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