HHsearch alignment for GI: 254780608 and conserved domain: PRK11180
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional.
Probab=100.00 E-value=0 Score=571.88 Aligned_cols=298 Identities=25% Similarity=0.409 Sum_probs=244.9
Q ss_pred EEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 999841136866899999876788989999999849903887884-5112117998899935655422233222234554
Q gi|254780608|r 9 YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVINALNHIIKEQKILDSS 87 (346)
Q Consensus 9 ~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~ 87 (346)
T Consensus 8 T~tV~~~~aG~RLD~fL~~~~~~~srs~i~k~ir~g~I~VNgk~v~k~~~~v~~GD~I~i~~~~~~~~------------ 75 (325)
T PRK11180 8 TATVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAEIEEEA------------ 75 (325)
T ss_pred EEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCCCCCCCCEEEECCCCCCCC------------
T ss_conf 99999100797399999975788899999999986988999999478212788999999816877634------------
Q ss_pred CCCCCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCC-CCCCHHHCCCC--CCCCCCCCCCCCCCCCCEEEEECCC
Q ss_conf 33432223454307861785688417653112235785332-33201101111--1001333544534222404621231
Q gi|254780608|r 88 VNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDS--KGQKPRLTHRLDQETSGILVVARTR 164 (346)
Q Consensus 88 ~~~~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~-~~~~l~~~~~~--~~~~~~lVHRLDr~TSGlll~AK~~ 164 (346)
T Consensus 76 ---~~~p~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~r~~iVHRLDr~TSGlll~AK~~ 152 (325)
T PRK11180 76 ---RFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTV 152 (325)
T ss_pred ---CCCCCCCCCCEEEECCCEEEEECCCCCEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCEEECCCCCCCEEEEECCCH
T ss_conf ---47722388518998388999988999447679898887799999875321047876766642799974146641759
Q ss_pred CHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEE
Q ss_conf 01222102333322111200013456541000000012234655432111335555555303430101343202442045
Q gi|254780608|r 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLE 244 (346)
Q Consensus 165 ~a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~ 244 (346)
T Consensus 153 ~a~~~l~~~f~~~~v~K~Y~Alv~G~~~-~~g~i~~pl~~~~~~-~~~~----~~~~~gk~A~T~~~vl~~~~-~~slv~ 225 (325)
T PRK11180 153 PAQTRLVEALQKREITREYEAVAIGHMT-AGGTVDEPISRHPTK-RTHM----AVHPMGKPAVTHYRIMEHFR-VHTRLR 225 (325)
T ss_pred HHHHHHHHHHHHCCCCEEEEEEEEEEEC-CCCEEECCCCCCCCC-CEEE----EECCCCEEECCHHHHHHHCC-CCEEEE
T ss_conf 9999999999738896599999810437-996585420137766-6289----97677702022101444358-845799
Q ss_pred EEECHHHHHHHHHHHHHCCCCEECCCCCCCCCCC------HHC--CCCCCCHHHHHHHHEEECCCCC-EEEEECCCCHHH
Q ss_conf 7861237899999999639800046444665221------000--1344624131100043758896-499983997899
Q gi|254780608|r 245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG------NFT--SPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHM 315 (346)
Q Consensus 245 ~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~------~~~--~~~~~r~~LHa~~l~f~hp~~~-~~~~~aplP~~f 315 (346)
T Consensus 226 ~~l~TGRtHQIRvHla~~G~PIvGD~~YG~~~~~~k~~~~~~~~~~~~~~R~~LHA~~L~f~HP~t~~~~~~~aplP~d~ 305 (325)
T PRK11180 226 LRLETGRTHQIRVHMAHITHPLVGDQVYGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPIPQDM 305 (325)
T ss_pred EEECCCCCHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHCCCCCCCCCCCCCEEEEECCCCHHH
T ss_conf 98275882899999998799563752468866555443477888761897664631845775789998799980690999
Q ss_pred HHHHHHHCCCCCC
Q ss_conf 9999980898752
Q gi|254780608|r 316 VKTWDSLGFKYDR 328 (346)
Q Consensus 316 ~~~l~~l~~~~d~ 328 (346)
T Consensus 306 ~~~l~~Lr~d~~~ 318 (325)
T PRK11180 306 VELIEALRADFEE 318 (325)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999998668976