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