HHsearch alignment for GI: 254780608 and conserved domain: cd02553

>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=99.61  E-value=1.5e-15  Score=118.16  Aligned_cols=140  Identities=19%  Similarity=0.263  Sum_probs=91.5

Q ss_pred             EEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             68841765311223578533233201101111100133354453422240462123101222102333322111200013
Q gi|254780608|r  108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLV  187 (346)
Q Consensus       108 livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~Aiv  187 (346)
T Consensus         2 YillnKP~G~v~t~~d~~~ktv~dll~~~~--~~~~l~~vGRLD~~s~GLLLlTNDG~l~~~l~h--P~~~i~K~Y~V~v   77 (167)
T cd02553           2 YLMLNKPAGVVCATKDPHHPTVIDLLPEPD--RRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTS--PKKHVPKTYEVTL   77 (167)
T ss_pred             EEEEECCCCEEECCCCCCCCCHHHHCCCCC--CCCCEEECCCCCCCCCCEEEECCCHHHHHHHHC--CCCCCCEEEEEEE
T ss_conf             999988999796988999997744335500--367556744568997622999188889976414--4478888999987


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCCCCE
Q ss_conf             456541000000012234655432111335555555-3034301013432024420457861237899999999639800
Q gi|254780608|r  188 WGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGA-NYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPI  266 (346)
Q Consensus       188 ~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g~Pi  266 (346)
T Consensus        78 ~~~i~~~~--l~~l-~~-G------v~-----i~dg~~~~~~~v~~~---~~--~~~~i~l~eGknrqIRrm~~~~g~~V  137 (167)
T cd02553          78 AGPLTEDD--IEAF-AE-G------VL-----LHDGYPTKPAKLEIL---SP--TTVRLTITEGKYHQVKRMFAAVGNKV  137 (167)
T ss_pred             CCCCCHHH--HHHH-HC-C------CE-----ECCCCEEEEEEEEEE---CC--CEEEEEEECCCCHHHHHHHHHCCCEE
T ss_conf             67899999--9999-76-9------89-----649859751799992---58--68999998884629999999869888


Q ss_pred             ECCCC
Q ss_conf             04644
Q gi|254780608|r  267 VGDHK  271 (346)
Q Consensus       267 vGD~~  271 (346)
T Consensus       138 ~~L~R  142 (167)
T cd02553         138 VALHR  142 (167)
T ss_pred             EEEEE
T ss_conf             58999