HHsearch alignment for GI: 254780277 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=2259.42  Aligned_cols=930  Identities=41%  Similarity=0.659  Sum_probs=791.5

Q ss_pred             EEEEECCHHHHHHHHCCCC---CCCCCCCCEECHHHHHHHHHHHHHHHHCC-CCCCCEEEEEEECCCCCHHHHCCHHHHC
Q ss_conf             8999662699988742675---44689885500699999999999998485-5479879999727488713240865216
Q gi|254780277|r    7 LFLVDGSSFIYRAFYATPL---LSRKHDGLPVNAIAGFCNMLWKLLQNSRK-ESIASHFAVIFDYPAVTFRNEIYPDYKA   82 (976)
Q Consensus         7 ~~liDg~~~~~ra~~a~p~---~~~~~~G~~t~ai~gf~~~l~~~i~~~~~-~~~~~~~~v~fD~~~~tfR~~~~~~YKa   82 (976)
T Consensus         1 L~LiDG~~lafRayfAl~~~~~~L~~~~G~~t~A~yGF~~~L~~~l~~~~Pm~----~~~~aFD~~~~TFR~e~Y~~YKa   76 (1005)
T TIGR00593         1 LLLIDGHSLAFRAYFALPNNKKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPMT----YVAVAFDSGTKTFRHEAYEEYKA   76 (1005)
T ss_pred             CEEEEHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCE----EEEEEECCCCCCHHHHHCHHHCC
T ss_conf             92340347999998862211466666788711677888999999997418951----69988768888516662533157


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCEEHHHHHHHHHHHHHHCCCCEEEECCCCHHHEECCC-CEEEEEC--CC
Q ss_conf             67987975886489999999970997995689016658999999998489949998687012122379-7599966--78
Q gi|254780277|r   83 NRPKIPEMLLPQLPLVRLATQAFGIPAIEIQGFEADDIIATYTYIAEKEGFAVTIISTDKDLMQLVSP-TTCLYDT--VK  159 (976)
Q Consensus        83 ~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~~~EADDviatla~~~~~~~~~v~i~s~DkD~~Qlv~~-~v~~~~~--~~  159 (976)
T Consensus        77 ~R~~tP~el~~Qi~~i~e~l~algi~~~e~~GYEADD~IaTLA~~a~~~G~~V~I~sgDrD~lQLvs~e~V~V~~~~~~~  156 (1005)
T TIGR00593        77 NRAKTPEELIEQIPLIKELLEALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDRDLLQLVSDENVKVLIPERKK  156 (1005)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCEEEEECCCCC
T ss_conf             88888874687689999999971981882288710128999888775468548998378462112178614886435456


Q ss_pred             C----CEECHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHH-----------HHHHH
Q ss_conf             8----35389999888489887877778751874358998776360249989841367899986-----------45420
Q gi|254780277|r  160 E----EKIDIEHVIKKWGIPPEKMVCLQALTGDSIDNIPGIPGIGYKTAALLLQEYGNLENILI-----------NASRI  224 (976)
Q Consensus       160 ~----~~~~~~~v~~~~gv~p~~~~d~~al~GD~sDnipGv~GiG~KtA~~ll~~~gsle~i~~-----------~~d~i  224 (976)
T Consensus       157 g~~~~~~~t~e~V~eKyGv~P~Q~~D~~AL~GD~SDNiPGV~GIGeKTA~kLL~~fgsLe~iy~~~ylkealr~~~~~~~  236 (1005)
T TIGR00593       157 GKTEFTEITPEYVVEKYGVTPSQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENTYLKEALRLDNLDQI  236 (1005)
T ss_pred             CCCCCEECCHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             75431011778987541867457887620468888785998973765689999872108999988778888747758622


Q ss_pred             HHHHHHHHHCCCHHHHHH--HHHHHHCCCCCCCCCCHHHH-CCCCCCHHHHHH-HHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             011223220035789997--65543203564224763552-126767688998-65323368999876531144544334
Q gi|254780277|r  225 KQKKRRENILEYAETARL--SRKLVMLRTDVPITIPLEHL-ILEDCNGPRLIS-FLKALEFTKLINRVATTYDCDAANIE  300 (976)
Q Consensus       225 ~~~k~~~~l~~~~e~a~l--s~~L~tL~~Dvpl~~~~~~l-~~~~~d~~~l~~-~~~~lef~~ll~rL~~~~~~~~~~~~  300 (976)
T Consensus       237 k~~~~~~~L~~~~e~a~~vfS~~La~i~~d~pl~~~~~~~~~~~~~~~~~l~~~~l~elef~s~~~~l~~~~~~~~~~~~  316 (1005)
T TIGR00593       237 KSEKLREKLIAHKEDAFLVFSKELATIVTDVPLEVDLEDLLRLSEPDREKLVEKLLQELEFKSLLKKLEKLESPEIDDHA  316 (1005)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             86578899998775378773176500037997434668873036775678999999975089999997202420004567


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCEE-------EC-
Q ss_conf             2111234332222333222222233332222233332112232112001121100001235556665035-------47-
Q gi|254780277|r  301 PVVLDINTTENKGIAIETEIDRDTTIKTSQFSSLSDQTSKINSEQTPQKLFLERLQKLSQYPINNDSYTK-------IV-  372 (976)
Q Consensus       301 ~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~p~~~~~~~~~~~~~~~~~~~~y~~-------I~-  372 (976)
T Consensus       317 p~~~~-------------~l~~~~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~V~~  365 (1005)
T TIGR00593       317 PALEA-------------DLSQAEAPEE------------------KEEFTLVAKESEEASPLANVAEKAERGGRSDVVL  365 (1005)
T ss_pred             CCCCC-------------CCCCCCCCCC------------------CCCCHHHHCCCCCCCCCCCCCHHHHHCCCCHHHH
T ss_conf             66510-------------0012676421------------------1242112013300267222103555136511343


Q ss_pred             --CHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCC-CC-CCCCCEECCCCCCC-----C--CCCCC
Q ss_conf             --99999999999986685232332224331100124420102577665-44-34550231374433-----3--45650
Q gi|254780277|r  373 --NTKDIQQWVQKLETIGSASFKIITDTMDAFHSKPIAIAISTLDQKDD-TS-FKVETIFIDLSVHT-----S--QDSTG  441 (976)
Q Consensus       373 --~~~~L~~li~~L~~~~~ia~DtETt~ld~~~~~ivGisls~~~~~~~-~~-~~~~~~yip~~~~~-----~--~d~~~  441 (976)
T Consensus       366 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  445 (1005)
T TIGR00593       366 ARDAIVLEDLLDQLKKARALAFATENQSLVAYISEADGISIADTELEGFSILVAEAEALYVALIKEDVSLLTILTDAKFA  445 (1005)
T ss_pred             HHHHHHHHCCHHHHHHCHHHHHHHHCCCCCCCCCCCCCCHHHHCCHHHCCCCCCCCCCCCCCCCCCCHHHHCCHHHHHHH
T ss_conf             33323220001121202033222121333310000014203322132123112132455223357722342001112789


Q ss_pred             CCCCHHHHHHHHHHHHCCCCCHHHHCCCCHHHHHHHHCCCCCC--C-CCCHHHHHHHHCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf             0178899997444420222100110032123788986188666--4-210023455431687667724667762244422
Q gi|254780277|r  442 KNTLTKEILSYLKKFFENEHFLKIGHNIKYDKLVLHRYGISMR--G-FEDIMLMSYVLDSGRSSHDIASIAQKWLSYTRK  518 (976)
Q Consensus       442 ~~~~~~evl~~L~~lle~~~i~kIgHN~KfD~~~L~~~GI~l~--~-i~DTmlaayLLdp~~~~~~L~~la~~yL~~~~~  518 (976)
T Consensus       446 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~K~~~~~L~~~g~~~~~~~~~~D~~laaYll~~~~~~~~l~~~~~~y~~~~~~  525 (1005)
T TIGR00593       446 EWLLKETIKKALEELLVSASKVKVAHDAKFLMHLLKRKGIELIEIGVIFDTMLAAYLLDPAQVSKDLDTLAKRYLVEELI  525 (1005)
T ss_pred             HHHHHCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHCCCCCC
T ss_conf             98740001455521002341012288999999999743773344211454899999843035640278999871343467


Q ss_pred             -C---CCCCCCCCCCCHHHCCHHHHHHHHH-------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             -3---3565432221000000123333222-------------------1111124567763222100013457886075
Q gi|254780277|r  519 -E---ILKSRKSSIPIDKISDSQVQEHAIE-------------------NSNVILQLWLLLRPKLIVEKLLHVYERLDKP  575 (976)
Q Consensus       519 -e---~~~~~k~~~~~~~i~~e~~~~Yaa~-------------------Da~~t~~L~~~l~~~L~~~~l~~l~~~iE~P  575 (976)
T Consensus       526 ~d~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~L~~~l~~~L~~eDaDitfrlyhylklrle~~~~~~L~~eiE~P  605 (1005)
T TIGR00593       526 LDDDRKEEGIKKLAKFADPDLEEAIEYLARKAAATARLAEELLKELDAEDADITFRLYHYLKLRLEENKLLSLYEEIELP  605 (1005)
T ss_pred             CCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHCCC
T ss_conf             78731345544334441121778899999999999999999888731132204667777888651638899999884200


Q ss_pred             CHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHH
Q ss_conf             01233221014310058999986434368999999999740345577776566679987420788755566545353178
Q gi|254780277|r  576 MIDVVSQMEITGIQIDQDLLKQVSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAKTKTGQWKTTAQ  655 (976)
Q Consensus       576 l~~vLa~ME~~Gi~vD~~~L~~l~~~l~~~l~~le~~i~~~aG~~FNinSpkQL~~vLf~~LgLp~~kKTktG~~ST~~~  655 (976)
T Consensus       606 l~~VL~~ME~~Gi~~D~~~L~~L~~e~~~~l~~lE~~Iy~~aG~~FNinSPKQL~~vLF~KL~Lp~~kK~KtG~YSTd~~  685 (1005)
T TIGR00593       606 LSKVLAEMEKTGIKVDKDYLQELSKEFGEELLDLEEEIYELAGEEFNINSPKQLGEVLFEKLGLPVGKKTKTGSYSTDAD  685 (1005)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCEECHH
T ss_conf             78999998776678708999999999999999999999987495206887335558869984788200346786213388


Q ss_pred             HHHHHHCCCCHH-HHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             877653047627-99999-9987888988653200111100123334533002221000001333433345563322224
Q gi|254780277|r  656 DLEQINCGDNPI-IKNIL-EWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMTGRLASLEPNLQNIPIKTDLGQKI  733 (976)
Q Consensus       656 ~Le~L~~~~hp~-~~~iL-eyR~l~KL~sTY~~~l~~~i~~~dgRIH~~f~q~~t~TGRlSs~~PNlQNiP~r~~~g~~i  733 (976)
T Consensus       686 vLe~L~-~~h~~~i~~~Ll~yR~L~KLksTY~d~Ll~~v~~~TgRiHT~F~Qt~TaTGRLSS~~PNLQNIPiR~~~Gr~I  764 (1005)
T TIGR00593       686 VLEKLA-EKHPIHIALILLEYRQLTKLKSTYVDGLLELVNPDTGRIHTTFNQTGTATGRLSSSNPNLQNIPIRSEEGRKI  764 (1005)
T ss_pred             HHHHHH-HCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCEEHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf             999887-4288836899987666654310120133898400028273131454563562004788854433227200133


Q ss_pred             CEEEECC-CCCEEEEEECCCCCEEEEEEEEEHHHHHHHHHCCCCHHHHHHHHHHCCCHHHCCHHHHHHHHHHHHHHHHCC
Q ss_conf             3024248-994899963265443687665103777873406988899999898099968899888863025135644077
Q gi|254780277|r  734 RRAFISP-PTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGI  812 (976)
Q Consensus       734 R~~F~a~-~g~~lv~aDySQiElRilA~ls~D~~l~~af~~g~DiH~~tA~~vf~~~~~~vt~~~R~~aK~infgi~YG~  812 (976)
T Consensus       765 R~AFva~~~g~~L~~ADYSQIELRiLAHlS~De~Li~AF~~~~DIH~~TA~~~Fgv~~~~vtp~~RR~AK~vNFGivYGm  844 (1005)
T TIGR00593       765 RKAFVAESKGWLLISADYSQIELRILAHLSQDENLIEAFKNGEDIHTQTASRLFGVEEEDVTPNMRRIAKAVNFGIVYGM  844 (1005)
T ss_pred             HHCCCCCCCCCEEEECCCCHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCCHHHCCHHHHCCCCEEEEHHHHCC
T ss_conf             22002468860688526337999999864078679999754887138899997298977449646047414430132101


Q ss_pred             CHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCEECCCCCEECCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             70356788199989999999999998888999999999999984988827787601898758837888778787701345
Q gi|254780277|r  813 SPFRLATQLRIPRSEAADYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPI  892 (976)
Q Consensus       813 ~~~~La~~l~is~~eA~~~i~~yf~~~p~v~~~~~~~~~~a~~~gyv~T~~GRrr~~p~i~s~~~~~r~~aeR~a~N~~i  892 (976)
T Consensus       845 SafgLA~~L~Is~~EA~~fIe~YF~~yPgv~~Y~~~~~~~ar~~GYV~Tl~gRRRY~~~i~s~n~~~R~~AER~A~NaPI  924 (1005)
T TIGR00593       845 SAFGLARELGISRKEAKEFIERYFERYPGVKEYLENTVEEARKKGYVTTLLGRRRYIPDINSRNRNLREAAERMAINAPI  924 (1005)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCEEEECCCEECCCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             20577775088888999999999763413899999999999736855630465611576322357779999998736753


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCEEEEECCHHHHHHHHHHHHHHHH-HCCCCCCCCCCCEEEEEEEECC
Q ss_conf             653899999999999999986599818999726389995598799999999999965-1013574444643888332089
Q gi|254780277|r  893 QGSAADITRRAMISVHKSLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHSME-KACLPKINLRVPLKVNIKVSNN  971 (976)
Q Consensus       893 QGsaAdi~k~am~~i~~~~~~~~~~~~~ilqVHDElv~ev~~~~~~~~~~~~~~~Me-~~~~~~~~l~VPl~v~~~~G~~  971 (976)
T Consensus       925 QGSAADI~K~AMikl~~~L~~~~L~~rlLLQVHDELl~E~P~~E~e~v~~l~k~~MED~A~----~L~VPL~v~~~~G~~ 1000 (1005)
T TIGR00593       925 QGSAADIMKIAMIKLDKALKERKLKSRLLLQVHDELLFEAPEEEAEEVKALVKEVMEDEAY----TLSVPLEVEVETGKN 1000 (1005)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEE----ECCCCCEEECCCCCC
T ss_conf             4687899999999999999732503334678655887234441378999999987146101----025763675245877


Q ss_pred             HHHHC
Q ss_conf             37819
Q gi|254780277|r  972 WQEEN  976 (976)
Q Consensus       972 W~e~~  976 (976)
T Consensus      1001 W~e~k 1005 (1005)
T TIGR00593      1001 WGEAK 1005 (1005)
T ss_pred             HHCCC
T ss_conf             11129