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