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=100.00 E-value=0 Score=822.04 Aligned_cols=502 Identities=22% Similarity=0.245 Sum_probs=396.2
Q ss_pred CCCEEEEEEHHHHHHHHHHHCCCCCC-CCCEEEHHHHHHHHCCCC---CHHHHHHHHCCCCCCH----HHHHCHHHHHHH
Q ss_conf 89819986307759999986299878-650454588999858899---9789999808898652----766376576641
Q gi|254780127|r 64 ETVMCVAHNSLFERILFKKTLGIDIP-SKRWICTSVLARTNGLPS---SLKNACLALNFSEHLT----KMEEGKALIARF 135 (675)
Q Consensus 64 ~~~~kv~HNa~FD~~vL~~~lGi~i~-~~~~~DTmi~A~~l~~p~---sL~~la~~lgl~~~~~----kd~~gk~li~~~ 135 (675)
T Consensus 464 a~~~~~~~~~K~~~~~L~~~-g~~~~~~~~~~D~~laaYll~~~~~~~~l~~~~~~y~~~~~~~d~~~~~~~~~~~~~~a 542 (1005)
T TIGR00593 464 ASKVKVAHDAKFLMHLLKRK-GIELIEIGVIFDTMLAAYLLDPAQVSKDLDTLAKRYLVEELILDDDRKEEGIKKLAKFA 542 (1005)
T ss_pred CCCCCCHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 41012288999999999743-77334421145489999984303564027899987134346778731345544334441
Q ss_pred HHHHHHHCCCCCCCC-CCHHH-HHHHHHHHHHHHHHHHHHHHHHCC----------CHHHHHHHHHHHHHHHHCCEECCH
Q ss_conf 002332013453112-58768-999898877539999999987200----------214310178999987516843088
Q gi|254780127|r 136 CKGSIDSPPYDCTRA-NHVQA-WQLFGEYCKRDVEATRELFKRLIP----------LSDGERDLWLLDQTINDRGYRIDL 203 (675)
Q Consensus 136 ~~~~~~~~~~~~~~~-~~~~~-~~~~~~Ya~~Dv~~~~~L~~~L~~----------~~~~E~~l~~~~~~me~~Gi~vD~ 203 (675)
T Consensus 543 ~~~~~~~~~~~~~~~~~~~~L~~~l~~~L~~eDaDitfrlyhylklrle~~~~~~L~~eiE~Pl~~VL~~ME~~Gi~~D~ 622 (1005)
T TIGR00593 543 DPDLEEAIEYLARKAAATARLAEELLKELDAEDADITFRLYHYLKLRLEENKLLSLYEEIELPLSKVLAEMEKTGIKVDK 622 (1005)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 12177889999999999999999988873113220466777788865163889999988420078999998776678708
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCCC---C-HHHHHHHHHH-CCCCCH-HHHH
Q ss_conf 99999999999999999999986305766888856889999999728999888---9-6588999974-489854-8999
Q gi|254780127|r 204 DLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDM---S-EGTLKSILSH-SNITQL-AKDL 277 (675)
Q Consensus 204 e~l~~~~~~~~~~~~~~~~~i~~~~g~~~~n~~S~~ql~~~L~~~~g~~~~~~---~-k~~~~~~l~~-~~~~~~-~~~l 277 (675)
T Consensus 623 ~~L~~L~~e~~~~l~~lE~~Iy~~aG~~F-NinSPKQL~~vLF~KL~Lp~~kK~KtG~YSTd~~vLe~L~~~h~~~i~~~ 701 (1005)
T TIGR00593 623 DYLQELSKEFGEELLDLEEEIYELAGEEF-NINSPKQLGEVLFEKLGLPVGKKTKTGSYSTDADVLEKLAEKHPIHIALI 701 (1005)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCHHHHHHHHHHHHCCCCCCCCCCCCCEECHHHHHHHHHCCCCCHHHH
T ss_conf 99999999999999999999998749520-68873355588699847882003467862133889998874288836899
Q ss_pred H-HHHHHHHHHCCHHHHHHHHHHCCC-CCCCCCEEECCCCCCHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCC
Q ss_conf 9-999997543000356688730568-84522002113221001110688855477776652345654431024445544
Q gi|254780127|r 278 I-LNRLASSGSAILKLNTLSEAVSSD-GRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIAD 355 (675)
Q Consensus 278 l-~~r~~~~~~~~~~~~~l~~~~~~d-GRih~~~~~~gAt~TGR~S~~~pNlQnlPr~~~~~~~~~~~~~~~~~~~~~~~ 355 (675)
T Consensus 702 Ll~yR~L~KLksT-Y~d~Ll~~v~~~TgRiHT~F~Qt~-TaTGRLSS~~PNLQNIP------------------------ 755 (1005)
T TIGR00593 702 LLEYRQLTKLKST-YVDGLLELVNPDTGRIHTTFNQTG-TATGRLSSSNPNLQNIP------------------------ 755 (1005)
T ss_pred HHHHHHHHHHHHC-CHHHHHHHHHHCCCCEEHHHHHHH-HHCCCCCCCCCCCCCCC------------------------
T ss_conf 9876666543101-201338984000282731314545-63562004788854433------------------------
Q ss_pred CCCCCCHHHHEEEECC-CCCEEEEEECCCCCEEEEEEECCCHHHHHHHHCCCCCCCCCHHHHHCCCCCCCCHHHHHCCCC
Q ss_conf 4322101321214769-987899973354850588662287678665404441000015776087511057022100642
Q gi|254780127|r 356 PLGLASDCVRSCIIAS-NGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKV 434 (675)
Q Consensus 356 ~~~~~~~~iR~~f~a~-~G~~lv~aDySqiElRvlA~ls~d~~li~~f~~g~D~h~~tA~~~~~~~~~~v~~~~R~~aK~ 434 (675)
T Consensus 756 iR~~~Gr~IR~AFva~~~g~~L~~ADYSQIELRiLAHlS~De~Li~AF~~~~DIH~~TA~~~Fgv~~~~vtp~~RR~AK~ 835 (1005)
T TIGR00593 756 IRSEEGRKIRKAFVAESKGWLLISADYSQIELRILAHLSQDENLIEAFKNGEDIHTQTASRLFGVEEEDVTPNMRRIAKA 835 (1005)
T ss_pred CCCCCHHHHHHCCCCCCCCCEEEECCCCHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHCCCHHHCCHHHHCCCCE
T ss_conf 22720013322002468860688526337999999864078679999754887138899997298977449646047414
Q ss_pred CHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCHHHHHHHHHHHHHHHC
Q ss_conf 10013307887789887887088864036666656667654788999999999875111010310889788999999867
Q gi|254780127|r 435 MELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKH 514 (675)
Q Consensus 435 ~~~gl~YG~G~~~l~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ea~~~~~~~~~~~ 514 (675)
T Consensus 836 vNFGivYGmSafgLA~--------------------------------------------~L~Is~~EA~~fIe~YF~~y 871 (1005)
T TIGR00593 836 VNFGIVYGMSAFGLAR--------------------------------------------ELGISRKEAKEFIERYFERY 871 (1005)
T ss_pred EEEHHHHCCCHHHHHH--------------------------------------------HHCCCHHHHHHHHHHHHHHC
T ss_conf 4301321012057777--------------------------------------------50888889999999997634
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCEEECCCCHHHCCCCCCHHHHHHCCCHHHHHHHHHHH
Q ss_conf 30789999999999999633721420132223443212445641122463113102452012332031001235776533
Q gi|254780127|r 515 QGVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYG 594 (675)
Q Consensus 515 p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~psGR~l~~~~~~~~~~~~~~~~~~~~r~~~~g 594 (675)
T Consensus 872 Pgv~~Y~~~~~~---~ar~~GY-----------------------V~Tl~gRRRY~~~i~s~n~~~R~---~AER~A--- 919 (1005)
T TIGR00593 872 PGVKEYLENTVE---EARKKGY-----------------------VTTLLGRRRYIPDINSRNRNLRE---AAERMA--- 919 (1005)
T ss_pred CHHHHHHHHHHH---HHHHCCC-----------------------EEEECCCEECCCCCCHHHHHHHH---HHHHHH---
T ss_conf 138999999999---9973685-----------------------56304656115763223577799---999987---
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----CC--CCEEEEECCEEEEECCCCHHHHHHHH-HHHHC-CCCCCCCCCCCEEE
Q ss_conf 5577767479899999999999996----79--81899953589996784789999999-99846-76302169841573
Q gi|254780127|r 595 GKLTENIVQAISRDILCEGMKNATK----NG--YDIVLTVHDEIVSETPDTPYFSVGTL-CSLMT-KNPSWAKGLPLKAE 666 (675)
Q Consensus 595 ~k~~n~~iQgtAaDi~k~am~~l~~----~g--~~ivl~VHDElv~evp~~~~~~~~~i-~~~M~-~~p~wa~~~pl~a~ 666 (675)
T Consensus 920 ---~NaPIQGSAADI~K~AMikl~~~L~~~~L~~rlLLQVHDELl~E~P~~E~e~v~~l~k~~MED~A~~--L~VPL~v~ 994 (1005)
T TIGR00593 920 ---INAPIQGSAADIMKIAMIKLDKALKERKLKSRLLLQVHDELLFEAPEEEAEEVKALVKEVMEDEAYT--LSVPLEVE 994 (1005)
T ss_pred ---HCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEE--CCCCCEEE
T ss_conf ---3675346878999999999999997325033346786558872344413789999999871461010--25763675
Q ss_pred CCCCCCCC
Q ss_conf 03114631
Q gi|254780127|r 667 GYEAKRYR 674 (675)
Q Consensus 667 ~~~~~~y~ 674 (675)
T Consensus 995 ~~~G~~W~ 1002 (1005)
T TIGR00593 995 VETGKNWG 1002 (1005)
T ss_pred CCCCCCHH
T ss_conf 24587711