CCCHHHHHHHHHHHHHHCCHHHHHHH---HHHHHHHHCCCEEE-----------------------ECCCEECCCCCCHH
T ss_conf             88888999999999763413899999---99999973685563-----------------------04656115763223


Q ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CC--CCEEEEECCEEEEECCCCHHHHH-HHHHH
Q ss_conf             0210100234567775314565545368899999999999996----79--81889952589997792489999-99999
Q gi|254781193|r  577 RSYLNTTTRQLTREYTYGGKLTENIVQAVSRDILAEGMMNATK----AG--YDIVLTVHDEIVCETPDTDEFNA-SMLYH  649 (675)
Q Consensus       577 ~~~~~~~~~~~~r~~~~~~k~~n~~iQgtaadi~k~ami~l~~----~g--~~ivl~VHDEiv~evp~~~~~~~-~~i~~  649 (675)
T Consensus       908 n~~~R~~---AER~A------~NaPIQGSAADI~K~AMikl~~~L~~~~L~~rlLLQVHDELl~E~P~~E~e~v~~l~k~  978 (1005)
T TIGR00593       908 NRNLREA---AERMA------INAPIQGSAADIMKIAMIKLDKALKERKLKSRLLLQVHDELLFEAPEEEAEEVKALVKE  978 (1005)
T ss_pred             HHHHHHH---HHHHH------HCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             5777999---99987------36753468789999999999999973250333467865588723444137899999998


Q ss_pred             HHC-CCCHHCCCCCCEEEECCCCCCC
Q ss_conf             845-6520215995157401004631
Q gi|254781193|r  650 LMT-SNPSWAKGLPLKAEGYESKRYR  674 (675)
Q Consensus       650 ~M~-~~~~w~~~~pl~ae~~~~~~y~  674 (675)
T Consensus       979 ~MED~A~~--L~VPL~v~~~~G~~W~ 1002 (1005)
T TIGR00593       979 VMEDEAYT--LSVPLEVEVETGKNWG 1002 (1005)
T ss_pred             HHCCEEEE--CCCCCEEECCCCCCHH
T ss_conf             71461010--2576367524587711