HHsearch alignment for GI: 254780610 and conserved domain: COG0564
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis].
Probab=100.00 E-value=0 Score=544.57 Aligned_cols=288 Identities=50% Similarity=0.808 Sum_probs=255.6
Q ss_pred EEEEEECHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEEECCCH-HCCHHHHHHH
Q ss_conf 499995711368757899998717688989999999859904998993286758048988999705601-1110233222
Q gi|254780610|r 11 IKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQ-KLNIAQENIP 89 (340)
Q Consensus 11 ~~~~~V~~~~~g~RLD~~L~~~l~~~~sR~~i~kli~~G~V~vnG~~~~~~~~~l~~gd~I~i~~~~~~-~~~~~~~~~~ 89 (340)
T Consensus 1 ~~~~~i~~~~~g~rld~~L~~-l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~ 77 (289)
T COG0564 1 MLEFEVPEEEAGQRLDKFLAK-LLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPGDVVRIPLPEEPEEEKLVPEDIP 77 (289)
T ss_pred CCEEEECCHHCCCCHHHHHHH-HCC-CCHHHHHHHHHCCCEEECCEECC-CCEEECCCCEEEEECCCCCCCCCCCCCCCC
T ss_conf 944883611135479999987-257-47999999988898899999835-871608999999535655433345654778
Q ss_pred HHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 22101440278996240111045678754210022222210244334444364324444332324057212035788889
Q gi|254780610|r 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLS 169 (340)
Q Consensus 90 ~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~ 169 (340)
T Consensus 78 l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~------~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~ 151 (289)
T COG0564 78 LDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDG------VERPGIVHRLDKDTSGLLLVAKNREAARELS 151 (289)
T ss_pred CCEEEECCCEEEEECCCCCEECCCCCCCCHHHHHHHHHHCCCC------CCCEEEECCCCCCCCEEEEEECCHHHHHHHH
T ss_conf 7779976999999889997167798875267999998752334------7864351488999856999995999999999
Q ss_pred HHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEE
Q ss_conf 99997211322133445432024332332110013434443322123444555553000012221011256677500123
Q gi|254780610|r 170 EQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLK 249 (340)
Q Consensus 170 ~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~ 249 (340)
T Consensus 152 ~~f~~----r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~~~~~--gk~A~T~~~~~~~~~~~----~tlv~ 221 (289)
T COG0564 152 EQFKQ----RKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKEGS--GKPAITHYEVLERFGDN----YTLVE 221 (289)
T ss_pred HHHHC----CCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCCCEEEECCCC--CCCEEEEEEEEEECCCC----CEEEE
T ss_conf 99851----8661799999968556668788354106767762169971688--98337999972063876----28999
Q ss_pred EEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEECCCCH
Q ss_conf 4431158999999998709786041544775544433457013554407980443210004246889768999849978
Q gi|254780610|r 250 CHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPE 328 (340)
Q Consensus 250 ~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~aplP~ 328 (340)
T Consensus 222 ~~~~TGRTHQIRvHl~~lghPI~GD~~Yg~~~-----------~~~~~~~~r~~LHA~~l~f~hp~t~~~~~~~a~~p~ 289 (289)
T COG0564 222 LKPETGRTHQIRVHLAHLGHPIVGDPLYGGKD-----------KSAGAGLKRQALHAYKLSFTHPLTGEELEFEAPLPE 289 (289)
T ss_pred EEECCCCHHHHHHHHHHCCCCEECCCCCCCCC-----------CCCCCCCCHHHHHHHHHCCCCCCCCCEEEEECCCCC
T ss_conf 99688985199999998799743874678742-----------112356214788753517788999977999568899