Citrus Sinensis ID: 026204

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-
Protein Sequence
MELVELEFNQVSVLALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ
Secondary Structure (PSIPRED)
cccccccHHHHHcccEEEccEEcccccccccccEEEEEEccccccccccccccccEEEEcccEEEEEcccccEEccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccEEEEcccccccEEEEEccHHHHHHHHHHHHcccccEEEEEEEEccccccccEEEEcccccccccEEEEEEcccccccccccccEEEEEEEEEccccEEEEEEEEccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHcccEEEccEEEEccEEEccccEEEEEccccccccEcccccccEEEEEcccEEEEEcccccEEcccccccccHHHHHHHHHcccccccccHHHcccccccccccccccEccccccEcccEEEEEcccccEEEEEEccHHHHHHHHHHHHHcccEEEEEEEEEccccccccEEEcccccccHHHcEEEEEccccccccccccEEHHHHHHEcccccEEEEEEEEEcccccc
Coil and Loop (DISEMBL)
MELVELEFNQVSVLALFLSMDklsvshnvkggdmvnctiselqplraeaedipldivyeddnvlvvnkpahmvvhpapgnatgtlvngilhhcslptlassnqeafsdaedisddeefsssisgasirpgivhrldkgtsgllvvakdehshahlseqfKLHTIERVYISLtsgvpsqssgrievpisrdpnnrirmaaipgsnkhgqarhAASRYKVIEILAGGGSALVEWRLETGRTHQ
Flexible Loop (DISEMBL)
MELVELEFNQVSVLALFLSMDKLSVshnvkggdmvNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSssisgasirpgiVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLtsgvpsqssgrievpisrdpnnRIRMAAipgsnkhgqarHAASRYKVIEILAGGGSALVEWRLETGRTHQ
Low Complexity Region (SEG)
MELVELEFNQVSVLALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQeafsdaedisddeefsssisGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ
Disordered region (IsUnstruct)
***VELEFNQVSVLALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPT********************************GIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLT*****************************************SRYKVIEILAGGGSALVEWRL*******
Disordered Region (DISOPRED)
****ELEFNQVSVLALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDI***********GASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRT**
Disordered Region (DISEMBL)
MELVELEFNQVSVLALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSN******************SISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSG********IEVPISRDPNNRIRMAAIPG*********AASRYKVIEILAGGGSALVEWRLETGRTHQ
Disordered Region (DISPRO)
MELVELEFNQVSVLALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLAS****************EFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETG****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MELVELEFNQVSVLALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	241	2.2.26 [Sep-21-2011]
Q3ECD0	430	RNA pseudourine synthase	yes	no	0.900	0.504	0.791	8e-96
Q5Z8P2	445	RNA pseudourine synthase	yes	no	0.896	0.485	0.708	4e-86
P50513	317	Ribosomal large subunit p	yes	no	0.763	0.580	0.425	4e-36
Q45826	316	Uncharacterized RNA pseud	yes	no	0.755	0.575	0.402	3e-35
P74346	327	Uncharacterized RNA pseud	N/A	no	0.763	0.562	0.399	4e-35
Q45480	303	Uncharacterized RNA pseud	yes	no	0.775	0.617	0.406	7e-35
O50310	327	Uncharacterized RNA pseud	yes	no	0.780	0.574	0.412	3e-34
O67638	316	Uncharacterized RNA pseud	yes	no	0.771	0.588	0.356	7e-31
Q8XYX8	358	Ribosomal large subunit p	yes	no	0.730	0.491	0.384	1e-30
Q9JVB6	374	Ribosomal large subunit p	yes	no	0.730	0.470	0.419	4e-30

>sp|Q3ECD0|PUS2_ARATH RNA pseudourine synthase 2, chloroplastic OS=Arabidopsis thaliana GN=At1g76050 PE=2 SV=1

 Score =  349 bits (896), Expect = 8e-96,   Method: Compositional matrix adjust.
 Identities = 175/221 (79%), Positives = 191/221 (86%), Gaps = 4/221 (1%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSHNVK GD VNCTISELQPL+AEAEDIPLDIVYED +VLVVNKPAHMVVHPAPGN TGT
Sbjct: 119 VSHNVKSGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGT 178

Query: 85  LVNGILHHCSLPTLASSNQEAFSDAE--DISDDEEFSSSIS--GASIRPGIVHRLDKGTS 140
           LVNGILHHCSLP +  SN E   D++    SDDEE ++S S   AS+RPGIVHRLDKGT+
Sbjct: 179 LVNGILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRLDKGTT 238

Query: 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAI 200
           GLLVVAKDEHSHAHL+EQFKLHTIERVY+SLT+GVPS   GRIE+PI RD +NRIRMAAI
Sbjct: 239 GLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRIEIPIGRDSSNRIRMAAI 298

Query: 201 PGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           PG  + G+ARHAASRYKVIE  AGGGSALVEWRLETGRTHQ
Sbjct: 299 PGGVRGGRARHAASRYKVIETFAGGGSALVEWRLETGRTHQ 339

Arabidopsis thaliana (taxid: 3702)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -

>sp|Q5Z8P2|PUS2_ORYSJ RNA pseudourine synthase 2, chloroplastic OS=Oryza sativa subsp. japonica GN=Os06g0717400 PE=2 SV=1

 Score =  317 bits (813), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 163/230 (70%), Positives = 179/230 (77%), Gaps = 14/230 (6%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSH VKGGD+V+CT+ ELQPLRAE EDIPLDIVYEDD++LVVNKPAHMVVHPAPGNA GT
Sbjct: 111 VSHMVKGGDIVSCTVLELQPLRAEPEDIPLDIVYEDDHLLVVNKPAHMVVHPAPGNANGT 170

Query: 85  LVNGILHHCSLPTLASSNQEAFSDAEDISDDE-------------EFSSSISGASIRPGI 131
           LVN ILHHC + T     + +  D    S D+             E SS +  A +RPGI
Sbjct: 171 LVNAILHHCKISTFTCLARNSIDDECPDSSDDDIDVFDIDQFTTGEVSSEVREALVRPGI 230

Query: 132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDP 191
           VHRLDKGTSGLLVVAKDEHSHA L+EQFKLHTI RVYISLT G P+ +SGRIEVPI+RDP
Sbjct: 231 VHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRRVYISLTCGAPNPNSGRIEVPIARDP 290

Query: 192 NNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           NNRIRM A PGS  H  ARHAASRYKV E+ AGGGSALVEWRLETGRTHQ
Sbjct: 291 NNRIRMIATPGSG-HRYARHAASRYKVREVFAGGGSALVEWRLETGRTHQ 339

Oryza sativa subsp. japonica (taxid: 39947)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|P50513|RLUD_ZYMMO Ribosomal large subunit pseudouridine synthase D OS=Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) GN=rluD PE=3 SV=2

 Score =  151 bits (381), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 91/214 (42%), Positives = 124/214 (57%), Gaps = 30/214 (14%)

Query: 28  NVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 87
            +K  D     I   +P   E +DIPL+IV+ED+++LVVNKPA MVVHPA GN   TLVN
Sbjct: 56  KIKSLDCFTVDIPLPRPAHNEPQDIPLEIVFEDEHLLVVNKPAGMVVHPAAGNYDNTLVN 115

Query: 88  GILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAK 147
            +L+HC+                         S I G + RPGIVHR+DK TSGLLVVAK
Sbjct: 116 ALLYHCAGKL----------------------SGIGGVA-RPGIVHRIDKDTSGLLVVAK 152

Query: 148 DEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHG 207
            + +HA L+ QF  H+I R Y ++  G PS   G ++ P++R   NR +MA +      G
Sbjct: 153 TDPAHAGLAAQFADHSINRRYRAIVDGHPSL-QGHVDAPLARSSVNRQKMAIV----SDG 207

Query: 208 QARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           + + A + Y++I  L    ++L+E RLETGRTHQ
Sbjct: 208 RGKRAVTHYRMITPLK--NASLIECRLETGRTHQ 239

Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA.

Zymomonas mobilis (strain ATCC 31821 / ZM4 / CP4) (taxid: 264203)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 3

>sp|Q45826|Y901_CHLAA Uncharacterized RNA pseudouridine synthase Caur_0901 OS=Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) GN=Caur_0901 PE=3 SV=2

 Score =  148 bits (374), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 87/216 (40%), Positives = 122/216 (56%), Gaps = 34/216 (15%)

Query: 26  SHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL 85
           S  V+ G ++  TI    P    AE IPLD+VYED ++ V+NKPA MVVHPAPG+  GTL
Sbjct: 63  SQPVRPGAVIQLTIPPPIPTELVAEPIPLDVVYEDADIAVINKPAGMVVHPAPGHPRGTL 122

Query: 86  VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVV 145
           VN +L     P LA                        G  +RPGIVHRLD+ TSGLLV+
Sbjct: 123 VNALL--ARYPDLA-----------------------IGGELRPGIVHRLDRDTSGLLVI 157

Query: 146 AKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNK 205
           A+ + +   L +Q +   + ++Y +L  G P + +G I+ PI RDP +R+RMA +P    
Sbjct: 158 ARHDQAMRSLVDQQQARRMRKIYQALVIGRPPE-TGTIDAPIGRDPRDRLRMAVVP---- 212

Query: 206 HGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
               R A + Y++++    G  +L+E +LETGRTHQ
Sbjct: 213 --DGRPARTHYRLLDTF--GDYSLLEVQLETGRTHQ 244

Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (taxid: 324602)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|P74346|Y1629_SYNY3 Uncharacterized RNA pseudouridine synthase slr1629 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=slr1629 PE=3 SV=1

 Score =  148 bits (373), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 85/213 (39%), Positives = 122/213 (57%), Gaps = 29/213 (13%)

Query: 29  VKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNG 88
           +K GD +   I EL PL   A++IPLDI+YED+ ++++NKPA +VVHP PG+  GT+VN 
Sbjct: 73  LKTGDRLVVNIPELIPLDVVAQNIPLDILYEDEQLIIINKPAGLVVHPGPGHPDGTVVNA 132

Query: 89  ILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKD 148
           +L HC  P LA                        G   RPGIVHRLDK T+G +VVAK 
Sbjct: 133 LLAHC--PDLAG----------------------IGGVQRPGIVHRLDKDTTGAMVVAKT 168

Query: 149 EHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQ 208
           E +  +L  Q K  T  R+Y  +  G P +  G + +P+ R P +R +M  +P   K G 
Sbjct: 169 ELALHNLQVQLKEKTARRLYWGIVYGSPKEIQGTVNLPVGRHPGDRQKMGIVP-VEKGG- 226

Query: 209 ARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
            R A + ++++E +  G  + +E++LETGRTHQ
Sbjct: 227 -REAVTHWRLLERI--GNHSWLEFQLETGRTHQ 256

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|Q45480|YLYB_BACSU Uncharacterized RNA pseudouridine synthase YlyB OS=Bacillus subtilis (strain 168) GN=ylyB PE=3 SV=3

 Score =  147 bits (371), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 89/219 (40%), Positives = 122/219 (55%), Gaps = 32/219 (14%)

Query: 23  LSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNAT 82
           +  ++ ++ GD V  T+ E + L   AE + LDI YED +VLVVNKP  MVVHPAPG+ T
Sbjct: 49  VKANYKIQPGDQVTVTVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLT 108

Query: 83  GTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 142
           GTLVNG++ HC+                D+       S I+G  +RPGIVHR+DK TSGL
Sbjct: 109 GTLVNGLMAHCT----------------DL-------SGINGV-MRPGIVHRIDKDTSGL 144

Query: 143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPG 202
           L+VAK++ +H  L  Q    T+ R Y ++  G+ S   G I+ PI RD  +R  M     
Sbjct: 145 LMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLISHDDGTIDAPIGRDKKDRQSMTVT-- 202

Query: 203 SNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
                  ++A + + V+E        LVE +LETGRTHQ
Sbjct: 203 ----RDGKNAVTHFHVLERFQ--DFTLVECQLETGRTHQ 235

Bacillus subtilis (strain 168) (taxid: 224308)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|O50310|Y723_CHLP8 Uncharacterized RNA pseudouridine synthase Cpar_0723 OS=Chlorobaculum parvum (strain NCIB 8327) GN=Cpar_0723 PE=3 SV=1

 Score =  145 bits (365), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 124/218 (56%), Gaps = 30/218 (13%)

Query: 26  SHNVKGGDMVNCTISELQPLRAE--AEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATG 83
           ++ VK  D ++ T   L+P   E   EDIP+ I+YEDD+++V++K A MVVHPA GN TG
Sbjct: 49  NYRVKSCDHIHLTF--LRPPAPELAPEDIPITILYEDDDLMVIDKEAGMVVHPAFGNWTG 106

Query: 84  TLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLL 143
           TL N ILHH               DA+++   E          +RPGIVHRLDK TSGL+
Sbjct: 107 TLANAILHHLG------------KDADELDKTE----------MRPGIVHRLDKDTSGLI 144

Query: 144 VVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGS 203
           ++AK+  +   L+ QF    +E+VY ++  GVP   SG I+  I R   NR  MA  P  
Sbjct: 145 IIAKNPTALHKLARQFANRQVEKVYKAIVWGVPKAESGTIKTNIGRSHKNRKVMANFPYE 204

Query: 204 NKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
              G  +HA + Y+V+E L  G  +L++  L TGRTHQ
Sbjct: 205 GAEG--KHAITDYQVVEDL--GYFSLMDVTLHTGRTHQ 238

Chlorobaculum parvum (strain NCIB 8327) (taxid: 517417)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|O67638|Y1758_AQUAE Uncharacterized RNA pseudouridine synthase aq_1758 OS=Aquifex aeolicus (strain VF5) GN=aq_1758 PE=3 SV=1

 Score =  134 bits (336), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 77/216 (35%), Positives = 118/216 (54%), Gaps = 30/216 (13%)

Query: 26  SHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL 85
           S  ++ G+ V   + E +PL  + E+IP++I+YED+++ VV KP  +VVHP+PG  +GTL
Sbjct: 54  SRKLREGERVILHVPEPEPLDVKPENIPINIIYEDEDIAVVEKPCGLVVHPSPGYTSGTL 113

Query: 86  VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVV 145
           VN +L+H                   I D     SSI G   RPGIVHRLDK T+G++V+
Sbjct: 114 VNALLYH-------------------IKD----LSSIGGVE-RPGIVHRLDKETAGVMVI 149

Query: 146 AKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNK 205
           AK+  +H +L  QF+    E+ Y  L  G+  +  G I+ PI+R P +R R         
Sbjct: 150 AKNNTAHRNLVRQFQERKTEKFYKVLVKGLVKKDYGAIDTPIARHPVDRKRFWV------ 203

Query: 206 HGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
             + + A + Y V++        L++ ++ TGRTHQ
Sbjct: 204 RKEGKEALTEYWVLKRYEKYEITLLKVKIHTGRTHQ 239

Aquifex aeolicus (strain VF5) (taxid: 224324)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: -

>sp|Q8XYX8|RLUD_RALSO Ribosomal large subunit pseudouridine synthase D OS=Ralstonia solanacearum (strain GMI1000) GN=rluD PE=3 SV=1

 Score =  133 bits (334), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 85/221 (38%), Positives = 123/221 (55%), Gaps = 45/221 (20%)

Query: 29  VKGGDMVNCTISELQPLRAE------AEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNAT 82
           V GGD +     E+ P RA+      AE + LD+VYEDD +LV+NKPA +VVHPA GN +
Sbjct: 90  VCGGDRI-----EVVPQRADDENAFVAEPVDLDVVYEDDTLLVINKPAGLVVHPAAGNWS 144

Query: 83  GTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL 142
           GT++NG+LH              +  A  +               R GIVHRLDK TSGL
Sbjct: 145 GTVLNGLLHR-------------YPQAAGLP--------------RAGIVHRLDKETSGL 177

Query: 143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPG 202
           +VVA+   +   L  Q +  T++R Y++L  G  +  +G I+ PI RDP +R RMA I  
Sbjct: 178 MVVARTLPAQTDLVRQLQARTVKRTYLALVWG-ETPEAGTIDAPIGRDPRDRTRMAII-- 234

Query: 203 SNKHGQARHAASRYKVIEILAGGGS--ALVEWRLETGRTHQ 241
             +    + A + +K ++++  G +  +LV+ +LETGRTHQ
Sbjct: 235 --ETASGKPARTHFKTLDVVDLGRAQVSLVQCQLETGRTHQ 273

Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA.

Ralstonia solanacearum (strain GMI1000) (taxid: 267608)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 3

>sp|Q9JVB6|RLUD_NEIMA Ribosomal large subunit pseudouridine synthase D OS=Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) GN=rluD PE=3 SV=1

 Score =  131 bits (330), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 89/212 (41%), Positives = 118/212 (55%), Gaps = 36/212 (16%)

Query: 31  GGDMVNCTISELQP-LRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGI 89
           GG+ +  T+   +  L    E + LDIVYEDD V+VVNKPA +VVHPA GN TGTL+NG+
Sbjct: 81  GGEQIRVTVRPSEENLAFVPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGL 140

Query: 90  LHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDE 149
           L HC  P L                     S I     R GIVHRLDK TSGL+VVAK  
Sbjct: 141 LAHC--PEL---------------------SQIP----RAGIVHRLDKETSGLMVVAKTL 173

Query: 150 HSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQA 209
            +   L  Q +  T++R+Y ++ +G+     G+IE  I RDP+NR++MA +    K G  
Sbjct: 174 PAQNSLVWQLQERTVKRIYRAVANGI-VPFDGKIETQIGRDPHNRLKMAVV----KFG-G 227

Query: 210 RHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           + A +  KV+E       + +E  LETGRTHQ
Sbjct: 228 KPAVTHVKVLERYL--AHSYIECSLETGRTHQ 257

Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA.

Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) (taxid: 122587)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 2

EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	241
224065743	444	predicted protein [Populus trichocarpa]	0.887	0.481	0.817	5e-97
6721111	980	T4O12.25 [Arabidopsis thaliana]	0.941	0.231	0.764	9e-96
255556673	399	ribosomal pseudouridine synthase, putati	0.900	0.543	0.802	1e-94
42572121	430	RNA pseudourine synthase 2 [Arabidopsis	0.900	0.504	0.791	4e-94
359492029	433	PREDICTED: RNA pseudourine synthase 2, c	0.900	0.501	0.755	2e-91
449450654	453	PREDICTED: RNA pseudourine synthase 2, c	0.896	0.476	0.760	4e-90
449500428	452	PREDICTED: LOW QUALITY PROTEIN: RNA pseu	0.892	0.475	0.764	2e-89
297839485	930	T4O12.25 [Arabidopsis lyrata subsp. lyra	0.850	0.220	0.777	2e-87
242097088	441	hypothetical protein SORBIDRAFT_10g03030	0.896	0.489	0.721	1e-86
413943106	350	hypothetical protein ZEAMMB73_425131 [Ze	0.896	0.617	0.717	3e-86

>gi|224065743|ref|XP_002301949.1| predicted protein [Populus trichocarpa] gi|222843675|gb|EEE81222.1| predicted protein [Populus trichocarpa]

 Score =  359 bits (922), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 179/219 (81%), Positives = 194/219 (88%), Gaps = 5/219 (2%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSHNVK GD VNC ISELQPLRAE E+IPLDIVYED+NVLVVNKPAHMVVHPAPGNATGT
Sbjct: 131 VSHNVKAGDKVNCVISELQPLRAEPENIPLDIVYEDENVLVVNKPAHMVVHPAPGNATGT 190

Query: 85  LVNGILHHCSLPTLASSNQEAFSDAEDISDDEE--FSSSISGASIRPGIVHRLDKGTSGL 142
           LVNGILHHCSLPT++S  QE  S AED+SDD++    SS   AS+RPGIVHRLDKGTSGL
Sbjct: 191 LVNGILHHCSLPTVSS--QEVLSGAEDVSDDDDEGLCSSSYAASVRPGIVHRLDKGTSGL 248

Query: 143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPG 202
           LVVAKDEHSHAHLSEQFKLHTI+RVY+SLT GVP+  +GRI+VPI RD +NRIRMAAI  
Sbjct: 249 LVVAKDEHSHAHLSEQFKLHTIKRVYVSLTCGVPAPMAGRIDVPIGRDVSNRIRMAAIVE 308

Query: 203 SNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
            N+ GQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ
Sbjct: 309 PNR-GQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 346

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6721111|gb|AAF26765.1|AC007396_14 T4O12.25 [Arabidopsis thaliana]

 Score =  355 bits (911), Expect = 9e-96,   Method: Compositional matrix adjust.
 Identities = 182/238 (76%), Positives = 199/238 (83%), Gaps = 11/238 (4%)

Query: 9   NQVSV-LALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN 67
           NQVS+ L LF       VSHNVK GD VNCTISELQPL+AEAEDIPLDIVYED +VLVVN
Sbjct: 658 NQVSISLTLF------QVSHNVKSGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVN 711

Query: 68  KPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAE--DISDDEEFSSSIS-- 123
           KPAHMVVHPAPGN TGTLVNGILHHCSLP +  SN E   D++    SDDEE ++S S  
Sbjct: 712 KPAHMVVHPAPGNPTGTLVNGILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSY 771

Query: 124 GASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRI 183
            AS+RPGIVHRLDKGT+GLLVVAKDEHSHAHL+EQFKLHTIERVY+SLT+GVPS   GRI
Sbjct: 772 AASVRPGIVHRLDKGTTGLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRI 831

Query: 184 EVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           E+PI RD +NRIRMAAIPG  + G+ARHAASRYKVIE  AGGGSALVEWRLETGRTHQ
Sbjct: 832 EIPIGRDSSNRIRMAAIPGGVRGGRARHAASRYKVIETFAGGGSALVEWRLETGRTHQ 889

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556673|ref|XP_002519370.1| ribosomal pseudouridine synthase, putative [Ricinus communis] gi|223541437|gb|EEF42987.1| ribosomal pseudouridine synthase, putative [Ricinus communis]

 Score =  352 bits (902), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 175/218 (80%), Positives = 192/218 (88%), Gaps = 1/218 (0%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSHNVK GD V CTISELQPLRAE ED+PLDIVYED+++LVVNKP HMVVHPAPGN TGT
Sbjct: 109 VSHNVKFGDKVTCTISELQPLRAEPEDMPLDIVYEDEHLLVVNKPPHMVVHPAPGNPTGT 168

Query: 85  LVNGILHHCSLPTLASSNQEAFSDAEDISDDEE-FSSSISGASIRPGIVHRLDKGTSGLL 143
           LVNGILHHC+LPT+A S+QE  SDAED SDD+E   SS   +SIRPGIVHRLDKGTSGLL
Sbjct: 169 LVNGILHHCNLPTVAISSQEVLSDAEDRSDDDERSYSSSCESSIRPGIVHRLDKGTSGLL 228

Query: 144 VVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGS 203
           VVAKDEH+HAHLSEQFK HTI+RVYISLTSGVPS  +GRI++PI RD NNRIRM AIPG 
Sbjct: 229 VVAKDEHAHAHLSEQFKQHTIQRVYISLTSGVPSALTGRIDIPIGRDVNNRIRMTAIPGP 288

Query: 204 NKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
            K G+ARHAASR+KV+E LAGGGSALVEWRLETGRTHQ
Sbjct: 289 IKQGRARHAASRFKVVETLAGGGSALVEWRLETGRTHQ 326

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42572121|ref|NP_974151.1| RNA pseudourine synthase 2 [Arabidopsis thaliana] gi|122215273|sp|Q3ECD0.1|PUS2_ARATH RecName: Full=RNA pseudourine synthase 2, chloroplastic; AltName: Full=RNA pseudouridylate synthase 2; AltName: Full=RNA-uridine isomerase 2; Flags: Precursor gi|332197669|gb|AEE35790.1| RNA pseudourine synthase 2 [Arabidopsis thaliana]

 Score =  349 bits (896), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 175/221 (79%), Positives = 191/221 (86%), Gaps = 4/221 (1%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSHNVK GD VNCTISELQPL+AEAEDIPLDIVYED +VLVVNKPAHMVVHPAPGN TGT
Sbjct: 119 VSHNVKSGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGT 178

Query: 85  LVNGILHHCSLPTLASSNQEAFSDAE--DISDDEEFSSSIS--GASIRPGIVHRLDKGTS 140
           LVNGILHHCSLP +  SN E   D++    SDDEE ++S S   AS+RPGIVHRLDKGT+
Sbjct: 179 LVNGILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRLDKGTT 238

Query: 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAI 200
           GLLVVAKDEHSHAHL+EQFKLHTIERVY+SLT+GVPS   GRIE+PI RD +NRIRMAAI
Sbjct: 239 GLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRIEIPIGRDSSNRIRMAAI 298

Query: 201 PGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           PG  + G+ARHAASRYKVIE  AGGGSALVEWRLETGRTHQ
Sbjct: 299 PGGVRGGRARHAASRYKVIETFAGGGSALVEWRLETGRTHQ 339

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359492029|ref|XP_003634352.1| PREDICTED: RNA pseudourine synthase 2, chloroplastic-like [Vitis vinifera] gi|302141717|emb|CBI18920.3| unnamed protein product [Vitis vinifera]

 Score =  341 bits (874), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 167/221 (75%), Positives = 188/221 (85%), Gaps = 4/221 (1%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSH ++ GD VNCTISELQPLRAE EDIPLDIVYED++VLVVNKPAHMVVHPAPGNA+GT
Sbjct: 114 VSHVIRAGDKVNCTISELQPLRAEPEDIPLDIVYEDEHVLVVNKPAHMVVHPAPGNASGT 173

Query: 85  LVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGAS----IRPGIVHRLDKGTS 140
           LVNGILHHCSLPT+A  N+++  D     +   F++  +  +    IRPGIVHRLDKGTS
Sbjct: 174 LVNGILHHCSLPTVALPNRDSEEDDISDDEFNSFAAGQNCGTCETNIRPGIVHRLDKGTS 233

Query: 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAI 200
           GLLVVAKDEHSHAHLSEQFKLH+I RVYISLTSGVP+  SGR+E+P+ RDPNNRIRM A+
Sbjct: 234 GLLVVAKDEHSHAHLSEQFKLHSIHRVYISLTSGVPTPLSGRVEIPVGRDPNNRIRMTAV 293

Query: 201 PGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           PG +  GQARHAASRYKVIEILA GGSALVEWRLETGRTHQ
Sbjct: 294 PGPSNSGQARHAASRYKVIEILAAGGSALVEWRLETGRTHQ 334

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449450654|ref|XP_004143077.1| PREDICTED: RNA pseudourine synthase 2, chloroplastic-like [Cucumis sativus]

 Score =  336 bits (862), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 168/221 (76%), Positives = 188/221 (85%), Gaps = 5/221 (2%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSHNVK GD++NCTISELQPLRAE EDI LDIVYED++VLVVNKPAHMVVHPAPGNATGT
Sbjct: 114 VSHNVKAGDVINCTISELQPLRAEPEDIDLDIVYEDEHVLVVNKPAHMVVHPAPGNATGT 173

Query: 85  LVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFS----SSISGASIRPGIVHRLDKGTS 140
           LVN IL+HCSLP +A+S  E  SD+ D+SDDE  S    S +S A IRPGIVHRLDKGTS
Sbjct: 174 LVNAILNHCSLPMVATSTGENESDS-DVSDDEFSSIGVFSRVSEAPIRPGIVHRLDKGTS 232

Query: 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAI 200
           GLLVVAKDEHSHAHLS QFK H+IERVYISLT GVP  ++GRIE+PI RDPNNRIRM AI
Sbjct: 233 GLLVVAKDEHSHAHLSAQFKQHSIERVYISLTCGVPPSTAGRIEMPICRDPNNRIRMTAI 292

Query: 201 PGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
            G+  +  A++AASRY V+EILA GGS+LVEWRLETGRTHQ
Sbjct: 293 DGTKNNPHAKYAASRYNVMEILAQGGSSLVEWRLETGRTHQ 333

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449500428|ref|XP_004161095.1| PREDICTED: LOW QUALITY PROTEIN: RNA pseudourine synthase 2, chloroplastic-like [Cucumis sativus]

 Score =  334 bits (857), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 169/221 (76%), Positives = 189/221 (85%), Gaps = 6/221 (2%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSHNVK GD++NCTISELQPLRAE EDI LDIVYED++VLVVNKPAHMVVHPAPGNATGT
Sbjct: 114 VSHNVKAGDVINCTISELQPLRAEPEDIDLDIVYEDEHVLVVNKPAHMVVHPAPGNATGT 173

Query: 85  LVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFS----SSISGASIRPGIVHRLDKGTS 140
           LVN IL+HCSLP +A+S  E  SD+ D+SDDE  S    S +S A IRPGIVHRLDKGTS
Sbjct: 174 LVNAILNHCSLPMVATSTGENESDS-DVSDDEFSSIGVFSRVSEAPIRPGIVHRLDKGTS 232

Query: 141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAI 200
           GLLVVAKDEHSHAHLS QFK H+IERVYISLT GVP  ++GRIE+PI RDPNNRIRM AI
Sbjct: 233 GLLVVAKDEHSHAHLSAQFKQHSIERVYISLTCGVPPSTAGRIEMPICRDPNNRIRMTAI 292

Query: 201 PGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
            G+N +  A++AASRY V+EILA GGS+LVEWRLETGRTHQ
Sbjct: 293 DGTN-NPHAKYAASRYNVMEILAQGGSSLVEWRLETGRTHQ 332

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297839485|ref|XP_002887624.1| T4O12.25 [Arabidopsis lyrata subsp. lyrata] gi|297333465|gb|EFH63883.1| T4O12.25 [Arabidopsis lyrata subsp. lyrata]

 Score =  327 bits (839), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 171/220 (77%), Positives = 181/220 (82%), Gaps = 15/220 (6%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSHNVK GD VNCTISELQPL+AEAEDIPLDIVYED +VLVVNKPAHMVVHPAPGN TGT
Sbjct: 621 VSHNVKAGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPGNPTGT 680

Query: 85  LVNGILHHCSLPTLASSNQE-AFSDAEDISDDEEF--SSSISGASIRPGIVHRLDKGTSG 141
           LVNGILHHCSLP ++ SN E   SD E  SDDEE   SSS   AS+RPGIVHRLDKGT+G
Sbjct: 681 LVNGILHHCSLPCVSYSNAEDDDSDEETFSDDEEMTTSSSSYAASVRPGIVHRLDKGTTG 740

Query: 142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIP 201
           LLVVAKDEHSHAHL+EQFKLHTIERVY            GRIE+PI RD +NRIRMAAIP
Sbjct: 741 LLVVAKDEHSHAHLAEQFKLHTIERVY------------GRIEIPIGRDSSNRIRMAAIP 788

Query: 202 GSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           G    G+ARHAASRYKVIE  AGGGSALVEWRLETGRTHQ
Sbjct: 789 GGLSGGRARHAASRYKVIETFAGGGSALVEWRLETGRTHQ 828

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242097088|ref|XP_002439034.1| hypothetical protein SORBIDRAFT_10g030300 [Sorghum bicolor] gi|241917257|gb|EER90401.1| hypothetical protein SORBIDRAFT_10g030300 [Sorghum bicolor]

 Score =  325 bits (833), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 166/230 (72%), Positives = 181/230 (78%), Gaps = 14/230 (6%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSH VKGGD+V+CT+SELQPLRAEAEDIPLDIVYEDD+VLVVNKPAHMVVHPAPGNA GT
Sbjct: 112 VSHTVKGGDLVSCTVSELQPLRAEAEDIPLDIVYEDDHVLVVNKPAHMVVHPAPGNANGT 171

Query: 85  LVNGILHHCSLPTLASSNQEAFSD-AEDISDD------------EEFSSSISGASIRPGI 131
           LVN ILHHC + T     + +  D   D SDD            E+ SS +  A +RPGI
Sbjct: 172 LVNAILHHCKISTFTCLARSSTGDECLDSSDDDIDVFNVDQFATEDASSEVRNALVRPGI 231

Query: 132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDP 191
           VHRLDKGTSGLLVVAKDEHSHA L+EQFKLHTI RVYISLT GVP+ +SGRIE  I+RDP
Sbjct: 232 VHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRRVYISLTCGVPNPNSGRIEASIARDP 291

Query: 192 NNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           NNRIRM AI GS  H  ARHAASRYKV E+  GGGSALVEWRLETGRTHQ
Sbjct: 292 NNRIRMIAIAGSG-HRYARHAASRYKVREVFVGGGSALVEWRLETGRTHQ 340

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413943106|gb|AFW75755.1| hypothetical protein ZEAMMB73_425131 [Zea mays]

 Score =  323 bits (829), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 165/230 (71%), Positives = 181/230 (78%), Gaps = 14/230 (6%)

Query: 25  VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGT 84
           VSH VKGGD+V+CT+SELQPLRAEAEDIPLDIVYEDD+VLVVNKPAHMVVHPAPGNA GT
Sbjct: 109 VSHTVKGGDLVSCTVSELQPLRAEAEDIPLDIVYEDDHVLVVNKPAHMVVHPAPGNAKGT 168

Query: 85  LVNGILHHCSLPTLA----SSNQEAFSDAEDISDD---------EEFSSSISGASIRPGI 131
           LVN ILHHC + T      SS  +   D+ D   D         E+ SS +  A +RPGI
Sbjct: 169 LVNAILHHCKISTFTCLARSSAGDECPDSTDEDTDVFHVDQFAAEDVSSEVRNALVRPGI 228

Query: 132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDP 191
           VHRLDKGTSGLLVVAKDEHSHA L+EQFKLHTI RVYISLT G P+ +SGRIE  I+RDP
Sbjct: 229 VHRLDKGTSGLLVVAKDEHSHARLAEQFKLHTIRRVYISLTCGAPNPNSGRIEASIARDP 288

Query: 192 NNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           NNRIRM AI GS  H  AR+AASRYKV E+ AGGGSALVEWRLETGRTHQ
Sbjct: 289 NNRIRMTAIAGSG-HRYARNAASRYKVREVFAGGGSALVEWRLETGRTHQ 337

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	241
TAIR|locus:2204355	430	AT1G76050 [Arabidopsis thalian	0.912	0.511	0.743	2.7e-84
TIGR_CMR|GSU_0082	322	GSU_0082 "ribosomal large subu	0.460	0.344	0.491	3.2e-41
TIGR_CMR|CHY_1505	305	CHY_1505 "ribosomal large subu	0.460	0.363	0.449	6.4e-37
TIGR_CMR|DET_1375	300	DET_1375 "ribosomal large subu	0.443	0.356	0.486	1.3e-36
TIGR_CMR|SPO_1408	342	SPO_1408 "ribosomal large subu	0.485	0.342	0.427	1.3e-32
UNIPROTKB|Q4K5V9	320	rluD "Pseudouridine synthase"	0.435	0.328	0.403	3.9e-31
TIGR_CMR|CPS_3915	324	CPS_3915 "ribosomal large subu	0.257	0.191	0.532	2.4e-28
UNIPROTKB|P33643	326	rluD "23S rRNA pseudouridine s	0.265	0.196	0.468	2.8e-28
UNIPROTKB|Q9KU20	324	rluD "Ribosomal large subunit	0.269	0.200	0.477	1.7e-25
TIGR_CMR|VC_0709	324	VC_0709 "ribosomal large subun	0.269	0.200	0.477	1.7e-25

TAIR|locus:2204355 AT1G76050 [Arabidopsis thaliana (taxid:3702)]

 Score = 844 (302.2 bits), Expect = 2.7e-84, P = 2.7e-84
 Identities = 168/226 (74%), Positives = 181/226 (80%)

Query:    20 MDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPG 79
             +DK  VSHNVK GD VNCTISELQPL+AEAEDIPLDIVYED +VLVVNKPAHMVVHPAPG
Sbjct:   116 VDK--VSHNVKSGDEVNCTISELQPLKAEAEDIPLDIVYEDKHVLVVNKPAHMVVHPAPG 173

Query:    80 NATGTLVNGILHHCSLPTLASSNQXXXXXXXXXXXXX----XXXXXXXGASIRPGIVHRL 135
             N TGTLVNGILHHCSLP +  SN                          AS+RPGIVHRL
Sbjct:   174 NPTGTLVNGILHHCSLPCVDYSNSEEDDDSDEETFSDDEEMTTSPSSYAASVRPGIVHRL 233

Query:   136 DKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRI 195
             DKGT+GLLVVAKDEHSHAHL+EQFKLHTIERVY+SLT+GVPS   GRIE+PI RD +NRI
Sbjct:   234 DKGTTGLLVVAKDEHSHAHLAEQFKLHTIERVYVSLTTGVPSPPQGRIEIPIGRDSSNRI 293

Query:   196 RMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
             RMAAIPG  + G+ARHAASRYKVIE  AGGGSALVEWRLETGRTHQ
Sbjct:   294 RMAAIPGGVRGGRARHAASRYKVIETFAGGGSALVEWRLETGRTHQ 339

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0009451 "RNA modification" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0009982 "pseudouridine synthase activity" evidence=IEA;ISS;TAS

TIGR_CMR|GSU_0082 GSU_0082 "ribosomal large subunit pseudouridine synthase D" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 272 (100.8 bits), Expect = 3.2e-41, Sum P(2) = 3.2e-41
 Identities = 58/118 (49%), Positives = 77/118 (65%)

Query:   124 GASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRI 183
             G  IRPGIVHR+DK TSG+LVVAK + +H  LS QF  HT++RVY++L  G P +  GRI
Sbjct:   130 GGEIRPGIVHRIDKDTSGVLVVAKSDRAHESLSRQFHDHTVKRVYLALVYGSPREDKGRI 189

Query:   184 EVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
             E  I R P +R +M+   G+ +HG  +HA + ++V     G    L+  RLETGRTHQ
Sbjct:   190 EGAIGRHPTDRKKMS---GAARHG--KHAVTHWRVAARFTG--VTLLRLRLETGRTHQ 240

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|CHY_1505 CHY_1505 "ribosomal large subunit pseudouridine synthase, RluA family" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 219 (82.2 bits), Expect = 6.4e-37, Sum P(2) = 6.4e-37
 Identities = 53/118 (44%), Positives = 71/118 (60%)

Query:   124 GASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRI 183
             G  +RPGIVHRLDK TSGLLVVAK++ +H  L+EQ K     R Y ++  G      G I
Sbjct:   128 GGVLRPGIVHRLDKDTSGLLVVAKNDLAHQSLAEQIKEKKAVREYWTIVHGYLKNKEGII 187

Query:   184 EVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
             ++PI R P +R +MA +  SN     + A + YKV+E     G  L++ +L TGRTHQ
Sbjct:   188 DLPIGRHPRDRQKMAVV--SN----GKTAQTVYKVLEEF-NKGFTLIQAKLLTGRTHQ 238

GO:0001522 "pseudouridine synthesis" evidence=ISS

GO:0009451 "RNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|DET_1375 DET_1375 "ribosomal large subunit pseudouridine synthase, RluA family" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 249 (92.7 bits), Expect = 1.3e-36, Sum P(2) = 1.3e-36
 Identities = 56/115 (48%), Positives = 76/115 (66%)

Query:   127 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVP 186
             +RPGIVHRLDK TSGLL+VAK+  + A+LS QFK  T+ + Y++L  G    + G IE P
Sbjct:   127 LRPGIVHRLDKDTSGLLLVAKNREALANLSAQFKERTVRKYYLTLVQGELHPAEGFIEAP 186

Query:   187 ISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
             + RDP NR ++A +  SN     R A + YKV+  + G   +L+E +LETGRTHQ
Sbjct:   187 LGRDPQNRQKIAVV--SN----GRPARTGYKVLRYIQG--YSLLEVKLETGRTHQ 233

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|SPO_1408 SPO_1408 "ribosomal large subunit pseudouridine synthase D" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 206 (77.6 bits), Expect = 1.3e-32, Sum P(2) = 1.3e-32
 Identities = 56/131 (42%), Positives = 74/131 (56%)

Query:   124 GASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRI 183
             G   RPGIVHR+DK TSGLLVVAK + +H  L+ QF  H+ ER Y +L  GVP  S  R+
Sbjct:   132 GGVKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAAQFAAHSAERHYTALCYGVPDGSDPRL 191

Query:   184 E-VP-ISRDPNNRIRMAAI----PGSNK------HGQARHAASRYKVIEILAGGGS-ALV 230
               V   S +P N +R+       P   +      HG  RHA +R +V+E      + +L+
Sbjct:   192 RGVKGASFEPGNILRLTTQLTRHPTDRQRQAVVFHG-GRHAVTRARVVESFGQPAAVSLI 250

Query:   231 EWRLETGRTHQ 241
             +  LETGRTHQ
Sbjct:   251 DCWLETGRTHQ 261

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

UNIPROTKB|Q4K5V9 rluD "Pseudouridine synthase" [Pseudomonas protegens Pf-5 (taxid:220664)]

 Score = 183 (69.5 bits), Expect = 3.9e-31, Sum P(2) = 3.9e-31
 Identities = 46/114 (40%), Positives = 62/114 (54%)

Query:   128 RPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPI 187
             R GIVHRLDK T+GL+VVAK   +   L  Q +  ++ R+Y  +  GV + + G+I  PI
Sbjct:   130 RAGIVHRLDKDTTGLMVVAKTIQAQTQLVAQLQSRSVSRIYECIVIGVVT-AGGKINAPI 188

Query:   188 SRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
              R    R RMA + G       + A S Y+V+E         V  +LETGRTHQ
Sbjct:   189 GRHGQQRQRMAVMEGG------KQAVSHYRVLERFRSHTHVRV--KLETGRTHQ 234

GO:0006364 "rRNA processing" evidence=ISS

TIGR_CMR|CPS_3915 CPS_3915 "ribosomal large subunit pseudouridine synthase D" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 182 (69.1 bits), Expect = 2.4e-28, Sum P(2) = 2.4e-28
 Identities = 33/62 (53%), Positives = 45/62 (72%)

Query:    31 GGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGIL 90
             GG+ ++        +R EA++IPL+IVYEDD +LV+NKPA +VVHP  GN  GTL+N +L
Sbjct:    61 GGEEIDINAKVEAEIRFEAQNIPLNIVYEDDYILVINKPAGLVVHPGAGNPDGTLLNALL 120

Query:    91 HH 92
             HH
Sbjct:   121 HH 122

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

UNIPROTKB|P33643 rluD "23S rRNA pseudouridine synthase" [Escherichia coli K-12 (taxid:83333)]

 Score = 171 (65.3 bits), Expect = 2.8e-28, Sum P(2) = 2.8e-28
 Identities = 30/64 (46%), Positives = 44/64 (68%)

Query:    29 VKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNG 88
             V GG+ V       +  R E +DIPLDIVYED++++++NKP  +VVHP  GN  GT++N 
Sbjct:    59 VLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNA 118

Query:    89 ILHH 92
             +LH+
Sbjct:   119 LLHY 122

GO:0000455 "enzyme-directed rRNA pseudouridine synthesis" evidence=IMP

GO:0000027 "ribosomal large subunit assembly" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0003723 "RNA binding" evidence=IEA

GO:0009982 "pseudouridine synthase activity" evidence=IEA;IDA

UNIPROTKB|Q9KU20 rluD "Ribosomal large subunit pseudouridine synthase D" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 161 (61.7 bits), Expect = 1.7e-25, Sum P(2) = 1.7e-25
 Identities = 32/67 (47%), Positives = 47/67 (70%)

Query:    29 VKGGDMVNCTISELQP-LRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 87
             V GG+++    +EL+   R EA+D+PL+IVYEDD+++V+NKP   VVHP  G A  T++N
Sbjct:    59 VMGGEVITVQ-AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLN 117

Query:    88 GILHHCS 94
              +L H S
Sbjct:   118 ALLFHYS 124

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|VC_0709 VC_0709 "ribosomal large subunit pseudouridine synthase D" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 161 (61.7 bits), Expect = 1.7e-25, Sum P(2) = 1.7e-25
 Identities = 32/67 (47%), Positives = 47/67 (70%)

Query:    29 VKGGDMVNCTISELQP-LRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 87
             V GG+++    +EL+   R EA+D+PL+IVYEDD+++V+NKP   VVHP  G A  T++N
Sbjct:    59 VMGGEVITVQ-AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLN 117

Query:    88 GILHHCS 94
              +L H S
Sbjct:   118 ALLFHYS 124

GO:0000154 "rRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q3ECD0	PUS2_ARATH	5, ., 4, ., 9, 9, ., -	0.7918	0.9004	0.5046	yes	no
Q5Z8P2	PUS2_ORYSJ	5, ., 4, ., 9, 9, ., -	0.7086	0.8962	0.4853	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	5.4.99	0.691

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	241
COG0564	289	COG0564, RluA, Pseudouridylate synthases, 23S RNA-	8e-64
TIGR00005	299	TIGR00005, rluA_subfam, pseudouridine synthase, Rl	6e-56
cd02869	185	cd02869, PseudoU_synth_RluCD_like, Pseudouridine s	2e-47
PRK11180	325	PRK11180, rluD, 23S rRNA pseudouridine synthase D;	3e-42
pfam00849	149	pfam00849, PseudoU_synth_2, RNA pseudouridylate sy	1e-26
cd02557	213	cd02557, PseudoU_synth_ScRIB2, Pseudouridine synth	7e-19
cd02563	223	cd02563, PseudoU_synth_TruC, tRNA pseudouridine is	9e-16
PRK10158	219	PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine sy	2e-11
PRK11025	317	PRK11025, PRK11025, 23S rRNA pseudouridylate synth	5e-09
TIGR01621	217	TIGR01621, RluA-like, pseudouridine synthase Rlu f	5e-09
cd02550	154	cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine	1e-08
cd02558	246	cd02558, PSRA_1, Pseudouridine synthase, a subgrou	8e-06
PRK11112	257	PRK11112, PRK11112, tRNA pseudouridine synthase C;	1e-04
PRK11112	257	PRK11112, PRK11112, tRNA pseudouridine synthase C;	0.002

>gnl|CDD|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]

 Score =  200 bits (510), Expect = 8e-64
 Identities = 89/214 (41%), Positives = 118/214 (55%), Gaps = 35/214 (16%)

Query: 29  VKGGDMVNCTISEL-QPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 87
           +K GD+V   + E  +  +   EDIPLDI+YED+++LVVNKPA +VVHP  G+  GTLVN
Sbjct: 52  LKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVN 111

Query: 88  GILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAK 147
            +L HC                                  RPGIVHRLDK TSGLL+VAK
Sbjct: 112 ALLRHCQD-----------------------------GVERPGIVHRLDKDTSGLLLVAK 142

Query: 148 DEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHG 207
           +  +   LSEQFK   +++ Y++L  G   +  G I+ PI RDP NR +MA +      G
Sbjct: 143 NREAARELSEQFKQRKVKKTYLALVRGHLPEDEGTIDAPIGRDPKNRKKMAVVK----EG 198

Query: 208 QARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
             + A + Y+V+E   G    LVE + ETGRTHQ
Sbjct: 199 SGKPAITHYEVLER-FGDNYTLVELKPETGRTHQ 231

Length = 289

>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family

 Score =  180 bits (458), Expect = 6e-56
 Identities = 78/213 (36%), Positives = 112/213 (52%), Gaps = 33/213 (15%)

Query: 29  VKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNG 88
           VK GD +   + E +      +DIPLDI++ED++++V+NKP+ +VVHP  GN  GT++N 
Sbjct: 47  VKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNA 106

Query: 89  ILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKD 148
           +L HC                                  R GIVHRLD+ TSGL+VVAK 
Sbjct: 107 LLAHCPPIAGVE---------------------------RVGIVHRLDRDTSGLMVVAKT 139

Query: 149 EHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQ 208
             +   L  Q K  T+ + Y++L  G      G ++ P+ R PNNR  MA  P S    +
Sbjct: 140 PLALRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRVPNNRGLMAVHPSS----E 195

Query: 209 ARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
            + A + ++V+E    G ++LVE  LETGRTHQ
Sbjct: 196 GKPAVTHFRVLE--RFGNASLVECELETGRTHQ 226

In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine [Protein synthesis, tRNA and rRNA base modification]. Length = 299

>gnl|CDD|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase, RsuA/RluD family

 Score =  154 bits (391), Expect = 2e-47
 Identities = 69/179 (38%), Positives = 93/179 (51%), Gaps = 34/179 (18%)

Query: 63  VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSI 122
           +LVVNKPA + VHP PG+ TGTLVN +L    L                           
Sbjct: 1   LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLL--------------------------- 33

Query: 123 SGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGR 182
            G   RPG+VHRLDK TSGLL+VAK++ + A LS+QFK   +++ Y++L  G P +  G 
Sbjct: 34  LGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYLALVDGKPPEDEGT 93

Query: 183 IEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           I+ P+ R    +     +         + A + YKV+E    G   LVE +LETGRTHQ
Sbjct: 94  IDAPLGRKKRKKRARVVV-----SEDGKPAITHYKVLE--RFGNVTLVELQLETGRTHQ 145

This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. Length = 185

>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional

 Score =  145 bits (368), Expect = 3e-42
 Identities = 80/213 (37%), Positives = 108/213 (50%), Gaps = 36/213 (16%)

Query: 29  VKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNG 88
           V GG+ V       +  R E +DIPLDIVYEDD++LV+NKP  +VVHP  GN  GT++N 
Sbjct: 59  VLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNA 118

Query: 89  ILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKD 148
           +LH+   P +A           D+               R GIVHRLDK T+GL+VVAK 
Sbjct: 119 LLHYY--PPIA-----------DVP--------------RAGIVHRLDKDTTGLMVVAKT 151

Query: 149 EHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQ 208
             +   L E  +   I R Y ++  G  +   G ++ PISR P  R  MA       H  
Sbjct: 152 VPAQTRLVEALQKREITREYEAVAIGHMTA-GGTVDEPISRHPTKRTHMAV------HPM 204

Query: 209 ARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
            + A + Y+++E         +  RLETGRTHQ
Sbjct: 205 GKPAVTHYRIMEHFR--VHTRLRLRLETGRTHQ 235

Length = 325

>gnl|CDD|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase

 Score =  100 bits (250), Expect = 1e-26
 Identities = 48/179 (26%), Positives = 75/179 (41%), Gaps = 37/179 (20%)

Query: 63  VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSI 122
            +VVNKPA + VHP   +                        + +    +++  +F    
Sbjct: 1   YIVVNKPAGVPVHPTDPSD---------------------LLSLTALLLVAELGKF---- 35

Query: 123 SGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGR 182
                R   VHRLD+ TSGLL++AKD  +   L++ F    +E+ Y++L  G P +  G 
Sbjct: 36  -----RLYPVHRLDRNTSGLLLLAKDGEAANKLNKLFPERKVEKEYLALVDG-PEEEEGT 89

Query: 183 IEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
           I+ PI +D     R               A +  +V+   +    +LVE  L TGR HQ
Sbjct: 90  IKAPIKKDKAVGFRKKEELDGKL------AVTHLRVLRSGSKEKYSLVELELVTGRKHQ 142

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. Length = 149

>gnl|CDD|211331 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2

 Score = 81.5 bits (202), Expect = 7e-19
 Identities = 49/190 (25%), Positives = 84/190 (44%), Gaps = 38/190 (20%)

Query: 53  PLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDI 112
           P+ IV+EDD++LVV+KP+ + VHP  G      V  IL                      
Sbjct: 15  PIKIVHEDDDLLVVDKPSGIPVHPT-GRYRYNTVTEILKS-------------------- 53

Query: 113 SDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLT 172
               E+  +     +RP   HRLD+ TSGLL+ AK   + + L +Q +   +++ Y++  
Sbjct: 54  ----EYGLT----ELRP--CHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARV 103

Query: 173 SGVPSQSSGRIEVPI-SRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVE 231
            G        ++ PI    P   +R      ++   + + A + +K +       +++V 
Sbjct: 104 KGEFPDGEVVVDQPIGLVSPKGGLR------NDVDEKGKDARTIFKRLSYNGDLNTSVVL 157

Query: 232 WRLETGRTHQ 241
            +  TGRTHQ
Sbjct: 158 CKPITGRTHQ 167

Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs. Length = 213

>gnl|CDD|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C

 Score = 73.1 bits (180), Expect = 9e-16
 Identities = 46/199 (23%), Positives = 77/199 (38%), Gaps = 48/199 (24%)

Query: 54  LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDIS 113
           L+I+Y+D++++ +NKP+ ++VH +                                  + 
Sbjct: 1   LEILYQDEHLVAINKPSGLLVHRSE---------------------------------LD 27

Query: 114 DDEEF-----SSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVY 168
             E            G  + P  VHRLD+ TSG+L+ A        L EQF  H + + Y
Sbjct: 28  RHETRFALQTLRDQLGQHVYP--VHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTY 85

Query: 169 ISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGS- 227
           +++  G   + SG I+ P+S +  +++             A        V E+    G  
Sbjct: 86  LAVVRGYVPE-SGTIDYPLSEEL-DKLADKFASDDKAPQAATTHYRLLAVEELPVVVGKY 143

Query: 228 -----ALVEWRLETGRTHQ 241
                +LVE    TGR HQ
Sbjct: 144 PTSRYSLVELTPHTGRKHQ 162

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. Length = 223

>gnl|CDD|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A; Provisional

 Score = 61.2 bits (148), Expect = 2e-11
 Identities = 54/188 (28%), Positives = 87/188 (46%), Gaps = 38/188 (20%)

Query: 54  LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDIS 113
           L I+Y+D++++VVNKP+ ++  P      G L     H  S+ T     Q  +  AE   
Sbjct: 14  LVILYQDEHIMVVNKPSGLLSVP------GRLEE---HKDSVMTRI---QRDYPQAES-- 59

Query: 114 DDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173
                             VHRLD  TSG++VVA  + +   L  QF+    ++ Y++   
Sbjct: 60  ------------------VHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVW 101

Query: 174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWR 233
           G PS + G +++P+  D  NR +      + K  Q     + Y+V+E  A   +A V  +
Sbjct: 102 GHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQ-----TEYEVVE-YAADNTARVVLK 155

Query: 234 LETGRTHQ 241
             TGR+HQ
Sbjct: 156 PITGRSHQ 163

Length = 219

>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C; Provisional

 Score = 55.1 bits (133), Expect = 5e-09
 Identities = 56/219 (25%), Positives = 91/219 (41%), Gaps = 66/219 (30%)

Query: 44  PLR-AEAEDIPLD------------IVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGIL 90
           P+R AE E+  +             I+YEDD++LV+NKP+   VH   G + G +     
Sbjct: 70  PVRVAEREEEAVSPKLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVI----- 124

Query: 91  HHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPG-----IVHRLDKGTSGLLVV 145
                        E                     ++RP      +VHRLD+ TSG+L+V
Sbjct: 125 -------------EGLR------------------ALRPEARFLELVHRLDRDTSGVLLV 153

Query: 146 AKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRD---PNNRIRMAAIPG 202
           AK   +   L EQ +   +++ Y++L  G        ++ P+ ++      RI   +   
Sbjct: 154 AKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRVS--- 210

Query: 203 SNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
                + + + +R+KV E  A   + LV     TGRTHQ
Sbjct: 211 ----QEGKPSETRFKVEERYA--FATLVRASPVTGRTHQ 243

Length = 317

>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein, TIGR01621

 Score = 54.5 bits (131), Expect = 5e-09
 Identities = 23/53 (43%), Positives = 35/53 (66%)

Query: 131 IVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRI 183
           +VHRLDK TSG+L++A +  S + LS+ F    IE+ Y++L+S  P +  G I
Sbjct: 46  LVHRLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLI 98

This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity [Protein synthesis, tRNA and rRNA base modification]. Length = 217

>gnl|CDD|211325 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine synthase, Rsu/Rlu family

 Score = 52.4 bits (126), Expect = 1e-08
 Identities = 42/183 (22%), Positives = 62/183 (33%), Gaps = 53/183 (28%)

Query: 63  VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSI 122
           +LV+NKP+ +V HP   +   T+V  +                                 
Sbjct: 1   ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGP--------------------------- 33

Query: 123 SGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGR 182
                R     RLDK TSGLL++  D      L+E      IE+ Y              
Sbjct: 34  -----RVHAAGRLDKDTSGLLLLTNDGRLQRRLTEP--RREIEKEY-------------L 73

Query: 183 IEVPISRDPNNRIRMAAIPGSNKHG----QARHAASRYKVIEILAGGGSALVEWRLETGR 238
           + V    D      +A +      G        A ++ +VI     GG+  +   L+TGR
Sbjct: 74  VTVRGELDEEGIEDLATVRRGRLSGLVDEGVPLAVTKVRVIG--EHGGTGRLRLTLKTGR 131

Query: 239 THQ 241
           THQ
Sbjct: 132 THQ 134

This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. Length = 154

>gnl|CDD|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA family

 Score = 45.3 bits (108), Expect = 8e-06
 Identities = 44/200 (22%), Positives = 76/200 (38%), Gaps = 57/200 (28%)

Query: 52  IPLD--IVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDA 109
           IP +  I+++D+++LV +KP  + V P     T TL+  +      P L           
Sbjct: 35  IPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGNPDLTP--------- 85

Query: 110 EDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYI 169
                                  HRLD+ T+GL++ +K   +       F    + + Y 
Sbjct: 86  ----------------------AHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYE 123

Query: 170 SLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQAR------HAASRYKVIEILA 223
           ++   VP+ +             +RI    + G     QAR      +A +R +++    
Sbjct: 124 AVAPYVPALTFPLTVR-------SRI----VKG-RGFFQAREVEGEPNAETRIELLARRG 171

Query: 224 GGGSALVEWRLE--TGRTHQ 241
           G G     +RL   TG+THQ
Sbjct: 172 GWG----LYRLSPHTGKTHQ 187

This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA. Length = 246

>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 34/126 (26%), Positives = 54/126 (42%), Gaps = 28/126 (22%)

Query: 132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISR-- 189
            HRLD+ TSG+L++A        L++QF+ H I++ Y ++  G        ++ P+    
Sbjct: 50  AHRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRGW-LMEEAVLDYPLKEEL 108

Query: 190 ----DPNNRIRMAAIPG-SNKHGQA---------RHAASRYKVIEILAGGGSALVEWRLE 235
               D   R   A  P  ++  G A         R+  +RY           +LVE   +
Sbjct: 109 DKIADKFAREDKAPQPAVTHYRGLATVEMPVATGRYPTTRY-----------SLVELEPK 157

Query: 236 TGRTHQ 241
           TGR HQ
Sbjct: 158 TGRKHQ 163

Length = 257

>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional

 Score = 38.1 bits (89), Expect = 0.002
 Identities = 11/22 (50%), Positives = 18/22 (81%)

Query: 54 LDIVYEDDNVLVVNKPAHMVVH 75
          L+I+Y+D+ ++ VNKPA  +VH
Sbjct: 2  LEILYQDEWLVAVNKPAGWLVH 23

Length = 257

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	241
COG0564	289	RluA Pseudouridylate synthases, 23S RNA-specific [	100.0
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	100.0
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	100.0
TIGR00005	299	rluA_subfam pseudouridine synthase, RluA family. m	100.0
cd02558	246	PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup	100.0
PRK10158	219	23S rRNA/tRNA pseudouridine synthase A; Provisiona	100.0
cd02557	213	PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps	100.0
cd02563	223	PseudoU_synth_TruC tRNA pseudouridine isomerase C:	100.0
TIGR01621	217	RluA-like pseudouridine synthase Rlu family protei	100.0
PRK11112	257	tRNA pseudouridine synthase C; Provisional	100.0
KOG1919	371	consensus RNA pseudouridylate synthases [RNA proce	100.0
PF00849	164	PseudoU_synth_2: RNA pseudouridylate synthase This	99.98
cd02550	154	PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu:	99.97
cd02869	185	PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD:	99.97
PRK10839	232	16S rRNA pseudouridylate synthase A; Provisional	99.97
cd02870	146	PseudoU_synth_RsuA_like Pseudouridine synthases ar	99.95
cd02556	167	PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi	99.95
PRK10700	289	23S rRNA pseudouridylate synthase B; Provisional	99.93
cd02553	167	PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi	99.93
cd02566	168	PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi	99.92
PRK10475	290	23S rRNA pseudouridine synthase F; Provisional	99.92
cd02555	177	PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup	99.87
PRK11394	217	23S rRNA pseudouridine synthase E; Provisional	99.86
COG1187	248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	99.84
cd02554	164	PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo	99.81
TIGR00093	128	pseudouridine synthase. This model identifies pane	99.79
cd02868	226	PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li	99.27
cd02572	182	PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li	98.02
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	97.79
PRK00989	230	truB tRNA pseudouridine synthase B; Provisional	97.77
cd00506	210	PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo	97.76
PRK04099	273	truB tRNA pseudouridine synthase B; Provisional	97.74
TIGR00431	209	TruB tRNA pseudouridine 55 synthase. TruB, the tRN	97.73
PRK00020	244	truB tRNA pseudouridine synthase B; Provisional	97.68
PRK02484	294	truB tRNA pseudouridine synthase B; Provisional	97.6
PRK14124	308	tRNA pseudouridine synthase B; Provisional	97.57
PRK14123	305	tRNA pseudouridine synthase B; Provisional	97.55
PRK03287	298	truB tRNA pseudouridine synthase B; Provisional	97.53
PRK02193	279	truB tRNA pseudouridine synthase B; Provisional	97.53
PRK00130	290	truB tRNA pseudouridine synthase B; Provisional	97.53
PRK14846	345	truB tRNA pseudouridine synthase B; Provisional	97.5
cd02573	277	PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou	97.5
PRK05389	305	truB tRNA pseudouridine synthase B; Provisional	97.5
PRK02755	295	truB tRNA pseudouridine synthase B; Provisional	97.49
PRK04270	300	H/ACA RNA-protein complex component Cbf5p; Reviewe	97.47
PRK01528	292	truB tRNA pseudouridine synthase B; Provisional	97.46
PRK05033	312	truB tRNA pseudouridine synthase B; Provisional	97.45
PRK01851	303	truB tRNA pseudouridine synthase B; Provisional	97.44
PRK01550	304	truB tRNA pseudouridine synthase B; Provisional	97.43
PRK14122	312	tRNA pseudouridine synthase B; Provisional	97.28
TIGR00425	322	CBF5 rRNA pseudouridine synthase, putative. This f	97.24
PRK04642	300	truB tRNA pseudouridine synthase B; Provisional	97.21
COG0130	271	TruB Pseudouridine synthase [Translation, ribosoma	96.97
cd02867	312	PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou	96.82
cd01291	87	PseudoU_synth PseudoU_synth: Pseudouridine synthas	94.17
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	93.87
PF14451	81	Ub-Mut7C: Mut7-C ubiquitin	93.47
COG1188	100	Ribosome-associated heat shock protein implicated	93.34
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	92.59
KOG2559	318	consensus Predicted pseudouridine synthase [Transl	92.03
PRK01777	95	hypothetical protein; Validated	91.28
smart00363	60	S4 S4 RNA-binding domain.	91.06
PF01509	149	TruB_N: TruB family pseudouridylate synthase (N te	89.31
PRK06437	67	hypothetical protein; Provisional	86.95
COG0522	205	RpsD Ribosomal protein S4 and related proteins [Tr	86.22
cd00754	80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	82.8
PRK10348	133	ribosome-associated heat shock protein Hsp15; Prov	82.36
PRK11507	70	ribosome-associated protein; Provisional	81.63
cd00565	65	ThiS ThiaminS ubiquitin-like sulfur carrier protei	81.11
PRK08364	70	sulfur carrier protein ThiS; Provisional	81.02
TIGR01682	80	moaD molybdopterin converting factor, subunit 1, n	80.33

>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.5e-46  Score=328.95  Aligned_cols=193  Identities=47%  Similarity=0.747  Sum_probs=169.7

Q ss_pred             eEEecCeecCCCceecCCCEEEEEecCCCC-ccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhc
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCTISELQP-LRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC   93 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~~~~~~~-~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~   93 (241)
                      +|.|||++++++++|..||+|.+...+... ....+++.+++|||||++++|||||+||+|||++++..+|+++.++.++
T Consensus        38 ~v~vNg~~v~~~~~l~~gd~i~~~~~~~~~~~~~~~~~~~l~IlyED~~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~  117 (289)
T COG0564          38 RVRVNGKKVKPSYKLKPGDVVRIPLPEEPEEEKLVPEDIPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNALLRHC  117 (289)
T ss_pred             CEEECCEEccCCeeeCCCCEEEEecccccccccccccCCCccEEEecCCEEEEECCCCCcCcCCCCCccHhHHHHHHHhc
Confidence            699999999999999999999998866332 3334455568899999999999999999999998888899999999886


Q ss_pred             CCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204           94 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      ...                             ..++++|||||++||||||+|||..+++.|+++|+.+.+.|+|+|+|.
T Consensus       118 ~~~-----------------------------~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~~r~v~K~Y~Alv~  168 (289)
T COG0564         118 QDG-----------------------------VERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVR  168 (289)
T ss_pred             ccc-----------------------------CCceeeeccCCCCCceEEEEECCHHHHHHHHHHHhcCcCcEEEEEEEE
Confidence            310                             367899999999999999999999999999999999999999999999


Q ss_pred             cccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       174 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      |.++.+.+.|+.||.++...+..+.+...    ..++.|.|+|++++++.. .+||++|+|+||||||
T Consensus       169 G~~~~~~~~i~~pi~r~~~~~~~~~v~~~----~~gk~A~T~~~~l~~~~~-~~tlv~~~~~TGRTHQ  231 (289)
T COG0564         169 GHLPEDEGTIDAPIGRDPKNRKKMAVVKE----GSGKPAITHYEVLERFGD-NYTLVELKPETGRTHQ  231 (289)
T ss_pred             CcccCCCCEEeeeeecCCcCCceEEEecc----CCCCceEEEEEehhccCC-ceEEEEEEeCCCCHhH
Confidence            99999999999999999888777777653    138999999999999632 2799999999999999

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=100.00  E-value=4.4e-40  Score=293.52  Aligned_cols=191  Identities=40%  Similarity=0.651  Sum_probs=157.4

Q ss_pred             eEEecCeec-CCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhc
Q 026204           15 ALFLSMDKL-SVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC   93 (241)
Q Consensus        15 ~v~vng~~~-~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~   93 (241)
                      .|.|||+++ ++++.|.+||.|.+...........+...+++|||||++++|+|||+||+|||+.+....|+.+.+..++
T Consensus        44 ~V~VNg~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~iiyed~~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~  123 (325)
T PRK11180         44 RVLVNGKVINKPKEKVLGGEQVAIDAEIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYY  123 (325)
T ss_pred             CEEECCEEccCCCcCcCCCCEEEEeeccccccCCCCCCCCCcEEEECCCEEEEECCCCCeEeCCCCCCCCcHHHHHHHHh
Confidence            489999987 5899999999999986543222222344568999999999999999999999988777779999888765


Q ss_pred             CCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204           94 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      ...                           ....++++|||||++||||||||||..++..|+++|+.+.++|+|+|+|.
T Consensus       124 ~~~---------------------------~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y~A~v~  176 (325)
T PRK11180        124 PPI---------------------------ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREYEAVAI  176 (325)
T ss_pred             hhc---------------------------cCCcccceeccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEEEEEEe
Confidence            210                           11245789999999999999999999999999999999999999999999


Q ss_pred             cccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       174 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      |.++ ..+.|+.||.+.......+....      .++.|.|+|+++...  .++||++|+|+||||||
T Consensus       177 G~~~-~~~~i~~~l~~~~~~~~~~~~~~------~gk~a~T~~~~l~~~--~~~slv~~~~~TGRtHQ  235 (325)
T PRK11180        177 GHMT-AGGTVDEPISRHPTKRTHMAVHP------MGKPAVTHYRIMEHF--RVHTRLRLRLETGRTHQ  235 (325)
T ss_pred             cCCC-CCCEEECceecCCCcCcEEEeCC------CCcEEeEEEEEeEEc--CCeEEEEEEeCCCCHHH
Confidence            9986 46899999987654444443333      678999999999874  57899999999999999

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=100.00  E-value=2.8e-40  Score=293.80  Aligned_cols=190  Identities=26%  Similarity=0.357  Sum_probs=150.2

Q ss_pred             eEEecCeecCCCceecCCCEEEEEecCCCCccCC--------CCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHH
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAE--------AEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLV   86 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~~~~~~~~~~~--------~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~   86 (241)
                      .|.|||+++++++.|+.||.|.+...........        ....+++|||||++++|||||+|++|||+.+.. .++.
T Consensus        46 ~V~VNg~~v~~~~~v~~GD~I~i~~~~~~~~~~~p~~~~~~~~~~~~~~Ilyed~~~lvvnKP~gl~~~~~~~~~-~~~~  124 (317)
T PRK11025         46 EVRVNKKRIKPEYKLEAGDEVRIPPVRVAEREEEAVSPKLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLS-FGVI  124 (317)
T ss_pred             CEEECCEEcCcccccCCCCEEEeCCCCccccccccccccccccccCcCCEEEECCCEEEEECCCCCcCcCCCCCC-ccHH
Confidence            4899999999999999999999864221110000        112457899999999999999999999986554 3566


Q ss_pred             HHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeE
Q 026204           87 NGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIER  166 (241)
Q Consensus        87 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K  166 (241)
                      +.+.....                              ....+++|||||++||||||||||+.+++.|+++|+.+.++|
T Consensus       125 ~~~~~~~~------------------------------~~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~v~K  174 (317)
T PRK11025        125 EGLRALRP------------------------------EARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQK  174 (317)
T ss_pred             HHHHHhcc------------------------------CCCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCCccE
Confidence            66554311                              113367899999999999999999999999999999999999


Q ss_pred             EEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          167 VYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       167 ~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      +|+|+|.|.++...++|+.||.++........+..    ...|+.|.|+|++++..  .++||++|+|+||||||
T Consensus       175 ~Y~a~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~----~~~gk~a~T~~~~l~~~--~~~sLv~~~~~TGRtHQ  243 (317)
T PRK11025        175 DYLALVRGQWQSHVKVVQAPLLKNILQSGERIVRV----SQEGKPSETRFKVEERY--AFATLVRASPVTGRTHQ  243 (317)
T ss_pred             EEEEEEeCcccCCCceEecccccCcccCCceEEec----CCCCccceEEEEEeEEc--CCcEEEEEEeCCCCHHH
Confidence            99999999998888999999987753322222211    12689999999999984  57899999999999999

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family

Probab=100.00  E-value=7.3e-40  Score=289.04  Aligned_cols=194  Identities=40%  Similarity=0.658  Sum_probs=159.0

Q ss_pred             eEEecCe-ecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhc
Q 026204           15 ALFLSMD-KLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC   93 (241)
Q Consensus        15 ~v~vng~-~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~   93 (241)
                      .|+|||+ ..++++.|++||.|.+...........+...+++|+|||++|+|+|||+|++||+..+...+|+.+.+..++
T Consensus        32 ~V~VNg~~~~~~~~~v~~gd~I~i~~~~~~~~~~~~~~~~~~i~~ed~~~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~  111 (299)
T TIGR00005        32 QVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEVPPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHC  111 (299)
T ss_pred             cEEECCEeccCcccCCCCCCEEEEecCCcccccCCccCCCccEEEeCCCEEEEECCCCCeEeCCCCCCcccHHHHHHHhc
Confidence            5899996 467999999999999976432222222333457899999999999999999999998777788999888765


Q ss_pred             CCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204           94 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      ...                           ....++++|||||++||||||||+|..+++.|+++|+++.+.|+|+|+|.
T Consensus       112 ~~~---------------------------~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~  164 (299)
T TIGR00005       112 PPI---------------------------AGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVH  164 (299)
T ss_pred             ccc---------------------------cCCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcceEEEEEEe
Confidence            310                           01245789999999999999999999999999999999999999999999


Q ss_pred             cccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       174 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      |.++.+.++|+.||.++..+...+.+...    .++++|.|+|+++..  ..++||++|+|+|||+||
T Consensus       165 g~~~~~~~~i~~~l~~~~~~~~~~~~~~~----~~~k~a~t~~~~l~~--~~~~slv~~~l~tGR~HQ  226 (299)
T TIGR00005       165 GQFDSGGGTVDAPLGRVPNNRGLMAVHPS----SEGKPAVTHFRVLER--FGNASLVECELETGRTHQ  226 (299)
T ss_pred             ccccCCCCEEeCceecCCCCCceEEEecC----CCCCeeeEEEEEeEE--cCCeEEEEEEeCCCChHH
Confidence            99988899999999886554444444331    258999999999987  357899999999999999

modifies uracil-65 in transfer RNAs to pseudouridine.

>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family

Probab=100.00  E-value=1.2e-39  Score=280.15  Aligned_cols=183  Identities=20%  Similarity=0.268  Sum_probs=147.6

Q ss_pred             EEecCeecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCC
Q 026204           16 LFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSL   95 (241)
Q Consensus        16 v~vng~~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~   95 (241)
                      +..||++++++++|+.||+|.++......   .+...+++|||||++|+|||||+|++|||+++...+|+.+.+...+. 
T Consensus         4 ~~~ng~~~~~~~~l~~gd~i~~~~~~~~~---~~~~~~~~Iiyed~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~-   79 (246)
T cd02558           4 VDADGEPLDPDSPYRPGTFVWYYRELPDE---PPIPFEETILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTG-   79 (246)
T ss_pred             ECCCCcCCCCCceecCCCEEEEeCCCCCC---CCCCCCcceEEecCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhC-
Confidence            34699999999999999999997532211   12223588999999999999999999999987777888888765532 


Q ss_pred             CccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecc
Q 026204           96 PTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGV  175 (241)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~  175 (241)
                                                    ...+++|||||++||||||||||+++++.|+.+|+.+.++|+|+|+|.|.
T Consensus        80 ------------------------------~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~YlA~v~G~  129 (246)
T cd02558          80 ------------------------------NPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARREVSKTYEAVAPYV  129 (246)
T ss_pred             ------------------------------CCcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcCCccEEEEEEEecC
Confidence                                          13467899999999999999999999999999999999999999999999


Q ss_pred             cCCCcc-EEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          176 PSQSSG-RIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       176 ~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      ++...+ .++.+|.++... ..+...      .+++.|.|+|++++..  .++|+++|+|+|||+||
T Consensus       130 ~~~~~~~~~~~~i~~~~~~-~~~~~~------~~~~~a~T~~~~l~~~--~~~slv~~~l~TGRtHQ  187 (246)
T cd02558         130 PALTFPLTVRSRIVKGRGF-FQAREV------EGEPNAETRIELLARR--GGWGLYRLSPHTGKTHQ  187 (246)
T ss_pred             CCCCCCcceeccccccCCc-ceeecc------CCCCCceEEEEEEEec--CCeEEEEEEeCCCCHHH
Confidence            864444 577777665432 122222      2567899999999873  57999999999999999

This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.

>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional

Probab=100.00  E-value=2.5e-36  Score=255.45  Aligned_cols=150  Identities=31%  Similarity=0.465  Sum_probs=126.4

Q ss_pred             CccEEEecCcEEEEECCCCceeecCCC-CCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccc
Q 026204           53 PLDIVYEDDNVLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI  131 (241)
Q Consensus        53 ~~~Ilyed~~llVinKPaGl~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (241)
                      .++|||||++++|+|||+|++||++.. ....++.+.+...+                                 ..+++
T Consensus        13 ~~~iiyed~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~---------------------------------~~~~~   59 (219)
T PRK10158         13 WLVILYQDEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY---------------------------------PQAES   59 (219)
T ss_pred             CCCEEEeCCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC---------------------------------CCCCE
Confidence            467999999999999999999998753 33456777665442                                 23678


Q ss_pred             cccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcc
Q 026204          132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH  211 (241)
Q Consensus       132 vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~  211 (241)
                      |||||++||||||+|+|.++++.|+++|+.+.+.|+|+|+|.|.++...++|+.||.++......+.+..     ++++.
T Consensus        60 vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~~v~K~Yla~v~G~~~~~~~~i~~~i~~~~~~~~~~~~~~-----~~gk~  134 (219)
T PRK10158         60 VHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCY-----ETGKP  134 (219)
T ss_pred             ECCCCCCCceEEEEECCHHHHHHHHHHHHhCCccEEEEEEEecccCCCCcEEecceecCCCCCceEEecC-----CCCce
Confidence            9999999999999999999999999999999999999999999998889999999987755544444432     26789


Q ss_pred             eEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          212 AASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       212 a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      |.|+|++++... .+.++++|+|+||||||
T Consensus       135 a~t~~~~l~~~~-~~~sll~~~~~TGRtHQ  163 (219)
T PRK10158        135 AQTEYEVVEYAA-DNTARVVLKPITGRSHQ  163 (219)
T ss_pred             eeEEEEEEEEcC-CCCEEEEEEeCCCCHHH
Confidence            999999998742 34589999999999999

>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like

Probab=100.00  E-value=3.3e-36  Score=253.71  Aligned_cols=153  Identities=27%  Similarity=0.377  Sum_probs=129.2

Q ss_pred             CccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCcccc
Q 026204           53 PLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIV  132 (241)
Q Consensus        53 ~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  132 (241)
                      +++|||||++++|+|||+|++|++++.....++.+.|...+.                               ...+++|
T Consensus        15 ~~~iiyed~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~-------------------------------~~~~~~v   63 (213)
T cd02557          15 PIKIVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYG-------------------------------LTELRPC   63 (213)
T ss_pred             CCcEEEECCCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcC-------------------------------CCCccCc
Confidence            578999999999999999999999876666788888876542                               1346789


Q ss_pred             ccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcce
Q 026204          133 HRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHA  212 (241)
Q Consensus       133 hRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a  212 (241)
                      ||||++||||||||+|++++++|+++|+++.++|+|+|+|.|.++.+.+.|+.||.++..........     ...++.|
T Consensus        64 hRLD~~TSGllllak~~~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~~~~~~~-----~~~~~~a  138 (213)
T cd02557          64 HRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGLVSPKGGLRNDV-----DEKGKDA  138 (213)
T ss_pred             cCCCCCCceEEEEECCHHHHHHHHHHHHcCCccEEEEEEEeCcCCCCCeEEecceeccCcCCceeecc-----CCCCcee
Confidence            99999999999999999999999999999999999999999999888999999998764322111111     1367899


Q ss_pred             EEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          213 ASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       213 ~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      .|+|+++......++||++|+|.|||+||
T Consensus       139 ~t~~~~~~~~~~~~~slv~v~~~TGR~HQ  167 (213)
T cd02557         139 RTIFKRLSYNGDLNTSVVLCKPITGRTHQ  167 (213)
T ss_pred             eEEEEEEEEcCCCCeEEEEEEeCCCCHHH
Confidence            99999999854348999999999999999

This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.

>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)

Probab=100.00  E-value=1.9e-35  Score=250.76  Aligned_cols=151  Identities=28%  Similarity=0.480  Sum_probs=120.0

Q ss_pred             ccEEEecCcEEEEECCCCceeecCCCCCCCC--HHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccc
Q 026204           54 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGT--LVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI  131 (241)
Q Consensus        54 ~~Ilyed~~llVinKPaGl~~~~~~~~~~~t--l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (241)
                      ++|||||++++|||||+|++|||.......+  +...+...+                                ...+++
T Consensus         1 ~~Ilyed~~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~   48 (223)
T cd02563           1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQL--------------------------------GQHVYP   48 (223)
T ss_pred             CcEEEecCCEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHc--------------------------------CCCccc
Confidence            3599999999999999999999976443333  222222221                                134678


Q ss_pred             cccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcc
Q 026204          132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH  211 (241)
Q Consensus       132 vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~  211 (241)
                      |||||++||||||||||+++++.|+++|+.+.++|+|+|+|.|.++. +++|+.||.++........+..    ...++.
T Consensus        49 vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~alv~G~~~~-~~~i~~~l~~~~~~~~~~~~~~----~~~~~~  123 (223)
T cd02563          49 VHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPE-SGTIDYPLSEELDKLADKFASD----DKAPQA  123 (223)
T ss_pred             ccCCCCCCeEEEEEEECHHHHHHHHHHHhcCceeEEEEEEEECccCC-CCeEEEeeeeCCCccceEEeec----CCCCce
Confidence            99999999999999999999999999999999999999999999875 7899999988765433333322    136789


Q ss_pred             eEEEEEEEEEe---------cCCCEEEEEEEcCCCCCCC
Q 026204          212 AASRYKVIEIL---------AGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       212 a~T~~~vl~~~---------~~~~~slv~~~l~TGR~HQ  241 (241)
                      |.|+|+++...         ...++||++|+|+||||||
T Consensus       124 a~t~~~~l~~~~~~~~~~~~~~~~~slv~~~~~TGR~HQ  162 (223)
T cd02563         124 ATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQ  162 (223)
T ss_pred             eEEEEEEeeecccccccccCCCCCeEEEEEEeCCCCHHH
Confidence            99999999752         1236899999999999999

No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.

>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621

Probab=100.00  E-value=1.5e-35  Score=250.31  Aligned_cols=146  Identities=28%  Similarity=0.433  Sum_probs=122.6

Q ss_pred             ccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccc
Q 026204           54 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVH  133 (241)
Q Consensus        54 ~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vh  133 (241)
                      ++|||||++++|||||+||+||++.+.  .++.+.+..+..                               ...+++||
T Consensus         2 ~~ilyed~~~lvvnKP~Gl~v~~~~~~--~~l~~~l~~~~~-------------------------------~~~~~~Vh   48 (217)
T TIGR01621         2 FEILFTHPDFLLINKHPGISVHKDDGE--TGLLQEVATQLG-------------------------------VGQVWLVH   48 (217)
T ss_pred             ceEEEeCCCEEEEECCCCCeECCCCCc--ChHHHHHHHhcC-------------------------------CCCccEec
Confidence            469999999999999999999987532  456666654321                               13578899


Q ss_pred             cCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceE
Q 026204          134 RLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAA  213 (241)
Q Consensus       134 RLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~  213 (241)
                      |||++||||||||+|+++++.|+++|+++.++|+|+|+|.|.++..+++|+.++.+...+...  +..     ..++.|.
T Consensus        49 RLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v~K~YlAlV~g~~~~~~~~i~~~~~~~~~~~~~--~~~-----~~~k~a~  121 (217)
T TIGR01621        49 RLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGDMEKSRRGSWK--LVN-----SQENPAI  121 (217)
T ss_pred             CCCCCCceEEEEEcCHHHHHHHHHHHhcCCccEEEEEEEeccccCCCCEEeCCcccCCCCCEE--EeC-----CCCCcee
Confidence            999999999999999999999999999999999999999999998999999999765443322  222     2568899


Q ss_pred             EEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          214 SRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       214 T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      |+|+++...  .++|+++|+|.||||||
T Consensus       122 t~~~~~~~~--~~~slv~~~~~TGR~HQ  147 (217)
T TIGR01621       122 TRFFSASAA--TGLRLFILKPHTGKTHQ  147 (217)
T ss_pred             EEEEEEEEc--CCeEEEEEEeCCCCHHH
Confidence            999999874  57999999999999999

This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.

>PRK11112 tRNA pseudouridine synthase C; Provisional

Probab=100.00  E-value=6e-35  Score=252.56  Aligned_cols=151  Identities=26%  Similarity=0.399  Sum_probs=118.8

Q ss_pred             ccEEEecCcEEEEECCCCceeecCCCCCCCCH--HHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccc
Q 026204           54 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL--VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGI  131 (241)
Q Consensus        54 ~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (241)
                      ++|||||++|+|||||+||+||+.......+.  ...+...+                                ...+++
T Consensus         2 l~IlyEd~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~   49 (257)
T PRK11112          2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQI--------------------------------GQHVFT   49 (257)
T ss_pred             CcEEEecCCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHh--------------------------------CCCcee
Confidence            46999999999999999999999754444332  22222221                                124678


Q ss_pred             cccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcc
Q 026204          132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH  211 (241)
Q Consensus       132 vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~  211 (241)
                      |||||++||||||||||+++++.|+++|+.+.++|+|+|+|.|.++ .+++|+.|+.++...........    ..++++
T Consensus        50 VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~Alv~G~~~-~~~~i~~~l~~~~~~~~~~~~~~----~~~~k~  124 (257)
T PRK11112         50 AHRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRGWLM-EEAVLDYPLKEELDKIADKFARE----DKAPQP  124 (257)
T ss_pred             eccCCCCCeeEEEEECCHHHHHHHHHHHHhCCcceEEEEEEEeEeC-CCCeEeeeeeecccccceeeccc----CCCCeE
Confidence            9999999999999999999999999999999999999999999885 56889999987643322222211    236899


Q ss_pred             eEEEEEEEEEec---------CCCEEEEEEEcCCCCCCC
Q 026204          212 AASRYKVIEILA---------GGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       212 a~T~~~vl~~~~---------~~~~slv~~~l~TGR~HQ  241 (241)
                      |.|+|+++....         +.++||++|+|.||||||
T Consensus       125 a~T~~~~l~~~~~~~~~~~~~~~~~slv~i~~~TGRtHQ  163 (257)
T PRK11112        125 AVTHYRGLATVEMPVATGRYPTTRYSLVELEPKTGRKHQ  163 (257)
T ss_pred             eEEEEEEEEEecccccccccCCCCeEEEEEEcCCCChHH
Confidence            999999998641         246899999999999999

>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]

Probab=100.00  E-value=5.7e-33  Score=248.25  Aligned_cols=204  Identities=31%  Similarity=0.434  Sum_probs=164.7

Q ss_pred             Ccceecccccee---------eeeEEecCeecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCC
Q 026204            1 MELVELEFNQVS---------VLALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAH   71 (241)
Q Consensus         1 ~~~~~~~~~~~~---------~~~v~vng~~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaG   71 (241)
                      +|++..||+.++         ...+.+||+.+..++.++.||.|.+..+...++.   ...++.|+|||++|+|||||+|
T Consensus        47 ~~~~~~ef~~~~~~~~~~~i~~g~v~~n~~~~~v~~i~k~~d~l~~~vhrh~p~~---~~~~~~Iv~ed~~~vVvnKP~g  123 (371)
T KOG1919|consen   47 VDVFVSEFRLRERAYYESAIKLGRVTVNGEQVRVSLIVKNGDVLCHTVHRHEPPV---AYLPIRIVFEDKDYVVVNKPHG  123 (371)
T ss_pred             HHHHHHHHhcCchHhhhhhhhcCceEECcEeeeeEEEeccCCEEEEeeccCCCCc---cccccceEEecCCEEEEeCCCC
Confidence            466777777776         3348999999999999999999999877654433   2247889999999999999999


Q ss_pred             ceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHH
Q 026204           72 MVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHS  151 (241)
Q Consensus        72 l~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~  151 (241)
                      ++|||.+....+++...+.....                               ...++++||||+.|||||+||+++.+
T Consensus       124 ipVhp~g~~~~n~i~~~l~~~~~-------------------------------~~~~~~~hRLDr~tSGllvlAkt~~~  172 (371)
T KOG1919|consen  124 IPVHPTGRYRENTITKILAALHK-------------------------------VEGLRPCHRLDRLTSGLLVLAKTKEA  172 (371)
T ss_pred             CceeccCccccccchHHHHHhcc-------------------------------ccccccccccCccccceEEEEechhH
Confidence            99999888888888777776421                               24467899999999999999999999


Q ss_pred             HHHHHHHhhcCeeeEEE-EEEEecccC-CCccEEEcceeeCCCCCeeEEEec-CCCCCCCCcceEEEEEEEEEecCCCEE
Q 026204          152 HAHLSEQFKLHTIERVY-ISLTSGVPS-QSSGRIEVPISRDPNNRIRMAAIP-GSNKHGQARHAASRYKVIEILAGGGSA  228 (241)
Q Consensus       152 ~~~L~~~f~~~~v~K~Y-~AlV~G~~~-~~~~~i~~~i~~~~~~~~~~~~~~-~~~~~~~~k~a~T~~~vl~~~~~~~~s  228 (241)
                      +..+++.|+++++.|.| +|-|.|.++ .+...|..++..... ..+|.+.. .+.+...++.|.|.|+++.++  ++.+
T Consensus       173 ~~~~~~~~r~~~~~k~Y~v~~v~g~fp~~~~~~i~~~~~~~~~-~~~~~l~~~~~~~~~~~k~a~T~~~~~~~~--~~ss  249 (371)
T KOG1919|consen  173 ADKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEER-PLRMGLNAVGVRDEVAAKDAKTLFKVLSYD--GGSS  249 (371)
T ss_pred             hHHHHHHHhcccceeEEEEEEEeccCCCCceEEeCCCcccccc-ccceEeeecccccccccccceeEEEEcccC--CceE
Confidence            99999999999999999 799999987 556677777765442 23333322 111223589999999999984  8999


Q ss_pred             EEEEEcCCCCCCC
Q 026204          229 LVEWRLETGRTHQ  241 (241)
Q Consensus       229 lv~~~l~TGR~HQ  241 (241)
                      +|+|+|+||||||
T Consensus       250 ~V~~~PlTGRtHQ  262 (371)
T KOG1919|consen  250 LVECRPLTGRTHQ  262 (371)
T ss_pred             EEEeeccCCcHHH
Confidence            9999999999999

>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family

Probab=99.98  E-value=1.4e-31  Score=215.91  Aligned_cols=148  Identities=37%  Similarity=0.554  Sum_probs=111.5

Q ss_pred             cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204           62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG  141 (241)
Q Consensus        62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG  141 (241)
                      +|+|||||+||+|++...................                           ......+++|||||++|||
T Consensus         1 ~~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~~v~RLD~~TsG   53 (164)
T PF00849_consen    1 NLIVVNKPAGVPVHPSDGNESKSVKELPALSLKR---------------------------GDDPPELYPVHRLDRDTSG   53 (164)
T ss_dssp             SEEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHH---------------------------CTTSGGGEESS---TT-EE
T ss_pred             CEEEEECCCCCeEecCCCCCcccccchhhhhhhh---------------------------ccCCCceEECCCCCccccC
Confidence            6899999999999998754443333333322210                           0234678999999999999


Q ss_pred             EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeC--CCCCeeEEEecCCCCCCCCcceEEEEEEE
Q 026204          142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRD--PNNRIRMAAIPGSNKHGQARHAASRYKVI  219 (241)
Q Consensus       142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~--~~~~~~~~~~~~~~~~~~~k~a~T~~~vl  219 (241)
                      |||||+|.++++.|+++|+.+.++|+|+|+|.|.+....+.++.++..+  ...........     .+++.+.|.|+++
T Consensus        54 lll~a~~~~~~~~l~~~f~~~~~~K~Y~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~t~~~~l  128 (164)
T PF00849_consen   54 LLLFAKDKEAAAKLSKQFPKRKVEKTYLALVEGGPVEEEGKINSPLGKDVGKNKSSNKDPPG-----RDGKPAITRYRVL  128 (164)
T ss_dssp             EEEEESSHHHHHHHHHHHHTTCSEEEEEEEECSSSSTTCEEEESHEEE-EECSSCTCCEEET-----TTSBTSEEEEEEE
T ss_pred             CeeccCCcccccccccccccCCCcEEEEEeEcccccccceeeeccccccccccccceeeeec-----ccccccceeeeee
Confidence            9999999999999999999999999999999988888899999999872  22222222222     3789999999999


Q ss_pred             EEe-------cCCCEEEEEEEcCCCCCCC
Q 026204          220 EIL-------AGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       220 ~~~-------~~~~~slv~~~l~TGR~HQ  241 (241)
                      ...       .+.++++++|+|.|||+||
T Consensus       129 ~~~~~~~~~~~~~~~s~v~~~l~tGr~HQ  157 (164)
T PF00849_consen  129 RSGSRTPSKDENAGCSLVECELITGRTHQ  157 (164)
T ss_dssp             EEETT---EECCSSEEEEEEEESS-STTH
T ss_pred             ccccccccccccCCCEEEEEEECcCCCHH
Confidence            986       5678999999999999999

This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....

>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family

Probab=99.97  E-value=4.1e-31  Score=212.02  Aligned_cols=134  Identities=31%  Similarity=0.438  Sum_probs=107.4

Q ss_pred             EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204           63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL  142 (241)
Q Consensus        63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl  142 (241)
                      |+|+|||+|++||++.+....++.+.+....                                ..++++|||||++||||
T Consensus         1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~~--------------------------------~~~~~~vhRLD~~TSGl   48 (154)
T cd02550           1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLH--------------------------------GPRVHAAGRLDKDTSGL   48 (154)
T ss_pred             CEEEECCCCCEEecCCCCCCCcHHHhhhccc--------------------------------CCceeEeccCCCCCeeE
Confidence            5899999999999988776677777554321                                24578899999999999


Q ss_pred             EEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEe
Q 026204          143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL  222 (241)
Q Consensus       143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~  222 (241)
                      ||||+|+++++.|+++  .+.+.|+|+|+|.|.++. ++.+..++.+.  ........      .+++.+.|+|+++.. 
T Consensus        49 ll~ak~~~~~~~l~~~--~~~v~K~Y~a~v~g~~~~-~~~~~~~~~~~--~~~~~~~~------~~~~~~~t~~~~l~~-  116 (154)
T cd02550          49 LLLTNDGRLQRRLTEP--RREIEKEYLVTVRGELDE-EGIEDLATVRR--GRLSGLVD------EGVPLAVTKVRVIGE-  116 (154)
T ss_pred             EEEEcCHHHHHHHhhh--hccCcEEEEEEEEeecCc-chheecccccc--CcceeEEc------CCCcccceEEEEEEe-
Confidence            9999999999999997  788999999999999864 45677776552  22222222      267889999999976 


Q ss_pred             cCCCEEEEEEEcCCCCCCC
Q 026204          223 AGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       223 ~~~~~slv~~~l~TGR~HQ  241 (241)
                       ..++|+++|+|.|||+||
T Consensus       117 -~~~~sll~~~l~tGR~HQ  134 (154)
T cd02550         117 -HGGTGRLRLTLKTGRTHQ  134 (154)
T ss_pred             -cCCcEEEEEEEcCCCcHH
Confidence             357899999999999999

This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.

>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family

Probab=99.97  E-value=7.2e-30  Score=209.68  Aligned_cols=145  Identities=48%  Similarity=0.796  Sum_probs=118.3

Q ss_pred             EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204           63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL  142 (241)
Q Consensus        63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl  142 (241)
                      ++|+|||+|++|++.......++...+.......                           .....+++|||||++||||
T Consensus         1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~v~RLD~~tsGl   53 (185)
T cd02869           1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLL---------------------------GEEFRPGLVHRLDKDTSGL   53 (185)
T ss_pred             CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhc---------------------------CCCCcCceecccCCCCceE
Confidence            5899999999999998877778877753222100                           1235678999999999999


Q ss_pred             EEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEe
Q 026204          143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL  222 (241)
Q Consensus       143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~  222 (241)
                      ||+|+|+++++.|++.|+.+.+.|+|+|+|.|.++...+.+..|+..+...........     .+++.+.|+|+++...
T Consensus        54 ll~ak~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~t~~~~l~~~  128 (185)
T cd02869          54 LLVAKNKKAAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRARVVVS-----EDGKPAITHYKVLERF  128 (185)
T ss_pred             EEEEcCHHHHHHHHHHHhcCceeEEEEEEEeCCCCCCccEEecccccCCccCceEEEEC-----CCCeEEEEEEEEEEEc
Confidence            99999999999999999999999999999999999889999999876522222222222     3678999999999873


Q ss_pred             cCCCEEEEEEEcCCCCCCC
Q 026204          223 AGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       223 ~~~~~slv~~~l~TGR~HQ  241 (241)
                        .++|+++|+|.|||+||
T Consensus       129 --~~~s~~~~~l~tGR~HQ  145 (185)
T cd02869         129 --GNVTLVELQLETGRTHQ  145 (185)
T ss_pred             --CCcEEEEEEeCcCCccH
Confidence              58899999999999999

This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.

>PRK10839 16S rRNA pseudouridylate synthase A; Provisional

Probab=99.97  E-value=2.2e-31  Score=227.17  Aligned_cols=159  Identities=16%  Similarity=0.216  Sum_probs=117.1

Q ss_pred             eEEecCeecC-CCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhc
Q 026204           15 ALFLSMDKLS-VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHC   93 (241)
Q Consensus        15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~   93 (241)
                      .|.|||+++. ++++|+.||.|.+......     +        .++++++|+|||+||+|||+... ..|+...+... 
T Consensus        26 ~V~VNg~~~~~~~~~l~~gd~I~l~~~~~~-----~--------~~~~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~-   90 (232)
T PRK10839         26 RVTVDGEIVKNGAFKLLPEHDVAYDGNPLA-----Q--------QHGPRYFMLNKPQGYVCSTDDPD-HPTVLYFLDEP-   90 (232)
T ss_pred             eEEECCEEeccCCcCcCCCCEEEECCEEcc-----c--------CCCCEEEEEECCCCeEecccCCC-CCeEEEecccc-
Confidence            5899999986 8999999999988531100     0        13568999999999999987443 24543322110 


Q ss_pred             CCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204           94 SLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                                                     ...++++|||||++||||||||+|..+++.|..  +.+.++|+|+|.+.
T Consensus        91 -------------------------------~~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~--~~~~i~K~Y~a~i~  137 (232)
T PRK10839         91 -------------------------------VAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRHHCEKTYLVTLE  137 (232)
T ss_pred             -------------------------------cccCceecCCCCCCceeEEEEecCHHHHHHHhC--CCCCCCeEEEEEEC
Confidence                                           113567899999999999999999999999986  78889999999877


Q ss_pred             cccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       174 G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      +.+..           +........+..      +++.|.|+|.+++...   .|+++|+|.||||||
T Consensus       138 ~~i~~-----------~~~~~~~~~~~~------~g~~a~t~~~~~~~~~---~sll~~~l~tGRtHQ  185 (232)
T PRK10839        138 SPVAD-----------DTAEQFAKGVQL------HNEKDLTKPAVLEVIT---PTQVRLTISEGRYHQ  185 (232)
T ss_pred             CCCCH-----------HHHHHHHCCeEE------CCCcccccccEEEEec---CCEEEEEEEcCcCHH
Confidence            65532           211111112222      4677899999998853   399999999999999

>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA

Probab=99.95  E-value=7.2e-29  Score=197.37  Aligned_cols=126  Identities=25%  Similarity=0.323  Sum_probs=97.5

Q ss_pred             EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204           63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL  142 (241)
Q Consensus        63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl  142 (241)
                      |+|+|||+|++|++.......++.+.+...                                 ..++.+|||||++||||
T Consensus         1 ~ivvnKP~G~~~~~~~~~~~~~l~~~l~~~---------------------------------~~~~~~vhRLD~~TsGl   47 (146)
T cd02870           1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDV---------------------------------GERLFPVGRLDYDTEGL   47 (146)
T ss_pred             CEEEECCCCcEecccCCCCCCEEeeecccc---------------------------------CCCEEECCCCCCCCeeE
Confidence            589999999999988765556665543211                                 23578999999999999


Q ss_pred             EEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEe
Q 026204          143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL  222 (241)
Q Consensus       143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~  222 (241)
                      ||||+|+++++.|+.  +.+.++|+|+|+|.|.++.+.+  .. +.       .....      .+++.+.|+|++++..
T Consensus        48 ll~ak~~~~~~~l~~--~~~~i~K~Y~a~v~g~~~~~~~--~~-~~-------~~~~~------~~~~~~~t~~~~l~~~  109 (146)
T cd02870          48 LLLTNDGELANRLTH--PRYGVEKTYLVKVRGVPSEEEL--RR-LR-------AGVEL------DDGKTAPAKVKVLSRD  109 (146)
T ss_pred             EEEeCCHHHHHHhhC--ccCCCCeEEEEEECCCCCHHHH--HH-HH-------CCeEe------CCceEcceEEEEeccC
Confidence            999999999999986  6778999999999999864432  11 10       00111      2567899999999763


Q ss_pred             cCCCEEEEEEEcCCCCCCC
Q 026204          223 AGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       223 ~~~~~slv~~~l~TGR~HQ  241 (241)
                        .++++++|+|.|||+||
T Consensus       110 --~~~sll~~~l~tGR~HQ  126 (146)
T cd02870         110 --PKNTLLEVTLHEGRNRQ  126 (146)
T ss_pred             --CCCcEEEEEEEeCCcHH
Confidence              46799999999999999

The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.

>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like

Probab=99.95  E-value=4.3e-28  Score=197.05  Aligned_cols=128  Identities=20%  Similarity=0.206  Sum_probs=100.4

Q ss_pred             cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204           62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG  141 (241)
Q Consensus        62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG  141 (241)
                      .++|+|||+|++||+.......++.+.+..+.                                ..++++|||||++|||
T Consensus         1 ~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~--------------------------------~~~~~~V~RLD~~TsG   48 (167)
T cd02556           1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLG--------------------------------IPRWISVGRLDLNTEG   48 (167)
T ss_pred             CEEEEECCCCcEECccCCCCCccHHHhhhhhc--------------------------------cCceEEcCcCCCCCee
Confidence            37899999999999876555678888775431                                1356789999999999


Q ss_pred             EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEE
Q 026204          142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEI  221 (241)
Q Consensus       142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~  221 (241)
                      |||||+|.++++.|+.  +++.+.|+|+|+|.|.++.+.  +. .+   . .    .+..     .+++.+.|+|+++..
T Consensus        49 Lll~ak~~~~~~~L~~--~~~~i~K~Y~a~V~g~~~~~~--~~-~~---~-~----gv~~-----~~~~~~~~~~~~~~~  110 (167)
T cd02556          49 LLLFTNDGELANRLMH--PSNEIEREYAVRVFGQVTDEQ--LK-SL---K-K----GVEL-----EDGFAGFKSIQLEGG  110 (167)
T ss_pred             EEEEECCHHHHHHHhC--CcCCCCeEEEEEECccCCHHH--HH-HH---H-c----CCEE-----CCCcCcceEEEEEec
Confidence            9999999999999976  888999999999999986543  11 00   0 0    1111     156778899999975


Q ss_pred             ecCCCEEEEEEEcCCCCCCC
Q 026204          222 LAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       222 ~~~~~~slv~~~l~TGR~HQ  241 (241)
                        ..++|+++|+|.|||+||
T Consensus       111 --~~~~sll~v~l~tGR~HQ  128 (167)
T cd02556         111 --EGKNSWYRVTLREGRNRE  128 (167)
T ss_pred             --CCCcEEEEEEEEeCCCHH
Confidence              346799999999999999

This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.

>PRK10700 23S rRNA pseudouridylate synthase B; Provisional

Probab=99.93  E-value=1e-25  Score=197.73  Aligned_cols=165  Identities=18%  Similarity=0.153  Sum_probs=115.2

Q ss_pred             eEEecCeecCCCceecCCC--EEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHh
Q 026204           15 ALFLSMDKLSVSHNVKGGD--MVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHH   92 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD--~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~   92 (241)
                      .|.|||+++.+++.|..+|  .|.+.......   . .     ..-||+.|+++|||+|++|++.......|+.+.+...
T Consensus        28 ~V~VNG~~~~~g~~V~~~~~d~I~v~g~~~~~---~-~-----~~~e~~~ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~   98 (289)
T PRK10700         28 RVSVDGKIATLGDRVEVTPGLKIRIDGHLISV---K-E-----SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKL   98 (289)
T ss_pred             CEEECCEeccCCCEeCCCCCeEEEECCEEeec---c-c-----ccccCCeEEEEECCCCCEeecCCCCCCccHHHHhhhh
Confidence            4899999999999998874  46553211100   0 0     0015578999999999999988766667898887642


Q ss_pred             cCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEE
Q 026204           93 CSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLT  172 (241)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV  172 (241)
                      .                                ..++++|||||++||||||||+|.++++.|.+  +.+.++|+|+|+|
T Consensus        99 ~--------------------------------~~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~--p~~~i~K~Y~v~V  144 (289)
T PRK10700         99 R--------------------------------GARWIAVGRLDVNTCGLLLFTTDGELANRLMH--PSREVEREYAVRV  144 (289)
T ss_pred             c--------------------------------CCceeEccCCCCCCceEEEEEcCHHHHHHHhC--ccCCCCeEEEEEE
Confidence            1                                13467899999999999999999999999987  8889999999999


Q ss_pred             ecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEec-CCCEEEEEEEcCCCCCCC
Q 026204          173 SGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILA-GGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       173 ~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~-~~~~slv~~~l~TGR~HQ  241 (241)
                      .|.+++...  . .+. .     .+.+.       ++.   |.+..+.... ....+++++.|.+||+||
T Consensus       145 ~G~~~~~~l--~-~l~-~-----Gv~l~-------~~~---~~~~~v~~~~~~~~~s~l~v~L~EGk~hQ  195 (289)
T PRK10700        145 FGQVDDAKL--R-QLS-R-----GVQLE-------DGP---AAFKTIKFSGGEGINQWYNVTLTEGRNRE  195 (289)
T ss_pred             ccCCCHHHH--H-HHH-c-----CCEeC-------Cce---eeeEEEEeccCCCCceEEEEEEeCCccHH
Confidence            998864332  1 110 0     01111       121   2233333321 234589999999999998

>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like

Probab=99.93  E-value=8.3e-26  Score=183.64  Aligned_cols=124  Identities=20%  Similarity=0.246  Sum_probs=90.7

Q ss_pred             EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204           63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL  142 (241)
Q Consensus        63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl  142 (241)
                      |+|+|||+|++||++. ....++.+.+..++.                               ..++++|||||++||||
T Consensus         2 ~ivvnKP~G~~~~~~~-~~~~tl~~~l~~~~~-------------------------------~~~~~~vhRLD~~TSGl   49 (167)
T cd02553           2 YLMLNKPAGVVCATKD-PHHPTVIDLLPEPDR-------------------------------RRDLFPVGRLDKDTTGL   49 (167)
T ss_pred             EEEEECCCCCEeCCCC-CCCCcHHHHhhhhcc-------------------------------cCCeEEcccCCCCCEEE
Confidence            7899999999999654 445788888766531                               13578899999999999


Q ss_pred             EEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEe
Q 026204          143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL  222 (241)
Q Consensus       143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~  222 (241)
                      ||||+|.++++.|.+  +.+.++|+|+|+|.|.++.+..  ....    .   .+....      +.+...+.+++++  
T Consensus        50 ll~ak~~~~~~~l~~--~~~~i~K~Y~a~V~G~~~~~~~--~~~~----~---~~~~~~------~~~~~~~~~~~~~--  110 (167)
T cd02553          50 LLLTNDGQLAHRLTS--PKKHVPKTYEVTLAGPLTEDDI--EAFA----E---GVLLHD------GYPTKPAKLEILS--  110 (167)
T ss_pred             EEEEeCHHHHHHhhC--CcCCCceEEEEEEccCCCHHHH--HHHH----C---CeEEcC------CCEeeeeEEEEeC--
Confidence            999999999988877  6788999999999999865432  1110    0   011111      1123445565553  


Q ss_pred             cCCCEEEEEEEcCCCCCCC
Q 026204          223 AGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       223 ~~~~~slv~~~l~TGR~HQ  241 (241)
                          .++++|+|.|||+||
T Consensus       111 ----~sll~v~l~tGR~HQ  125 (167)
T cd02553         111 ----PTTVRLTITEGKYHQ  125 (167)
T ss_pred             ----CcEEEEEEEeCCCHH
Confidence                299999999999999

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.

>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE

Probab=99.92  E-value=1.3e-25  Score=182.74  Aligned_cols=136  Identities=17%  Similarity=0.224  Sum_probs=93.0

Q ss_pred             EEEEECCCCceeecCCC-CCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204           63 VLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG  141 (241)
Q Consensus        63 llVinKPaGl~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG  141 (241)
                      ++|+|||+|++||+... ....++.+.+..                                   .++++|||||++|||
T Consensus         1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~~-----------------------------------~~~~~v~RLD~~TsG   45 (168)
T cd02566           1 LILFNKPYGVLSQFTDESEKHKTLKDYIDD-----------------------------------PGVYAAGRLDRDSEG   45 (168)
T ss_pred             CEEEECCCCCEEecCCCcCCCccHHHHcCc-----------------------------------CCeEEccCCCCCCeE
Confidence            58999999999998765 444566655421                                   235789999999999


Q ss_pred             EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccE-EEccee-eCCC-CCeeEEEecCCCCCCCCcceEEEEEE
Q 026204          142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGR-IEVPIS-RDPN-NRIRMAAIPGSNKHGQARHAASRYKV  218 (241)
Q Consensus       142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~-i~~~i~-~~~~-~~~~~~~~~~~~~~~~~k~a~T~~~v  218 (241)
                      |||||+|+++++.|.+  +.+.++|+|+|+|.|.++.+... +...+. .+.. .........      .+....|.|++
T Consensus        46 lll~a~d~~~~~~l~~--~~~~v~K~Y~a~v~g~~~~~~~~~l~~g~~~~~~~~~~~~v~~~~------~~~~~~~~~~~  117 (168)
T cd02566          46 LLLLTDDGRLQHRITD--PSFKHPKTYYVQVEGVPTEDALEQLRNGVELGDGLTLPAKVEKVD------EPPWLWEREPP  117 (168)
T ss_pred             EEEEEeCHHHHHHHHC--CCCCCCEEEEEEECCcCCHHHHHHHhCCcEECCeEecceEEEEec------ccccccccccc
Confidence            9999999999888877  45679999999999998643210 011111 1111 111111111      22345566666


Q ss_pred             EEEecCCCEEEEEEEcCCCCCCC
Q 026204          219 IEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       219 l~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      +....+.+.|+++|+|.|||+||
T Consensus       118 ~~~~~~~~~sll~v~l~tGR~HQ  140 (168)
T cd02566         118 IRFRKNIPTSWIEITICEGKNRQ  140 (168)
T ss_pred             cccccCCCccEEEEEEecCccHH
Confidence            76543456789999999999999

This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.

>PRK10475 23S rRNA pseudouridine synthase F; Provisional

Probab=99.92  E-value=2.7e-25  Score=194.69  Aligned_cols=116  Identities=22%  Similarity=0.312  Sum_probs=94.9

Q ss_pred             eEEecCeecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcC
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS   94 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~   94 (241)
                      .|.|||+++.+++.|.+||.|.+.....     .+      ..+||++|+|+|||+|++||+... ...|+.+.+...  
T Consensus        32 ~V~VNGk~v~~~~~V~~gD~V~v~g~~i-----~~------~~~ed~~~lvlnKP~G~~~~~~~~-~~~tv~~~l~~~--   97 (290)
T PRK10475         32 NVFINGKRATIGDQVKAGDVVKVNGQLI-----EP------REAEDLVLIALNKPVGIVSTTEDG-ERDNIVDFVNHS--   97 (290)
T ss_pred             cEEECCEEccCCCCcCCCCEEEECCEEc-----cc------cccCCCeEEEEECCCCCCcCCCCC-CCCcHHHHhhcc--
Confidence            4899999999999999999999864211     11      013788999999999999997765 356887776532  


Q ss_pred             CCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEec
Q 026204           95 LPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSG  174 (241)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G  174 (241)
                                                      .++++|||||++||||||||+|.++++.|.+  +.+.++|+|+|+|.|
T Consensus        98 --------------------------------~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~--p~~~i~K~Y~v~V~g  143 (290)
T PRK10475         98 --------------------------------KRVFPIGRLDKDSQGLIFLTNHGDLVNKILR--AGNDHEKEYLVTVDK  143 (290)
T ss_pred             --------------------------------ccccccccCCCCCcceEEEecCHHHHHHhhC--cCCCCCeEEEEEECC
Confidence                                            2467899999999999999999999999977  667899999999999


Q ss_pred             ccCC
Q 026204          175 VPSQ  178 (241)
Q Consensus       175 ~~~~  178 (241)
                      .+++
T Consensus       144 ~~~~  147 (290)
T PRK10475        144 PITD  147 (290)
T ss_pred             CCCH
Confidence            8854

>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family

Probab=99.87  E-value=1.4e-22  Score=165.93  Aligned_cols=89  Identities=21%  Similarity=0.274  Sum_probs=64.4

Q ss_pred             CccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCcc-EEEcceeeCCCCCeeEEEecCCCCC
Q 026204          128 RPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSG-RIEVPISRDPNNRIRMAAIPGSNKH  206 (241)
Q Consensus       128 ~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~  206 (241)
                      ++++|||||++||||||||+|..+++.|++  +.+.+.|+|+|+|.|.++.+.. .+..++..+.               
T Consensus        46 ~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~--~~~~i~K~Y~v~v~g~~~~~~l~~l~~g~~~~~---------------  108 (177)
T cd02555          46 RLAPIGPLDKDASGLLVFSQDGRVLRKLIG--DASRLEQEYLVEVRGELTAGGLERLNHGLTYDG---------------  108 (177)
T ss_pred             ceeEecCCCCCCeeEEEEECCHHHHHHHhC--hhcCCCEEEEEEEcccCCHHHHHHHhcCcccCC---------------
Confidence            577899999999999999999999999999  5678999999999999865321 1222221110               


Q ss_pred             CCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          207 GQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       207 ~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      ...+++.+.+        .+.+++++.|.|||+||
T Consensus       109 ~~~~~~~~~~--------~~~~~l~i~l~tGr~hQ  135 (177)
T cd02555         109 RELPPAKVSW--------QNEQRLRFALKEPQPGQ  135 (177)
T ss_pred             eecceEEEEE--------cCCCEEEEEEECCcChH
Confidence            0011223222        13589999999999998

This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.

>PRK11394 23S rRNA pseudouridine synthase E; Provisional

Probab=99.86  E-value=6.1e-22  Score=166.35  Aligned_cols=83  Identities=24%  Similarity=0.340  Sum_probs=69.5

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      ..|+++|||+|++|++.......++.+.+..                                   .++++|||||++||
T Consensus        39 ~~ylllnKP~G~l~~~~d~~~~~tl~d~l~~-----------------------------------~~~~~vgRLD~~Ts   83 (217)
T PRK11394         39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIPV-----------------------------------QGVYAAGRLDRDSE   83 (217)
T ss_pred             CEEEEEECCCCCEEeeCCccCCcchHHhccc-----------------------------------CCeEEecCCCCCCe
Confidence            3599999999999997655555677766531                                   24678999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCc
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSS  180 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~  180 (241)
                      ||||+|+|.++++.|.+  +++.+.|+|+|+|.|.++.+.
T Consensus        84 GllLlt~d~~~~~~L~~--~~~~i~K~Y~~~v~g~~~~~~  121 (217)
T PRK11394         84 GLLVLTNNGALQARLTQ--PGKRTGKIYYVQVEGIPTQDA  121 (217)
T ss_pred             eEEEEECCHHHHHHHhC--cccCCCEEEEEEECCCCCHHH
Confidence            99999999999999999  577899999999999986544

>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]

Probab=99.84  E-value=1.2e-20  Score=160.98  Aligned_cols=164  Identities=20%  Similarity=0.223  Sum_probs=114.4

Q ss_pred             eEEecCeecC-CCceecCCC-EEEEEecCCCCccCCCCCCCccEEE-ecCcEEEEECCCCceeecCCCCCCCCHHHHHHH
Q 026204           15 ALFLSMDKLS-VSHNVKGGD-MVNCTISELQPLRAEAEDIPLDIVY-EDDNVLVVNKPAHMVVHPAPGNATGTLVNGILH   91 (241)
Q Consensus        15 ~v~vng~~~~-~~~~l~~GD-~i~~~~~~~~~~~~~~~~~~~~Ily-ed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~   91 (241)
                      .|.|||++++ .+..+.+++ .|.+....              +.+ +...|+++|||.|+.|+......+.|+.+.+..
T Consensus        28 ~V~VnG~v~~~~~~~v~~~~~~i~v~g~~--------------~~~~~~~~y~llnKP~G~v~s~~D~~gr~tv~D~lp~   93 (248)
T COG1187          28 RVTVNGKVATLGGVVVDPDDDVVEVDGKR--------------IELKEERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPE   93 (248)
T ss_pred             CEEECCEEeccCCeEeCCCCcEEEECCEE--------------eeccccceEEEEECCCCeEecccCCCCCceeeeeccc
Confidence            4899999876 677888774 66663311              222 233399999999999998766667788777654


Q ss_pred             hcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEE
Q 026204           92 HCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISL  171 (241)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~Al  171 (241)
                      ..                              +...++++|+|||++||||||++.|.+++++|.+  ++..++|+|+|.
T Consensus        94 ~~------------------------------~~~~~~~pvGRLD~dTeGLLLLTnDG~la~rL~~--P~~~~~K~Y~v~  141 (248)
T COG1187          94 RL------------------------------PRKKRLFPVGRLDKDTEGLLLLTNDGELAHRLMH--PSSEVEKEYLVR  141 (248)
T ss_pred             cc------------------------------ccccceeeccccCCCCeeEEEEeCCHHHHHHhcC--CCCCCCEEEEEE
Confidence            31                              1135688999999999999999999999999988  999999999999


Q ss_pred             EecccCCCcc-EEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          172 TSGVPSQSSG-RIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       172 V~G~~~~~~~-~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      |.|.++++.. .+...+.          ..       ++....+....+......+.|++++.|..||+||
T Consensus       142 v~g~~~~~~l~~l~~Gv~----------l~-------d~~~~~~~~~~l~~~~~~~~s~~~itl~EGrnrQ  195 (248)
T COG1187         142 VEGPVTEEDLEKLRKGVT----------LD-------DGETKPAKPASLEKEPGKNNSWLRITLTEGRNRQ  195 (248)
T ss_pred             EecCCCHHHHHHHhCCcE----------ec-------CcccccceeEEEEecCCCCceEEEEEEeCCcCHH
Confidence            9998754321 0111111          11       2222233322232221226799999999999998

>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like

Probab=99.81  E-value=4.3e-20  Score=149.34  Aligned_cols=120  Identities=17%  Similarity=0.155  Sum_probs=84.9

Q ss_pred             EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204           63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL  142 (241)
Q Consensus        63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl  142 (241)
                      |+++|||+|++|++... ...++.+++..                                  ..++++|||||++||||
T Consensus         2 y~~lnKP~G~l~s~~~~-~~~tv~~~l~~----------------------------------~~~~~~vgRLD~~tsGl   46 (164)
T cd02554           2 YIAYNKPVGIDCTLERA-DEDNIIDFVNP----------------------------------PPRIFPIGRLDKDSEGL   46 (164)
T ss_pred             EEEEECCCCcEeecCCC-CCCcHHHHhcC----------------------------------cCCEEEccCCCCCCeeE
Confidence            68999999999998754 34677766532                                  13578899999999999


Q ss_pred             EEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEe
Q 026204          143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEIL  222 (241)
Q Consensus       143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~  222 (241)
                      ||||+|.+++++|+.  +...+.|+|+|.|.|.+.....      ..-..+   +.. .      +   +.|....++..
T Consensus        47 ll~t~dg~~~~~L~~--p~~~~~K~Y~V~v~~~l~~~~l------~~l~~G---~~~-~------~---~~~~~~~v~~~  105 (164)
T cd02554          47 ILLTNDGDLVNKILH--ADNNHEKEYLVTVNKPITDEFI------EGMSNG---VVI-L------G---TVTKPCKVERL  105 (164)
T ss_pred             EEEEcCHHHHHHHhh--hhcCCCeEEEEEECCCCCHHHH------HHHhCC---CEE-C------C---eEEcceEEEEC
Confidence            999999999999976  6677999999999998764321      000000   000 1      1   23333334432


Q ss_pred             cCCCEEEEEEEcCCCCCCC
Q 026204          223 AGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       223 ~~~~~slv~~~l~TGR~HQ  241 (241)
                      .  . +.++|.|.+||+||
T Consensus       106 ~--~-~~l~i~l~eGr~~q  121 (164)
T cd02554         106 A--K-DKFRIVLTQGLNRQ  121 (164)
T ss_pred             C--C-CEEEEEEECCcCHH
Confidence            1  2 35999999999998

This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.

>TIGR00093 pseudouridine synthase

Probab=99.79  E-value=1.2e-19  Score=141.17  Aligned_cols=90  Identities=22%  Similarity=0.396  Sum_probs=70.9

Q ss_pred             cccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcc
Q 026204          132 VHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARH  211 (241)
Q Consensus       132 vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~  211 (241)
                      |||||++||||||||+|+++++.|..  +.+.+.|+|+|+|.|.++.+.  ++ ++..      ... ..      +++.
T Consensus         1 v~RLD~~TSGlll~akd~~~~~~L~~--~~~~i~K~Y~a~v~g~~~~~~--~~-~~~~------g~~-~~------~~~~   62 (128)
T TIGR00093         1 AGRLDRDSEGLLLLTNDGELVHRLTH--PGHHCEKTYLVTVEGPVTDED--LE-ALRK------GVQ-LE------DGPT   62 (128)
T ss_pred             CCCCCCCCEEEEEEEeCHHHHHHHhC--CCCCCCeEEEEEECCCCCHHH--HH-HHhC------CeE-EC------CcEE
Confidence            79999999999999999999999988  788899999999999886543  11 1210      011 11      4556


Q ss_pred             eEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          212 AASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       212 a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      +.+.|+++..  ..+.++++|+|.|||+||
T Consensus        63 ~~~~~~~l~~--~~~~~~l~~~l~tGR~HQ   90 (128)
T TIGR00093        63 KPAKLEVITE--PGFPTWLRITLSEGRNRQ   90 (128)
T ss_pred             eeeEEEEEcc--CCCceEEEEEEeCCCCHH
Confidence            7888998875  245789999999999999

This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.

>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like

Probab=99.27  E-value=7e-12  Score=106.18  Aligned_cols=76  Identities=24%  Similarity=0.243  Sum_probs=56.6

Q ss_pred             cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204           62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG  141 (241)
Q Consensus        62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG  141 (241)
                      .++|||||+||.++...    +.+...+...+.                              .....+.|||||.+|||
T Consensus         1 GilvvnKP~Gi~s~~~~----~~~~~~l~~~~~------------------------------~~k~~~~vhrLD~~aSG   46 (226)
T cd02868           1 GLFAVYKPPGVHWKHVR----DTIESNLLKYFP------------------------------EDKVLVGVHRLDAFSSG   46 (226)
T ss_pred             CEEEEEcCCCCChhHHH----HHHHHHHHHHcc------------------------------ccceeeEccccCCCCce
Confidence            37999999999876431    333333333322                              11235678999999999


Q ss_pred             EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      +|+||+++.+  +|...|..+.+.|+|+|...
T Consensus        47 vl~~a~~~~t--kl~~~~~~~~~~K~Y~~~~~   76 (226)
T cd02868          47 VLVLGVNHGN--KLLSHLYSNHPTRVYTIRGL   76 (226)
T ss_pred             EEEEEeChhH--hHHHHHHhcCCCeEEEEEEE
Confidence            9999999986  69999999999999997644

This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).

>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like

Probab=98.02  E-value=1.7e-05  Score=65.33  Aligned_cols=70  Identities=21%  Similarity=0.256  Sum_probs=54.8

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.++++|||.|+-+|        .++..+...+.                               ..+++..+-||-..|
T Consensus         2 ~g~l~i~Kp~g~tS~--------~~v~~~k~~~~-------------------------------~kkvGH~GTLDp~A~   42 (182)
T cd02572           2 YGVINLDKPSGPSSH--------EVVAWIKRILG-------------------------------VEKTGHSGTLDPKVT   42 (182)
T ss_pred             CeEEEEecCCCCCHH--------HHHHHHHHHhC-------------------------------CCccCcCCCCCCcCe
Confidence            469999999999775        46777776654                               246788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-+.  +.++...+..  ..|+|.|.+.
T Consensus        43 GvLiv~~g~--~Tk~~~~~~~--~~K~Y~a~v~   71 (182)
T cd02572          43 GCLPVCIDR--ATRLVKSQQE--AGKEYVCVMR   71 (182)
T ss_pred             eEEEEEECH--HhhhhHHHhC--CCCEEEEEEE
Confidence            999999997  3555555554  4599999876

This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r

>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes

Probab=97.79  E-value=3.8e-05  Score=51.68  Aligned_cols=43  Identities=35%  Similarity=0.505  Sum_probs=35.2

Q ss_pred             eEEecCeec-CCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEE
Q 026204           15 ALFLSMDKL-SVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVN   67 (241)
Q Consensus        15 ~v~vng~~~-~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVin   67 (241)
                      +|.+||+++ +++..+.+||.|.+.....          +..|+|||++++|+|
T Consensus        27 ~V~vn~~~~~~~~~~v~~~d~i~i~~~~~----------~~~i~~ed~~~lvv~   70 (70)
T cd00165          27 HVLVNGKVVTKPSYKVKPGDVIEVDGKSI----------EEDIVYEDKKLLVVN   70 (70)
T ss_pred             CEEECCEEccCCccCcCCCCEEEEcCCCc----------ccceeeccCCEEEeC
Confidence            488999998 7999999999998864211          127999999999986

>PRK00989 truB tRNA pseudouridine synthase B; Provisional

Probab=97.77  E-value=5.8e-05  Score=64.08  Aligned_cols=71  Identities=18%  Similarity=0.341  Sum_probs=56.4

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||.|+-+|        .++..+...+.                               ..+++..+.||-..|
T Consensus         9 ~G~l~i~KP~g~TS~--------dvv~~ikk~~~-------------------------------~kKvGH~GTLDP~At   49 (230)
T PRK00989          9 EGILLVDKPQGRTSF--------SLIRSLTKLIG-------------------------------VKKIGHAGTLDPFAT   49 (230)
T ss_pred             CEEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCcCccCCCCCe
Confidence            479999999999775        46777777654                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-.+ .+.+|.+.+..  ..|+|+|.+.
T Consensus        50 GvLiv~vG~-~aTkl~~~~~~--~~K~Y~~~~~   79 (230)
T PRK00989         50 GVMVMLIGR-KFTRLSDILLF--EDKEYAAVAH   79 (230)
T ss_pred             eEEEEEECC-chhhhHHHhcC--CCcEEEEEEE
Confidence            999999876 34556666655  7899999876

>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family

Probab=97.76  E-value=7.9e-05  Score=62.62  Aligned_cols=69  Identities=22%  Similarity=0.287  Sum_probs=55.1

Q ss_pred             cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204           62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG  141 (241)
Q Consensus        62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG  141 (241)
                      .++.||||.|+-+|        .+++.++..+.                               ..+++..+.||-..||
T Consensus         1 Gil~i~KP~g~tS~--------~vv~~ik~~~~-------------------------------~kKvGH~GTLDP~AsG   41 (210)
T cd00506           1 GLFAVDKPQGPSSH--------DVVDTIRRIFL-------------------------------AEKVGHGGTLDPFATG   41 (210)
T ss_pred             CEEEEEcCCCCCHH--------HHHHHHHHHhC-------------------------------ccccCCCCcCCCcCee
Confidence            37899999999775        46777776653                               2467889999999999


Q ss_pred             EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      +|+++-+..  .++...|..  ..|+|.|.+.
T Consensus        42 vLiv~vG~a--Tkl~~~~~~--~~K~Y~~~~~   69 (210)
T cd00506          42 VLVVGIGKA--TKLLKHLLA--ATKDYTAIGR   69 (210)
T ss_pred             EEEEEECHH--HhhhHHHhc--CCceEEEEEE
Confidence            999999973  556666655  8999999876

This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker

>PRK04099 truB tRNA pseudouridine synthase B; Provisional

Probab=97.74  E-value=8.7e-05  Score=64.60  Aligned_cols=70  Identities=23%  Similarity=0.319  Sum_probs=56.1

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.++++|||+|+-+|        .++.+++..+.                               ..+.+..+-||-..|
T Consensus         2 ngil~vdKP~g~tS~--------~vv~~ikk~~~-------------------------------~kKvGH~GTLDP~At   42 (273)
T PRK04099          2 NRLFVANKPAGMSSN--------AFLSRLKRKYG-------------------------------VKKAGFSGTLDPFAK   42 (273)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCccCCCCCe
Confidence            368999999999875        47788887654                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-.+.  .+|...+..  ..|+|.|.+.
T Consensus        43 GvLiv~iG~a--TKl~~~l~~--~~K~Y~a~~~   71 (273)
T PRK04099         43 GVLIVAFGQY--TKLFRFLKK--TPKTYRATLW   71 (273)
T ss_pred             eEEEEEEChH--hhhHHHhcc--CCceEEEEEE
Confidence            9999999975  446666655  4899999866

>TIGR00431 TruB tRNA pseudouridine 55 synthase

Probab=97.73  E-value=9.2e-05  Score=62.11  Aligned_cols=70  Identities=19%  Similarity=0.291  Sum_probs=56.1

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||.|+-+|        .+++.+...+.                               ..+++..+.||-..|
T Consensus         2 ~G~l~v~KP~g~tS~--------~vv~~vkk~~~-------------------------------~kKvGH~GTLDP~As   42 (209)
T TIGR00431         2 NGVLLLDKPQGMTSF--------DALAKVRRLLN-------------------------------VKKVGHTGTLDPFAT   42 (209)
T ss_pred             CeEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCCCCCCCCcCc
Confidence            368999999999764        46777777654                               246788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-+..+  +|...+.  ...|+|.|.+.
T Consensus        43 GvLiv~vG~~T--kl~~~~~--~~~K~Y~~~~~   71 (209)
T TIGR00431        43 GVLPILVGKAT--KLSPYLT--DLDKEYRAEIR   71 (209)
T ss_pred             eEEEEEEChHh--hhhHHHc--CCCCeEEEEEE
Confidence            99999999853  6666665  48999999865

TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific

>PRK00020 truB tRNA pseudouridine synthase B; Provisional

Probab=97.68  E-value=0.00013  Score=62.50  Aligned_cols=70  Identities=20%  Similarity=0.327  Sum_probs=55.1

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.++++|||.|+-+|        .++..++..+.                               ..+++..+-||-..|
T Consensus        10 ~Gil~vdKP~G~TS~--------dvv~~vkr~~~-------------------------------~kKvGH~GTLDP~At   50 (244)
T PRK00020         10 DGVLLLDKPVGLSSN--------HALQRAKRTVD-------------------------------AAKAGHTGTLDPFAT   50 (244)
T ss_pred             CeEEEEecCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCcCCcCCCcCe
Confidence            479999999999775        46777777654                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-..  +.+|...+..  ..|+|+|.+.
T Consensus        51 GvLiv~iG~--aTKl~~~l~~--~~K~Y~a~~~   79 (244)
T PRK00020         51 GLLVCCMGR--ATKISGRMLE--ADKTYQATLQ   79 (244)
T ss_pred             eEEEEEECH--HhhhhHHhcc--CCcEEEEEEE
Confidence            999999997  3555555544  5599999865

>PRK02484 truB tRNA pseudouridine synthase B; Provisional

Probab=97.60  E-value=0.00018  Score=63.39  Aligned_cols=70  Identities=21%  Similarity=0.245  Sum_probs=55.4

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.++++|||+|+-+|        .++..++..+.                               ..+++..+.||-..|
T Consensus         3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At   43 (294)
T PRK02484          3 NGIINLKKEAGMTSH--------DAVFKLRKILQ-------------------------------TKKIGHGGTLDPDVV   43 (294)
T ss_pred             ceEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCCCCCCCCe
Confidence            368999999999875        46777777654                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-...  .++.+.+..  ..|+|.|.+.
T Consensus        44 GvL~i~vG~a--Tkl~~~l~~--~~K~Y~a~~~   72 (294)
T PRK02484         44 GVLPIAVGKA--TRLIEYMTE--AGKVYEGEIT   72 (294)
T ss_pred             eEEEEEEChh--hhhhHHhcc--CCcEEEEEEE
Confidence            9999999974  446665654  4599999876

>PRK14124 tRNA pseudouridine synthase B; Provisional

Probab=97.57  E-value=0.00025  Score=62.85  Aligned_cols=70  Identities=24%  Similarity=0.330  Sum_probs=55.7

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.++++|||.|+-+|        .++..++..+.                               ..+++..+-||-..|
T Consensus         3 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At   43 (308)
T PRK14124          3 HGFLVAYKPKGPTSH--------DVVDEVRKKLK-------------------------------TRKVGHAGTLDPFAT   43 (308)
T ss_pred             ceEEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCccCcCcCCCCCCc
Confidence            368999999999875        46777777654                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-+..  .+|.+.+..  -.|+|+|.+.
T Consensus        44 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~   72 (308)
T PRK14124         44 GVLIVGVNKA--TRLLEYLKN--EKKVYYVKMR   72 (308)
T ss_pred             EEEEEEEChH--HhhhHHHhc--CCceEEEEEE
Confidence            9999999974  446666655  3899999876

>PRK14123 tRNA pseudouridine synthase B; Provisional

Probab=97.55  E-value=0.00023  Score=63.06  Aligned_cols=70  Identities=20%  Similarity=0.253  Sum_probs=56.2

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||.|+-+|        .++..++..+.                               ..+++..+.||-..|
T Consensus         3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At   43 (305)
T PRK14123          3 NGILPVYKERGLTSH--------DVVFKLRKILK-------------------------------TKKIGHTGTLDPEVA   43 (305)
T ss_pred             ceEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCcCCCCcCe
Confidence            369999999999875        46777777654                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-.+.  .+|.+.+..  ..|+|.|.+.
T Consensus        44 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~~~~~   72 (305)
T PRK14123         44 GVLPVCIGNA--TRVSDYVMD--MGKAYEATVS   72 (305)
T ss_pred             eEEEEEEChh--hhhHHHhcC--CCcEEEEEEE
Confidence            9999999985  356666655  7899999875

>PRK03287 truB tRNA pseudouridine synthase B; Provisional

Probab=97.53  E-value=0.00023  Score=62.81  Aligned_cols=71  Identities=24%  Similarity=0.384  Sum_probs=56.0

Q ss_pred             cCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCC
Q 026204           60 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT  139 (241)
Q Consensus        60 d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T  139 (241)
                      -+.+++||||.|+-+|        .++..++..+.                               ..+++..+-||-..
T Consensus         8 ~~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~A   48 (298)
T PRK03287          8 GSGLVVVDKPAGMTSH--------DVVARCRRLFG-------------------------------TRKVGHAGTLDPMA   48 (298)
T ss_pred             cCeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCcCccCCCcc
Confidence            3579999999999775        46777777654                               24678899999999


Q ss_pred             ceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          140 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       140 SGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      ||+|+++-..  +.++...+.+  ..|+|.|.+.
T Consensus        49 tGvL~i~vG~--aTKl~~~l~~--~~K~Y~a~~~   78 (298)
T PRK03287         49 TGVLVLGVER--ATKLLGHLTL--TDKSYTATIR   78 (298)
T ss_pred             eeEEEEEeCh--hhhhhHHHhc--CCcEEEEEEE
Confidence            9999999996  3555555655  4899999865

>PRK02193 truB tRNA pseudouridine synthase B; Provisional

Probab=97.53  E-value=0.00024  Score=62.10  Aligned_cols=68  Identities=24%  Similarity=0.362  Sum_probs=53.7

Q ss_pred             EEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceE
Q 026204           63 VLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGL  142 (241)
Q Consensus        63 llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGl  142 (241)
                      ++++|||.|+-+|        .++..+...+.                               ..+++..+.||-..||+
T Consensus         2 il~i~KP~G~tS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~AtGv   42 (279)
T PRK02193          2 IKLLYKPKGISSF--------KFIKNFAKTNN-------------------------------IKKIGHTGTLDPLASGL   42 (279)
T ss_pred             EEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCccccCccCCCcCeeE
Confidence            6899999999875        36677776653                               25678899999999999


Q ss_pred             EEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          143 LVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       143 ll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+++-.+.  .++...+.+  ..|+|.|.+.
T Consensus        43 L~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~   69 (279)
T PRK02193         43 LLVATDED--TKLIDYLDQ--KDKTYIAKIK   69 (279)
T ss_pred             EEEEEChh--hhhhHHhcc--CCcEEEEEEE
Confidence            99999973  556666633  7899999866

>PRK00130 truB tRNA pseudouridine synthase B; Provisional

Probab=97.53  E-value=0.00027  Score=62.22  Aligned_cols=70  Identities=21%  Similarity=0.248  Sum_probs=55.8

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.++++|||.|+-+|        .++..++..+.                               ..+++..+-||-..|
T Consensus         2 ~Gil~i~KP~G~tS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At   42 (290)
T PRK00130          2 DGILNILKPPGMTSF--------DVVRKIRKIAK-------------------------------IKKVGHTGTLDPLAS   42 (290)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccCcCCCCCCCCe
Confidence            368999999999775        46777777654                               246788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-...  .+|.+.+..  ..|+|.|.+.
T Consensus        43 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~a~~~   71 (290)
T PRK00130         43 GVLPVCLGKA--TKIVDYLME--GKKTYRAEIK   71 (290)
T ss_pred             eEEEEEEChh--hhhHHHhcc--CCcEEEEEEE
Confidence            9999999973  456666655  4899999876

>PRK14846 truB tRNA pseudouridine synthase B; Provisional

Probab=97.50  E-value=0.00031  Score=62.73  Aligned_cols=70  Identities=21%  Similarity=0.218  Sum_probs=55.3

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||.|+-+|        .+++.++..+.                               ..+++..+.||-..|
T Consensus         3 nGiL~idKP~G~TS~--------dvv~~vrk~l~-------------------------------~kKVGH~GTLDP~At   43 (345)
T PRK14846          3 NYWLNIYKPRGISSA--------QLVSIVKKILG-------------------------------KTKIGHAGTLDVEAE   43 (345)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCcCccCCCcCc
Confidence            479999999999875        46777777654                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-...  .++...+..  ..|+|+|.+.
T Consensus        44 GVL~i~vG~a--TKl~~~l~~--~~K~Y~a~~~   72 (345)
T PRK14846         44 GILPFAVGEA--TKLIHLLID--ARKTYIFTVK   72 (345)
T ss_pred             eEEEEEEChh--hhhhHHHhc--CCceEEEEEE
Confidence            9999999873  555555544  6789999865

>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like

Probab=97.50  E-value=0.0003  Score=61.55  Aligned_cols=69  Identities=23%  Similarity=0.363  Sum_probs=55.2

Q ss_pred             cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204           62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG  141 (241)
Q Consensus        62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG  141 (241)
                      .++.+|||.|+-+|        .++..++..+.                               ..+++..+-||-..||
T Consensus         1 Gil~i~KP~G~tS~--------~vv~~vr~~~~-------------------------------~kKvGH~GTLDP~AtG   41 (277)
T cd02573           1 GILLLDKPAGLTSH--------DVVQKVRRLLG-------------------------------TKKVGHTGTLDPLATG   41 (277)
T ss_pred             CEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------cCccCCCCCCCCcCeE
Confidence            37899999999875        46777777654                               2467889999999999


Q ss_pred             EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      +|+++-+..  .+|...+..  ..|+|+|.+.
T Consensus        42 vL~v~vG~a--Tkl~~~l~~--~~K~Y~~~~~   69 (277)
T cd02573          42 VLPIALGEA--TKLSQYLLD--ADKTYRATVR   69 (277)
T ss_pred             EEEEEEChH--HhhHHHhcC--CCcEEEEEEE
Confidence            999999974  456666655  6999999876

This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.

>PRK05389 truB tRNA pseudouridine synthase B; Provisional

Probab=97.50  E-value=0.00029  Score=62.41  Aligned_cols=70  Identities=21%  Similarity=0.204  Sum_probs=55.6

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||.|+-+|        .++..++..+.                               ..+++..+-||-..|
T Consensus        13 ~Gil~i~KP~G~TS~--------dvv~~vrk~~~-------------------------------~kKvGH~GTLDP~At   53 (305)
T PRK05389         13 SGWLILDKPAGMTST--------EAVSKVKWLFD-------------------------------AQKAGHAGTLDPLAS   53 (305)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhc-------------------------------ccccCCcccCCCCCc
Confidence            579999999999875        46777777654                               246788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-..  +.+|...+..  ..|+|+|.+.
T Consensus        54 GvL~v~vG~--aTkl~~~l~~--~~K~Y~a~~~   82 (305)
T PRK05389         54 GVLPIALGE--ATKTVPYVMD--GTKRYRFTVA   82 (305)
T ss_pred             eEEEEEECh--hhhhhHHhcc--CCcEEEEEEE
Confidence            999999987  3555565644  4899999865

>PRK02755 truB tRNA pseudouridine synthase B; Provisional

Probab=97.49  E-value=0.00031  Score=61.95  Aligned_cols=69  Identities=23%  Similarity=0.252  Sum_probs=55.1

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.++++|||.|+-+|        .++..++..+.                               ..+++..+-||-..|
T Consensus         3 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At   43 (295)
T PRK02755          3 FGFLNLDKPAGLTSH--------DCVARLRRLLR-------------------------------LKRVGHGGTLDPAAT   43 (295)
T ss_pred             ceEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccccCCCCCCcCe
Confidence            369999999999875        46777777654                               246788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-.+.+  +|.+.+..   .|+|.|.+.
T Consensus        44 GvL~i~vG~aT--kl~~~l~~---~K~Y~a~~~   71 (295)
T PRK02755         44 GVLPIALGKAT--RLLPYLPG---EKTYRGTIR   71 (295)
T ss_pred             eEEEEEEChhh--hhHHHhCC---CcEEEEEEE
Confidence            99999999854  56666642   699999865

>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed

Probab=97.47  E-value=0.00033  Score=62.12  Aligned_cols=71  Identities=17%  Similarity=0.209  Sum_probs=55.7

Q ss_pred             cCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCC
Q 026204           60 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT  139 (241)
Q Consensus        60 d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T  139 (241)
                      -+.++++|||.|+-+|        .+++.++..+.                               ..+++..+-||-..
T Consensus        21 ~~g~l~i~Kp~g~tS~--------~~v~~~r~~~~-------------------------------~kkvGH~GTLDp~A   61 (300)
T PRK04270         21 KFGVVNLDKPPGPTSH--------EVAAWVRDILG-------------------------------VEKAGHGGTLDPKV   61 (300)
T ss_pred             CCCEEEEECCCCCCHH--------HHHHHHHHHhc-------------------------------cccccCCCCCCCcC
Confidence            4579999999999775        46777777653                               24678899999999


Q ss_pred             ceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          140 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       140 SGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      ||+|+++-+..  .+|.+.+..  ..|+|.|.+.
T Consensus        62 ~GvL~v~~g~a--tk~~~~~~~--~~K~Y~~~~~   91 (300)
T PRK04270         62 TGVLPVALGKA--TKVVQALLE--SGKEYVCVMH   91 (300)
T ss_pred             eEEEEEEEChH--hhhhHHhcc--CCcEEEEEEE
Confidence            99999999873  566666654  4599999865

>PRK01528 truB tRNA pseudouridine synthase B; Provisional

Probab=97.46  E-value=0.00038  Score=61.24  Aligned_cols=70  Identities=21%  Similarity=0.253  Sum_probs=54.8

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||.|+-+|        .++..++..+.                               ..+++..+-||-..|
T Consensus         3 ~GiL~i~KP~G~TS~--------dvv~~vrk~~~-------------------------------~kKvGH~GTLDP~At   43 (292)
T PRK01528          3 NYWLNIYKPRGISSA--------KLVSIVKKILG-------------------------------KVKIGHAGTLDVEAE   43 (292)
T ss_pred             CEEEEEeCCCCCCHH--------HHHHHHHHHcC-------------------------------CCccCcCccCCCcCc
Confidence            479999999999775        46777777653                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-...  .++...+..  ..|+|.|.+.
T Consensus        44 GvL~v~vG~a--TKl~~~l~~--~~K~Y~~~~~   72 (292)
T PRK01528         44 GVLPLAVGEA--TKLVQLLID--AKKTYIFTVK   72 (292)
T ss_pred             eEEEEEEChH--hhhhHHHhc--CCceEEEEEE
Confidence            9999999873  455555544  5699999865

>PRK05033 truB tRNA pseudouridine synthase B; Provisional

Probab=97.45  E-value=0.00039  Score=61.69  Aligned_cols=70  Identities=19%  Similarity=0.289  Sum_probs=56.0

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||.|+-+|        .++..++..+.                               ..+++..+-||-..|
T Consensus        10 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At   50 (312)
T PRK05033         10 NGVLLLDKPQGMSSN--------DALQKVKRLFN-------------------------------ANKAGHTGALDPLAT   50 (312)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCCCCcCCCcCe
Confidence            579999999999875        36777777653                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-.+.  .+|.+.+..  ..|+|.|.+.
T Consensus        51 GvL~v~vG~a--Tkl~~~~~~--~~K~Y~a~~~   79 (312)
T PRK05033         51 GMLPICLGEA--TKFSQYLLD--SDKRYRVTAR   79 (312)
T ss_pred             eEEEEEECHH--hhhhHHhcC--CCcEEEEEEE
Confidence            9999999974  446666655  5899999876

>PRK01851 truB tRNA pseudouridine synthase B; Provisional

Probab=97.44  E-value=0.00043  Score=61.19  Aligned_cols=70  Identities=20%  Similarity=0.288  Sum_probs=55.6

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||.|+-+|        .++..++..+.                               ..+++..+-||-..|
T Consensus        16 ~Gil~i~KP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~At   56 (303)
T PRK01851         16 DGVLLLDKPLGLSSN--------DALQRAKRLLR-------------------------------AKKAGHTGTLDPLAT   56 (303)
T ss_pred             CeEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------cccCCCCCCCCCCCc
Confidence            589999999999875        46777777654                               246788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-...  .+|.+.+..  ..|+|.|.+.
T Consensus        57 GvL~v~vG~a--Tkl~~~l~~--~~K~Y~~~~~   85 (303)
T PRK01851         57 GLLPLCFGEA--TKFSQDLLD--ADKTYEATLR   85 (303)
T ss_pred             eEEEEEECHH--HhhhHHhcc--cCeEEEEEEE
Confidence            9999999974  446666655  4599999865

>PRK01550 truB tRNA pseudouridine synthase B; Provisional

Probab=97.43  E-value=0.00041  Score=61.43  Aligned_cols=70  Identities=21%  Similarity=0.293  Sum_probs=55.6

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||.||-+|        .++..++..+.                               ..+++..+-||-..|
T Consensus         2 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At   42 (304)
T PRK01550          2 NGVLLLHKPRGMTSH--------DCVFKLRKILR-------------------------------TKKVGHTGTLDPEVS   42 (304)
T ss_pred             CeEEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCCcccCCCCCCcCe
Confidence            368999999999875        46777777654                               246788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-...  .+|.+.+..  ..|+|.|.+.
T Consensus        43 GvL~i~vG~a--Tkl~~~l~~--~~K~Y~a~~~   71 (304)
T PRK01550         43 GVLPICVGRA--TKIAEYLTD--EGKTYEGEVT   71 (304)
T ss_pred             eEEEEEEChh--hhhhHHhcC--CCcEEEEEEE
Confidence            9999999974  446666655  4899999876

>PRK14122 tRNA pseudouridine synthase B; Provisional

Probab=97.28  E-value=0.00074  Score=59.93  Aligned_cols=69  Identities=26%  Similarity=0.396  Sum_probs=54.6

Q ss_pred             cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204           62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG  141 (241)
Q Consensus        62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG  141 (241)
                      .+++||||.|+-+|        .++..++..+.                               ..+++..+-||-..||
T Consensus         2 ~il~idKP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~AtG   42 (312)
T PRK14122          2 PVYAVDKPLGLTSH--------DVVNRARRALG-------------------------------TRRVGHTGTLDPLATG   42 (312)
T ss_pred             cEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------CCCCCCCCCCCCcCee
Confidence            37899999999775        46777777654                               2567889999999999


Q ss_pred             EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      +|+++-...  .+|...+.  ...|+|.|.+.
T Consensus        43 vL~i~iG~a--TKl~~~l~--~~~K~Y~a~~~   70 (312)
T PRK14122         43 VLVLCTDDS--TKLVPFLS--AEDKEYLAWVS   70 (312)
T ss_pred             eEEEEEChh--hhhhHHhc--CCCceEEEEEE
Confidence            999999974  34766663  37899999875

>TIGR00425 CBF5 rRNA pseudouridine synthase, putative

Probab=97.24  E-value=0.00073  Score=60.46  Aligned_cols=71  Identities=20%  Similarity=0.276  Sum_probs=56.2

Q ss_pred             cCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCC
Q 026204           60 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT  139 (241)
Q Consensus        60 d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T  139 (241)
                      .+.++++|||.|+-+|        .++..++..+.                               ..+++..+-||-..
T Consensus        33 ~~G~l~i~KP~g~tS~--------~~v~~vr~~~~-------------------------------~kkvGH~GTLDP~A   73 (322)
T TIGR00425        33 SYGVVNLDKPSGPSSH--------EVVAWVRRILN-------------------------------VEKTGHGGTLDPKV   73 (322)
T ss_pred             CCCEEEEeCCCCCCHH--------HHHHHHHHHhc-------------------------------ccccCCCCCCCCCC
Confidence            3579999999999875        46777777654                               24678899999999


Q ss_pred             ceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          140 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       140 SGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      ||+|+++-..  +.+|.+.+..  ..|+|+|.+.
T Consensus        74 ~GvL~v~~G~--aTkl~~~~~~--~~K~Y~~~v~  103 (322)
T TIGR00425        74 TGVLPVCIER--ATRLVKSLQE--APKEYVCLMR  103 (322)
T ss_pred             ceEEEEEECh--HhhccHHhcc--CCCEEEEEEE
Confidence            9999999987  3566666654  7899998875

This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.

>PRK04642 truB tRNA pseudouridine synthase B; Provisional

Probab=97.21  E-value=0.00096  Score=58.91  Aligned_cols=70  Identities=19%  Similarity=0.244  Sum_probs=56.0

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||.|+-+|        .+++.++..+.                               ..+++..+-||-..|
T Consensus        10 ~Gil~i~KP~G~TS~--------dvv~~vrr~~~-------------------------------~kKvGH~GTLDP~At   50 (300)
T PRK04642         10 DGILLLDKPAGLSSN--------NALQAARRLLR-------------------------------AEKGGHTGSLDPLAT   50 (300)
T ss_pred             CeEEEEecCCCCCHH--------HHHHHHHHHhC-------------------------------CCcccCCCccCCcCe
Confidence            579999999999875        47788877764                               246788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-..  +.+|.+.+..  ..|+|+|.+.
T Consensus        51 GvL~v~~G~--aTkl~~~l~~--~~K~Y~a~~~   79 (300)
T PRK04642         51 GLLPLCFGE--ATKIAGLLLG--SAKAYDAEIV   79 (300)
T ss_pred             eeEEEEECh--hhhhhHHhcC--CCcEEEEEEE
Confidence            999999987  3566666654  6899999874

>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]

Probab=96.97  E-value=0.002  Score=56.11  Aligned_cols=69  Identities=17%  Similarity=0.241  Sum_probs=55.0

Q ss_pred             cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204           62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG  141 (241)
Q Consensus        62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG  141 (241)
                      .++++|||.|+-+|        .++.++...++                               ..+.+..+-||-..||
T Consensus        16 Gil~ldKP~G~tS~--------~~v~~vkkil~-------------------------------~~K~GH~GTLDP~atG   56 (271)
T COG0130          16 GVINLDKPPGPTSH--------EVVAWVKRILG-------------------------------VEKAGHGGTLDPLATG   56 (271)
T ss_pred             ceEEeeCCCCCCHH--------HHHHHHHHHhC-------------------------------ccccccccccCCcccc
Confidence            89999999999775        46777777764                               2566789999999999


Q ss_pred             EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      +|.+|-. + +.+|.+.+..  ..|+|.|.+.
T Consensus        57 vLpi~ig-~-aTKl~~~l~~--~~K~Y~a~~~   84 (271)
T COG0130          57 VLPICLG-E-ATKLVQYLLD--ADKEYVATVR   84 (271)
T ss_pred             eEEEEec-h-hHhHHHHHhh--CCcEEEEEEE
Confidence            9999998 3 4555555544  7899999976

>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4

Probab=96.82  E-value=0.0035  Score=55.72  Aligned_cols=93  Identities=17%  Similarity=0.207  Sum_probs=55.3

Q ss_pred             cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCcccccccccccccccccccccccc-----ccCCCCCCccccccCC
Q 026204           62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSS-----SISGASIRPGIVHRLD  136 (241)
Q Consensus        62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~vhRLD  136 (241)
                      .+++||||.|+-++        .+++.++..+.....-..   .+..+   .... |+.     .......+++..+-||
T Consensus         1 Gil~i~KP~G~TS~--------~vv~~lk~~l~~s~~~~~---~~~~~---~~~~-~~~~~~~~~~~~~~~KiGH~GTLD   65 (312)
T cd02867           1 GVFAINKPSGITSA--------QVLNDLKPLFLNSALFKD---KIQRA---VAKR-GKKARRRKGRKRSKLKIGHGGTLD   65 (312)
T ss_pred             CeEEEeCCCCCCHH--------HHHHHHHHHhcccccccc---hhhhh---hhhh-hhhhhhhccccccccccccccccC
Confidence            37899999999775        467777776642100000   00000   0000 000     0011125788899999


Q ss_pred             CCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          137 KGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       137 ~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      -..||+|+++-... .+.++ .|..  ..|+|.|.+.
T Consensus        66 PlAsGVLvvgvG~a-TK~l~-~~l~--~~K~Y~~~~~   98 (312)
T cd02867          66 PLATGVLVVGVGAG-TKQLQ-DYLS--CSKTYEATGL   98 (312)
T ss_pred             CccceeEEEEECcH-HHHHH-HHhc--CCceEEEEEE
Confidence            99999999999874 34444 4444  8999999865

This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).

>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)

Probab=94.17  E-value=0.19  Score=35.82  Aligned_cols=29  Identities=21%  Similarity=0.179  Sum_probs=25.8

Q ss_pred             CCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          126 SIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       126 ~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      ..+++.++++|+.++|+++++                   ++|...+.
T Consensus        23 ~~~i~~aG~kDk~a~t~q~v~-------------------n~f~i~~r   51 (87)
T cd01291          23 PKRVGYAGRKDKRAVTTQLVS-------------------NRFTITLR   51 (87)
T ss_pred             hheEEECccCCCCeeEEEEEc-------------------ccEEEEEE
Confidence            356789999999999999999                   88888887

Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA

Probab=93.87  E-value=0.056  Score=35.82  Aligned_cols=23  Identities=9%  Similarity=0.209  Sum_probs=20.9

Q ss_pred             eEEecCeec-CCCceecCCCEEEE
Q 026204           15 ALFLSMDKL-SVSHNVKGGDMVNC   37 (241)
Q Consensus        15 ~v~vng~~~-~~~~~l~~GD~i~~   37 (241)
                      .|+|||+++ +++++|++||.|.+
T Consensus        35 ~V~VNg~~~~~~~~~l~~Gd~v~i   58 (59)
T TIGR02988        35 EVLVNGELENRRGKKLYPGDVIEI   58 (59)
T ss_pred             CEEECCEEccCCCCCCCCCCEEEe
Confidence            489999998 68999999999986

This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.

>PF14451 Ub-Mut7C: Mut7-C ubiquitin

Probab=93.47  E-value=0.13  Score=36.63  Aligned_cols=28  Identities=18%  Similarity=0.171  Sum_probs=24.9

Q ss_pred             eeeEEecCeecCCCceecCCCEEEEEec
Q 026204           13 VLALFLSMDKLSVSHNVKGGDMVNCTIS   40 (241)
Q Consensus        13 ~~~v~vng~~~~~~~~l~~GD~i~~~~~   40 (241)
                      |..|.|||+.+..++++++||+|.++..
T Consensus        49 V~~i~vNG~~v~~~~~~~~Gd~v~V~P~   76 (81)
T PF14451_consen   49 VGLILVNGRPVDFDYRLKDGDRVAVYPV   76 (81)
T ss_pred             eEEEEECCEECCCcccCCCCCEEEEEec
Confidence            4568999999999999999999999754

>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]

Probab=93.34  E-value=0.1  Score=38.46  Aligned_cols=27  Identities=19%  Similarity=0.272  Sum_probs=24.6

Q ss_pred             eEEecCeecCCCceecCCCEEEEEecC
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCTISE   41 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~~~~   41 (241)
                      .|.+||.+++++..|+.||+|.+.+..
T Consensus        35 rV~vNG~~aKpS~~VK~GD~l~i~~~~   61 (100)
T COG1188          35 RVKVNGQRAKPSKEVKVGDILTIRFGN   61 (100)
T ss_pred             eEEECCEEcccccccCCCCEEEEEeCC
Confidence            499999999999999999999998754

>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=92.59  E-value=0.1  Score=32.82  Aligned_cols=21  Identities=24%  Similarity=0.227  Sum_probs=19.2

Q ss_pred             eEEecCeecC-CCceecCCCEE
Q 026204           15 ALFLSMDKLS-VSHNVKGGDMV   35 (241)
Q Consensus        15 ~v~vng~~~~-~~~~l~~GD~i   35 (241)
                      .|+|||++++ +++.|.+||+|
T Consensus        27 ~V~VNg~~v~~~~~~v~~~d~I   48 (48)
T PF01479_consen   27 RVKVNGKVVKDPSYIVKPGDVI   48 (48)
T ss_dssp             TEEETTEEESSTTSBESTTEEE
T ss_pred             EEEECCEEEcCCCCCCCCcCCC
Confidence            4899999988 99999999986

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....

>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]

Probab=92.03  E-value=0.11  Score=44.30  Aligned_cols=22  Identities=32%  Similarity=0.416  Sum_probs=19.3

Q ss_pred             CccccccCCCCCceEEEeecCH
Q 026204          128 RPGIVHRLDKGTSGLLVVAKDE  149 (241)
Q Consensus       128 ~~~~vhRLD~~TSGlll~Ak~~  149 (241)
                      .+.++||||-.|||+++|.-+-
T Consensus        90 ~V~v~h~l~~~~sgvl~~gVgh  111 (318)
T KOG2559|consen   90 DVQVVHVLPLATSGVLLFGVGH  111 (318)
T ss_pred             ceeeEEeecccccceEEEecCc
Confidence            4688999999999999998764

>PRK01777 hypothetical protein; Validated

Probab=91.28  E-value=0.25  Score=36.28  Aligned_cols=28  Identities=11%  Similarity=0.037  Sum_probs=24.9

Q ss_pred             eeEEecCeecCCCceecCCCEEEEEecC
Q 026204           14 LALFLSMDKLSVSHNVKGGDMVNCTISE   41 (241)
Q Consensus        14 ~~v~vng~~~~~~~~l~~GD~i~~~~~~   41 (241)
                      ..+-|||+.++.++.|+.||+|+++.+.
T Consensus        50 ~~vgI~Gk~v~~d~~L~dGDRVeIyrPL   77 (95)
T PRK01777         50 NKVGIYSRPAKLTDVLRDGDRVEIYRPL   77 (95)
T ss_pred             ceEEEeCeECCCCCcCCCCCEEEEecCC
Confidence            4578999999999999999999998654

>smart00363 S4 S4 RNA-binding domain

Probab=91.06  E-value=0.25  Score=31.38  Aligned_cols=26  Identities=23%  Similarity=0.142  Sum_probs=22.9

Q ss_pred             eeEEecCeec-CCCceecCCCEEEEEe
Q 026204           14 LALFLSMDKL-SVSHNVKGGDMVNCTI   39 (241)
Q Consensus        14 ~~v~vng~~~-~~~~~l~~GD~i~~~~   39 (241)
                      .+|+|||+++ .++..+..||.|.+..
T Consensus        26 g~i~vng~~~~~~~~~l~~gd~i~~~~   52 (60)
T smart00363       26 GRVKVNGKKVTKPSYIVKPGDVISVRG   52 (60)
T ss_pred             CCEEECCEEecCCCeEeCCCCEEEEcc
Confidence            3589999998 7999999999998865

>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones

Probab=89.31  E-value=0.46  Score=37.80  Aligned_cols=43  Identities=23%  Similarity=0.282  Sum_probs=32.7

Q ss_pred             CCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          127 IRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       127 ~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      .+++..+.||-..||||+++-+..  .+|...+..  ..|+|.|.+.
T Consensus         7 ~KvGH~GTLDP~AsGvL~v~vg~~--Tkl~~~l~~--~~K~Y~~~~~   49 (149)
T PF01509_consen    7 KKVGHGGTLDPFASGVLVVGVGKA--TKLLSYLQN--SDKEYVATIR   49 (149)
T ss_dssp             SSEEESS-SSTT-EEEEEEEEGGG--GGGHHHHTT--SEEEEEEEEE
T ss_pred             ceeccccccCCcceEEEEEEECCc--chHHHHhhc--cCCEEEEEEE
Confidence            577889999999999999999873  446666655  5599999865

Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....

>PRK06437 hypothetical protein; Provisional

Probab=86.95  E-value=0.92  Score=30.91  Aligned_cols=25  Identities=24%  Similarity=0.159  Sum_probs=22.6

Q ss_pred             eEEecCeecCCCceecCCCEEEEEe
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCTI   39 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~~   39 (241)
                      ++-+||+.+..++.|+.||+|.+..
T Consensus        38 aV~vNg~iv~~~~~L~dgD~Veiv~   62 (67)
T PRK06437         38 VVIVNGSPVLEDHNVKKEDDVLILE   62 (67)
T ss_pred             EEEECCEECCCceEcCCCCEEEEEe
Confidence            7789999999999999999999853

>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]

Probab=86.22  E-value=0.82  Score=38.35  Aligned_cols=27  Identities=15%  Similarity=0.210  Sum_probs=24.1

Q ss_pred             eEEecCeecC-CCceecCCCEEEEEecC
Q 026204           15 ALFLSMDKLS-VSHNVKGGDMVNCTISE   41 (241)
Q Consensus        15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~   41 (241)
                      .|.|||+++. |++.|.+||.+.|....
T Consensus       120 HI~VnGk~V~iPSy~V~~gdei~V~~k~  147 (205)
T COG0522         120 HILVNGKRVNIPSYLVSPGDEISVREKS  147 (205)
T ss_pred             eEEECCEEeccCcEEecCCCEEEeeecc
Confidence            4899999988 99999999999997654

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins

Probab=82.80  E-value=1.6  Score=30.18  Aligned_cols=28  Identities=14%  Similarity=0.250  Sum_probs=25.1

Q ss_pred             eeeeeEEecCeecCCCceecCCCEEEEE
Q 026204           11 VSVLALFLSMDKLSVSHNVKGGDMVNCT   38 (241)
Q Consensus        11 ~~~~~v~vng~~~~~~~~l~~GD~i~~~   38 (241)
                      .+...+.|||+.++.++.|+.||+|.+.
T Consensus        47 ~~~~~v~vNg~~v~~~~~l~~gD~v~i~   74 (80)
T cd00754          47 LARVRIAVNGEYVRLDTPLKDGDEVAII   74 (80)
T ss_pred             hhcEEEEECCeEcCCCcccCCCCEEEEe
Confidence            4667899999999999999999999985

MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional

Probab=82.36  E-value=1.5  Score=34.17  Aligned_cols=25  Identities=8%  Similarity=-0.039  Sum_probs=22.9

Q ss_pred             eEEecCeecCCCceecCCCEEEEEe
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCTI   39 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~~   39 (241)
                      .|.|||+++|++..|..||.|.|..
T Consensus        35 ~V~vnG~~~Kps~~V~~gd~l~v~~   59 (133)
T PRK10348         35 KVHYNGQRSKPSKIVELNATLTLRQ   59 (133)
T ss_pred             CEEECCEECCCCCccCCCCEEEEEE
Confidence            4899999999999999999999965

>PRK11507 ribosome-associated protein; Provisional

Probab=81.63  E-value=1.6  Score=30.18  Aligned_cols=24  Identities=8%  Similarity=0.062  Sum_probs=21.1

Q ss_pred             eEEecCeecC-CCceecCCCEEEEE
Q 026204           15 ALFLSMDKLS-VSHNVKGGDMVNCT   38 (241)
Q Consensus        15 ~v~vng~~~~-~~~~l~~GD~i~~~   38 (241)
                      .|.|||+... .+.+|.+||.|.+.
T Consensus        38 ~V~VNGeve~rRgkKl~~GD~V~~~   62 (70)
T PRK11507         38 QVKVDGAVETRKRCKIVAGQTVSFA   62 (70)
T ss_pred             ceEECCEEecccCCCCCCCCEEEEC
Confidence            4899999865 79999999999994

>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein

Probab=81.11  E-value=1.6  Score=29.26  Aligned_cols=26  Identities=19%  Similarity=0.286  Sum_probs=22.3

Q ss_pred             eeEEecCeecCCC----ceecCCCEEEEEe
Q 026204           14 LALFLSMDKLSVS----HNVKGGDMVNCTI   39 (241)
Q Consensus        14 ~~v~vng~~~~~~----~~l~~GD~i~~~~   39 (241)
                      .+|-+||+.+..+    +.|+.||+|.+..
T Consensus        31 i~V~vNg~~v~~~~~~~~~L~~gD~V~ii~   60 (65)
T cd00565          31 VAVALNGEIVPRSEWASTPLQDGDRIEIVT   60 (65)
T ss_pred             EEEEECCEEcCHHHcCceecCCCCEEEEEE
Confidence            3788999999877    8999999999853

ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.

>PRK08364 sulfur carrier protein ThiS; Provisional

Probab=81.02  E-value=2  Score=29.43  Aligned_cols=25  Identities=20%  Similarity=0.106  Sum_probs=22.4

Q ss_pred             eeEEecCeecCCCceecCCCEEEEE
Q 026204           14 LALFLSMDKLSVSHNVKGGDMVNCT   38 (241)
Q Consensus        14 ~~v~vng~~~~~~~~l~~GD~i~~~   38 (241)
                      -++-+||+.+..++.|+.||+|.+.
T Consensus        40 v~v~vNg~iv~~~~~l~~gD~Veii   64 (70)
T PRK08364         40 AIAKVNGKVALEDDPVKDGDYVEVI   64 (70)
T ss_pred             EEEEECCEECCCCcCcCCCCEEEEE
Confidence            5678999999999999999999985

>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal

Probab=80.33  E-value=2.2  Score=29.75  Aligned_cols=29  Identities=10%  Similarity=0.105  Sum_probs=24.9

Q ss_pred             ceeeeeEEecCeecCCCceecCCCEEEEE
Q 026204           10 QVSVLALFLSMDKLSVSHNVKGGDMVNCT   38 (241)
Q Consensus        10 ~~~~~~v~vng~~~~~~~~l~~GD~i~~~   38 (241)
                      ..+...|.+|++.+..+..|+.||+|.+.
T Consensus        46 ~~~~~~v~vn~~~v~~~~~l~dgDevai~   74 (80)
T TIGR01682        46 SRGQVMVAVNEEYVTDDALLNEGDEVAFI   74 (80)
T ss_pred             hccceEEEECCEEcCCCcCcCCCCEEEEe
Confidence            34556799999999999999999999985

The C-terminal Gly-Gly of this model is critical to function.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	241
1v9f_A	325	Crystal Structure Of Catalytic Domain Of Pseudourid		3e-26
1qyu_A	349	Structure Of The Catalytic Domain Of 23s Rrna Pseud		1e-24
1prz_A	252	Crystal Structure Of Pseudouridine Synthase Rlud Ca		1e-23
2i82_A	217	Crystal Structure Of Pseudouridine Synthase Rlua: I		5e-09
1xpi_A	231	Crystal Structure Of The Catalytic Domain Of E. Col		3e-08
1v9k_A	228	The Crystal Structure Of The Catalytic Domain Of Ps		1e-07

>pdb|1V9F|A Chain A, Crystal Structure Of Catalytic Domain Of Pseudouridine Synthase Rlud From Escherichia Coli Length = 325

Iteration: 1
 Score =  114 bits (286), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 76/214 (35%), Positives = 107/214 (50%), Gaps = 36/214 (16%)
Query: 28  NVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 87
            V GG+ V       +  R E +DIPLDIVYED++++++NKP  +VVHP  GN  GT++N
Sbjct: 57  KVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLN 116
Query: 88  GILHHCSLPTLASSNQXXXXXXXXXXXXXXXXXXXXGASIRPGIVHRLDKGTSGLLVVAK 147
            +LH+   P +A                            R GIVHRLDK T+GL+VVAK
Sbjct: 117 ALLHY--YPPIADVP-------------------------RAGIVHRLDKDTTGLMVVAK 149
Query: 148 DEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHG 207
              +   L E  +   I R Y ++  G  + + G ++ PISR P  R  MA       H 
Sbjct: 150 TVPAQTRLVESLQRREITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMAV------HP 202
Query: 208 QARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
             + A + Y+++E         +  RLETGRTHQ
Sbjct: 203 MGKPAVTHYRIMEHFR--VHTRLRLRLETGRTHQ 234

>pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna Pseudouridine Synthase Rlud Length = 349

Iteration: 1
 Score =  109 bits (273), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 75/214 (35%), Positives = 104/214 (48%), Gaps = 36/214 (16%)
Query: 28  NVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVN 87
            V GG+ V       +  R E +DIPLDIVYED++++++NKP  +VVHP  GN  GT++N
Sbjct: 81  KVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLN 140
Query: 88  GILHHCSLPTLASSNQXXXXXXXXXXXXXXXXXXXXGASIRPGIVHRLDKGTSGLLVVAK 147
            +LH+   P +A                            R GIVHRLDK T+GL VVAK
Sbjct: 141 ALLHY--YPPIADVP-------------------------RAGIVHRLDKDTTGLXVVAK 173
Query: 148 DEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHG 207
              +   L E  +   I R Y ++  G  + + G ++ PISR P  R   A       H 
Sbjct: 174 TVPAQTRLVESLQRREITREYEAVAIGHXT-AGGTVDEPISRHPTKRTHXAV------HP 226
Query: 208 QARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
             + A + Y++ E         +  RLETGRTHQ
Sbjct: 227 MGKPAVTHYRIXEHFR--VHTRLRLRLETGRTHQ 258

>pdb|1PRZ|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlud Catalytic Module Length = 252

Iteration: 1
 Score =  106 bits (265), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 72/196 (36%), Positives = 98/196 (50%), Gaps = 36/196 (18%)
Query: 46  RAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQXX 105
           R E +DIPLDIVYED++++V+NKP  +VVHP  GN  GT++N +LH+   P +A      
Sbjct: 2   RFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYY--PPIADVP--- 56
Query: 106 XXXXXXXXXXXXXXXXXXGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIE 165
                                 R GIVHRLDK T+GL VVAK   +   L E  +   I 
Sbjct: 57  ----------------------RAGIVHRLDKDTTGLXVVAKTVPAQTRLVESLQRREIT 94
Query: 166 RVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGG 225
           R Y ++  G  + + G ++ PISR P  R   A       H   + A + Y++ E     
Sbjct: 95  REYEAVAIGHXT-AGGTVDEPISRHPTKRTHXAV------HPXGKPAVTHYRIXEHFR-- 145
Query: 226 GSALVEWRLETGRTHQ 241
               +  RLETGRTHQ
Sbjct: 146 VHTRLRLRLETGRTHQ 161

>pdb|2I82|A Chain A, Crystal Structure Of Pseudouridine Synthase Rlua: Indirect Sequence Readout Through Protein-induced Rna Structure Length = 217

Iteration: 1
 Score = 57.8 bits (138), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 83/188 (44%), Gaps = 38/188 (20%)
Query: 54  LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQXXXXXXXXXX 113
           L I+Y+DD++ VVNKP+ ++  P      G L     H  S+ T    +           
Sbjct: 12  LVILYQDDHIXVVNKPSGLLSVP------GRLEE---HKDSVXTRIQRDYPQAES----- 57
Query: 114 XXXXXXXXXXGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173
                             VHRLD  TSG++VVA  + +   L  QF+    ++ Y++   
Sbjct: 58  ------------------VHRLDXATSGVIVVALTKAAERELKRQFREREPKKQYVARVW 99
Query: 174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWR 233
           G PS + G +++P+  D  NR +      + K  Q     + Y+V+E  A   +A V  +
Sbjct: 100 GHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQ-----TEYEVVE-YAADNTARVVLK 153
Query: 234 LETGRTHQ 241
             TGR+HQ
Sbjct: 154 PITGRSHQ 161

>pdb|1XPI|A Chain A, Crystal Structure Of The Catalytic Domain Of E. Coli Pseudouridine Synthase Rluc Length = 231

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 85/194 (43%), Gaps = 53/194 (27%)
Query: 56  IVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQXXXXXXXXXXXX 115
           I+YEDD++LV+NKP+   VH   G + G ++ G+                          
Sbjct: 7   ILYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGL-------------------------- 39
Query: 116 XXXXXXXXGASIRPG-----IVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYIS 170
                     ++RP      +VHRLD+ TSG+L+VAK   +   L EQ +   +++ Y++
Sbjct: 40  ---------RALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLA 90
Query: 171 LTSGVPSQSSGRIEVPISRD---PNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGS 227
           L  G        ++ P+ ++      RI   +  G       + + +R+KV E  A   +
Sbjct: 91  LVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEG-------KPSETRFKVEERYA--FA 141
Query: 228 ALVEWRLETGRTHQ 241
            LV     TGRTHQ
Sbjct: 142 TLVRCSPVTGRTHQ 155

>pdb|1V9K|A Chain A, The Crystal Structure Of The Catalytic Domain Of Pseudouridine Synthase Rluc From Escherichia Coli Length = 228

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 83/194 (42%), Gaps = 53/194 (27%)
Query: 56  IVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQXXXXXXXXXXXX 115
           I YEDD++LV+NKP+   VH   G + G ++ G+                          
Sbjct: 4   IXYEDDHILVLNKPSGTAVHGGSGLSFG-VIEGL-------------------------- 36
Query: 116 XXXXXXXXGASIRPG-----IVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYIS 170
                     ++RP      +VHRLD+ TSG+L+VAK   +   L EQ +    ++ Y++
Sbjct: 37  ---------RALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGXQKDYLA 87
Query: 171 LTSGVPSQSSGRIEVPISRD---PNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGS 227
           L  G        ++ P+ ++      RI   +  G       + + +R+KV E  A   +
Sbjct: 88  LVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEG-------KPSETRFKVEERYA--FA 138
Query: 228 ALVEWRLETGRTHQ 241
            LV     TGRTHQ
Sbjct: 139 TLVRCSPVTGRTHQ 152

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	241
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	2e-87
2i82_A	217	Ribosomal large subunit pseudouridine synthase A;	8e-73
1v9k_A	228	Ribosomal large subunit pseudouridine synthase C;	2e-62

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Length = 325

 Score =  261 bits (669), Expect = 2e-87
 Identities = 75/216 (34%), Positives = 106/216 (49%), Gaps = 36/216 (16%)

Query: 26  SHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTL 85
              V GG+ V       +  R E +DIPLDIVYED++++++NKP  +VVHP  GN  GT+
Sbjct: 55  KEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTV 114

Query: 86  VNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVV 145
           +N +LH+                             I+    R GIVHRLDK T+GL+VV
Sbjct: 115 LNALLHYY--------------------------PPIAD-VPRAGIVHRLDKDTTGLMVV 147

Query: 146 AKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNK 205
           AK   +   L E  +   I R Y ++  G  + + G ++ PISR P  R  MA  P    
Sbjct: 148 AKTVPAQTRLVESLQRREITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMAVHPMG-- 204

Query: 206 HGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ 241
               + A + Y+++E         +  RLETGRTHQ
Sbjct: 205 ----KPAVTHYRIMEHF--RVHTRLRLRLETGRTHQ 234

>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Length = 217

 Score =  220 bits (562), Expect = 8e-73
 Identities = 48/196 (24%), Positives = 83/196 (42%), Gaps = 38/196 (19%)

Query: 46  RAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEA 105
               ++  L I+Y+DD+++VVNKP+ ++  P         V   +     P         
Sbjct: 4   YNPPQEPWLVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRD-YP--------- 53

Query: 106 FSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIE 165
                                 +   VHRLD  TSG++VVA  + +   L  QF+    +
Sbjct: 54  ----------------------QAESVHRLDMATSGVIVVALTKAAERELKRQFREREPK 91

Query: 166 RVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGG 225
           + Y++   G PS + G +++P+  D  NR +        + G  + A + Y+V+E     
Sbjct: 92  KQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCY---ETG--KPAQTEYEVVEYA-AD 145

Query: 226 GSALVEWRLETGRTHQ 241
            +A V  +  TGR+HQ
Sbjct: 146 NTARVVLKPITGRSHQ 161

>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A Length = 228

 Score =  193 bits (494), Expect = 2e-62
 Identities = 46/188 (24%), Positives = 76/188 (40%), Gaps = 37/188 (19%)

Query: 54  LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDIS 113
             I+YEDD++LV+NKP+   VH   G + G +  G+                        
Sbjct: 2   DVIMYEDDHILVLNKPSGTAVHGGSGLSFGVI-EGLRALR-------------------- 40

Query: 114 DDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS 173
                       +    +VHRLD+ TSG+L+VAK   +   L EQ +   +++ Y++L  
Sbjct: 41  ----------PEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVR 90

Query: 174 GVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWR 233
           G        ++ P+ ++                   + + +R+KV E      + LV   
Sbjct: 91  GQWQSHVKSVQAPLLKNILQSGERIVRVSQE----GKPSETRFKVEERY--AFATLVRCS 144

Query: 234 LETGRTHQ 241
             TGRTHQ
Sbjct: 145 PVTGRTHQ 152

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	241
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	100.0
2i82_A	217	Ribosomal large subunit pseudouridine synthase A;	100.0
1v9k_A	228	Ribosomal large subunit pseudouridine synthase C;	100.0
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	99.97
2oml_A	189	Ribosomal large subunit pseudouridine synthase E;	99.97
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	99.97
2olw_A	217	Ribosomal large subunit pseudouridine synthase E;	99.97
3dh3_A	290	Ribosomal large subunit pseudouridine synthase F;	99.95
2gml_A	237	Ribosomal large subunit pseudouridine synthase F;	99.91
1k8w_A	327	TRNA pseudouridine synthase B; protein-RNA complex	97.32
2aus_C	334	Pseudouridine synthase; isomerase, structural prot	97.3
1r3e_A	309	TRNA pseudouridine synthase B; RNA modification, p	97.26
1sgv_A	316	TRNA pseudouridine synthase B; hinged motion, tRNA	97.18
2apo_A	357	Probable tRNA pseudouridine synthase B; protein-pr	97.18
3u28_A	400	H/ACA ribonucleoprotein complex subunit 4; pseudou	97.0
2k6p_A	92	Uncharacterized protein HP_1423; alpha-L motif, RN	96.71
1dm9_A	133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	90.47
2hj1_A	97	Hypothetical protein; structural genomics, PSI, pr	89.94
2q5w_D	77	Molybdopterin converting factor, subunit 1; MOCO,	85.97
3po0_A	89	Small archaeal modifier protein 1; ubiquitin-like	83.46
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	81.3
1fm0_D	81	Molybdopterin convertin factor, subunit 1; molybde	80.64
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	80.49
1vjk_A	98	Molybdopterin converting factor, subunit 1; struct	80.43

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A

Probab=100.00  E-value=8.1e-42  Score=303.51  Aligned_cols=190  Identities=39%  Similarity=0.637  Sum_probs=138.4

Q ss_pred             EEecCee-cCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcC
Q 026204           16 LFLSMDK-LSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS   94 (241)
Q Consensus        16 v~vng~~-~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~   94 (241)
                      |.|||++ .++++.|++||.|.+...........++..+++|+|||++++|+|||+||+||++.+....|+.+.+..++.
T Consensus        44 V~VNG~~v~~~~~~v~~gD~I~v~~~~~~~~~~~~~~~~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~~  123 (325)
T 1v9f_A           44 VLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYP  123 (325)
T ss_dssp             --------------------------------CCCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCG
T ss_pred             EEECCEEccCCCCEeCCCCEEEEeccccccccCCcccCCCeEEEECCCEEEEECCCCCeEecCCCCCCccHHHHHHHHHH
Confidence            8899998 789999999999999765433222334455688999999999999999999999887777899999887753


Q ss_pred             CCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEec
Q 026204           95 LPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSG  174 (241)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G  174 (241)
                      ..                           ....++++|||||++||||||||+|.++++.|+++|+.+.++|+|+|+|.|
T Consensus       124 ~~---------------------------~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~G  176 (325)
T 1v9f_A          124 PI---------------------------ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIG  176 (325)
T ss_dssp             GG---------------------------GGSGGGGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEES
T ss_pred             hc---------------------------CCCCceeeecCCCCCCeeEEEEEcCHHHHHHHHHHHHcCCeeEEEEEEEeC
Confidence            10                           012467899999999999999999999999999999999999999999999


Q ss_pred             ccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          175 VPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       175 ~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      .++. +|+|+.||.++..+..++.+..      +|+.|.|+|++++..  .++|+++|+|.||||||
T Consensus       177 ~~~~-~g~i~~~i~~~~~~~~~~~v~~------~gk~a~t~~~vl~~~--~~~slv~~~l~TGR~HQ  234 (325)
T 1v9f_A          177 HMTA-GGTVDEPISRHPTKRTHMAVHP------MGKPAVTHYRIMEHF--RVHTRLRLRLETGRTHQ  234 (325)
T ss_dssp             CCCC-CEEEECCEEECSSCTTCEEECT------TSBCCEEEEEEEEEC--SSEEEEEEEESCCCTTH
T ss_pred             CCCC-CCEEeeeeeECCCCCEEEEECC------CCeeEEEEEEEeEEc--CCeEEEEEEECCCCcHH
Confidence            9987 8999999999877777777754      789999999999984  57999999999999999

>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli}

Probab=100.00  E-value=3.5e-37  Score=259.15  Aligned_cols=149  Identities=32%  Similarity=0.483  Sum_probs=129.2

Q ss_pred             ccEEEecCcEEEEECCCCceeecCCC-CCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCcccc
Q 026204           54 LDIVYEDDNVLVVNKPAHMVVHPAPG-NATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIV  132 (241)
Q Consensus        54 ~~Ilyed~~llVinKPaGl~~~~~~~-~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  132 (241)
                      ++|+|||++++|+|||+|++||++.+ ....++.+.+...+                                 .++++|
T Consensus        12 ~~ilyed~~~lvvnKP~G~~~~~~~~~~~~~tl~~~l~~~~---------------------------------~~~~~v   58 (217)
T 2i82_A           12 LVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY---------------------------------PQAESV   58 (217)
T ss_dssp             CCEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHHHHHHC---------------------------------TTCEES
T ss_pred             ceEEEECCCEEEEECCCCCeEeCCCCCCchhHHHHHHHHHC---------------------------------CCCcee
Confidence            78999999999999999999998764 34578988887653                                 135789


Q ss_pred             ccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcce
Q 026204          133 HRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHA  212 (241)
Q Consensus       133 hRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a  212 (241)
                      ||||++||||||||+|.++++.|+++|+++.++|+|+|+|.|.++.+.+.|+.||.++..+...+.+..     .+++.|
T Consensus        59 hRLD~~TSGlll~ak~~~~~~~l~~~f~~~~v~K~Y~a~v~G~~~~~~g~i~~~l~~~~~~~~~~~v~~-----~~gk~a  133 (217)
T 2i82_A           59 HRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCY-----ETGKPA  133 (217)
T ss_dssp             SCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCSSSEEEEECCEEECGGGTTCEEECT-----TTCBCC
T ss_pred             ecCCCCCeEEEEEEeCHHHHHHHHHHHHhCCeeEEEEEEEecccCCCCcEEecceeecCCCCcEEEEeC-----CCCcEE
Confidence            999999999999999999999999999999999999999999998888999999998765544455432     378999


Q ss_pred             EEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          213 ASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       213 ~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      .|+|++++... .++|+++|+|.|||+||
T Consensus       134 ~t~~~vl~~~~-~~~slv~~~l~TGR~HQ  161 (217)
T 2i82_A          134 QTEYEVVEYAA-DNTARVVLKPITGRSHQ  161 (217)
T ss_dssp             EEEEEEEEEET-TTEEEEEEEESSCCTTH
T ss_pred             EEEEEEEEECC-CCeEEEEEEECCCCcHH
Confidence            99999999852 23899999999999999

>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A

Probab=100.00  E-value=7e-36  Score=253.03  Aligned_cols=148  Identities=30%  Similarity=0.449  Sum_probs=126.2

Q ss_pred             cEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCcccccc
Q 026204           55 DIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHR  134 (241)
Q Consensus        55 ~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhR  134 (241)
                      +|+|||++++|+|||+|++|||+.+ ...++.+.+...+.                              ...++++|||
T Consensus         3 ~Ilyed~~~lvvnKP~G~~~~~~~~-~~~~l~~~l~~~~~------------------------------~~~~~~~VhR   51 (228)
T 1v9k_A            3 VIMYEDDHILVLNKPSGTAVHGGSG-LSFGVIEGLRALRP------------------------------EARFLELVHR   51 (228)
T ss_dssp             CEEEECSSEEEEEECTTSCSSCCSS-SBCCHHHHHHHHST------------------------------TCSCCEESSC
T ss_pred             CEEEECCCEEEEECCCCCeEecCCC-hHHHHHHHHHHHcC------------------------------CCCccceEec
Confidence            4999999999999999999999765 45678887765532                              1245788999


Q ss_pred             CCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCC--CeeEEEecCCCCCCCCcce
Q 026204          135 LDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNN--RIRMAAIPGSNKHGQARHA  212 (241)
Q Consensus       135 LD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~--~~~~~~~~~~~~~~~~k~a  212 (241)
                      ||++||||||||+|.++++.|+++|+++.++|+|+|+|.|.++.+.+.|+.||.++...  ...+.+..      +|+.|
T Consensus        52 LD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~g~~~~~~~~------~gk~a  125 (228)
T 1v9k_A           52 LDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQ------EGKPS  125 (228)
T ss_dssp             CCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCTTCCEECCCEEEEECTTSCEEEEECT------TSBCC
T ss_pred             CCCCCeEEEEEEeCHHHHHHHHHHHHhCCeeEEEEEEEecccCCCCCEEeCceeccCCCCCceEEEECC------CCcEE
Confidence            99999999999999999999999999999999999999999998899999999876432  23344432      68999


Q ss_pred             EEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          213 ASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       213 ~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      .|+|++++..  .++|+++|+|.||||||
T Consensus       126 ~t~~~vl~~~--~~~slv~~~l~TGR~HQ  152 (228)
T 1v9k_A          126 ETRFKVEERY--AFATLVRCSPVTGRTHQ  152 (228)
T ss_dssp             CEEEEEEEEC--SSEEEEEEEESSCCTTH
T ss_pred             EEEEEEEEEc--CCeEEEEEEECCCCchH
Confidence            9999999984  56999999999999999

>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A*

Probab=99.97  E-value=5.5e-33  Score=236.04  Aligned_cols=158  Identities=16%  Similarity=0.189  Sum_probs=121.1

Q ss_pred             eEEecCeecC-CCceecCCCEEEEEecCCCCccCCCCCCCccEEEe-cCcEEEEECCCCceeecCCCCCCCCHHHHHHHh
Q 026204           15 ALFLSMDKLS-VSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYE-DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHH   92 (241)
Q Consensus        15 ~v~vng~~~~-~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilye-d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~   92 (241)
                      .|.|||++++ +++.|++||.|.+..              ..|+|| |++++|+|||+||+|||..+. ..|+.+.+..+
T Consensus        29 ~V~VNG~~v~~~~~~v~~gD~I~v~~--------------~~i~~e~d~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~   93 (234)
T 1ksk_A           29 RVTVDGEIVRNAAFKLLPEHDVAYDG--------------NPLAQQHGPRYFMLNKPQGYVCSTDDPD-HPTVLYFLDEP   93 (234)
T ss_dssp             CEEETTEECCCTTCEECTTCCEEETT--------------EEECCCCCCCEEEEEECTTCBSSSSCSS-SCBGGGGCCCT
T ss_pred             eEEECCEEeCCCCCCCCCCCEEEEeC--------------eEeecCCCCEEEEEECCCCCEeCCCCCC-CCcHHHHhhhh
Confidence            4899999986 999999999998831              138999 999999999999999998764 56776654332


Q ss_pred             cCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEE
Q 026204           93 CSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLT  172 (241)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV  172 (241)
                      +                                ..++++|||||++||||||||+|.++++.|.+  +.+.++|+|+|+|
T Consensus        94 ~--------------------------------~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~--~~~~v~K~Y~a~v  139 (234)
T 1ksk_A           94 V--------------------------------AWKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRHHCEKTYLVTL  139 (234)
T ss_dssp             T--------------------------------GGGCEESSCCCTTCEEEEEEESCHHHHHHHHC--TTSCCCEEEEEEE
T ss_pred             h--------------------------------cCCeeEcCCCCCCCeeEEEEEcCHHHHHHHhC--CCCCCCeEEEEEE
Confidence            1                                13578999999999999999999999998876  7889999999999


Q ss_pred             ecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          173 SGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       173 ~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      .|.++...  |+.+..  .     +....   ....+++|.  |++++      +|+++|+|.||||||
T Consensus       140 ~g~~~~~~--i~~~~~--g-----~~~~~---~~~~~~~a~--~~~~~------~s~~~~~l~tGR~HQ  188 (234)
T 1ksk_A          140 ESPVADDT--AEQFAK--G-----VQLHN---EKDLTKPAV--LEVIT------PTQVRLTISEGRYHQ  188 (234)
T ss_dssp             SSCCCTTH--HHHHHH--C-----CCCTT---CSSCCCCCE--EEEEE------TTEEEEEESCCCTTH
T ss_pred             ccCCCHHH--HHHHHC--C-----eEECC---CCcccceEE--EEEeC------CeEEEEEEccCCCHH
Confidence            99987652  333321  0     00110   001345554  56664      489999999999999

>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli}

Probab=99.97  E-value=2e-33  Score=231.54  Aligned_cols=145  Identities=18%  Similarity=0.189  Sum_probs=106.2

Q ss_pred             ccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccc
Q 026204           54 LDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVH  133 (241)
Q Consensus        54 ~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vh  133 (241)
                      ..|||||++++|+|||+||+||+..+....|+.+.+.                                   ..++++||
T Consensus         4 ~~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~-----------------------------------~~~~~~vh   48 (189)
T 2oml_A            4 RKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-----------------------------------VQGVYAAG   48 (189)
T ss_dssp             ----CCCCCEEEEEECTTBCSCSSCCTTCBCGGGTCC-----------------------------------CSSCEESS
T ss_pred             cccccCCCeEEEEECCCCCEecCCCCCCCCCHHHHcC-----------------------------------CCCceECC
Confidence            3599999999999999999999987766667654332                                   02468899


Q ss_pred             cCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCc-cEEEcceeeCCCC-C-eeEEEecCCCCCCCCc
Q 026204          134 RLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSS-GRIEVPISRDPNN-R-IRMAAIPGSNKHGQAR  210 (241)
Q Consensus       134 RLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~-~~i~~~i~~~~~~-~-~~~~~~~~~~~~~~~k  210 (241)
                      |||++||||||||+|.++++.|+++  .+.++|+|+|+|.|.++.+. +.+..++..+... . .......     ....
T Consensus        49 RLD~~TSGlll~ak~~~~~~~l~~~--~~~v~K~Y~a~v~G~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~-----~~~~  121 (189)
T 2oml_A           49 RLDRDSEGLLVLTNNGALQARLTQP--GKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVD-----EPAW  121 (189)
T ss_dssp             CCCTTCEEEEEEESCHHHHHHHHST--TSCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEEC-----CCTT
T ss_pred             CCCCCCeeEEEEEcCHHHHHHHhCc--cCCCcEEEEEEEcCCCCHHHHHHHHcCceeCCceeeeeEEEEec-----cccc
Confidence            9999999999999999999999996  67899999999999987654 3566676533211 1 1111111     1122


Q ss_pred             ceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          211 HAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       211 ~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      .+.|.|+++... ..++|+++|+|.|||+||
T Consensus       122 ~~~t~~~v~~~~-~~~~slv~~~l~TGR~HQ  151 (189)
T 2oml_A          122 LWPRNPPIRERK-SIPTSWLKITLYEGRNRQ  151 (189)
T ss_dssp             CCCCSSCCC-CT-TSCEEEEEEEESCCCTTH
T ss_pred             cccccccccccc-CCCcEEEEEEEeeCCCHH
Confidence            346888888752 247999999999999999

>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5

Probab=99.97  E-value=1.3e-32  Score=235.05  Aligned_cols=158  Identities=16%  Similarity=0.201  Sum_probs=119.1

Q ss_pred             eEEecCeec-CCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCc-EEEEECCCCceeecCCCCCCCCHHHHHHHh
Q 026204           15 ALFLSMDKL-SVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDN-VLVVNKPAHMVVHPAPGNATGTLVNGILHH   92 (241)
Q Consensus        15 ~v~vng~~~-~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~-llVinKPaGl~~~~~~~~~~~tl~~~l~~~   92 (241)
                      .|.|||+++ ++++.|.+||.|.+.              +..|+|||++ ++|+|||+||+||+..+. ..|+.+.|..+
T Consensus        28 ~V~VNG~~v~~~~~~v~~gD~I~v~--------------~~~i~~ed~~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~~   92 (243)
T 1vio_A           28 AVKINGEIVKSGSVQISQEDEIYFE--------------DELLTWIEEGQYFMLNKPQGCVCSNDDGD-YPTIYQFFDYP   92 (243)
T ss_dssp             CEEETTEECCCTTCEECTTSCEEET--------------TEECCSSCCCCEEEEEECTTCBSSCCC---CCBGGGGSCTT
T ss_pred             cEEECCEEeCCCCCCcCCCCEEEEe--------------ccccccCCCCEEEEEECCCCCEeCCCCCC-CCcHHHHHhHH
Confidence            489999998 599999999988873              1248999999 999999999999998764 56776654432


Q ss_pred             cCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEE
Q 026204           93 CSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLT  172 (241)
Q Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV  172 (241)
                      +                                ..++++|||||++||||||||+|++++..+..  +.+.++|+|+|+|
T Consensus        93 ~--------------------------------~~~~~~vhRLD~~TsGlll~ak~~~~a~~l~~--~~~~v~K~Y~a~v  138 (243)
T 1vio_A           93 L--------------------------------AGKLHSAGRLDVDTTGLVLLTDDGQWSHRITS--PKHHCEKTYLVTL  138 (243)
T ss_dssp             G--------------------------------GGGCEESSCCCTTCEEEEEEESCHHHHHHHHC--TTSCCCEEEEEEE
T ss_pred             h--------------------------------cCCEeEccCCCCCCeEEEEEEECHHHHHHHhC--CCCCCCEEEEEEE
Confidence            1                                13578899999999999999999998888865  7889999999999


Q ss_pred             ecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          173 SGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       173 ~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      .|.++.+  .|+.+..  .     +.+..   ....+++|.  |++++      +|+++|+|.||||||
T Consensus       139 ~g~~~~~--~i~~~~~--g-----~~~~~---~~~~~~~a~--~~~l~------~sl~~~~l~tGR~HQ  187 (243)
T 1vio_A          139 ADPVEEN--YSAACAE--G-----ILLRG---EKEPTKPAK--LEILD------DYNVNLTISEGRYHQ  187 (243)
T ss_dssp             SSCCCTT--HHHHHHH--C-----CCCTT---CSSCCCCCE--EEECS------SSEEEEEESCCCTTH
T ss_pred             eCCCCHH--HHHHHhC--C-----eEECC---CCccceeEE--EEEeC------CEEEEEEEccCCcHH
Confidence            9998765  2333321  0     00111   011356665  45553      599999999999999

>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli}

Probab=99.97  E-value=8.2e-32  Score=226.39  Aligned_cols=146  Identities=18%  Similarity=0.201  Sum_probs=99.2

Q ss_pred             CccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCcccc
Q 026204           53 PLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIV  132 (241)
Q Consensus        53 ~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  132 (241)
                      .+.|||||++++|+|||+|++||+..+....|+.+.+.                                   ..++++|
T Consensus        31 ~~~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~tl~~~l~-----------------------------------~~~~~~V   75 (217)
T 2olw_A           31 RRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-----------------------------------VQGVYAA   75 (217)
T ss_dssp             ------CCCCEEEEEECTTBCSCSSCCTTSBCGGGTCC-----------------------------------CCSCEES
T ss_pred             cCceEeeCCcEEEEECCCCCEeccCCCCCCccHHHHhC-----------------------------------cCCceEC
Confidence            56799999999999999999999987766667655332                                   0246889


Q ss_pred             ccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCc-cEEEcceeeCC-CC-CeeEEEecCCCCCCCC
Q 026204          133 HRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSS-GRIEVPISRDP-NN-RIRMAAIPGSNKHGQA  209 (241)
Q Consensus       133 hRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~-~~i~~~i~~~~-~~-~~~~~~~~~~~~~~~~  209 (241)
                      ||||++||||||||+|.++++.|++.  .+.++|+|+|+|.|.++.+. +.|..++..+. .. .....+...     ..
T Consensus        76 hRLDr~TSGllllAk~~~~~~~L~~~--~~~v~K~Y~A~V~G~~~~~~~~~i~~~i~~~~g~~~~~~~~~~~~-----~~  148 (217)
T 2olw_A           76 GRLDRDSEGLLVLTNNGALQARLTQP--GKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDE-----PA  148 (217)
T ss_dssp             SCCCTTCEEEEEEESCHHHHHHHHCT--TCCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECC-----CT
T ss_pred             CCCCCCCeeEEEEEcCHHHHHHHHcc--cccCCEEEEEEEccCCCHHHHHHHhCCEEeCCCcccceEEEEecC-----Cc
Confidence            99999999999999999999999995  67899999999999987655 45666664321 11 111111110     00


Q ss_pred             cceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          210 RHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       210 k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                       .+.+.+.++......++|+++|+|.|||+||
T Consensus       149 -~~~~~~~~v~~~~~~~~slv~~~l~TGRtHQ  179 (217)
T 2olw_A          149 -WLWPRNPPIRERKSIPTSWLKITLYEGRNRQ  179 (217)
T ss_dssp             -TCCCCSSCCC-CCSSCEEEEEEEESCCCTTH
T ss_pred             -cccccccceeccCCCCcEEEEEEECcCCCHH
Confidence             1122222222222247899999999999999

>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}

Probab=99.95  E-value=1.5e-29  Score=220.67  Aligned_cols=157  Identities=20%  Similarity=0.241  Sum_probs=116.1

Q ss_pred             eEEecCeecCCCceecCCCEEEEEecCCCCccCCCCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcC
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCTISELQPLRAEAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCS   94 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~~~~~~~~~~~~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~   94 (241)
                      .|.|||+++++++.|.+||.|.+......     +      ..|||++|+|+|||+|++||+.... ..|+.+.+..   
T Consensus        32 ~V~VNG~~v~~~~~V~~gD~I~v~~~~i~-----~------~~~ed~~~lvvnKP~G~~~~~~~~~-~~tl~~~l~~---   96 (290)
T 3dh3_A           32 NVFLNGKRATIGDQVKPGDVVKVNGQLIE-----P------REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFVNH---   96 (290)
T ss_dssp             CEEETTEECCTTCEECTTCCEEETTEEEC-----C------CCGGGCCEEEEEECTTCBCCCCSSC-TTBHHHHHTC---
T ss_pred             CEEECCEEccCCcCcCCCCEEEecccccc-----c------cccccceEEEEECCCccccCCCCCC-CCcHHHHhhc---
Confidence            48999999999999999999999542211     1      1278999999999999999998754 5688776642   


Q ss_pred             CCccccccccccccccccccccccccccCCCCCCccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEec
Q 026204           95 LPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSG  174 (241)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G  174 (241)
                                                     ..++++|||||++||||||||+|.++++.|.+  +.+.++|+|+|+|.|
T Consensus        97 -------------------------------~~~~~~VhRLD~dTSGLllla~d~~~~~~L~~--~~~~v~K~Y~a~V~G  143 (290)
T 3dh3_A           97 -------------------------------SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILR--AGNDHEKEYLVTVDK  143 (290)
T ss_dssp             -------------------------------SSCCEESSCCCTTCEEEEEEESCTTHHHHHHC--GGGCCCEEEEEEESS
T ss_pred             -------------------------------cCceeeeccCCCCCcceEEEcCCHHHHHHHHH--hhCCcCEEEEEEECC
Confidence                                           14678899999999999999999999999988  567899999999999


Q ss_pred             ccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          175 VPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       175 ~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      .++++..  . .+. .+   .  .. .    ....+++.  ++.      .+.++++|.|.|||+||
T Consensus       144 ~~~~~~i--~-~l~-~G---v--~l-~----~~~~~~~~--v~~------~~~~~l~l~l~tGR~HQ  188 (290)
T 3dh3_A          144 PITEEFI--R-GMS-AG---V--PI-L----GTVTKKCK--VKK------EAPFVFRITLVQGLNRQ  188 (290)
T ss_dssp             CCCHHHH--H-HHH-TC---C--BC-S----SSBCCCCE--EEE------CSSSEEEEEESCCCTTH
T ss_pred             CCCHHHH--H-HHh-cC---c--cc-C----CcccceEE--EEE------cCCeEEEEEEeCCCChH
Confidence            9865431  1 010 00   0  00 1    00112232  222      24589999999999998

>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli}

Probab=99.91  E-value=3.5e-25  Score=187.43  Aligned_cols=123  Identities=19%  Similarity=0.198  Sum_probs=91.7

Q ss_pred             cCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCC
Q 026204           60 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT  139 (241)
Q Consensus        60 d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T  139 (241)
                      ++.|||+|||+|++|++... ...|+.+.+..                                  ..++++|||||++|
T Consensus        13 ~~~~lvlnKPaG~vs~~~~~-~~~tv~dll~~----------------------------------~~rl~~VgRLD~dT   57 (237)
T 2gml_A           13 DLVLIALNKPVGIVSTTEDG-ERDNIVDFVNH----------------------------------SKRVFPIGRLDKDS   57 (237)
T ss_dssp             CCCEEEEEECTTCBCCSSSS-CSSBHHHHSCC----------------------------------SSCCEEESCCCTTC
T ss_pred             CCEEEEEECCCCCEeCCCCC-CCCCHHHHhhc----------------------------------cCCeeEecCCCCCC
Confidence            46799999999999998755 45677765421                                  13578999999999


Q ss_pred             ceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEE
Q 026204          140 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVI  219 (241)
Q Consensus       140 SGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl  219 (241)
                      |||||||+|.+++.+|.+  +.+.++|+|+|+|.|.++++..  +. +. .  +   +.+ .      +++.+.+.++++
T Consensus        58 SGLLLlT~dg~~a~~L~~--p~~~v~K~Y~a~V~G~~~~~~i--~~-l~-~--G---v~l-~------~~~~~~a~~~~l  119 (237)
T 2gml_A           58 QGLIFLTNHGDLVNKILR--AGNDHEKEYLVTVDKPITEEFI--RG-MS-A--G---VPI-L------GTVTKKCKVKKE  119 (237)
T ss_dssp             EEEEEEESCHHHHHHHHH--HHHHSCEEEEEEESSCCCHHHH--HH-HS-S--C---CEE-T------TEECCCCEEEEE
T ss_pred             eeEEEEEcCHHHHHHHhC--ccCCCCEEEEEEEcccCCHHHH--HH-HH-c--C---eEe-C------CcccccEEEEEe
Confidence            999999999999999988  6778999999999999865431  11 11 0  0   111 1      233344556666


Q ss_pred             EEecCCCEEEEEEEcCCCCCCC
Q 026204          220 EILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       220 ~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      .      .++++|.|.|||+||
T Consensus       120 ~------~s~l~i~L~tGR~HQ  135 (237)
T 2gml_A          120 A------PFVFRITLVQGLNRQ  135 (237)
T ss_dssp             E------TTEEEEEECCCSTTH
T ss_pred             C------CEEEEEEEecCCcHH
Confidence            3      389999999999999

>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A

Probab=97.32  E-value=0.00021  Score=62.58  Aligned_cols=72  Identities=21%  Similarity=0.337  Sum_probs=56.4

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||+||-+|        .++..++..+.                               ..+++..+.||-..|
T Consensus        25 ~Gil~vdKP~G~TS~--------dvv~~vr~~l~-------------------------------~kKvGH~GTLDP~At   65 (327)
T 1k8w_A           25 NGVLLLDKPQGMSSN--------DALQKVKRIYN-------------------------------ANRAGHTGALDPLAT   65 (327)
T ss_dssp             CEEEEEEECTTCCHH--------HHHHHHHHHTT-------------------------------CSCEEESSCCCTTCE
T ss_pred             CeEEEEECCCCCCHH--------HHHHHHHHhhc-------------------------------cceeccCCCCCCCCe
Confidence            569999999999875        47777877654                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe-cc
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS-GV  175 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~-G~  175 (241)
                      |+|+++-...+  ++...+..  ..|+|.|.+. |.
T Consensus        66 GvL~i~~G~aT--Kl~~~l~~--~~K~Y~a~~~lG~   97 (327)
T 1k8w_A           66 GMLPICLGEAT--KFSQYLLD--SDKRYRVIARLGQ   97 (327)
T ss_dssp             EEEEEEEGGGG--GGTHHHHT--SCEEEEEEEEETE
T ss_pred             eEEEEEECHHH--hHHHHhcc--CCcEEEEEEEECC
Confidence            99999998753  35555554  3899999876 44

>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A

Probab=97.30  E-value=0.00017  Score=63.60  Aligned_cols=71  Identities=23%  Similarity=0.275  Sum_probs=56.6

Q ss_pred             cCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCC
Q 026204           60 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT  139 (241)
Q Consensus        60 d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T  139 (241)
                      .+.+++||||+|+-+|        .++..+...+.                               ..+.+..+-||-..
T Consensus        45 ~~Gil~vdKP~g~tS~--------~vv~~vr~~~~-------------------------------~~KvGH~GTLDP~a   85 (334)
T 2aus_C           45 QYGVINLDKPPGPTSH--------EVVAWIKRILN-------------------------------LEKAGHGGTLDPKV   85 (334)
T ss_dssp             HTEEEEEEECSSSCHH--------HHHHHHHHHTT-------------------------------CSCEEESSCCCTTC
T ss_pred             cCcEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------cceeccccccCCcc
Confidence            4679999999999875        47778877764                               25678899999999


Q ss_pred             ceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          140 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       140 SGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      ||+|+++-...  .++.+.+..  ..|+|.|.+.
T Consensus        86 tGvL~v~~g~a--Tk~~~~l~~--~~K~Y~~~~~  115 (334)
T 2aus_C           86 SGVLPVALERA--TRVVQALLP--AGKEYVALMH  115 (334)
T ss_dssp             EEEEEEEEGGG--GGGGGGGTT--CCEEEEEEEE
T ss_pred             ceeEEEEeChh--hhhHHHhcc--cCcEEEEEEE
Confidence            99999999753  356565655  5899999876

>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A

Probab=97.26  E-value=0.00018  Score=62.55  Aligned_cols=70  Identities=21%  Similarity=0.341  Sum_probs=56.0

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.++++|||+|+-||        .++..++..+.                               ..+.+..+.||-..|
T Consensus         3 ~Gil~vdKP~G~TS~--------~vv~~vrr~l~-------------------------------~kKvGH~GTLDP~At   43 (309)
T 1r3e_A            3 HGILVAYKPKGPTSH--------DVVDEVRKKLK-------------------------------TRKVGHGGTLDPFAC   43 (309)
T ss_dssp             CEEEEEEECSSSCHH--------HHHHHHHHHTT-------------------------------CSCEEESSCCCTTCE
T ss_pred             CeEEEEECCCCCCHH--------HHHHHHHHHhc-------------------------------cceecccccCCCCcc
Confidence            469999999999875        47788887764                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-.+.  .++...+..  ..|+|.|.+.
T Consensus        44 GvL~i~iG~a--TKl~~~l~~--~~K~Y~a~~~   72 (309)
T 1r3e_A           44 GVLIIGVNQG--TRILEFYKD--LKKVYWVKMR   72 (309)
T ss_dssp             EEEEEEEGGG--GGGGGGGTT--SCEEEEEEEE
T ss_pred             eeEEEEECHH--HhHHHHhCc--cCcEEEEEEE
Confidence            9999999874  355555554  4899999876

>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2

Probab=97.18  E-value=0.00024  Score=61.93  Aligned_cols=71  Identities=21%  Similarity=0.342  Sum_probs=56.7

Q ss_pred             cCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCC
Q 026204           60 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT  139 (241)
Q Consensus        60 d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T  139 (241)
                      .+.++++|||.||-||        .++..++..+.                               ..+++..+.||-..
T Consensus         5 ~~Gil~vdKP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~A   45 (316)
T 1sgv_A            5 GPGIVVIDKPAGMTSH--------DVVGRCRRIFA-------------------------------TRRVGHAGTLDPMA   45 (316)
T ss_dssp             CSEEEEEEECTTCCHH--------HHHHHHHHHTT-------------------------------CSCEEESSCCCTTC
T ss_pred             CCeEEEEECCCCCCHH--------HHHHHHHHHhc-------------------------------cccccccccCCCCC
Confidence            3579999999999875        47788887764                               25678899999999


Q ss_pred             ceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          140 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       140 SGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      ||+|+++-.+.  .++...+..  ..|+|.|.+.
T Consensus        46 tGvL~i~iG~a--TKl~~~l~~--~~K~Y~~~~~   75 (316)
T 1sgv_A           46 TGVLVIGIERA--TKILGLLTA--APKSYAATIR   75 (316)
T ss_dssp             EEEEEEEEGGG--GGGGGGTTT--SCEEEEEEEE
T ss_pred             eEEEEEEECHH--HhHHHHhCc--CCcEEEEEEE
Confidence            99999999874  345555544  5999999876

>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2

Probab=97.18  E-value=0.00025  Score=62.91  Aligned_cols=71  Identities=21%  Similarity=0.269  Sum_probs=56.9

Q ss_pred             cCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCC
Q 026204           60 DDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGT  139 (241)
Q Consensus        60 d~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~T  139 (241)
                      .+.+++||||+|+-+|        .++..++..+.                               ..+.+..+-||-..
T Consensus        65 ~~Gil~vdKP~G~TS~--------~vv~~vr~~l~-------------------------------~~KvGH~GTLDP~A  105 (357)
T 2apo_A           65 KYGVVVVDKPRGPTSH--------EVSTWVKKILN-------------------------------LDKAGHGGTLDPKV  105 (357)
T ss_dssp             HTEEEEEEECSSSCHH--------HHHHHHHHHTT-------------------------------CSCEEESSCCCTTC
T ss_pred             cCcEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------ccccccccccCCCc
Confidence            5679999999999875        47788887764                               25678899999999


Q ss_pred             ceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          140 SGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       140 SGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      ||+|+++-...  .++...+..  ..|+|.|.+.
T Consensus       106 tGvL~v~~G~a--Tk~~~~l~~--~~K~Y~~~~~  135 (357)
T 2apo_A          106 TGVLPVALERA--TKTIPMWHI--PPKEYVCLMH  135 (357)
T ss_dssp             EEEEEEEEGGG--GGGGGGTTS--SCEEEEEEEE
T ss_pred             eeEEEEEeCHH--HhHHHHhcc--CCcEEEEEEE
Confidence            99999999753  356565655  7899999876

>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A

Probab=97.00  E-value=0.00054  Score=61.45  Aligned_cols=74  Identities=20%  Similarity=0.264  Sum_probs=57.3

Q ss_pred             ecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCC
Q 026204           59 EDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKG  138 (241)
Q Consensus        59 ed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~  138 (241)
                      -.+.+|+||||+|+-+|        .++..++..+.                               ..+.+..+-||-.
T Consensus        57 ~~~Gil~ldKP~G~TS~--------dvv~~vrr~l~-------------------------------~kKvGH~GTLDP~   97 (400)
T 3u28_A           57 ISSGVINLDKPSNPSSH--------EVVAWIKRILR-------------------------------CEKTGHSGTLDPK   97 (400)
T ss_dssp             HHTEEEEEEECSSSCHH--------HHHHHHHHHHT-------------------------------CSCEEESSCCCTT
T ss_pred             ccCcEEEEECCCCCCHH--------HHHHHHHHHhC-------------------------------cCcccccCCCCCC
Confidence            34689999999999876        47788887764                               2567889999999


Q ss_pred             CceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe-cc
Q 026204          139 TSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS-GV  175 (241)
Q Consensus       139 TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~-G~  175 (241)
                      .||+|+++-.+.  .++...+..  ..|+|.|.+. |.
T Consensus        98 AtGvL~v~iG~a--TKl~~~l~~--~~K~Y~a~~~lG~  131 (400)
T 3u28_A           98 VTGCLIVCIDRA--TRLVKSQQG--AGKEYVCIVRLHD  131 (400)
T ss_dssp             CEEEEEEEEGGG--GGGHHHHHH--SCEEEEEEEEESS
T ss_pred             CeEEEEEEEChH--HhHhHHhcC--CCcEEEEEEEeCC
Confidence            999999999763  344455544  5899999875 44

>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}

Probab=96.71  E-value=0.00055  Score=48.73  Aligned_cols=49  Identities=14%  Similarity=0.097  Sum_probs=34.4

Q ss_pred             eEEecCeecCCCceecCCCEEEEEecCCCCc-c-------CCCCCCCccEEEecCcE
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCTISELQPL-R-------AEAEDIPLDIVYEDDNV   63 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~~~~~~~~-~-------~~~~~~~~~Ilyed~~l   63 (241)
                      .|+|||+++++++.|++||.|.+...+.... .       .......+.++|||+++
T Consensus        27 ~V~VNg~~~~~~~~v~~gd~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~~lyed~~~   83 (92)
T 2k6p_A           27 AVWLNGSCAKASKEVKAGDTISLHYLKGIEEYTILQIPALKNVPRKDTHLYIAPKTK   83 (92)
T ss_dssp             CCEETTEECCTTCBCCTTCEEEECCSSCCEEEEECCCCCCSCCCSSSTTSSEEECCC
T ss_pred             cEEECCEEcCCCCCcCCCCEEEEEeCCceEEEEEeccccccCCCHHHHHHHHHhcCC
Confidence            3899999999999999999999976442211 0       01222347899998764

>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A

Probab=90.47  E-value=0.22  Score=37.68  Aligned_cols=27  Identities=7%  Similarity=-0.020  Sum_probs=23.9

Q ss_pred             eEEecCeecCCCceecCCCEEEEEecC
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCTISE   41 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~~~~   41 (241)
                      .|.|||+++++++.|..||.|.|....
T Consensus        35 ~V~VNG~~vk~s~~V~~GD~I~I~~~~   61 (133)
T 1dm9_A           35 KVHYNGQRSKPSKIVELNATLTLRQGN   61 (133)
T ss_dssp             CEEETTEECCTTCBCCTTCEEEEEETT
T ss_pred             cEEECCEEcCCCCEeCCCCEEEEEeCC
Confidence            389999999999999999999997643

>2hj1_A Hypothetical protein; structural genomics, PSI, protein structure initiative, NEW research center for structural genomics, nysgxrc; 2.10A {Haemophilus influenzae} SCOP: d.15.3.4

Probab=89.94  E-value=0.16  Score=36.32  Aligned_cols=27  Identities=11%  Similarity=0.115  Sum_probs=24.6

Q ss_pred             eeEEecCeecCCCceecCCCEEEEEec
Q 026204           14 LALFLSMDKLSVSHNVKGGDMVNCTIS   40 (241)
Q Consensus        14 ~~v~vng~~~~~~~~l~~GD~i~~~~~   40 (241)
                      .+|-|||+.++.++.|+.||+|+|+..
T Consensus        59 ~~V~Vng~~v~~d~~L~dGDRVEIyrp   85 (97)
T 2hj1_A           59 NKIGIFSRPIKLTDVLKEGDRIEIYRP   85 (97)
T ss_dssp             SEEEEEECSCCTTCBCCTTCEEEECCC
T ss_pred             cEEEEcCEECCCCccCCCCCEEEEEec
Confidence            578999999999999999999999754

>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B*

Probab=85.97  E-value=0.81  Score=30.53  Aligned_cols=24  Identities=13%  Similarity=0.109  Sum_probs=22.4

Q ss_pred             eEEecCeecCCCceecCCCEEEEE
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCT   38 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~   38 (241)
                      .+.|||+.+..++.|+.||+|.+.
T Consensus        48 ~v~vNg~~v~~~~~L~~gD~V~i~   71 (77)
T 2q5w_D           48 QVAVNEEFVQKSDFIQPNDTVALI   71 (77)
T ss_dssp             EEEETTEEECTTSEECTTCEEEEE
T ss_pred             EEEECCEECCCCCCcCCCCEEEEE
Confidence            689999999999999999999985

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A

Probab=83.46  E-value=0.89  Score=31.34  Aligned_cols=27  Identities=7%  Similarity=0.108  Sum_probs=23.8

Q ss_pred             eeeEEecCeecCCCceecCCCEEEEEe
Q 026204           13 VLALFLSMDKLSVSHNVKGGDMVNCTI   39 (241)
Q Consensus        13 ~~~v~vng~~~~~~~~l~~GD~i~~~~   39 (241)
                      ...+.|||+.+..++.|+.||+|.+..
T Consensus        58 ~~~v~VN~~~v~~~~~l~~gDeV~i~P   84 (89)
T 3po0_A           58 HINVLRNGEAAALGEATAAGDELALFP   84 (89)
T ss_dssp             TSEEEETTEECCTTSBCCTTCEEEEEC
T ss_pred             cEEEEECCEECCCCcccCCCCEEEEEC
Confidence            357899999999999999999999953

>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C

Probab=81.30  E-value=1  Score=34.98  Aligned_cols=26  Identities=15%  Similarity=0.212  Sum_probs=22.6

Q ss_pred             eEEecCeec-CCCceecCCCEEEEEec
Q 026204           15 ALFLSMDKL-SVSHNVKGGDMVNCTIS   40 (241)
Q Consensus        15 ~v~vng~~~-~~~~~l~~GD~i~~~~~   40 (241)
                      .|.|||+++ ++++.|.+||.|.+...
T Consensus        77 ~V~VNG~~v~~ps~~V~~gD~I~V~~~  103 (159)
T 1c05_A           77 HILVDGSRVNIPSYRVKPGQTIAVREK  103 (159)
T ss_dssp             CEEETTEECCCSSCBCCTTCEEEECGG
T ss_pred             CEEECCEEeCcCCcEeCCCCEEEEeCc
Confidence            489999998 59999999999999643

>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} SCOP: d.15.3.1 PDB: 1fma_D 1jw9_D 1jwa_D* 1jwb_D* 3bii_D 1nvi_D

Probab=80.64  E-value=1.6  Score=29.30  Aligned_cols=24  Identities=21%  Similarity=0.224  Sum_probs=22.2

Q ss_pred             eEEecCeecCCCceecCCCEEEEE
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCT   38 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~   38 (241)
                      .+.|||+.+..++.|+.||+|.+.
T Consensus        52 ~v~vN~~~v~~~~~l~~gD~V~i~   75 (81)
T 1fm0_D           52 LAAVNQTLVSFDHPLTDGDEVAFF   75 (81)
T ss_dssp             EEEETTEECCTTCBCCTTCEEEEE
T ss_pred             EEEECCEECCCCCCCCCCCEEEEe
Confidence            599999999999999999999985

>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6

Probab=80.49  E-value=0.58  Score=31.76  Aligned_cols=24  Identities=8%  Similarity=0.039  Sum_probs=20.6

Q ss_pred             eEEecCeec-CCCceecCCCEEEEE
Q 026204           15 ALFLSMDKL-SVSHNVKGGDMVNCT   38 (241)
Q Consensus        15 ~v~vng~~~-~~~~~l~~GD~i~~~   38 (241)
                      .|+|||+++ ++++.|.+||.|.+.
T Consensus        47 ~V~VNG~~v~~~~~~v~~gd~I~v~   71 (79)
T 1p9k_A           47 QVKVDGAVETRKRCKIVAGQTVSFA   71 (79)
T ss_dssp             HHEETTBCCCCSSCCCCSSEEEEET
T ss_pred             EEEECCEEecCCCCCCCCCCEEEEC
Confidence            389999987 689999999988873

>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PSI, protein structure INI southeast collaboratory for structural genomics; 1.51A {Pyrococcus furiosus} SCOP: d.15.3.1

Probab=80.43  E-value=1.3  Score=31.22  Aligned_cols=27  Identities=19%  Similarity=0.246  Sum_probs=24.0

Q ss_pred             eeeeEEecCeecCCCceecCCCEEEEE
Q 026204           12 SVLALFLSMDKLSVSHNVKGGDMVNCT   38 (241)
Q Consensus        12 ~~~~v~vng~~~~~~~~l~~GD~i~~~   38 (241)
                      +...|.|||+.+..++.|+.||+|.+.
T Consensus        66 ~~v~v~VNg~~v~~~~~L~dGDeV~i~   92 (98)
T 1vjk_A           66 ADVNIAVNGRYVSWDEELKDGDVVGVF   92 (98)
T ss_dssp             SSBEEEETTBCCCTTCBCCTTCEEEEE
T ss_pred             CcEEEEECCEECCCCCCCCCCCEEEEE
Confidence            445799999999999999999999985

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	241
d1v9fa_	250	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	2e-27
d1v9ka_	227	d.265.1.3 (A:) Ribosomal large subunit pseudouridi	2e-23

>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Length = 250

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase D, RluD
species: Escherichia coli [TaxId: 562]

 Score =  103 bits (256), Expect = 2e-27
 Identities = 68/194 (35%), Positives = 95/194 (48%), Gaps = 36/194 (18%)

Query: 48  EAEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFS 107
           E +DIPLDIVYED++++++NKP  +VVHP  GN  GT++N +LH+               
Sbjct: 2   EPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYY-------------- 47

Query: 108 DAEDISDDEEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERV 167
                               R GIVHRLDK T+GL+VVAK   +   L E  +   I R 
Sbjct: 48  -------------PPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITRE 94

Query: 168 YISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGS 227
           Y ++       + G ++ PISR P  R  MA  P        + A + Y+++E       
Sbjct: 95  YEAVA-IGHMTAGGTVDEPISRHPTKRTHMAVHPM------GKPAVTHYRIME--HFRVH 145

Query: 228 ALVEWRLETGRTHQ 241
             +  RLETGRTHQ
Sbjct: 146 TRLRLRLETGRTHQ 159

>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Length = 227

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase C, RluC
species: Escherichia coli [TaxId: 562]

 Score = 92.3 bits (228), Expect = 2e-23
 Identities = 46/186 (24%), Positives = 76/186 (40%), Gaps = 37/186 (19%)

Query: 56  IVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDD 115
           I+YEDD++LV+NKP+   VH   G + G +  G+                          
Sbjct: 3   IMYEDDHILVLNKPSGTAVHGGSGLSFGVI-EGLRALR---------------------- 39

Query: 116 EEFSSSISGASIRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGV 175
                     +    +VHRLD+ TSG+L+VAK   +   L EQ +   +++ Y++L  G 
Sbjct: 40  --------PEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQ 91

Query: 176 PSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEILAGGGSALVEWRLE 235
                  ++ P+ ++                   + + +R+KV E      + LV     
Sbjct: 92  WQSHVKSVQAPLLKNILQSGERIVRVSQE----GKPSETRFKVEERY--AFATLVRCSPV 145

Query: 236 TGRTHQ 241
           TGRTHQ
Sbjct: 146 TGRTHQ 151

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	241
d1v9fa_	250	Ribosomal large subunit pseudouridine synthase D,	100.0
d1v9ka_	227	Ribosomal large subunit pseudouridine synthase C,	100.0
d1vioa1	174	Ribosomal small subunit pseudouridine 516 synthase	99.86
d1kska4	172	Ribosomal small subunit pseudouridine 516 synthase	99.8
d1k8wa5	242	Pseudouridine synthase II TruB {Escherichia coli [	97.52
d1r3ea2	228	Pseudouridine synthase II TruB {Thermotoga maritim	97.4
d1sgva2	233	Pseudouridine synthase II TruB {Mycobacterium tube	97.33
d2ey4a2	245	Pseudouridine synthase II TruB {Archaeon Pyrococcu	97.33
d2apoa2	230	Pseudouridine synthase II TruB {Archaeon Methanoco	97.19
d1dm9a_	104	Heat shock protein 15 kD {Escherichia coli [TaxId:	94.26
d1c06a_	159	Ribosomal protein S4 {Bacillus stearothermophilus	91.55
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	90.36
d2gy9d1	204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	89.94
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	89.62
d2uubd1	208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	87.66
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	84.71
d1vjka_	88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	83.94
d2g1la1	102	Kinesin-like protein kif1c {Human (Homo sapiens) [	80.83
d2hj1a1	77	Hypothetical protein HI0395 {Haemophilus influenza	80.42

>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase D, RluD
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.9e-39  Score=275.21  Aligned_cols=157  Identities=43%  Similarity=0.739  Sum_probs=138.1

Q ss_pred             CCCCCccEEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCC
Q 026204           49 AEDIPLDIVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIR  128 (241)
Q Consensus        49 ~~~~~~~Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (241)
                      |++.+++|||||++++|||||+||+|||+.+...+|+.+.+..++...                           .....
T Consensus         3 P~~~~l~IlyeD~~~ivvnKP~gl~~hp~~~~~~~t~~~~l~~~~~~~---------------------------~~~~~   55 (250)
T d1v9fa_           3 PQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPI---------------------------ADVPR   55 (250)
T ss_dssp             CCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGG---------------------------GGSGG
T ss_pred             CCCCCCCEEEECCCEEEEECCCCCCCcCCCCCCCccHHHHHHHHhhhc---------------------------cCCCc
Confidence            456688999999999999999999999998888889999998876421                           12346


Q ss_pred             ccccccCCCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCC
Q 026204          129 PGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQ  208 (241)
Q Consensus       129 ~~~vhRLD~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~  208 (241)
                      +++|||||++||||||||||+.+++.|+++|+++.+.|+|+|+|.|.++ ..+.++.|+.........+.+.+      +
T Consensus        56 ~~~vHRLDr~TSGlll~Ak~~~a~~~l~~~f~~~~v~K~Y~a~~~g~~~-~~~~~~~~~~~~~~~~~~~~~~~------~  128 (250)
T d1v9fa_          56 AGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMT-AGGTVDEPISRHPTKRTHMAVHP------M  128 (250)
T ss_dssp             GGBCCCCCTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCC-CCEEEECCEEECSSCTTCEEECT------T
T ss_pred             eeEEeecCCCCcceEEEecccHHHHhhhhhhccceEeEEeeeeeccccc-cccccccccccCCcccceeEECC------C
Confidence            7889999999999999999999999999999999999999999999985 46788889988777777777665      7


Q ss_pred             CcceEEEEEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          209 ARHAASRYKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       209 ~k~a~T~~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      |++|.|+|++++..  +++|+++|+|+||||||
T Consensus       129 gk~a~T~~~~l~~~--~~~slv~~~~~TGR~HQ  159 (250)
T d1v9fa_         129 GKPAVTHYRIMEHF--RVHTRLRLRLETGRTHQ  159 (250)
T ss_dssp             SBCCEEEEEEEEEC--SSEEEEEEEESCCCTTH
T ss_pred             Ceeccccchhhhcc--cCceeEEEEecccchHH
Confidence            89999999999984  68999999999999999

>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal large subunit pseudouridine synthase C, RluC
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=7.6e-38  Score=262.86  Aligned_cols=149  Identities=30%  Similarity=0.433  Sum_probs=125.7

Q ss_pred             EEEecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccC
Q 026204           56 IVYEDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRL  135 (241)
Q Consensus        56 Ilyed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRL  135 (241)
                      |||||++++|||||+||+|||+.+.. .++.+.+.....                              ....+++||||
T Consensus         3 IlyeD~~ilvvnKP~gl~~h~~~~~~-~~~~~~l~~~~~------------------------------~~~~~~~vHRL   51 (227)
T d1v9ka_           3 IMYEDDHILVLNKPSGTAVHGGSGLS-FGVIEGLRALRP------------------------------EARFLELVHRL   51 (227)
T ss_dssp             EEEECSSEEEEEECTTSCSSCCSSSB-CCHHHHHHHHST------------------------------TCSCCEESSCC
T ss_pred             EEEeCCCEEEEECCCCCccCCCCCCc-chHHHHHHHhCC------------------------------CCcccceeeec
Confidence            99999999999999999999986554 456666665432                              12456889999


Q ss_pred             CCCCceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEE
Q 026204          136 DKGTSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASR  215 (241)
Q Consensus       136 D~~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~  215 (241)
                      |++||||||||||+++++.|+++|+++.+.|+|+|+|.|.++...+.++.|+..+........+..    ..+++.|.|.
T Consensus        52 D~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~a~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~gk~a~t~  127 (227)
T d1v9ka_          52 DRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRV----SQEGKPSETR  127 (227)
T ss_dssp             CTTCEEEEEEESSHHHHHHHHHHHHTTCSEEEEEEEEESCCCTTCCEECCCEEEEECTTSCEEEEE----CTTSBCCCEE
T ss_pred             cceeeeeeeeecchHHHHHHHHHHhcccccceecccccCccccccCccccccccccccceeeeeec----CCCCccccee
Confidence            999999999999999999999999999999999999999999999999999987644333222222    1388999999


Q ss_pred             EEEEEEecCCCEEEEEEEcCCCCCCC
Q 026204          216 YKVIEILAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       216 ~~vl~~~~~~~~slv~~~l~TGR~HQ  241 (241)
                      |++++..  .++||++|+|.||||||
T Consensus       128 ~~~l~~~--~~~slv~~~~~TGRtHQ  151 (227)
T d1v9ka_         128 FKVEERY--AFATLVRCSPVTGRTHQ  151 (227)
T ss_dssp             EEEEEEC--SSEEEEEEEESSCCTTH
T ss_pred             ehhhhhc--CCcEEEEEEeccCchHH
Confidence            9999984  68999999999999999

>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal small subunit pseudouridine 516 synthase RsuA
species: Haemophilus influenzae [TaxId: 727]

Probab=99.86  E-value=1.6e-23  Score=168.18  Aligned_cols=86  Identities=20%  Similarity=0.270  Sum_probs=68.0

Q ss_pred             ecCcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCC
Q 026204           59 EDDNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKG  138 (241)
Q Consensus        59 ed~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~  138 (241)
                      |++.|+++|||+|++|+..... ..++.+++...                                ...++++|||||++
T Consensus         1 e~~~Yi~lNKP~G~~~~~~~~~-~~~v~~~l~~~--------------------------------~~~~l~~V~RLD~~   47 (174)
T d1vioa1           1 EEGQYFMLNKPQGCVCSNDDGD-YPTIYQFFDYP--------------------------------LAGKLHSAGRLDVD   47 (174)
T ss_dssp             CCCCEEEEEECTTCBSSCCC---CCBGGGGSCTT--------------------------------GGGGCEESSCCCTT
T ss_pred             CCCEEEEEECCCCEEeCCCCCC-CCcHHHhCccc--------------------------------ccCceEEEecCChh
Confidence            5789999999999999865443 44665543221                                12456889999999


Q ss_pred             CceEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCC
Q 026204          139 TSGLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQS  179 (241)
Q Consensus       139 TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~  179 (241)
                      ||||||||+|.++++.+..  +...+.|.|.+.|.|.+.+.
T Consensus        48 TsGLll~t~d~~~~~~l~~--~~~~~~k~y~v~v~~~~~~~   86 (174)
T d1vioa1          48 TTGLVLLTDDGQWSHRITS--PKHHCEKTYLVTLADPVEEN   86 (174)
T ss_dssp             CEEEEEEESCHHHHHHHHC--TTSCCCEEEEEEESSCCCTT
T ss_pred             HhceEEEeecccccccccc--cccceeeeeeeEEecccchh
Confidence            9999999999999999976  66779999999999988654

>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase RsuA/RluD
domain: Ribosomal small subunit pseudouridine 516 synthase RsuA
species: Escherichia coli [TaxId: 562]

Probab=99.80  E-value=2.3e-21  Score=155.15  Aligned_cols=125  Identities=18%  Similarity=0.289  Sum_probs=86.0

Q ss_pred             cEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCce
Q 026204           62 NVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTSG  141 (241)
Q Consensus        62 ~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSG  141 (241)
                      .|+++|||+|+.|+...... .++.+.+..                                ....++++|||||++|||
T Consensus         2 ~yi~lNKP~G~l~s~~~~~~-~~~~~~l~~--------------------------------~~~~~l~~vgRLD~~tsG   48 (172)
T d1kska4           2 RYFMLNKPQGYVCSTDDPDH-PTVLYFLDE--------------------------------PVAWKLHAAGRLDIDTTG   48 (172)
T ss_dssp             CEEEEEECTTCBSSSSCSSS-CBGGGGCCC--------------------------------TTGGGCEESSCCCTTCEE
T ss_pred             EEEEEECCCCEEECCcCCCC-CcEEEecCc--------------------------------cccCcEEEeecCCccccc
Confidence            48999999999998654433 344332211                                112457899999999999


Q ss_pred             EEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecccCCCccEEEcceeeCCCCCeeEEEecCCCCCCCCcceEEEEEEEEE
Q 026204          142 LLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGVPSQSSGRIEVPISRDPNNRIRMAAIPGSNKHGQARHAASRYKVIEI  221 (241)
Q Consensus       142 lll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~  221 (241)
                      |||||+|.++++.|.+  +...++|+|+|.|.|.++.....   .+.+.        +..      .+..+.+.+..++.
T Consensus        49 LlL~tndg~~~~~l~~--~~~~i~k~Y~v~v~~~i~~~~~~---~l~~g--------v~i------~~~~~~~~~~~v~~  109 (172)
T d1kska4          49 LVLMTDDGQWSHRITS--PRHHCEKTYLVTLESPVADDTAE---QFAKG--------VQL------HNEKDLTKPAVLEV  109 (172)
T ss_dssp             EEEEESCHHHHHHHHC--TTSCCCEEEEEEESSCCCTTHHH---HHHHC--------CCC------TTCSSCCCCCEEEE
T ss_pred             cEEEecccceeeeecc--ccccccEEEEEEEeccCCHHHHH---Hhhcc--------eEE------cCccccccceEEee
Confidence            9999999999999988  66779999999999988754321   11110        111      22223344344444


Q ss_pred             ecCCCEEEEEEEcCCCCCCC
Q 026204          222 LAGGGSALVEWRLETGRTHQ  241 (241)
Q Consensus       222 ~~~~~~slv~~~l~TGR~HQ  241 (241)
                      ..   .++++|.+.|||+||
T Consensus       110 ~~---~~~l~i~l~~Gr~~q  126 (172)
T d1kska4         110 IT---PTQVRLTISEGRYHQ  126 (172)
T ss_dssp             EE---TTEEEEEESCCCTTH
T ss_pred             cc---CcEEEEEEecCccHH
Confidence            32   246899999999998

>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Escherichia coli [TaxId: 562]

Probab=97.52  E-value=3.4e-05  Score=63.01  Aligned_cols=70  Identities=20%  Similarity=0.318  Sum_probs=53.9

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      +.+++||||+|+-++        .+++.++..+.                               ..+++..+.||--.|
T Consensus         4 ~G~l~v~KP~g~tS~--------~vv~~~k~~l~-------------------------------~kKvGh~GTLDP~As   44 (242)
T d1k8wa5           4 NGVLLLDKPQGMSSN--------DALQKVKRIYN-------------------------------ANRAGHTGALDPLAT   44 (242)
T ss_dssp             CEEEEEEECTTCCHH--------HHHHHHHHHTT-------------------------------CSCEEESSCCCTTCE
T ss_pred             cEEEEEecCCCCCHH--------HHHHHHHHHhC-------------------------------CCcCCcCCcCCCccc
Confidence            579999999999775        46777777653                               356788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-+..  .++...|..  ..|+|.|.+.
T Consensus        45 GvL~i~ig~a--TK~~~~~~~--~~K~Y~~~i~   73 (242)
T d1k8wa5          45 GMLPICLGEA--TKFSQYLLD--SDKRYRVIAR   73 (242)
T ss_dssp             EEEEEEEGGG--GGGTHHHHT--SCEEEEEEEE
T ss_pred             ceEEEEEchh--hhhhhhhhh--hhheeeEEEE
Confidence            9999999763  344445544  4699999865

>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Thermotoga maritima [TaxId: 2336]

Probab=97.40  E-value=5.6e-05  Score=61.22  Aligned_cols=70  Identities=21%  Similarity=0.341  Sum_probs=55.2

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      ..+++||||.|+-++        .+++.++..+.                               ..+.+..++||-..|
T Consensus         3 ~G~l~i~Kp~g~tS~--------~~v~~vk~~l~-------------------------------~~KvGh~GTLDP~As   43 (228)
T d1r3ea2           3 HGILVAYKPKGPTSH--------DVVDEVRKKLK-------------------------------TRKVGHGGTLDPFAC   43 (228)
T ss_dssp             CEEEEEEECSSSCHH--------HHHHHHHHHTT-------------------------------CSCEEESSCCCTTCE
T ss_pred             ceEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------CCccCcCcccCCcce
Confidence            468999999999775        47788887764                               246788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-+..  .++...+.+  ..|+|.|.+.
T Consensus        44 GvL~i~ig~~--tkl~~~~~~--~~K~Y~~~~~   72 (228)
T d1r3ea2          44 GVLIIGVNQG--TRILEFYKD--LKKVYWVKMR   72 (228)
T ss_dssp             EEEEEEEGGG--GGGGGGGTT--SCEEEEEEEE
T ss_pred             eeEEEEEccc--ccchhhhhc--ccceEEEEEE
Confidence            9999999863  355555644  5799999866

>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.33  E-value=6.3e-05  Score=61.09  Aligned_cols=70  Identities=21%  Similarity=0.346  Sum_probs=54.9

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      ..+++||||.|+-++        .+++.++..+.                               ..+++..++||-..|
T Consensus         4 ~G~l~v~KP~G~TS~--------~~v~~vk~~~~-------------------------------~kKvGh~GTLDP~At   44 (233)
T d1sgva2           4 PGIVVIDKPAGMTSH--------DVVGRCRRIFA-------------------------------TRRVGHAGTLDPMAT   44 (233)
T ss_dssp             SEEEEEEECTTCCHH--------HHHHHHHHHTT-------------------------------CSCEEESSCCCTTCE
T ss_pred             CEEEEEEcCCCCCHH--------HHHHHHHHHhC-------------------------------cCccccCcCCCCcce
Confidence            579999999999664        47777777654                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-..  +.++...|..  ..|+|.|.+.
T Consensus        45 GvL~i~ig~--aTK~~~~~~~--~~K~Y~~~~~   73 (233)
T d1sgva2          45 GVLVIGIER--ATKILGLLTA--APKSYAATIR   73 (233)
T ss_dssp             EEEEEEEGG--GGGGGGGTTT--SCEEEEEEEE
T ss_pred             eeEEEEech--hhhhhhhhcc--CceEEEEEEE
Confidence            999999986  3555555554  4799999865

>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.33  E-value=9.2e-05  Score=60.32  Aligned_cols=70  Identities=23%  Similarity=0.271  Sum_probs=56.4

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      ..+++||||.|+-+|        .+++.+...+.                               ..+++..+.||-..|
T Consensus        42 ~G~l~idKP~G~TS~--------~vv~~vkk~l~-------------------------------~kKvGH~GTLDP~At   82 (245)
T d2ey4a2          42 FGVINLDKPPGPTSH--------EVVAWIKKILN-------------------------------LEKAGHGGTLDPKVS   82 (245)
T ss_dssp             TEEEEEEECSSSCHH--------HHHHHHHHHTT-------------------------------CSCEEESSCCCTTCE
T ss_pred             CcEEEEeCCCCCCHH--------HHHHHHHHHhC-------------------------------cCCCCcCccCCCcce
Confidence            479999999999775        57888888764                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEe
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTS  173 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~  173 (241)
                      |+|+++-...  .++.+.|..  ..|+|.|.+.
T Consensus        83 GvL~i~iG~a--TKl~~~~~~--~~K~Y~~~~~  111 (245)
T d2ey4a2          83 GVLPVALEKA--TRVVQALLP--AGKEYVALMH  111 (245)
T ss_dssp             EEEEEEEGGG--GGGHHHHTT--SCEEEEEEEE
T ss_pred             eeEEEEecHH--HHHHHHhcc--CCcEEEEEEE
Confidence            9999999764  455555543  8899999876

>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.19  E-value=0.00011  Score=59.38  Aligned_cols=72  Identities=21%  Similarity=0.233  Sum_probs=56.9

Q ss_pred             CcEEEEECCCCceeecCCCCCCCCHHHHHHHhcCCCccccccccccccccccccccccccccCCCCCCccccccCCCCCc
Q 026204           61 DNVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTLASSNQEAFSDAEDISDDEEFSSSISGASIRPGIVHRLDKGTS  140 (241)
Q Consensus        61 ~~llVinKPaGl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TS  140 (241)
                      ..+++||||.|+-++        .+++.+...+.                               ..+++..+-||-..|
T Consensus        29 ~G~l~idKP~G~TS~--------~vv~~ikk~l~-------------------------------~kKvGH~GTLDP~At   69 (230)
T d2apoa2          29 YGVVVVDKPRGPTSH--------EVSTWVKKILN-------------------------------LDKAGHGGTLDPKVT   69 (230)
T ss_dssp             TEEEEEEECSSSCHH--------HHHHHHHHHTT-------------------------------CSCEEESSCCCTTCE
T ss_pred             CcEEEEECCCCCCHH--------HHHHHHHHHcC-------------------------------CCCCCcccccCccce
Confidence            479999999999775        47888888764                               256788999999999


Q ss_pred             eEEEeecCHHHHHHHHHHhhcCeeeEEEEEEEecc
Q 026204          141 GLLVVAKDEHSHAHLSEQFKLHTIERVYISLTSGV  175 (241)
Q Consensus       141 Glll~Ak~~~~~~~L~~~f~~~~v~K~Y~AlV~G~  175 (241)
                      |+|+++-.+.  .++...|..  ..|+|.|.+.=.
T Consensus        70 GvL~v~iG~a--TKl~~~~~~--~~K~Y~~~~~~g  100 (230)
T d2apoa2          70 GVLPVALERA--TKTIPMWHI--PPKEYVCLMHLH  100 (230)
T ss_dssp             EEEEEEEGGG--GGGGGGTTS--SCEEEEEEEEES
T ss_pred             eeeeeeecHH--HHHHHHHhc--cCceEEEEEEee
Confidence            9999999873  345555544  579999987643

>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Heat shock protein 15 kD
domain: Heat shock protein 15 kD
species: Escherichia coli [TaxId: 562]

Probab=94.26  E-value=0.018  Score=40.25  Aligned_cols=26  Identities=8%  Similarity=-0.032  Sum_probs=23.6

Q ss_pred             eEEecCeecCCCceecCCCEEEEEec
Q 026204           15 ALFLSMDKLSVSHNVKGGDMVNCTIS   40 (241)
Q Consensus        15 ~v~vng~~~~~~~~l~~GD~i~~~~~   40 (241)
                      .|.|||+++++++.|++||.|.+...
T Consensus        31 ~V~vNg~~vKps~~vk~GDvI~i~~~   56 (104)
T d1dm9a_          31 KVHYNGQRSKPSKIVELNATLTLRQG   56 (104)
T ss_dssp             CEEETTEECCTTCBCCTTCEEEEEET
T ss_pred             CeeeCCeeccccccCCCCCEEEEEeC
Confidence            38999999999999999999999654

>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=91.55  E-value=0.052  Score=40.68  Aligned_cols=25  Identities=16%  Similarity=0.255  Sum_probs=22.6

Q ss_pred             eEEecCeecC-CCceecCCCEEEEEe
Q 026204           15 ALFLSMDKLS-VSHNVKGGDMVNCTI   39 (241)
Q Consensus        15 ~v~vng~~~~-~~~~l~~GD~i~~~~   39 (241)
                      -|.|||++++ |++.|++||.|.+..
T Consensus        77 hi~vNgk~v~iPSy~vk~GDvIsvke  102 (159)
T d1c06a_          77 HILVDGSRVNIPSYRVKPGQTIAVRE  102 (159)
T ss_dssp             CEEETTEECCCSSCCCCSSCEEEECG
T ss_pred             ceEccceEEEecceeecCCcEEeecc
Confidence            4899999988 999999999999964

>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=90.36  E-value=0.084  Score=32.40  Aligned_cols=25  Identities=12%  Similarity=0.033  Sum_probs=21.9

Q ss_pred             eEEecCeecC-CCceecCCCEEEEEe
Q 026204           15 ALFLSMDKLS-VSHNVKGGDMVNCTI   39 (241)
Q Consensus        15 ~v~vng~~~~-~~~~l~~GD~i~~~~   39 (241)
                      .|.|||+.++ +++.|.+||.|.+..
T Consensus        27 ~V~Vng~~v~~~~~~v~~~d~I~~~g   52 (58)
T d1vioa2          27 AVKINGEIVKSGSVQISQEDEIYFED   52 (58)
T ss_dssp             CEEETTEECCCTTCEECTTSCEEETT
T ss_pred             eEEECCEEeCCCCCCCCCCCEEEECC
Confidence            4899999976 899999999999843

>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Escherichia coli [TaxId: 562]

Probab=89.94  E-value=0.069  Score=41.58  Aligned_cols=25  Identities=20%  Similarity=0.220  Sum_probs=22.7

Q ss_pred             eEEecCeecC-CCceecCCCEEEEEe
Q 026204           15 ALFLSMDKLS-VSHNVKGGDMVNCTI   39 (241)
Q Consensus        15 ~v~vng~~~~-~~~~l~~GD~i~~~~   39 (241)
                      -|.|||++++ |++.|++||.|.+..
T Consensus       120 hi~VNgk~VnIPSy~vk~GDvIsvke  145 (204)
T d2gy9d1         120 AIMVNGRVVNIASYQVSPNDVVSIRE  145 (204)
T ss_dssp             CEEESSSBCCCTTCBCCTTCBEEECT
T ss_pred             ceecCCEEEEeccEeecCCCEEEecc
Confidence            4899999998 899999999999964

>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.62  E-value=0.11  Score=31.94  Aligned_cols=25  Identities=4%  Similarity=-0.053  Sum_probs=22.0

Q ss_pred             eEEecCeec-CCCceecCCCEEEEEe
Q 026204           15 ALFLSMDKL-SVSHNVKGGDMVNCTI   39 (241)
Q Consensus        15 ~v~vng~~~-~~~~~l~~GD~i~~~~   39 (241)
                      .|.|||+++ ++++.|.++|.|.+..
T Consensus        26 ~V~Vng~~v~~~~~~V~~~d~I~~dg   51 (59)
T d1kska3          26 RVTVDGEIVRNAAFKLLPEHDVAYDG   51 (59)
T ss_dssp             CEEETTEECCCTTCEECTTCCEEETT
T ss_pred             cEEECCEEeecCCcCcCCCCEEEECC
Confidence            489999987 5999999999999954

>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Thermus thermophilus [TaxId: 274]

Probab=87.66  E-value=0.16  Score=39.50  Aligned_cols=25  Identities=16%  Similarity=0.224  Sum_probs=22.6

Q ss_pred             eEEecCeecC-CCceecCCCEEEEEe
Q 026204           15 ALFLSMDKLS-VSHNVKGGDMVNCTI   39 (241)
Q Consensus        15 ~v~vng~~~~-~~~~l~~GD~i~~~~   39 (241)
                      -|.|||++++ |++.|++||.|.+..
T Consensus       124 ~i~vNg~~v~ips~~~~~gd~I~vre  149 (208)
T d2uubd1         124 HITVNGRRVDLPSYRVRPGDEIAVAE  149 (208)
T ss_dssp             CEEETTEECCCTTCBCCTTCEEEECG
T ss_pred             CeecCCeEEEeccEEecCCceeehhh
Confidence            4899999988 899999999999964

>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: YbcJ-like
domain: Hypothetical protein YbcJ
species: Escherichia coli [TaxId: 562]

Probab=84.71  E-value=0.15  Score=33.39  Aligned_cols=23  Identities=9%  Similarity=0.043  Sum_probs=20.7

Q ss_pred             EEecCeec-CCCceecCCCEEEEE
Q 026204           16 LFLSMDKL-SVSHNVKGGDMVNCT   38 (241)
Q Consensus        16 v~vng~~~-~~~~~l~~GD~i~~~   38 (241)
                      |.|||+++ ++++.|.+||.|.+.
T Consensus        48 V~VNG~~~~~p~~~V~~~d~I~vd   71 (79)
T d1p9ka_          48 VKVDGAVETRKRCKIVAGQTVSFA   71 (79)
T ss_dssp             HEETTBCCCCSSCCCCSSEEEEET
T ss_pred             cccCCEEeccccccCCCCCEEEEC
Confidence            78999997 599999999999884

>d1vjka_ d.15.3.1 (A:) Molybdopterin synthase subunit MoaD {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: MoaD
domain: Molybdopterin synthase subunit MoaD
species: Pyrococcus furiosus [TaxId: 2261]

Probab=83.94  E-value=0.48  Score=30.99  Aligned_cols=29  Identities=17%  Similarity=0.216  Sum_probs=25.3

Q ss_pred             ceeeeeEEecCeecCCCceecCCCEEEEE
Q 026204           10 QVSVLALFLSMDKLSVSHNVKGGDMVNCT   38 (241)
Q Consensus        10 ~~~~~~v~vng~~~~~~~~l~~GD~i~~~   38 (241)
                      .++...+.|||+.+..++.|+.||+|.+.
T Consensus        56 ~~~~i~iavN~~~~~~d~~L~~gDevai~   84 (88)
T d1vjka_          56 EDADVNIAVNGRYVSWDEELKDGDVVGVF   84 (88)
T ss_dssp             TTSSBEEEETTBCCCTTCBCCTTCEEEEE
T ss_pred             ccccEEEEEcceEcCCCcCcCCCCEEEEe
Confidence            34566789999999999999999999985

>d2g1la1 b.26.1.2 (A:498-599) Kinesin-like protein kif1c {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SMAD/FHA domain
superfamily: SMAD/FHA domain
family: FHA domain
domain: Kinesin-like protein kif1c
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.83  E-value=0.48  Score=32.06  Aligned_cols=24  Identities=8%  Similarity=0.146  Sum_probs=21.3

Q ss_pred             eeEEecCeecCCCceecCCCEEEE
Q 026204           14 LALFLSMDKLSVSHNVKGGDMVNC   37 (241)
Q Consensus        14 ~~v~vng~~~~~~~~l~~GD~i~~   37 (241)
                      ..++|||+++.....|+.||+|.+
T Consensus        69 ~gt~VNg~~i~~~~~L~~gD~I~~   92 (102)
T d2g1la1          69 AETYVNGKLVTEPLVLKSGNRIVM   92 (102)
T ss_dssp             CCEEETTEECCSCEECCTTCEEEE
T ss_pred             CCeEECCeEccceeEcCCCCEEEE
Confidence            358999999987799999999998

>d2hj1a1 d.15.3.4 (A:11-87) Hypothetical protein HI0395 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: MoaD/ThiS
family: HI0395-like
domain: Hypothetical protein HI0395
species: Haemophilus influenzae [TaxId: 727]

Probab=80.42  E-value=0.36  Score=31.37  Aligned_cols=25  Identities=12%  Similarity=0.169  Sum_probs=21.6

Q ss_pred             EEecCeecCCCceecCCCEEEEEec
Q 026204           16 LFLSMDKLSVSHNVKGGDMVNCTIS   40 (241)
Q Consensus        16 v~vng~~~~~~~~l~~GD~i~~~~~   40 (241)
                      +=|=|+.++.++.|+.||+|+++.+
T Consensus        51 vGIfGk~v~~~~~L~~gDRVEIYRP   75 (77)
T d2hj1a1          51 IGIFSRPIKLTDVLKEGDRIEIYRP   75 (77)
T ss_dssp             EEEEECSCCTTCBCCTTCEEEECCC
T ss_pred             EeEECcCcCCCCcCCCCCEEEEeec
Confidence            4566999999999999999999753