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