HHsearch alignment for GI: 254780277 and conserved domain: cd06444

>cd06444 DNA_pol_A DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol I has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide po
Probab=100.00  E-value=0  Score=906.99  Aligned_cols=379  Identities=54%  Similarity=0.882  Sum_probs=371.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHH
Q ss_conf             05899998643436899999999974034557777656667998742078875556654535317887765304762799
Q gi|254780277|r  590 IDQDLLKQVSAEISKNLLSLEENIYDLSGEKFNLSSPKQLGDILFTKLKFPSGAKTKTGQWKTTAQDLEQINCGDNPIIK  669 (976)
Q Consensus       590 vD~~~L~~l~~~l~~~l~~le~~i~~~aG~~FNinSpkQL~~vLf~~LgLp~~kKTktG~~ST~~~~Le~L~~~~hp~~~  669 (976)
T Consensus         1 id~~~~~~~~~~l~~~l~~l~~~~~~~~g~~fn~~S~~ql~~~L~~~lg~~~~~~~~~~-~st~~~~l~~~-~~~hp~~~   78 (379)
T cd06444           1 VDKEELEELSAELEKELEELEKEIYELAGEEFNINSPKQLGEVLFEKLGLPVSKKTKTG-YSTDEEVLEKL-AEAHPIIA   78 (379)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCC-CCCCHHHHHHH-HHCCCHHH
T ss_conf             98899999999999999999999999969907999999999999985499989888899-99859999976-43384899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEE
Q ss_conf             99999878889886532001111001233345330022210000013334333455633222243024248994899963
Q gi|254780277|r  670 NILEWRQLSKIKSTYADSLPNHINKRTQRVHTFYSLASTMTGRLASLEPNLQNIPIKTDLGQKIRRAFISPPTKKLISAD  749 (976)
Q Consensus       670 ~iLeyR~l~KL~sTY~~~l~~~i~~~dgRIH~~f~q~~t~TGRlSs~~PNlQNiP~r~~~g~~iR~~F~a~~g~~lv~aD  749 (976)
T Consensus        79 ~ile~R~~~kl~st~~~~~~~~~~~~~gRih~~~~q~gt~TGR~Ss~~PNlQniP~~~~~~~~~R~~f~~~~G~~lv~aD  158 (379)
T cd06444          79 LILEYRKLAKLKSTYVDALPKLINPKTGRIHTSFNQTVTATGRLSSSNPNLQNIPIRTEEGREIRKAFVAPPGYVLLSAD  158 (379)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHEEECCCCCEEEEEC
T ss_conf             99999999999999999998760689997966885277540012467876457888871167675247479998799842


Q ss_pred             CCCCCEEEEEEEEEHHHHHHHHHCCCCHHHHHHHHHHCCCHHHCCHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHH
Q ss_conf             26544368766510377787340698889999989809996889988886302513564407770356788199989999
Q gi|254780277|r  750 YSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVNIEKVSPQMRRHAKTINFSIIYGISPFRLATQLRIPRSEAA  829 (976)
Q Consensus       750 ySQiElRilA~ls~D~~l~~af~~g~DiH~~tA~~vf~~~~~~vt~~~R~~aK~infgi~YG~~~~~La~~l~is~~eA~  829 (976)
T Consensus       159 ySqiElRvlA~ls~D~~l~~~f~~g~Dih~~~A~~~~~~~~~~v~~~~R~~aK~~~fgl~YG~G~~~la~~l~~s~~eA~  238 (379)
T cd06444         159 YSQIELRILAHLSGDPALIEAFNNGEDIHSRTAAEVFGVPEEEVTKEERRKAKAINFGIIYGMGAFGLAEQLGISREEAK  238 (379)
T ss_pred             HHHCHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHCCCHHHCCHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCHHHHH
T ss_conf             31121888888717699999987388789999999839984435988998865767575328345329750199999999


Q ss_pred             HHHHHHHHHCHHHHHHHHHHHHHHHHCCCEECCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999888899999999999998498882778760189875883788877878770134565389999999999999
Q gi|254780277|r  830 DYIKRYFHRFPGIHEYIEKTKNFVRQNGYVETIFGRRIHYDEINSPKSSIRNINERAAINAPIQGSAADITRRAMISVHK  909 (976)
Q Consensus       830 ~~i~~yf~~~p~v~~~~~~~~~~a~~~gyv~T~~GRrr~~p~i~s~~~~~r~~aeR~a~N~~iQGsaAdi~k~am~~i~~  909 (976)
T Consensus       239 ~~~~~f~~~~p~v~~~~~~~~~~a~~~g~v~T~~GR~r~~~~~~~~~~~~~~~~~r~a~N~~iQGsaAdi~k~ami~i~~  318 (379)
T cd06444         239 EFIDRYFATYPGVKEYLEKTVEEAREGGYVETLFGRRRYLPEINSPNKNVRSAAERQAINTPIQGSAADIIKLAMIKIEK  318 (379)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCCCEECCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999786566789999999997797766778853477556788889878766567787465899999999999999


Q ss_pred             HHHHCCCCEEEEEEECCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEECCHHH
Q ss_conf             99865998189997263899955987999999999999651013574444643888332089378
Q gi|254780277|r  910 SLEDHKLATKMLLQIHDELVFEVPEEEITTASQIIVHSMEKACLPKINLRVPLKVNIKVSNNWQE  974 (976)
Q Consensus       910 ~~~~~~~~~~~ilqVHDElv~ev~~~~~~~~~~~~~~~Me~~~~~~~~l~VPl~v~~~~G~~W~e  974 (976)
T Consensus       319 ~l~~~~~~~~lv~~VHDEiv~ev~~~~~~~~~~~i~~~Me~a~----~l~VPl~v~~~iG~~Wge  379 (379)
T cd06444         319 LLKEKGLDARLLLQVHDELIFEVPEEELEEAAALVKENMENAV----KLSVPLKVDIKIGKNWGE  379 (379)
T ss_pred             HHHHCCCCCEEEEEECEEEEEEECHHHHHHHHHHHHHHHHCCC----CCCCCEEEECCCCCCCCC
T ss_conf             9996299978999725424899879999999999999985635----778837866372699999