HHsearch alignment for GI: 254780271 and conserved domain: COG4650

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms].

Probab=97.54  E-value=0.00011  Score=53.35  Aligned_cols=89  Identities=26%  Similarity=0.491  Sum_probs=61.4

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHH------HCCCEEEHHHHHHHHHHHCCCCCCCHHHHHH--------HHHHHHHHHH
Q ss_conf             5683588407332176999999987------1853131012211111103556330357788--------7654227765
Q gi|254780271|r  112 AKSNILLVGPTGCGKTYLAQTLARI------IDVPFTMADATTLTEAGYVGEDVENIILKLL--------QAADYNVERA  177 (424)
Q Consensus       112 ~~~NILliGPTGvGKTelAr~LAk~------l~~PF~~vdaT~~TE~GYvG~Dvesii~~L~--------~~a~~~v~~a  177 (424)
T Consensus       207 sr~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~-----amsalfghvkgaftga~~~r~gllrsa  281 (531)
T COG4650         207 SRAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDT-----AMSALFGHVKGAFTGARESREGLLRSA  281 (531)
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCH-----HHHHHHHHHHCCCCCCHHHHHHHHCCC
T ss_conf             469768646887436689999999998887537862788630004752-----889987640013146334554424337


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             422333223332002333333443210256898875310587
Q gi|254780271|r  178 QRGIVYIDEVDKISRKSDNPSITRDVSGEGVQQALLKIMEGT  219 (424)
Q Consensus       178 ~~~iv~iDEidKi~~~~~~~~~~~dvs~~gvq~~LLkileg~  219 (424)
T Consensus       282 dggmlfldeigelgad--------------eqamllkaieek  309 (531)
T COG4650         282 DGGMLFLDEIGELGAD--------------EQAMLLKAIEEK  309 (531)
T ss_pred             CCCEEEHHHHHHCCCC--------------HHHHHHHHHHHH
T ss_conf             7865756743324752--------------788999998871