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