HHsearch alignment for GI: 254780608 and conserved domain: cd02550

>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=100.00  E-value=2.1e-38  Score=262.24  Aligned_cols=151  Identities=26%  Similarity=0.374  Sum_probs=118.3

Q ss_pred             EEEECCCCCCEEECCCCCCCC-CCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             688417653112235785332-3320110111110013335445342224046212310122210233332211120001
Q gi|254780608|r  108 IYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL  186 (346)
Q Consensus       108 livinKPaGl~vhp~~g~~~~-~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Ai  186 (346)
T Consensus         1 iivvnKP~G~~~~~~~~~~~~~~~~~l~---~~~~~~l~~vhRLDr~TSGlll~ak~~~~~~~l~~~--~~~v~K~Y~a~   75 (154)
T cd02550           1 ILVLNKPSGLVCHPTDRDRDPTVVVRLD---KLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RREIEKEYLVT   75 (154)
T ss_pred             CEEEECCCCCEEECCCCCCCCCHHHHHH---HHCCCCEEEECCCCCCCCCCEEECCCHHHHHHHHHH--HCCCCEEEEEE
T ss_conf             9999999997185899999970999987---517986137126899997856773798999999850--05650579999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCCCCE
Q ss_conf             34565410000000122346554321113355555553034301013432024420457861237899999999639800
Q gi|254780608|r  187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI  266 (346)
Q Consensus       187 v~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g~Pi  266 (346)
T Consensus        76 v~g~~~~~-~~~~~~~~~~~-------~~~~~~~~~~~~~~t~~~~~~~~~-~~slv~~~l~TGR~HQIR~hl~~~G~PI  146 (154)
T cd02550          76 VRGELDEE-GIEDLATVRRG-------RLSGLVDEGVPLAVTKVRVIGEHG-GTGRLRLTLKTGRTHQIRRHCAAVGFPV  146 (154)
T ss_pred             EEEECCHH-HHEECCCCCCC-------CCEEEECCCCEECCCEEEEECCCC-CCEEEEEEECCCCCHHHHHHHHHCCCEE
T ss_conf             98727858-82444456424-------551266599620432889931479-9489999979886699999999869939


Q ss_pred             ECCCCC
Q ss_conf             046444
Q gi|254780608|r  267 VGDHKY  272 (346)
Q Consensus       267 vGD~~Y  272 (346)
T Consensus       147 l~l~R~  152 (154)
T cd02550         147 LRLHRV  152 (154)
T ss_pred             EEEEEE
T ss_conf             568998