HHsearch alignment for GI: 254780608 and conserved domain: COG0564
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis].
Probab=100.00 E-value=0 Score=526.47 Aligned_cols=285 Identities=35% Similarity=0.583 Sum_probs=234.9
Q ss_pred EEEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 49998411368668999998767889899999998499038878845112117998899935655422233222234554
Q gi|254780608|r 8 QYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87 (346)
Q Consensus 8 ~~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~ 87 (346)
T Consensus 2 ~~~~i~~~~~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~~~~~l~~gd~i~~~~~~~~~~-----~------ 69 (289)
T COG0564 2 LEFEVPEEEAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVKPSYKLKPGDVVRIPLPEEPEE-----E------ 69 (289)
T ss_pred CEEEECCHHCCCCHHHHHHHHCC-CCHHHHHHHHHCCCEEECCEECCCCEEECCCCEEEEECCCCCCC-----C------
T ss_conf 44883611135479999987257-47999999988898899999835871608999999535655433-----3------
Q ss_pred CCCCCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCC--CCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf 33432223454307861785688417653112235785332--3320110111110013335445342224046212310
Q gi|254780608|r 88 VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA 165 (346)
Q Consensus 88 ~~~~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~--~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~ 165 (346)
T Consensus 70 ---~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~-~~~~~~vHRLDkdTSGlll~AK~~~ 145 (289)
T COG0564 70 ---KLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDG-VERPGIVHRLDKDTSGLLLVAKNRE 145 (289)
T ss_pred ---CCCCCCCCCCEEEECCCEEEEECCCCCEECCCCCCCCHHHHHHHHHHCCCC-CCCEEEECCCCCCCCEEEEEECCHH
T ss_conf ---456547787779976999999889997167798875267999998752334-7864351488999856999995999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEE
Q ss_conf 12221023333221112000134565410000000122346554321113355555553034301013432024420457
Q gi|254780608|r 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245 (346)
Q Consensus 166 a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~ 245 (346)
T Consensus 146 a~~~l~~~f~~r~v~K~Y~Alv~G~~~~~~~~i~~pi~r~~~~~~~~~v~-~~--~~gk~A~T~~~~~~~~~~~~tlv~~ 222 (289)
T COG0564 146 AARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVV-KE--GSGKPAITHYEVLERFGDNYTLVEL 222 (289)
T ss_pred HHHHHHHHHHCCCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCCCEEEE-CC--CCCCCEEEEEEEEEECCCCCEEEEE
T ss_conf 99999999851866179999996855666878835410676776216997-16--8898337999972063876289999
Q ss_pred EECHHHHHHHHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCE-EEEECCCCH
Q ss_conf 86123789999999963980004644466522100013446241311000437588964-999839978
Q gi|254780608|r 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPA 313 (346)
Q Consensus 246 ~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP~ 313 (346)
T Consensus 223 ~~~TGRTHQIRvHl~~lghPI~GD~~Yg~~~--~~~~~~~~r~~LHA~~l~f~hp~t~~~~~~~a~~p~ 289 (289)
T COG0564 223 KPETGRTHQIRVHLAHLGHPIVGDPLYGGKD--KSAGAGLKRQALHAYKLSFTHPLTGEELEFEAPLPE 289 (289)
T ss_pred EECCCCHHHHHHHHHHCCCCEECCCCCCCCC--CCCCCCCCHHHHHHHHHCCCCCCCCCEEEEECCCCC
T ss_conf 9688985199999998799743874678742--112356214788753517788999977999568899