HHsearch alignment for GI: 254780608 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=409.40  Aligned_cols=210  Identities=30%  Similarity=0.457  Sum_probs=162.2

Q ss_pred             CEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCC
Q ss_conf             30786178568841765311223578533233201101111100133354453422240462123101222102333322
Q gi|254780608|r   99 SILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRR  178 (346)
Q Consensus        99 ~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~  178 (346)
T Consensus         1 l~IvyED~~ilvvnKP~Gl~~hp~~~~~~~~~~~~~~~~~~~~~~~~~vHRLDr~TSGllv~Ak~~~a~~~l~~~f~~~~   80 (223)
T cd02563           1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLGQHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHR   80 (223)
T ss_pred             CEEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEECCCCCCCCCEEEEECCHHHHHHHHHHHHHCC
T ss_conf             97999679999999999982658999988369999998875378753404778987635999845899999999987551


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH----------HCCCCEEEEEEC
Q ss_conf             1112000134565410000000122346554321113355555553034301013432----------024420457861
Q gi|254780608|r  179 IQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCF----------AQKFCWLEMQPH  248 (346)
Q Consensus       179 v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~----------~~~~slv~~~l~  248 (346)
T Consensus        81 v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~  156 (223)
T cd02563          81 VHKTYLAVVRGYVP-ESGTIDYPLSEELDKLADK---FASDDKAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPH  156 (223)
T ss_pred             CCCEEEEEEEEECC-CCCEEEEECCCCCCCCCCE---EEECCCCCCCEEEEEEEEEEEECCEEECCCCCCCEEEEEEEEC
T ss_conf             12269999984079-9987986545467755636---8742788763488988765532000101147774799999967


Q ss_pred             HHHHHHHHHHHHHCCCCEECCCCCCCCCCCHH--CCCCCCCHHHHHHHHEEECCCCCE-EEEECCCC
Q ss_conf             23789999999963980004644466522100--013446241311000437588964-99983997
Q gi|254780608|r  249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGNF--TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP  312 (346)
Q Consensus       249 TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~~--~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP  312 (346)
T Consensus       157 TGRtHQIRvHla~lG~PIvGD~~YG~~~~~~~~~~~~~~~rl~LHA~~L~F~HP~tge~i~~eaPl~  223 (223)
T cd02563         157 TGRKHQLRRHLAHIRHPIIGDTTHGDGRHNRFFREHFGCHRLLLAATRLEFTHPVTGERLLIEAPLD  223 (223)
T ss_pred             CCCHHHHHHHHHHCCCCEECCCCCCCCCCCHHHHHCCCCCCHHHHCCEEEEECCCCCCEEEEECCCC
T ss_conf             6870899999998799782772568754350235304996864740874838859998899983699