HHsearch alignment for GI: 254780610 and conserved domain: cd02563

>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=100.00  E-value=0  Score=406.27  Aligned_cols=217  Identities=33%  Similarity=0.515  Sum_probs=167.4

Q ss_pred             HHHCCCCCEEEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             22101440278996240111045678754210022222210244334444364324444332324057212035788889
Q gi|254780610|r   90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLS  169 (340)
Q Consensus        90 ~~IlyED~~llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~  169 (340)
T Consensus         1 l~IvyED~~ilvvnKP~Gl~~hp~~~~~~~~~~~~--~~~~~~~-----~~~~~~vHRLDr~TSGllv~Ak~~~a~~~l~   73 (223)
T cd02563           1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFAL--QTLRDQL-----GQHVYPVHRLDRPTSGVLLFALSSEVARKLG   73 (223)
T ss_pred             CEEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHH--HHHHHHC-----CCCCCEECCCCCCCCCEEEEECCHHHHHHHH
T ss_conf             97999679999999999982658999988369999--9988753-----7875340477898763599984589999999


Q ss_pred             HHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEEC------CCCCC
Q ss_conf             999972113221334454320243323321100134344433221234445555530000122210112------56677
Q gi|254780610|r  170 EQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYN------KNSNF  243 (340)
Q Consensus       170 ~~f~~~~~~~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~------~~~~~  243 (340)
T Consensus        74 ~~f~----~~~v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (223)
T cd02563          74 EQFT----EHRVHKTYLAVVRGYVP-ESGTIDYPLSEELDKLADKFA--SDDKAPQAATTHYRLLAVEELPVVVGKYPTS  146 (223)
T ss_pred             HHHH----HCCCCCEEEEEEEEECC-CCCEEEEECCCCCCCCCCEEE--ECCCCCCCEEEEEEEEEEEECCEEECCCCCC
T ss_conf             9987----55112269999984079-998798654546775563687--4278876348898876553200010114777


Q ss_pred             CCCEEEEEECHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCHHHHHCEEEEECCCCCCEEEEE
Q ss_conf             50012344311589999999987097860415447755444334570135544079804432100042468897689998
Q gi|254780610|r  244 AVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQ  323 (340)
Q Consensus       244 ~~slv~~~~~TGRtHQIRvhla~lG~PIvGD~~YG~~~~~~~~~~~~~~~~~~~~~~r~~LHA~~l~f~hP~t~~~~~f~  323 (340)
T Consensus       147 ~~slv~~~~~TGRtHQIRvHla~lG~PIvGD~~YG~~~~~~-------~~~~~~~~~rl~LHA~~L~F~HP~tge~i~~e  219 (223)
T cd02563         147 RYSLVELTPHTGRKHQLRRHLAHIRHPIIGDTTHGDGRHNR-------FFREHFGCHRLLLAATRLEFTHPVTGERLLIE  219 (223)
T ss_pred             CEEEEEEEECCCCHHHHHHHHHHCCCCEECCCCCCCCCCCH-------HHHHCCCCCCHHHHCCEEEEECCCCCCEEEEE
T ss_conf             47999999676870899999998799782772568754350-------23530499686474087483885999889998


Q ss_pred             CCCC
Q ss_conf             4997
Q gi|254780610|r  324 VPIP  327 (340)
Q Consensus       324 aplP  327 (340)
T Consensus       220 aPl~  223 (223)
T cd02563         220 APLD  223 (223)
T ss_pred             CCCC
T ss_conf             3699