HHsearch alignment for GI: 254780406 and conserved domain: cd01291

>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Probab=97.05  E-value=0.00036  Score=46.08  Aligned_cols=86  Identities=13%  Similarity=0.098  Sum_probs=55.6

Q ss_pred             CCCCEEEECCCCCCCCCCCCEEECCCCCCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHH
Q ss_conf             78751563144333364421011023432002665543323202223676410001234457404775211245564678
Q gi|254780406|r   79 HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL  158 (354)
Q Consensus        79 ~KP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~p~~~~~k~Y~v~v~~~~~~~~~  158 (354)
T Consensus         2 ~K~~~~t~~~~~~~~~-----~~~~~~~~v~~aG~kDk~a~t~Q~~s-----------------n~f~i~lr--------   51 (87)
T cd01291           2 YKPGGDTMEAARQLAK-----LLGIPPKRVGYAGRKDKRAVTTQLVS-----------------NRFTITLR--------   51 (87)
T ss_pred             CCCCCCHHHHHHHHHH-----HHCCCHHHEEECCCCCCCEEEEEEEE-----------------EEEEEEEC--------
T ss_conf             6568789999999999-----82998777517446666554788764-----------------43589821--------


Q ss_pred             HHHHHHHHCCCEEEECCCEEEEECCCCEEEEEEEEEECCHHHHHHHHHHCC
Q ss_conf             887400000876750343036402688079999995184289999999839
Q gi|254780406|r  159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN  209 (354)
Q Consensus       159 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~l~eGr~~qIrr~~~~~g  209 (354)
T Consensus        52 -------------~~~~~~~~~~~~~~~~~l~f~L--~~~~yat~~lrel~   87 (87)
T cd01291          52 -------------VKPLNLKWPEERKRALVLEFTL--PRGSYATMLLRELG   87 (87)
T ss_pred             -------------CCCCCCCCHHHHHHHEEEEEEC--CCCHHHHHHHHHCC
T ss_conf             -------------6466777678864115789852--67407899898619