HHsearch alignment for GI: 254780237 and conserved domain: CHL00013
>CHL00013 rpoA RNA polymerase alpha subunit.
Probab=100.00 E-value=0 Score=773.64 Aligned_cols=303 Identities=32% Similarity=0.501 Sum_probs=274.1
Q ss_pred CCCEEEECC----CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 420158636----7888158999961697566788899999874169830688999887144314664624449999984
Q gi|254780237|r 13 NNIEYIVLG----QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88 (340)
Q Consensus 13 ~~i~~~~~~----~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLN 88 (340)
T Consensus 11 ~~~~~~Cie~~~~~~~~~YgrF~~~Ple~G~g~TlGNaLRRvLLssl~G~aIt~vkI~Gv~HEfsti~GV~EdV~eIiLN 90 (333)
T CHL00013 11 RTLQWKCVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRVKIEGVPHEYSTIVGIRESVHEILLN 90 (333)
T ss_pred CCCEEEEEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCCHHHHHHC
T ss_conf 55248985027526876278999705888742146788988877458850789999889653105789864479999856
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 91 LK~i~~k~~~~~~~~~~l~~~Gp~~VtA~Di~~p~~veivNpd~~IATl~~~~~l~mel~ie~G~GY~~~~~~~---~~~ 167 (333)
T CHL00013 91 LKEIVLRSNLYGTQIASICVQGPGYVTAQDIILPPSVEIVDPTQYIATLTEPIDLCIELKIERGRGYRLKNPNN---FQD 167 (333)
T ss_pred HHHEEEECCCCCCEEEEEEEECCCEEEEHHCCCCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCC---CCC
T ss_conf 45438972479857999996078058803416888539977987999967997799999997686865177566---777
Q ss_pred CEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHH--
Q ss_conf 302124311114422357764116887762189999993896177799999999999988876224444322100000--
Q gi|254780237|r 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246 (340)
Q Consensus 169 g~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~-- 246 (340)
T Consensus 168 g~i~iDaiFsPV~kVny~Ve~~rvg~~~-~ekL~lEI~TnGsI~P~eAL~~AakIL~~~f~~~~~~~~~~~~~~~~~~~~ 246 (333)
T CHL00013 168 GSYPIDAVFMPVRNVNYSIHSYGNGNEK-QEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQNKV 246 (333)
T ss_pred CEEECCCCCCCCCEEEEEEEECCCCCCC-CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 6077677667502378999975678755-626999999589789999999999999999998744432112333344434
Q ss_pred --------------CCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf --------------000011233311122101105888989883983718887449888861889886449999999998
Q gi|254780237|r 247 --------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340)
Q Consensus 247 --------------~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340)
T Consensus 247 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IeeLeLSvRs~NCLKra~I~tvgdLv~~se~dLl~ikNfGkKSl~EI~ekL~e 326 (333)
T CHL00013 247 TLPLFTFHDRLANLRKNKKEIALKQIFIDQLELSVRAYNCLKRANIHTLLDLLNYSQEDLLKIKNFGQKSVKQVLDALEK 326 (333)
T ss_pred CCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 45543320012110100111200277088821878877436373893799986389999941899863029999999988
Q ss_pred HCCCCCCCCC
Q ss_conf 0831267687
Q gi|254780237|r 313 MGLFLGMNLP 322 (340)
Q Consensus 313 ~gl~lg~~l~ 322 (340)
T Consensus 327 ~---~Gi~Lp 333 (333)
T CHL00013 327 R---FGIDLP 333 (333)
T ss_pred H---HCCCCC
T ss_conf 6---299798