HHsearch alignment for GI: 254780295 and conserved domain: cd02570

>cd02570 PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA. psi38 and psi39 in tRNAs are highly phylogenetically conserved. P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators.
Probab=100.00  E-value=0  Score=556.31  Aligned_cols=239  Identities=47%  Similarity=0.769  Sum_probs=234.2

Q ss_pred             EEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHHHHCC
Q ss_conf             99997166872004875387788999999999709956999711213861222346886406321104689999986188
Q gi|254780295|r    6 MIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLKI   85 (247)
Q Consensus         6 ~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN~~L~~   85 (247)
T Consensus         1 l~i~Y~Gt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~l~~~LN~~L--   78 (239)
T cd02570           1 LTIEYDGTNFSGWQRQPNGRTVQGELEKALSKIAGEPVRVIGAGRTDAGVHALGQVAHFDTPSEIPLEKLIKALNSLL--   78 (239)
T ss_pred             CEEEEECCCEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHC--
T ss_conf             989995898027707869989999999999998498648998415677854101199997478899999999998549--


Q ss_pred             CCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECCCCCCC
Q ss_conf             87654344322677755000210022355685244320233321024433333566556567652001100102456553
Q gi|254780295|r   86 SDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQA  165 (247)
Q Consensus        86 p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~~~~~~  165 (247)
T Consensus        79 P~dI~i~~i~~v~~~F~aR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~~~~a~~~~~G~HdF~~F~~~~~~~  158 (239)
T cd02570          79 PPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRPVPSPFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFRAAGCQS  158 (239)
T ss_pred             CCCEEEEEEEECCCCCCEEEECCEEEEEEEECCCCCCCHHHCCCEEEECCCCCHHHHHHHHHHCCCCCCHHHHCCCCCCC
T ss_conf             99869999698288756176033479999961688899667774566646465999999998705881356432799999


Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEE
Q ss_conf             33211033111123332001131588889999999999999997689988899999835882116663698984763304
Q gi|254780295|r  166 SSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLYFDSVE  245 (247)
Q Consensus       166 ~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~  245 (247)
T Consensus       159 ~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mvG~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~  238 (239)
T cd02570         159 KSTVRTIYRADVYREGDLIVFEIRANGFLYHMVRNIVGTLLEVGRGKLSPEDIKEILEAKDRTAAGPTAPAHGLYLVKVE  238 (239)
T ss_pred             CCCEEEEEEEEEEECCCEEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEECCCC
T ss_conf             99708999999998599899998677789999999999999998799999999999867885558673489876890039


Q ss_pred             E
Q ss_conf             3
Q gi|254780295|r  246 Y  246 (247)
Q Consensus       246 Y  246 (247)
T Consensus       239 Y  239 (239)
T cd02570         239 Y  239 (239)
T ss_pred             C
T ss_conf             9