HHsearch alignment for GI: 254780237 and conserved domain: COG0202
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription].
Probab=100.00 E-value=0 Score=606.44 Aligned_cols=313 Identities=47% Similarity=0.771 Sum_probs=291.0
Q ss_pred CCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 17974201586367888158999961697566788899999874169830688999887144314664624449999984
Q gi|254780237|r 9 LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88 (340)
Q Consensus 9 ~~~P~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLN 88 (340)
T Consensus 1 ~~~p~~i~i~~---~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I~~v~hef~s~~gv~Edvl~~~Ln 77 (317)
T COG0202 1 FLKPKKVKIEE---LSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEGVQEDVLAHRLN 77 (317)
T ss_pred CCCCCCEEEEE---CCCCCCCEEEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHC
T ss_conf 98665258997---146634089998540785035789999999748430479999961322334676747999999846
Q ss_pred HCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCC
Q ss_conf 01141777279827999999447169963351389859988880899977896499999974687632034444655754
Q gi|254780237|r 89 IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168 (340)
Q Consensus 89 LK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~i 168 (340)
T Consensus 78 Lk~L~~k~~~~~~~~~~~~~~g~g~v~a~d~~~~~~lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~~~~~~~~~~v 157 (317)
T COG0202 78 LKPLAVKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNREDDPPV 157 (317)
T ss_pred CCEEEEECCCCCCEEEEEECCCCCCCCHHHCCCCEEEEEECCCCEEEECCCCCCEEEEEEEECCCCEECCCCCCCCCCCC
T ss_conf 83276203456640799850578622175646540489978985356506786047999998176176265454447874
Q ss_pred CEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCC
Q ss_conf 30212431111442235776411688776218999999389617779999999999998887622444432210000000
Q gi|254780237|r 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248 (340)
Q Consensus 169 g~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~~ 248 (340)
T Consensus 158 ~~i~~D~~~spv~kvqy~ve~~r~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~~~~~~~~e~~-- 235 (317)
T COG0202 158 GPIAVDAPFSPVRKVQYIVEEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKAVEIEEEKP-- 235 (317)
T ss_pred EEEECCCCEEEEEECEEEEEEEEEECCCCCEEEEEEEEECCEEEHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCC--
T ss_conf 064079840366412079986798446774069999764637502799999999889999998753655440101565--
Q ss_pred CCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCH
Q ss_conf 001123331112210110588898988398371888744988886188988644999999999808312676878986
Q gi|254780237|r 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326 (340)
Q Consensus 249 ~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~ 326 (340)
T Consensus 236 ~~~~~~~~~~~I~~l~lsvrs~ncLk~~~i~~i~~L~~~se~~l~~v~n~G~ksleEi~~kl~~~~l~l~~~~e~~~~ 313 (317)
T COG0202 236 EFPILLVLEAPIDELDLSVRSYNCLKREGIETIGELVQRTEEELLKVENLGKKSLEEIKEKLAELGLELGMELENWPP 313 (317)
T ss_pred CCCCCCCCCCCCCCCCCCEEEEHHHCCCCCHHHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHCCC
T ss_conf 442332334653412313335012311581146877745798885043656699999999999851332356400156