HHsearch alignment for GI: 254780127 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=618.02 Aligned_cols=366 Identities=22% Similarity=0.287 Sum_probs=315.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCH---HHHHHHHHH-CCCCCHHHH
Q ss_conf 0889999999999999999999998630576688885688999999972899988896---588999974-489854899
Q gi|254780127|r 201 IDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSE---GTLKSILSH-SNITQLAKD 276 (675)
Q Consensus 201 vD~e~l~~~~~~~~~~~~~~~~~i~~~~g~~~~n~~S~~ql~~~L~~~~g~~~~~~~k---~~~~~~l~~-~~~~~~~~~ 276 (675)
T Consensus 1 id~~~~~~~~~~l~~~l~~l~~~~~~~~g~~f-n~~S~~ql~~~L~~~lg~~~~~~~~~~~st~~~~l~~~~~~hp~~~~ 79 (379)
T cd06444 1 VDKEELEELSAELEKELEELEKEIYELAGEEF-NINSPKQLGEVLFEKLGLPVSKKTKTGYSTDEEVLEKLAEAHPIIAL 79 (379)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHH
T ss_conf 98899999999999999999999999969907-99999999999998549998988889999859999976433848999
Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHC-CCCCCCCCEEECCCCCCHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCC
Q ss_conf 999999975430003566887305-6884522002113221001110688855477776652345654431024445544
Q gi|254780127|r 277 LILNRLASSGSAILKLNTLSEAVS-SDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIAD 355 (675)
Q Consensus 277 ll~~r~~~~~~~~~~~~~l~~~~~-~dGRih~~~~~~gAt~TGR~S~~~pNlQnlPr~~~~~~~~~~~~~~~~~~~~~~~ 355 (675)
T Consensus 80 ile~R~~~kl~s-t~~~~~~~~~~~~~gRih~~~~q~g-t~TGR~Ss~~PNlQniP~~~~-------------------- 137 (379)
T cd06444 80 ILEYRKLAKLKS-TYVDALPKLINPKTGRIHTSFNQTV-TATGRLSSSNPNLQNIPIRTE-------------------- 137 (379)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHCCCCCEEEEEEECCC-CCCCCCCCCCCCCCCCCCCCH--------------------
T ss_conf 999999999999-9999998760689997966885277-540012467876457888871--------------------
Q ss_pred CCCCCCHHHHEEEECCCCCEEEEEECCCCCEEEEEEECCCHHHHHHHHCCCCCCCCCHHHHHCCCCCCCCHHHHHCCCCC
Q ss_conf 43221013212147699878999733548505886622876786654044410000157760875110570221006421
Q gi|254780127|r 356 PLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVM 435 (675)
Q Consensus 356 ~~~~~~~~iR~~f~a~~G~~lv~aDySqiElRvlA~ls~d~~li~~f~~g~D~h~~tA~~~~~~~~~~v~~~~R~~aK~~ 435 (675)
T Consensus 138 ----~~~~~R~~f~~~~G~~lv~aDySqiElRvlA~ls~D~~l~~~f~~g~Dih~~~A~~~~~~~~~~v~~~~R~~aK~~ 213 (379)
T cd06444 138 ----EGREIRKAFVAPPGYVLLSADYSQIELRILAHLSGDPALIEAFNNGEDIHSRTAAEVFGVPEEEVTKEERRKAKAI 213 (379)
T ss_pred ----HHHHHHHEEECCCCCEEEEECHHHCHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHCCCHHHCCHHHHHHHHHH
T ss_conf ----1676752474799987998423112188888871769999998738878999999983998443598899886576
Q ss_pred HHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCHHHHHHHHHHHHHHHCC
Q ss_conf 00133078877898878870888640366666566676547889999999998751110103108897889999998673
Q gi|254780127|r 436 ELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQ 515 (675)
Q Consensus 436 ~~gl~YG~G~~~l~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ea~~~~~~~~~~~p 515 (675)
T Consensus 214 ~fgl~YG~G~~~la~--------------------------------------------~l~~s~~eA~~~~~~f~~~~p 249 (379)
T cd06444 214 NFGIIYGMGAFGLAE--------------------------------------------QLGISREEAKEFIDRYFATYP 249 (379)
T ss_pred HHHHHHCCCHHHHHH--------------------------------------------CCCCCHHHHHHHHHHHHHHCC
T ss_conf 757532834532975--------------------------------------------019999999999999999786
Q ss_pred CHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCEEECCCCHHHCCCCCCHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 07899999999999996337214201322234432124456411224631131024520123320310012357765335
Q gi|254780127|r 516 GVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGG 595 (675)
Q Consensus 516 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~~psGR~l~~~~~~~~~~~~~~~~~~~~r~~~~g~ 595 (675)
T Consensus 250 ~v~~~~~~~~~~a~~---~g-----------------------~v~T~~GR~r~~~~~~~~~~~~~---~~~~r------ 294 (379)
T cd06444 250 GVKEYLEKTVEEARE---GG-----------------------YVETLFGRRRYLPEINSPNKNVR---SAAER------ 294 (379)
T ss_pred CHHHHHHHHHHHHHH---CC-----------------------CEECCCCCEECCCCCCCCCHHHH---HHHHH------
T ss_conf 566789999999997---79-----------------------77667788534775567888898---78766------
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHC------CCCEEEEECCEEEEECCCCHHHHHH-HHHHHHCCCCCCCCCCCCEEECC
Q ss_conf 5777674798999999999999967------9818999535899967847899999-99998467630216984157303
Q gi|254780127|r 596 KLTENIVQAISRDILCEGMKNATKN------GYDIVLTVHDEIVSETPDTPYFSVG-TLCSLMTKNPSWAKGLPLKAEGY 668 (675)
Q Consensus 596 k~~n~~iQgtAaDi~k~am~~l~~~------g~~ivl~VHDElv~evp~~~~~~~~-~i~~~M~~~p~wa~~~pl~a~~~ 668 (675)
T Consensus 295 ~a~N~~iQGsaAdi~k~ami~i~~~l~~~~~~~~lv~~VHDEiv~ev~~~~~~~~~~~i~~~Me~a~~l--~VPl~v~~~ 372 (379)
T cd06444 295 QAINTPIQGSAADIIKLAMIKIEKLLKEKGLDARLLLQVHDELIFEVPEEELEEAAALVKENMENAVKL--SVPLKVDIK 372 (379)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECEEEEEEECHHHHHHHHHHHHHHHHCCCCC--CCCEEEECC
T ss_conf 567787465899999999999999999629997899972542489987999999999999998563577--883786637
Q ss_pred CCCCCC
Q ss_conf 114631
Q gi|254780127|r 669 EAKRYR 674 (675)
Q Consensus 669 ~~~~y~ 674 (675)
T Consensus 373 iG~~Wg 378 (379)
T cd06444 373 IGKNWG 378 (379)
T ss_pred CCCCCC
T ss_conf 269999