HHsearch alignment for GI: 254780608 and conserved domain: cd00506

>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=96.42  E-value=0.002  Score=41.59  Aligned_cols=69  Identities=22%  Similarity=0.282  Sum_probs=46.0

Q ss_pred             CEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             56884176531122357853323320110111110013335445342224046212310122210233332211120001
Q gi|254780608|r  107 KIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL  186 (346)
Q Consensus       107 ~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Ai  186 (346)
T Consensus         1 Gil~i~KP~G~TS~~-------vv~~vk~~~~--~kKvGH~GTLDP~AtGvL~i~vG~a-TK-~~~~~~~--~~K~Y~~~   67 (210)
T cd00506           1 GLFAVDKPQGPSSHD-------VVDTIRRIFL--AEKVGHGGTLDPFATGVLVVGIGKA-TK-LLKHLLA--ATKDYTAI   67 (210)
T ss_pred             CEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCEEEEEECHH-HH-HHHHHCC--CCCEEEEE
T ss_conf             989996799999899-------9999999858--7735768666974524289997788-87-9998755--99778799


Q ss_pred             CC
Q ss_conf             34
Q gi|254780608|r  187 VW  188 (346)
Q Consensus       187 v~  188 (346)
T Consensus        68 ~~   69 (210)
T cd00506          68 GR   69 (210)
T ss_pred             EE
T ss_conf             99