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