HHsearch alignment for GI: 254781218 and conserved domain: COG1508

>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription].
Probab=96.11  E-value=0.069  Score=31.47  Aligned_cols=102  Identities=20%  Similarity=0.207  Sum_probs=69.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH-
Q ss_conf             9889999984899999998877998889999999999828999996145322100002321345546777999999999-
Q gi|254781218|r   45 KTQKEMAIGANQLESAVNLFENGMCSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTNKKRLDPYAIGARLKSIRK-  123 (205)
Q Consensus        45 ltQ~elA~~~gis~~~is~~E~G~~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~~~~~d~~~iG~rLk~lR~-  123 (205)
T Consensus       331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLk~FFs~~i~s~~gg~~~S-------------~~~Ik~~Ik~lI~~  397 (444)
T COG1508         331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGEASS-------------TEAIKALIKKLIEA  397 (444)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCEEEHHHHHHHHCCCCCCCCCCC-------------HHHHHHHHHHHHHH
T ss_conf             31999998837128889999825410488633448988777416788876444-------------89999999998753


Q ss_pred             ---HCCCCHHHHHHHH-----CCCHHHHHHHHCCCCCCCHHHHH
Q ss_conf             ---7298389999997-----79999999974148899989999
Q gi|254781218|r  124 ---DKGMSQIEFGKLL-----GMPNSTLSNYEQGRTIPEIKPAR  159 (205)
Q Consensus       124 ---~~glsq~elA~~l-----gis~~tis~~E~g~~~Ps~~~l~  159 (205)
T Consensus       398 E~~~~pLSD~kIa~lLkekGi~iARRTVAKYRe~L~I~sS~~Rk  441 (444)
T COG1508         398 EDKKKPLSDSKIAELLKEKGIDVARRTVAKYREELNIPSSSQRK  441 (444)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             16778887899999999719842588599999880899565540