HHsearch alignment for GI: 254780610 and conserved domain: pfam00849

>pfam00849 PseudoU_synth_2 RNA pseudouridylate synthase. Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.
Probab=100.00  E-value=1.2e-39  Score=255.99  Aligned_cols=151  Identities=37%  Similarity=0.506  Sum_probs=121.5

Q ss_pred             EEEEECCCHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf             78996240111045678754210022222210244334444364324444332324057212035788889999972113
Q gi|254780610|r   99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKS  178 (340)
Q Consensus        99 llvinKPaGl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~lVHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~~~  178 (340)
T Consensus         1 ~lvvnKP~Gl~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~f~----~   69 (151)
T pfam00849         1 YIVVNKPAGVPVHPTDLSDLLSLTELLLVAE-------LGKFRLYPVHRLDRDTSGLLLLAKDGEAANKLNKLFP----E   69 (151)
T ss_pred             CEEEECCCCCEEECCCCCCCCCHHHHHHHHC-------CCCCCEEEECCCCCCCCCEEEECCCHHHHHHHHHHHH----H
T ss_conf             9999999998582189987862888655551-------5997355851778888544786232688888999866----5


Q ss_pred             CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCEEECCCCCCCCCEEEEEECHHHHH
Q ss_conf             22133445432024332332110013434443322123444555553000012221011256677500123443115899
Q gi|254780610|r  179 TRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTH  258 (340)
Q Consensus       179 ~~v~K~Y~Aiv~G~~~~~~g~i~~~l~~~~~~~~~~~~~~~~~~~~k~a~T~~~~l~~~~~~~~~~~slv~~~~~TGRtH  258 (340)
T Consensus        70 ~~v~K~Y~a~v~g~~-~~~~~~~~~~~~~~~~~~~~---~~~~~~~k~a~t~~~~l~~~~--~~~~~slv~~~l~TGR~H  143 (151)
T pfam00849        70 RKVEKEYLALVDGPE-EEEGTIKAPIKKDKNKVPRR---KKEELDGKKAVTHLRVLRSGS--KIEDVSLVELELVTGRKH  143 (151)
T ss_pred             CCCCEEEEEEEECCC-CCCCEEEEECCCCCCCCEEE---EEECCCCCCCCEEEEEEEECC--CCCCEEEEEEEECCCHHH
T ss_conf             355428999996777-87708981011367777279---875699842425999988725--689969999996728379


Q ss_pred             HHHHHHHH
Q ss_conf             99999987
Q gi|254780610|r  259 QIRVHMAH  266 (340)
Q Consensus       259 QIRvhla~  266 (340)
T Consensus       144 QIRvhlas  151 (151)
T pfam00849       144 QIRAHLAA  151 (151)
T ss_pred             HHHHHHCC
T ss_conf             99998669