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