HHsearch alignment for GI: 254781193 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=644.23  Aligned_cols=367  Identities=22%  Similarity=0.294  Sum_probs=326.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCC---CCHHHHHHHHHCCCCHHHH
Q ss_conf             3799999999999999999999999872885476788799988777755888888988---5338998721304823899
Q gi|254781193|r  199 VDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTE---TTCQRVLSSNKKLTPQAIQ  275 (675)
Q Consensus       199 vD~e~l~~l~~~~~~~~~~l~~~i~~~~~~~~~n~~S~~ql~~~L~~~lg~~~~~~~k---~t~~~~L~~~~~~~~~~~~  275 (675)
T Consensus         1 id~~~~~~~~~~l~~~l~~l~~~~~~~~g-~~fn~~S~~ql~~~L~~~lg~~~~~~~~~~~st~~~~l~~~~~~hp~~~~   79 (379)
T cd06444           1 VDKEELEELSAELEKELEELEKEIYELAG-EEFNINSPKQLGEVLFEKLGLPVSKKTKTGYSTDEEVLEKLAEAHPIIAL   79 (379)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHH
T ss_conf             98899999999999999999999999969-90799999999999998549998988889999859999976433848999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCC-CCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             999999976551013357887408-6896767788400013221124788844488888651134554310123333455
Q gi|254781193|r  276 VFNNRMRASRSAVLKLNTLVEAMN-SDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDP  354 (675)
Q Consensus       276 ~l~~r~~~~k~~~~~~~~~~~~~~-~dgRih~~~~~~gat~TGR~S~~~pNlQnlPr~~~~~~~~~~~~~~~~~~~~~~~  354 (675)
T Consensus        80 ile~R-~~~kl~st~~~~~~~~~~~~~gRih~~~~q~g-t~TGR~Ss~~PNlQniP~~~~~~------------------  139 (379)
T cd06444          80 ILEYR-KLAKLKSTYVDALPKLINPKTGRIHTSFNQTV-TATGRLSSSNPNLQNIPIRTEEG------------------  139 (379)
T ss_pred             HHHHH-HHHHHHHHHHHHHHHHHCCCCCEEEEEEECCC-CCCCCCCCCCCCCCCCCCCCHHH------------------
T ss_conf             99999-99999999999998760689997966885277-54001246787645788887116------------------


Q ss_pred             CCCCCCHHHHHEEEECCCCCEEEEEECCCCCHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHCCCCHHHHCCHHHHHCCC
Q ss_conf             44321003333012668987899983453723333231146201134541133101014764487956706201110165
Q gi|254781193|r  355 DPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKV  434 (675)
Q Consensus       355 ~~~~~~~~~iR~~f~a~~G~~lv~aDySqiElRvlA~ls~d~~l~~af~~g~D~h~~tA~~~~g~~~~~~~~~~R~~aK~  434 (675)
T Consensus       140 -------~~~R~~f~~~~G~~lv~aDySqiElRvlA~ls~D~~l~~~f~~g~Dih~~~A~~~~~~~~~~v~~~~R~~aK~  212 (379)
T cd06444         140 -------REIRKAFVAPPGYVLLSADYSQIELRILAHLSGDPALIEAFNNGEDIHSRTAAEVFGVPEEEVTKEERRKAKA  212 (379)
T ss_pred             -------HHHHHEEECCCCCEEEEECHHHCHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHCCCHHHCCHHHHHHHHH
T ss_conf             -------7675247479998799842311218888887176999999873887899999998399844359889988657


Q ss_pred             CEEEEECCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHC
Q ss_conf             20210028888889987987088831134556555455556788889999887643100010220788899999999878
Q gi|254781193|r  435 MELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKH  514 (675)
Q Consensus       435 ~~~g~~YG~G~~~l~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ea~~~~~~~r~~~  514 (675)
T Consensus       213 ~~fgl~YG~G~~~la~---~l-----------------------------------------~~s~~eA~~~~~~f~~~~  248 (379)
T cd06444         213 INFGIIYGMGAFGLAE---QL-----------------------------------------GISREEAKEFIDRYFATY  248 (379)
T ss_pred             HHHHHHHCCCHHHHHH---CC-----------------------------------------CCCHHHHHHHHHHHHHHC
T ss_conf             6757532834532975---01-----------------------------------------999999999999999978


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCHHHHCCHHHHHHHHHHHH
Q ss_conf             87899999999999999754917962154211332223445640232476631016786621021010023456777531
Q gi|254781193|r  515 SRVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYG  594 (675)
Q Consensus       515 p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~GR~~~~~~~~~~~~~~~~~~~~~~r~~~~~  594 (675)
T Consensus       249 p~v~~~~~~~~~~a~~--------------------------~g~v~T~~GR~r~~~~~~~~~~~~~~~---~~r-----  294 (379)
T cd06444         249 PGVKEYLEKTVEEARE--------------------------GGYVETLFGRRRYLPEINSPNKNVRSA---AER-----  294 (379)
T ss_pred             CCHHHHHHHHHHHHHH--------------------------CCCEECCCCCEECCCCCCCCCHHHHHH---HHH-----
T ss_conf             6566789999999997--------------------------797766778853477556788889878---766-----


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHC------CCCEEEEECCEEEEECCCCHHHH-HHHHHHHHCCCCHHCCCCCCEEEE
Q ss_conf             45655453688999999999999967------98188995258999779248999-999999845652021599515740
Q gi|254781193|r  595 GKLTENIVQAVSRDILAEGMMNATKA------GYDIVLTVHDEIVCETPDTDEFN-ASMLYHLMTSNPSWAKGLPLKAEG  667 (675)
Q Consensus       595 ~k~~n~~iQgtaadi~k~ami~l~~~------g~~ivl~VHDEiv~evp~~~~~~-~~~i~~~M~~~~~w~~~~pl~ae~  667 (675)
T Consensus       295 -~a~N~~iQGsaAdi~k~ami~i~~~l~~~~~~~~lv~~VHDEiv~ev~~~~~~~~~~~i~~~Me~a~~l--~VPl~v~~  371 (379)
T cd06444         295 -QAINTPIQGSAADIIKLAMIKIEKLLKEKGLDARLLLQVHDELIFEVPEEELEEAAALVKENMENAVKL--SVPLKVDI  371 (379)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECEEEEEEECHHHHHHHHHHHHHHHHCCCCC--CCCEEEEC
T ss_conf             -567787465899999999999999999629997899972542489987999999999999998563577--88378663


Q ss_pred             CCCCCCC
Q ss_conf             1004631
Q gi|254781193|r  668 YESKRYR  674 (675)
Q Consensus       668 ~~~~~y~  674 (675)
T Consensus       372 ~iG~~Wg  378 (379)
T cd06444         372 KIGKNWG  378 (379)
T ss_pred             CCCCCCC
T ss_conf             7269999