HHsearch alignment for GI: 254780142 and conserved domain: PRK08566
>PRK08566 DNA-directed RNA polymerase subunit alpha; Validated.
Probab=100.00 E-value=0 Score=1674.31 Aligned_cols=780 Identities=27% Similarity=0.395 Sum_probs=607.4
Q ss_pred CCCCCCCEEEEEEECCCHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 56786405368984588678850144897175542545687568873362136856677215664156344883567578
Q gi|254780142|r 11 PWTDDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCG 90 (1398)
Q Consensus 11 ~~~~~~~i~~i~f~l~spe~I~~~S~~ev~~~et~n~~~~kP~~~Gl~d~ri~g~~~d~~c~Cg~~~~~~~~g~~C~~Cg 90 (1398)
T Consensus 2 ~~~~p~~I~~I~f~~~S~~eI~~~S~~eI~~~~~~~~~-~~p~~gGl~D~rmG~~~---------------~~~~C~TCg 65 (881)
T PRK08566 2 MMDVPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDD-GYPIEGGLMDPRLGVID---------------PGLRCKTCG 65 (881)
T ss_pred CCCCCEEECEEEEEECCHHHHHHHCEEEEECCCCCCCC-CCCCCCCCCCCCCCCCC---------------CCCCCCCCC
T ss_conf 88887301459998158999986257899561238889-98588997761118999---------------729789999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHCCCHHHHHHHHHHCC----EE--EECCCCCCHHHHCCC---
Q ss_conf 853047757876772002776220130122578999980999656301332111----23--217886510432236---
Q gi|254780142|r 91 VEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERVLYFES----YV--VVDPGLSSLEKYQIL--- 161 (1398)
Q Consensus 91 ~~~~~~~~r~ghfGhIeLa~PV~Hi~f~k~~~~~i~~~l~~~~~~~~~v~y~~~----~~--~~~~~~~~~~~~~~~--- 161 (1398)
T Consensus 66 ~~~~~Cp---GHfGHIeLa~PV~hp~f~~~i~----~iL~~~C~~C~rl~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 138 (881)
T PRK08566 66 GRAGECP---GHFGHIELARPVIHVGFAKLIY----KLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGGLAKDLIKEI 138 (881)
T ss_pred CCCCCCC---CCCEEEEECCCCCCHHHHHHHH----HHHHCCCCHHCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9789589---9684874067510287899999----99956011230185779999999999987643115699999999
Q ss_pred -CHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEE
Q ss_conf -9999988676358555061155267788877267488999999873103220347886447788866663489851128
Q gi|254780142|r 162 -TEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMI 240 (1398)
Q Consensus 162 -~~~~~~~~~~~~~~~~~~~~~g~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~Pewmi 240 (1398)
T Consensus 139 ~k~~~k~~~C~~Cg~~~~~i~~~--------~~~~f~~~~~~~~~~L~p~~v~~il~~I~~ed~~~Lg~~~~~~rPe~~i 210 (881)
T PRK08566 139 KKEAAKRMVCPHCGEEQYKIKFE--------KPTTFYEERKEGAVKLTPSEIRERLEKIPDEDLELLGINPEVARPEWMV 210 (881)
T ss_pred HHHHHHCCCCCCCCCCCCEEEEE--------CCHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHCCCCCCCCHHHHH
T ss_conf 99875245685558857203631--------5436766203230357999999999718987899848996668807834
Q ss_pred EEECCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCC-C
Q ss_conf 630450762235138846973131003789999999869999998739835677769999999888874277678772-4
Q gi|254780142|r 241 IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVV-T 319 (1398)
Q Consensus 241 l~~lpV~P~~~RP~v~~~~g~~~~dDlt~~~~~Ii~~N~~Lk~~~~~~ap~~i~~~~~~lLQ~~v~~~~dn~~~~~~~-~ 319 (1398)
T Consensus 211 l~~lpVpP~~~RP~i~~~~g~~~~ddlt~~l~~Ii~~n~~l~~~~~~~a~~~~i~~~~~~LQ~~V~~~~Dn~~~~~~~~~ 290 (881)
T PRK08566 211 LTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNELPGIPPAR 290 (881)
T ss_pred HHCCCCCCCCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 22255799767874023787345773889999999999999999876995767899999999999999725778987434
Q ss_pred CCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCEECHHHHHHHHHHHH-----HH---HHHHHCC
Q ss_conf 787650678998610237820003465100457740341255435462003489877612899-----99---9999879
Q gi|254780142|r 320 GANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPF-----LY---AQLEKKG 391 (1398)
Q Consensus 320 ~~~~rp~ks~~~rlkgK~GrfR~nl~GKRVdfs~RsVI~pdP~l~~~evgvP~~~A~~L~~P~-----~~---~~L~~~g 391 (1398)
T Consensus 291 ~~~~r~~k~i~q~L~gK~GrfR~nlmGKRVd~saRSVIspDP~L~~~evGvP~~~A~~Lt~pe~Vt~~N~~~l~~~v~nG 370 (881)
T PRK08566 291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTPWNIEELREYVLNG 370 (881)
T ss_pred CCCCCCCCCHHHHHCCCCCEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHCCCCEEEEHHHHHHHHHHHHCC
T ss_conf 56898564188885466630100224453355430343268876367025879999757868076087899999999739
Q ss_pred CCCCCCCCCCEEE------------------CCCCCEEHHHHHHHCCCEEEECCCCCCEECCEEEEEEEEECCCEEEEEC
Q ss_conf 8666300010012------------------2488250132666569789975763101114012358994495479731
Q gi|254780142|r 392 YVSTVKQAKKFVE------------------KERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHP 453 (1398)
Q Consensus 392 ~~~~i~~~k~~i~------------------~~~~~v~~v~rhl~~gd~Vl~NRqPsLHr~Simah~~~v~~~~t~rln~ 453 (1398)
T Consensus 371 ~~--~~pga~~i~~~~g~~~~l~~~~~~~~~~~l~~g~iV~Rhl~dgD~Vl~NRqPTLHr~sima~~v~v~~gktirln~ 448 (881)
T PRK08566 371 PD--KHPGANYVIRPDGRRIKLTDKNKEELAERLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNL 448 (881)
T ss_pred CC--CCCCCEEEECCCCCEEEHHHHHHHHHHHHCCCCCEEEEEEECCCEEEECCCCHHHHHCCCCEEEEEEECCEEEECC
T ss_conf 85--5677437882578366425756999998526786896564359667752773354420001037997434577566
Q ss_pred CCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCCCEECCHH
Q ss_conf 22545467877545699746899999999998767505423788782044025899999987336788744681417999
Q gi|254780142|r 454 LVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMG 533 (1398)
Q Consensus 454 ~vc~pyNADFDGDEMnlHvPqs~eAraEa~~Lm~~~~niisP~~g~Pi~~~~QD~i~G~y~lT~~~~~~~~~~~~f~~~~ 533 (1398)
T Consensus 449 ~vc~~yNADFDGDeMn~HvPqs~~A~aEa~~Lm~~~~nilsP~~G~Pii~~~QD~vlg~y~LT~~~--------~f~~k~ 520 (881)
T PRK08566 449 AVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIHDHISGAYLLTRKS--------TLFTKE 520 (881)
T ss_pred CCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHCHHCCCCCCCCCCEEEEHHHHHHHHHHHHCCC--------CCCCHH
T ss_conf 567870677644102331257898999999986263026337899824651188887789986487--------668999
Q ss_pred HHHHHHHC----CCCCCCCEEEEEECCCCCCCCCCCEE--------ECCC----CCC----CCCCEEEECCCCCEEEEEC
Q ss_conf 99999988----89867852365204645667614245--------2179----775----1122055458751017751
Q gi|254780142|r 534 EVYHALEN----KIVTLHSKIRGRYKSVDKDGNSISKI--------YDTT----PGR----MIIGEILPRHHEISFDICN 593 (1398)
Q Consensus 534 ~~~~~~~~----~~~~~~a~i~~~~~~~~~~~~~~~~~--------~~tt----~Gr----~~~~~ilp~~~~~~~~~~~ 593 (1398)
T Consensus 521 ~~~~ll~~~~~~~~~~~pai~kp~~~wTGkqi~s~iLP~~~~~~~~~~~~~~~~~~~~~~~~~d~~v~I~~G~ll~G~ld 600 (881)
T PRK08566 521 EALDLLGAVGIDELPPEPAIENGKEYWTGKQIFSLFLPKDLNLVFKAKICSKCDECKKEDCEHDAYVVIKNGKLLKGVID 600 (881)
T ss_pred HHHHHHHHCCCCCCCCCCHHCCCCCCCCHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCCCCEEEEECCEEEEEECC
T ss_conf 99999983585656775200278412538999998746887525431024675544334577876699876977762046
Q ss_pred CHHCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHH----HHHHHHHHHHHHHHHHHHHH
Q ss_conf 10020136669999999808178999875588999999985398613212326836----99999999978999999886
Q gi|254780142|r 594 QEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPES----KEKIIAEADKMVKEYENQYN 669 (1398)
Q Consensus 594 ~~~~k~~~~~li~~i~~~~G~~~~~~~l~~~~~l~~~~l~~~GfSigi~D~~~~~~----k~~~i~~a~~~~~~~~~~~~ 669 (1398)
T Consensus 601 K~~lG~~~~~LI~~i~~~yG~~~a~~fLd~lq~L~~~~l~~~GFSvGi~Dl~i~~~~~~~i~e~i~~~~~~v~~l~~~~~ 680 (881)
T PRK08566 601 KKAIGAEQGSILDRIVKEYGPERARRFLDSVTKLAIRFIMLRGFTTGIDDEDIPEEAYEEIDEIIEEAEKRVEELIEAYE 680 (881)
T ss_pred HHHHCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCEEEEHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 77734343439999999859799999999999999999997784766644275889999999999999999999999998
Q ss_pred CCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCC---HHHEEEEEE
Q ss_conf 4897-------667888788642346589999999999876115654322224688376422555578---424112001
Q gi|254780142|r 670 DGLI-------TRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGG 739 (1398)
Q Consensus 670 ~G~~-------t~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~~M~~SGAKGS---~~qi~ql~G 739 (1398)
T Consensus 681 ~g~l~~~~~~t~~e~~E~~i~~~l~~~r~~~~~i~~~~l------------~~~N~~~~Mv~SGAKGS~~Ni~Qi~g~lG 748 (881)
T PRK08566 681 NGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYL------------GLDNPAVIMARTGARGSMLNITQMAACVG 748 (881)
T ss_pred HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC------------CCCCCHHHHHHCCCCCCHHHHHHHHHCCC
T ss_conf 298665889867899999999999999999999998628------------99995775311367677999999995345
Q ss_pred ECCCCCCC--C---CCCCCC-------C-----CCCHHHCCCCHHHHHHCCCCCCHHHHCCCCCCCCCCEEEEHHHHHHC
Q ss_conf 00002464--4---344456-------6-----63011108889897640576103221012101567401101542301
Q gi|254780142|r 740 MRGLIAKP--S---GEIIES-------P-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQ 802 (1398)
Q Consensus 740 qq~l~gkp--~---G~~~~~-------P-----V~~sF~~GL~p~EfFfhamgGReGLiDTAvKTA~SGYlqRrLvk~~e 802 (1398)
T Consensus 749 QQ~~~G~Ri~~~~~~RtLP~f~~~d~~~~a~GfI~~sF~~GL~p~Efffh~m~gReGLiDTAvKTa~sGYlqRrLvk~lE 828 (881)
T PRK08566 749 QQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEYFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQ 828 (881)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCHHCCCHHHHCCCCCCCCHHHHHHHHHHHC
T ss_conf 61048976746777888899988898867895161245379988999970521040186677314752099999999861
Q ss_pred CCEEEEECCCCCC--CCEEEEEEECCEEEEEEC---------CCCCCCCCHHHC
Q ss_conf 4327751388766--651211100884886500---------010122114420
Q gi|254780142|r 803 NCVVNQVDCNTKK--GLTITHIVDSGQVVYSLG---------SRVLGRTALDDI 845 (1398)
Q Consensus 803 Dl~V~~~D~~t~~--g~~~~~~~~~~~~~~~l~---------~~~~~r~~~~di 845 (1398)
T Consensus 829 dl~v~-yD~tVR~~~~~ivq-f~YG~Dg~dp~~~~~~~~~~~~~~~~~~~~~~~ 880 (881)
T PRK08566 829 DLKVE-YDGTVRDTRGNIVQ-FKYGEDGVDPMKSDHGKPVDVDRIIERVLGKEV 880 (881)
T ss_pred CEEEE-CCCCEECCCCCEEE-EECCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf 86992-79973869997899-765787768000258973349999999754007