HHsearch alignment for GI: 254780406 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=99.73 E-value=2.9e-18 Score=134.84 Aligned_cols=154 Identities=19% Similarity=0.195 Sum_probs=100.3
Q ss_pred CCCCEEEEECCCCCEEEECCCCCCCCCC--CCEEECCC-CCCEECCCCCCCCCCCEEEECCCCCCCCCCCC--CCCCCEE
Q ss_conf 5564389602787515631443333644--21011023-43200266554332320222367641000123--4457404
Q gi|254780406|r 69 KAERTRLWLYHKPIGLVTTHSDPDGRST--VFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLR 143 (354)
Q Consensus 69 ~~~~~~~~~~~KP~g~~~~~~~~~~~~~--~~~~~~~~-~~~~~~vgRLD~~t~GLlllTndg~l~~~l~~--p~~~~~k 143 (354)
T Consensus 4 vyED~~ilvvnKP~Gl~~hp~~~~~~~~~~~~~~~~~~~~~~~~~vHRLDr~TSGllv~Ak~~~a~~~l~~~f~~~~v~K 83 (223)
T cd02563 4 LYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLGQHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHK 83 (223)
T ss_pred EEECCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEECCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCC
T ss_conf 99679999999999982658999988369999998875378753404778987635999845899999999987551122
Q ss_pred EEEEEECCCCCHHHHHH--H-------HHHHHCCCEEEECC--CEEEE-----------ECCCCEEEEEEEEEECCHHHH
Q ss_conf 77521124556467888--7-------40000087675034--30364-----------026880799999951842899
Q gi|254780406|r 144 VYRVRFHGQVDQDKLNL--L-------KKGIVIQGICYGDM--QVTLD-----------TQKGSNAWVTVGLREGKNREI 201 (354)
Q Consensus 144 ~Y~v~v~~~~~~~~~~~--~-------~~g~~~~~~~~~~~--~~~~~-----------~~~~~~~~~~v~l~eGr~~qI 201 (354)
T Consensus 84 ~Y~Alv~G~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~slv~~~~~TGRtHQI 163 (223)
T cd02563 84 TYLAVVRGYVPESGTIDYPLSEELDKLADKFASDDKAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQL 163 (223)
T ss_pred EEEEEEEEECCCCCEEEEECCCCCCCCCCEEEECCCCCCCEEEEEEEEEEEECCEEECCCCCCCEEEEEEEECCCCHHHH
T ss_conf 69999984079998798654546775563687427887634889887655320001011477747999999676870899
Q ss_pred HHHHHHCCCEEEEEEEEEECCEE
Q ss_conf 99999839868688975870545
Q gi|254780406|r 202 KKVFEFFNWKVNRLIRISYGPFQ 224 (354)
Q Consensus 202 rr~~~~~g~~V~~L~Rv~~G~~~ 224 (354)
T Consensus 164 RvHla~lG~PIvGD--~~YG~~~ 184 (223)
T cd02563 164 RRHLAHIRHPIIGD--TTHGDGR 184 (223)
T ss_pred HHHHHHCCCCEECC--CCCCCCC
T ss_conf 99999879978277--2568754