Citrus Sinensis ID: 042710

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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-------
Protein Sequence
GVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYCSRL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccEEEEEEEEccccccccccccccccHHHHHHHHHHHHHccccccEEEEEcccccccccccccEEEEEcccccccHHHHHHHHHcccccccEEEEEEEccccccccccccccEEEEEEEcccccccccccEEEEEcccccHHHHHHHHHHccccccHHHHcccccccccccccEEEEEEEEEEEccEEEEEEEEccHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEccccccccccccccccEEEEEEEEEccccccccEEccccccHHHHHHHHHHHHHHHHcccEEEEEEcccccccEEccEEEEEccccccccHHHHHHHHHHHccccEEEEEEEEccccccccccccEEEEEEEEEEccccccccccccEEEcccccHHHHHHHHHHHcEEEEcHHHcccccccccccccEEEEEEEEEEcccEEEEEEEcHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
gvgvvglegtnntvkpptddsfpgfkwRLVIgydgtryagwqfqtspptIQCIVEKALIRVTKLEREdlrlvgasrtdtgvhawgqvahfitpfsydGLESIHAALngllppdirVREISAAVPEFHARFSAKSKIYHYKiyndavmdpfqhhyayHSVYKLNTTLMREAAEYFVGKHDFSAFVNIqrndralnpvksifrfDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYCSRL
Flexible Loop (DISEMBL)
gvgvvglegtnntvkpptddsfpgfKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLrlvgasrtdtgvhawGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYCSRL
Low Complexity Region (SEG)
GVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYCSRL
Disordered region (IsUnstruct)
*********************FPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSY****
Disordered Region (DISOPRED)
***********************GFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQR**RALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYCSRL
Disordered Region (DISEMBL)
GVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYCSRL
Disordered Region (DISPRO)
GVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYCSRL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
GVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYCSRL
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	237	2.2.26 [Sep-21-2011]
Q6MEE7	256	tRNA pseudouridine syntha	yes	no	0.843	0.781	0.450	7e-46
Q8R7Y7	240	tRNA pseudouridine syntha	yes	no	0.822	0.812	0.447	2e-38
A8F526	245	tRNA pseudouridine syntha	yes	no	0.818	0.791	0.427	6e-37
P70973	247	tRNA pseudouridine syntha	yes	no	0.835	0.801	0.425	3e-36
B8I814	245	tRNA pseudouridine syntha	yes	no	0.822	0.795	0.430	3e-36
Q9PJT0	267	tRNA pseudouridine syntha	yes	no	0.810	0.719	0.410	6e-36
Q8XLQ0	248	tRNA pseudouridine syntha	yes	no	0.827	0.790	0.398	1e-35
B3E0A0	255	tRNA pseudouridine syntha	yes	no	0.835	0.776	0.423	2e-35
A3DJK8	244	tRNA pseudouridine syntha	yes	no	0.827	0.803	0.420	3e-35
B0K5S6	244	tRNA pseudouridine syntha	yes	no	0.822	0.799	0.402	5e-35

>sp|Q6MEE7|TRUA1_PARUW tRNA pseudouridine synthase A 1 OS=Protochlamydia amoebophila (strain UWE25) GN=truA1 PE=3 SV=1

 Score =  183 bits (465), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 92/204 (45%), Positives = 134/204 (65%), Gaps = 4/204 (1%)

Query: 27  WRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ 86
           ++L I YDGT Y+GWQ Q +  +IQ  +++AL  +  L++E + LVG+ RTD GVHA GQ
Sbjct: 4   YKLTIAYDGTNYSGWQIQPNASSIQQKIQEALCIL--LKKEKVVLVGSGRTDAGVHAKGQ 61

Query: 87  VAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAV 146
           VAHF     Y  L  +H +LNGLLP DIR++ +    P FH+++SA  K YHY ++ + V
Sbjct: 62  VAHFHFQ-DYIDLSRLHVSLNGLLPRDIRIKAVEPVSPRFHSQYSAIRKEYHYYLHLNKV 120

Query: 147 MDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVN-IQRNDRALNPVKSIFRFDVI 205
           MDPFQ  Y++H   K++  ++++AA  F G HDF++F N   R   A NPV++++R D+ 
Sbjct: 121 MDPFQRLYSWHFQRKIDVNILKKAAILFTGTHDFTSFANEAHRGTAAKNPVRTLYRLDIK 180

Query: 206 EMGALLQLEVEGSGFLYRQVRNMV 229
                L+LE EG GFLY+ VRN+V
Sbjct: 181 PNEGGLRLEFEGDGFLYKMVRNIV 204

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.
Protochlamydia amoebophila (strain UWE25) (taxid: 264201)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: 1EC: 2

>sp|Q8R7Y7|TRUA_THETN tRNA pseudouridine synthase A OS=Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) GN=truA PE=3 SV=1

 Score =  159 bits (402), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 90/201 (44%), Positives = 123/201 (61%), Gaps = 6/201 (2%)

Query: 29  LVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 88
           L+I YDGT Y GWQ+Q +  T+Q ++EKA+ +VT    E + L+G+SRTDTGVHA  QVA
Sbjct: 2   LIIEYDGTNYHGWQYQKNAITVQEVLEKAIEKVTG---EKVNLIGSSRTDTGVHALYQVA 58

Query: 89  HFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMD 148
           +F T       E +  ALN +LP D+ V +       FHAR+SA+SK Y Y I N     
Sbjct: 59  NFKTKTKIPP-EKLPYALNAVLPDDVVVVKAKEVDKSFHARYSARSKRYRYLILNRQFPM 117

Query: 149 PFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMG 208
           P   +Y +H  Y L+   M++AA +F G HDFSAF      ++ +NPVK+IF   V + G
Sbjct: 118 PTMRNYCWHVPYPLDVEAMKKAAFFFRGTHDFSAFK--ASGNKKVNPVKTIFDLTVEKEG 175

Query: 209 ALLQLEVEGSGFLYRQVRNMV 229
            L+++EVE  GFLY  VR +V
Sbjct: 176 DLIKIEVEADGFLYNMVRIIV 196

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.

Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (taxid: 273068)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|A8F526|TRUA_THELT tRNA pseudouridine synthase A OS=Thermotoga lettingae (strain ATCC BAA-301 / DSM 14385 / TMO) GN=truA PE=3 SV=1

 Score =  154 bits (388), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 86/201 (42%), Positives = 121/201 (60%), Gaps = 7/201 (3%)

Query: 30  VIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAH 89
           ++ YDGT + G+Q Q    T+Q + E+AL R+ K   + +  + A RTDTGVHA GQ+  
Sbjct: 7   IVSYDGTNFCGFQVQKDVRTVQGMFEQALERILK---QRVITIAAGRTDTGVHANGQIVC 63

Query: 90  FITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDP 149
           F      D  ES+  A+N  LP DI VR++      FH RF AK +IYHY IYN    + 
Sbjct: 64  FDCYLDIDE-ESMKNAMNANLPDDIYVRKVVEVDKNFHPRFDAKRRIYHYLIYNSQEPNL 122

Query: 150 FQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEM-G 208
           F  +YA+   YKLN   MREAA++F G+HDF +F  ++  D   N V++I+R  V+++ G
Sbjct: 123 FIRNYAWWFPYKLNICKMREAAKFFEGEHDFRSF--MKSGDHRENTVRTIYRVRVLQLRG 180

Query: 209 ALLQLEVEGSGFLYRQVRNMV 229
            ++ + VEG  FL R VRNMV
Sbjct: 181 GIILIRVEGRSFLRRMVRNMV 201

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.

Thermotoga lettingae (strain ATCC BAA-301 / DSM 14385 / TMO) (taxid: 416591)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|P70973|TRUA_BACSU tRNA pseudouridine synthase A OS=Bacillus subtilis (strain 168) GN=truA PE=3 SV=2

 Score =  152 bits (383), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 86/202 (42%), Positives = 117/202 (57%), Gaps = 4/202 (1%)

Query: 25  FKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAW 84
            + +  I YDG  + G+Q Q    T+Q  +EKAL  + K  ++ + +V + RTD+GVHA 
Sbjct: 1   MRLKCTISYDGHLFNGYQVQPGKRTVQDELEKALAVLHK-SKDRIPVVSSGRTDSGVHAA 59

Query: 85  GQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYND 144
           GQV HF TP S    E    ALN LLP DI V++   A   FHARFSA  K Y Y +Y +
Sbjct: 60  GQVIHFDTPLSIPA-ERWPYALNALLPDDIAVKQAEIADDGFHARFSAVKKEYRYFVYTE 118

Query: 145 AVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDV 204
              D F+ HYAYH  Y+LN   MREAA++ +G HDF++F   +      + V++I+  D 
Sbjct: 119 KHPDVFKRHYAYHFSYRLNVQDMREAAKHLIGTHDFTSFCAAKTE--VQDKVRTIYELDW 176

Query: 205 IEMGALLQLEVEGSGFLYRQVR 226
            E    LQ+ + GSGFLY  VR
Sbjct: 177 TETADGLQMRITGSGFLYNMVR 198

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.

Bacillus subtilis (strain 168) (taxid: 224308)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|B8I814|TRUA_CLOCE tRNA pseudouridine synthase A OS=Clostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10) GN=truA PE=3 SV=1

 Score =  151 bits (382), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 87/202 (43%), Positives = 118/202 (58%), Gaps = 7/202 (3%)

Query: 26  KWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 85
           K RL I YDGT Y GWQ Q +  T+Q +++KAL   +KL  ED+ + G SRTD GVHA+G
Sbjct: 3   KIRLTIEYDGTNYHGWQIQKNAKTVQEVIQKAL---SKLLGEDVGVTGCSRTDVGVHAYG 59

Query: 86  QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 145
           QVAHF+T     G +    A+N LLP DI ++       EFHAR+SAK K Y Y IYN  
Sbjct: 60  QVAHFLTDSKIPG-DKFSYAINNLLPDDIVIKNSEEVPEEFHARYSAKGKKYRYLIYNSP 118

Query: 146 VMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDV- 204
                  + + H   +LN   M++AA YF G+HDF AF       R+   V+ I+  +V 
Sbjct: 119 HASAIMRNRSCHVRPELNVAEMQKAAGYFKGEHDFLAFQATGGQVRS--TVREIYGMEVY 176

Query: 205 IEMGALLQLEVEGSGFLYRQVR 226
           ++   ++ +EV G+GFLY  VR
Sbjct: 177 VKEDNMISIEVSGNGFLYNMVR 198

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.

Clostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10) (taxid: 394503)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|Q9PJT0|TRUA_CHLMU tRNA pseudouridine synthase A OS=Chlamydia muridarum (strain MoPn / Nigg) GN=truA PE=3 SV=1

 Score =  150 bits (380), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 85/207 (41%), Positives = 124/207 (59%), Gaps = 15/207 (7%)

Query: 29  LVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 88
           L I Y GT Y+GWQ+Q +  +IQ ++E  L    K+ R  + ++ + RTD GVHA GQVA
Sbjct: 7   LRIAYQGTAYSGWQYQPNALSIQEVLETLL---QKISRTRISVIASGRTDAGVHAQGQVA 63

Query: 89  HFITP----FSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYND 144
           HF  P    FS  G   I   LN LLP DI +R++ A   +FH+RFSA +K YHY +   
Sbjct: 64  HFCCPDHPHFSDPG--QIKKMLNALLPHDIVIRDVIATNEDFHSRFSAITKEYHYTL--S 119

Query: 145 AVMDPFQHH--YAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRF 202
            +  P  HH  + +   +KL    MREAA+Y VG HDF++F N+ R   +   V++++  
Sbjct: 120 LLPKPLPHHRLFCFSPRHKLCLESMREAAKYLVGTHDFASFANLGREYSST--VRTLYAL 177

Query: 203 DVIEMGALLQLEVEGSGFLYRQVRNMV 229
           D++E   L+ +  +G+GFLY+ VRN+V
Sbjct: 178 DLLEQEHLVTVICKGNGFLYKMVRNIV 204

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.

Chlamydia muridarum (strain MoPn / Nigg) (taxid: 243161)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|Q8XLQ0|TRUA1_CLOPE tRNA pseudouridine synthase A 1 OS=Clostridium perfringens (strain 13 / Type A) GN=truA1 PE=3 SV=1

 Score =  149 bits (377), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 82/206 (39%), Positives = 121/206 (58%), Gaps = 10/206 (4%)

Query: 28  RLVIGYDGTRYAGWQFQ----TSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHA 83
           ++ + YDG++Y GWQ Q    ++  T+Q  +EK L   TK+  E+++L+G  RTD+GVHA
Sbjct: 5   KITLDYDGSKYKGWQKQNQKGSNVSTVQDKLEKVL---TKMTSEEIQLIGCGRTDSGVHA 61

Query: 84  WGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYN 143
              VA+F T  S   LE I   +N  LP DIRV EI  A   FHARF+ KSK Y Y I N
Sbjct: 62  KNYVANFKTN-SLMTLEQIIEYINEYLPEDIRVTEIREASERFHARFNVKSKTYEYTIDN 120

Query: 144 DAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFD 203
           +   D F   YA+H   KL+   M E A+Y +G HDF +F +++  +++   +++I   +
Sbjct: 121 NKFKDVFLRKYAWHVEEKLDLEAMEEGAKYLLGTHDFKSFTSLKSKNKS--TLRTINSIE 178

Query: 204 VIEMGALLQLEVEGSGFLYRQVRNMV 229
             E   +L +++ G+GFL   VR MV
Sbjct: 179 FHENNNILSIKINGNGFLLNMVRIMV 204

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.

Clostridium perfringens (strain 13 / Type A) (taxid: 195102)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|B3E0A0|TRUA_METI4 tRNA pseudouridine synthase A OS=Methylacidiphilum infernorum (isolate V4) GN=truA PE=3 SV=1

 Score =  149 bits (376), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 86/203 (42%), Positives = 118/203 (58%), Gaps = 5/203 (2%)

Query: 27  WRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ 86
           ++L + Y G+ + GWQ Q   PT+Q  +E+A   V K+  E + + GA RTD GVHA GQ
Sbjct: 8   YKLTLSYCGSGFHGWQRQGELPTVQRALEEA---VAKIWEEPIPVEGAGRTDAGVHAKGQ 64

Query: 87  VAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAV 146
           VA F  P   +  E +  ALN  LP  +RV +      EF ARF A SK Y Y ++ND V
Sbjct: 65  VASFAAPRKLEP-EVLKRALNYHLPDTVRVWDARIVPREFSARFDAVSKTYQYLLWNDPV 123

Query: 147 MDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIE 206
           MDPF    A+H    ++  +M EAA  F+GKH+F+AFV+        NPV+++     +E
Sbjct: 124 MDPFYLGRAWHIPRAMDVEMMNEAARLFLGKHNFAAFVS-NPGMPVKNPVRTVLDCFFLE 182

Query: 207 MGALLQLEVEGSGFLYRQVRNMV 229
            G+L+   V+  GFLYR VRNMV
Sbjct: 183 QGSLVFFNVKADGFLYRMVRNMV 205

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.

Methylacidiphilum infernorum (isolate V4) (taxid: 481448)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|A3DJK8|TRUA_CLOTH tRNA pseudouridine synthase A OS=Clostridium thermocellum (strain ATCC 27405 / DSM 1237) GN=truA PE=3 SV=1

 Score =  148 bits (373), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 85/202 (42%), Positives = 114/202 (56%), Gaps = 6/202 (2%)

Query: 28  RLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQV 87
           +L+I YDGT Y GWQ Q +  T+Q  +E+A   +  L  E + L+GASRTD GVHA GQV
Sbjct: 5   KLIIEYDGTNYHGWQKQKNAKTVQDTIERA---IKGLTGEKVDLIGASRTDFGVHALGQV 61

Query: 88  AHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVM 147
           A+FIT     G +    ALN +LP DI ++E      +FHAR+ AK K Y Y IYN    
Sbjct: 62  ANFITNSGIPG-DRFSYALNRMLPDDIVIKESQEVDMDFHARYKAKGKRYRYLIYNSQFP 120

Query: 148 DPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEM 207
                H  YH  +KL+   M+ AA YF+G HDFSAF +      A   V++I    +   
Sbjct: 121 SALLRHRTYHVSHKLDFESMQRAASYFLGTHDFSAFRS--SGSSAKTSVRTITDVSLERE 178

Query: 208 GALLQLEVEGSGFLYRQVRNMV 229
             +++ E+ G GFLY  VR +V
Sbjct: 179 DKIVKFEIAGDGFLYNMVRIIV 200

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.

Clostridium thermocellum (strain ATCC 27405 / DSM 1237) (taxid: 203119)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|B0K5S6|TRUA_THEPX tRNA pseudouridine synthase A OS=Thermoanaerobacter sp. (strain X514) GN=truA PE=3 SV=1

 Score =  147 bits (372), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 81/201 (40%), Positives = 117/201 (58%), Gaps = 6/201 (2%)

Query: 29  LVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 88
           +V+ YDGT Y GWQ+Q +  T+Q +++KA+ +VT    E++ L+GASRTDTGVHA  QVA
Sbjct: 6   IVVEYDGTNYHGWQYQKNAVTVQEVLQKAIKKVTG---EEVNLIGASRTDTGVHALYQVA 62

Query: 89  HFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMD 148
           +F T       E +  ALN +LP DI V +       FHAR+SAK K Y Y I N     
Sbjct: 63  NFKTNTKIPA-EKLPYALNSVLPDDIVVVQAKDVEDSFHARYSAKRKRYKYIILNRKFQM 121

Query: 149 PFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMG 208
           P   +Y +H  Y LN   M++AA Y +G HDFSAF          + +++++   + +  
Sbjct: 122 PTMRNYCWHISYPLNIEEMKKAASYLIGTHDFSAFK--ASGSSKTSTIRTVYDLTIEKNE 179

Query: 209 ALLQLEVEGSGFLYRQVRNMV 229
             + +E+E +GFLY  VR +V
Sbjct: 180 DFINIEIEANGFLYNMVRIIV 200

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.

Thermoanaerobacter sp. (strain X514) (taxid: 399726)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

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	237
225432191	336	PREDICTED: tRNA pseudouridine synthase A	0.890	0.627	0.848	1e-102
297736816	326	unnamed protein product [Vitis vinifera]	0.890	0.647	0.848	1e-102
255556594	344	pseudouridylate synthase, putative [Rici	0.864	0.595	0.809	2e-96
357479187	322	tRNA pseudouridine synthase family prote	0.894	0.658	0.763	8e-96
449441496	335	PREDICTED: tRNA pseudouridine synthase A	0.890	0.629	0.777	1e-95
357479185	350	tRNA pseudouridine synthase family prote	0.894	0.605	0.763	2e-95
356545824	327	PREDICTED: tRNA pseudouridine synthase A	0.869	0.629	0.786	2e-95
356564676	309	PREDICTED: tRNA pseudouridine synthase A	0.894	0.686	0.754	1e-92
147865780	403	hypothetical protein VITISV_020811 [Viti	0.801	0.471	0.817	1e-90
30680075	323	tRNA pseudouridine synthase A [Arabidops	0.936	0.687	0.693	3e-89

>gi|225432191|ref|XP_002275097.1| PREDICTED: tRNA pseudouridine synthase A 1-like [Vitis vinifera]

 Score =  378 bits (970), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 179/211 (84%), Positives = 190/211 (90%)

Query: 19  DDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTD 78
           + S  G+KWRLVI Y+GTRY+GWQ+Q SPPTIQCIVEKAL R TKLEREDL LVGASRTD
Sbjct: 49  NTSASGYKWRLVIAYEGTRYSGWQYQQSPPTIQCIVEKALTRATKLEREDLYLVGASRTD 108

Query: 79  TGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYH 138
           TGVHAWGQVAHF+TPF+YDGLESIHAALNGLLPPDIRVREIS AVPEFHARFS KSKIYH
Sbjct: 109 TGVHAWGQVAHFLTPFNYDGLESIHAALNGLLPPDIRVREISPAVPEFHARFSVKSKIYH 168

Query: 139 YKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKS 198
           YKIYNDAVMDPF  HY YHSVYKLNT  MREAA++F GKHDFSAFVN   NDR+ NPVK+
Sbjct: 169 YKIYNDAVMDPFLRHYVYHSVYKLNTLAMREAAKHFTGKHDFSAFVNASHNDRSPNPVKN 228

Query: 199 IFRFDVIEMGALLQLEVEGSGFLYRQVRNMV 229
           IFRFDV EMGALLQLEVEGSGFLYRQVRNMV
Sbjct: 229 IFRFDVNEMGALLQLEVEGSGFLYRQVRNMV 259

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736816|emb|CBI26017.3| unnamed protein product [Vitis vinifera]

 Score =  378 bits (970), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 179/211 (84%), Positives = 190/211 (90%)

Query: 19  DDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTD 78
           + S  G+KWRLVI Y+GTRY+GWQ+Q SPPTIQCIVEKAL R TKLEREDL LVGASRTD
Sbjct: 39  NTSASGYKWRLVIAYEGTRYSGWQYQQSPPTIQCIVEKALTRATKLEREDLYLVGASRTD 98

Query: 79  TGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYH 138
           TGVHAWGQVAHF+TPF+YDGLESIHAALNGLLPPDIRVREIS AVPEFHARFS KSKIYH
Sbjct: 99  TGVHAWGQVAHFLTPFNYDGLESIHAALNGLLPPDIRVREISPAVPEFHARFSVKSKIYH 158

Query: 139 YKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKS 198
           YKIYNDAVMDPF  HY YHSVYKLNT  MREAA++F GKHDFSAFVN   NDR+ NPVK+
Sbjct: 159 YKIYNDAVMDPFLRHYVYHSVYKLNTLAMREAAKHFTGKHDFSAFVNASHNDRSPNPVKN 218

Query: 199 IFRFDVIEMGALLQLEVEGSGFLYRQVRNMV 229
           IFRFDV EMGALLQLEVEGSGFLYRQVRNMV
Sbjct: 219 IFRFDVNEMGALLQLEVEGSGFLYRQVRNMV 249

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556594|ref|XP_002519331.1| pseudouridylate synthase, putative [Ricinus communis] gi|223541646|gb|EEF43195.1| pseudouridylate synthase, putative [Ricinus communis]

 Score =  357 bits (917), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 166/205 (80%), Positives = 182/205 (88%)

Query: 25  FKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAW 84
           FKWRLVI YDGTRYAGWQFQ SPPTIQC +EKALI+VTKL+R+DL LVGASRTDTGVHA+
Sbjct: 71  FKWRLVIAYDGTRYAGWQFQQSPPTIQCYLEKALIQVTKLDRKDLLLVGASRTDTGVHAF 130

Query: 85  GQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYND 144
           GQVAHF+TPF+Y  L++IHAALNGLLPPDIRVREIS AVPEFHARFS  SK+YHYKIYND
Sbjct: 131 GQVAHFVTPFNYPSLDTIHAALNGLLPPDIRVREISPAVPEFHARFSTISKLYHYKIYND 190

Query: 145 AVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDV 204
             MDPF  HYAYHS YKLN   MR+AA+YF+G HDFSAF N  R+DR  NPVK+IFRFDV
Sbjct: 191 TFMDPFLRHYAYHSTYKLNAAAMRQAAKYFIGSHDFSAFANASRDDRVPNPVKTIFRFDV 250

Query: 205 IEMGALLQLEVEGSGFLYRQVRNMV 229
           IEMGALLQLEVEG+GFLYRQVRNMV
Sbjct: 251 IEMGALLQLEVEGTGFLYRQVRNMV 275

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357479187|ref|XP_003609879.1| tRNA pseudouridine synthase family protein [Medicago truncatula] gi|355510934|gb|AES92076.1| tRNA pseudouridine synthase family protein [Medicago truncatula]

 Score =  355 bits (911), Expect = 8e-96,   Method: Compositional matrix adjust.
 Identities = 165/216 (76%), Positives = 186/216 (86%), Gaps = 4/216 (1%)

Query: 14  VKPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVG 73
           VKP  D    G+KWRL++ YDGTRYAGWQ+Q SPPT+QC VEKALIR TKL+R+DL+LVG
Sbjct: 35  VKPNQD----GYKWRLLLSYDGTRYAGWQYQESPPTVQCAVEKALIRATKLQRKDLQLVG 90

Query: 74  ASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAK 133
           ASRTD GVHAWGQVAHF+TPF+YD L+S+HAALNGLLP DIRVREIS A  EFHARFS K
Sbjct: 91  ASRTDAGVHAWGQVAHFLTPFNYDNLDSVHAALNGLLPSDIRVREISPASAEFHARFSVK 150

Query: 134 SKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRAL 193
           SKIYHYKIY+D +MDPFQ H+AYH++YKLN+  MREAA YF+GKHDF+AF N   NDR  
Sbjct: 151 SKIYHYKIYSDTIMDPFQRHFAYHNMYKLNSAAMREAARYFIGKHDFTAFENASHNDRIP 210

Query: 194 NPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMV 229
           +PVK IFRFDV EMGALLQLEVEGSGFLYRQVRNMV
Sbjct: 211 DPVKHIFRFDVKEMGALLQLEVEGSGFLYRQVRNMV 246

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449441496|ref|XP_004138518.1| PREDICTED: tRNA pseudouridine synthase A 1-like [Cucumis sativus] gi|449518841|ref|XP_004166444.1| PREDICTED: tRNA pseudouridine synthase A 1-like [Cucumis sativus]

 Score =  355 bits (910), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 164/211 (77%), Positives = 182/211 (86%)

Query: 19  DDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTD 78
           + SFP FKWRL+I YDGTRYAGWQ+Q SPPTIQC++E+ALI  TKLER+DL LVGASRTD
Sbjct: 48  EPSFPCFKWRLLIAYDGTRYAGWQYQRSPPTIQCLIEEALIGATKLERKDLHLVGASRTD 107

Query: 79  TGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYH 138
            GVHAWGQVAHF+TPF+YD LES+HAALNGLLP DIRVRE+S AVP+FHARFS  SK+YH
Sbjct: 108 KGVHAWGQVAHFVTPFNYDSLESVHAALNGLLPVDIRVREMSPAVPDFHARFSTLSKVYH 167

Query: 139 YKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKS 198
           YKIY+  +MDPFQ  Y YH VYKLN   M+EAA YFVGKHDFSAF N   NDR +NPVK 
Sbjct: 168 YKIYSGTIMDPFQRCYTYHCVYKLNYAAMKEAANYFVGKHDFSAFTNAAHNDRVVNPVKV 227

Query: 199 IFRFDVIEMGALLQLEVEGSGFLYRQVRNMV 229
           IFRFDVIEMGAL+QLEVEGSGFLYRQVRNMV
Sbjct: 228 IFRFDVIEMGALVQLEVEGSGFLYRQVRNMV 258

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357479185|ref|XP_003609878.1| tRNA pseudouridine synthase family protein [Medicago truncatula] gi|355510933|gb|AES92075.1| tRNA pseudouridine synthase family protein [Medicago truncatula]

 Score =  354 bits (908), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 165/216 (76%), Positives = 186/216 (86%), Gaps = 4/216 (1%)

Query: 14  VKPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVG 73
           VKP  D    G+KWRL++ YDGTRYAGWQ+Q SPPT+QC VEKALIR TKL+R+DL+LVG
Sbjct: 63  VKPNQD----GYKWRLLLSYDGTRYAGWQYQESPPTVQCAVEKALIRATKLQRKDLQLVG 118

Query: 74  ASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAK 133
           ASRTD GVHAWGQVAHF+TPF+YD L+S+HAALNGLLP DIRVREIS A  EFHARFS K
Sbjct: 119 ASRTDAGVHAWGQVAHFLTPFNYDNLDSVHAALNGLLPSDIRVREISPASAEFHARFSVK 178

Query: 134 SKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRAL 193
           SKIYHYKIY+D +MDPFQ H+AYH++YKLN+  MREAA YF+GKHDF+AF N   NDR  
Sbjct: 179 SKIYHYKIYSDTIMDPFQRHFAYHNMYKLNSAAMREAARYFIGKHDFTAFENASHNDRIP 238

Query: 194 NPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMV 229
           +PVK IFRFDV EMGALLQLEVEGSGFLYRQVRNMV
Sbjct: 239 DPVKHIFRFDVKEMGALLQLEVEGSGFLYRQVRNMV 274

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356545824|ref|XP_003541334.1| PREDICTED: tRNA pseudouridine synthase A 1-like [Glycine max]

 Score =  353 bits (907), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 162/206 (78%), Positives = 181/206 (87%)

Query: 24  GFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHA 83
           G+KWR+V+ YDGT+YAGWQ+Q SPPT+QC VEKAL + TKL+R+DL LVGASRTD GVHA
Sbjct: 43  GYKWRIVLAYDGTQYAGWQYQESPPTVQCTVEKALTQATKLQRKDLCLVGASRTDAGVHA 102

Query: 84  WGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYN 143
           WGQVAHF TPF+YD LE +HAALNGLLP DIR+REIS A  EFHARFSAKSKIYHYKIYN
Sbjct: 103 WGQVAHFFTPFNYDNLEQLHAALNGLLPTDIRIREISPASAEFHARFSAKSKIYHYKIYN 162

Query: 144 DAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFD 203
           DA+MDPFQ H+AYHSVYKLN+ +MREAA YFVGKHDFSAF N   NDR  +PVK +FRFD
Sbjct: 163 DAIMDPFQRHFAYHSVYKLNSAVMREAATYFVGKHDFSAFANASHNDRVPDPVKHVFRFD 222

Query: 204 VIEMGALLQLEVEGSGFLYRQVRNMV 229
           + EMGALLQLEVEGSGFLYRQVRNMV
Sbjct: 223 LKEMGALLQLEVEGSGFLYRQVRNMV 248

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356564676|ref|XP_003550576.1| PREDICTED: tRNA pseudouridine synthase A 1-like [Glycine max]

 Score =  345 bits (885), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 163/216 (75%), Positives = 182/216 (84%), Gaps = 4/216 (1%)

Query: 14  VKPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVG 73
           VKP  D     +KWRLV+ YDGT+YAGWQ+Q SPPT+QC +EKAL R TKL+R+D  LVG
Sbjct: 19  VKPIQD----WYKWRLVLAYDGTKYAGWQYQQSPPTVQCTLEKALTRATKLQRKDFCLVG 74

Query: 74  ASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAK 133
           ASRTD GVHAWGQVAHF TPF+YD LE +HAALNGLLP DIRVREIS A  EFHARFSA 
Sbjct: 75  ASRTDAGVHAWGQVAHFFTPFNYDNLEELHAALNGLLPTDIRVREISPASAEFHARFSAI 134

Query: 134 SKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRAL 193
           SKIYHYKIYNDA+MDPFQ H+AYHSVYKLN+ +MREAA+YFVGKHDFSAF N   ND   
Sbjct: 135 SKIYHYKIYNDAIMDPFQRHFAYHSVYKLNSAVMREAAKYFVGKHDFSAFANASNNDGVP 194

Query: 194 NPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMV 229
           +PVK +FRFD+ EMGALLQ+EVEGSGFLYRQVRNMV
Sbjct: 195 DPVKHVFRFDLKEMGALLQIEVEGSGFLYRQVRNMV 230

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865780|emb|CAN81146.1| hypothetical protein VITISV_020811 [Vitis vinifera]

 Score =  338 bits (866), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 166/203 (81%), Positives = 173/203 (85%), Gaps = 13/203 (6%)

Query: 40  GWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGL 99
           GWQ+Q SPPTIQCIVEKAL R TKLEREDL LVGASRTDTGVHAWGQVAHF+TPF+YDGL
Sbjct: 124 GWQYQQSPPTIQCIVEKALTRATKLEREDLYLVGASRTDTGVHAWGQVAHFLTPFNYDGL 183

Query: 100 ESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSV 159
           ESIHAALNGLLPPDIRVREIS AVPEFHARFS KSKIYHYKIYNDAVMDPF  HY YHSV
Sbjct: 184 ESIHAALNGLLPPDIRVREISPAVPEFHARFSXKSKIYHYKIYNDAVMDPFLRHYVYHSV 243

Query: 160 YKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEM------------ 207
           YKLNT  MREAA++F GKHDFSAFVN   NDR+ NPVK+IFRFDV EM            
Sbjct: 244 YKLNTLAMREAAKHFTGKHDFSAFVNASHNDRSPNPVKNIFRFDVNEMMFLELIVNCIIA 303

Query: 208 -GALLQLEVEGSGFLYRQVRNMV 229
            GALLQLEVEGSGFLYRQVRNMV
Sbjct: 304 QGALLQLEVEGSGFLYRQVRNMV 326

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30680075|ref|NP_187351.2| tRNA pseudouridine synthase A [Arabidopsis thaliana] gi|119360081|gb|ABL66769.1| At3g06950 [Arabidopsis thaliana] gi|332640958|gb|AEE74479.1| tRNA pseudouridine synthase A [Arabidopsis thaliana]

 Score =  333 bits (855), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 156/225 (69%), Positives = 185/225 (82%), Gaps = 3/225 (1%)

Query: 5   VGLEGTNNTVKPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKL 64
           + +   N++VK    DS   +KWRLVI YDGTR+AGWQ+Q SPPTIQ ++EKALI++T+L
Sbjct: 24  ISMTNLNSSVK--VSDS-GAYKWRLVIAYDGTRFAGWQYQESPPTIQSMLEKALIQITEL 80

Query: 65  EREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVP 124
            R++L+L+GA RTD GVHAWGQVAHF+TPF+Y  L+S HAALNGLLP DIRVRE+SAAVP
Sbjct: 81  GRKELQLIGAGRTDAGVHAWGQVAHFVTPFNYTSLDSFHAALNGLLPKDIRVRELSAAVP 140

Query: 125 EFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFV 184
           EFHARFSA SK+Y Y+IYND  MDPFQ H+AYH  YKLN + MREAA  FVGKHDFSAF 
Sbjct: 141 EFHARFSASSKVYRYQIYNDTFMDPFQRHWAYHCAYKLNASKMREAANLFVGKHDFSAFA 200

Query: 185 NIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMV 229
           N  R D   +P+K+I RFDVI+MG+LLQLEVEGSGFLYRQVRNMV
Sbjct: 201 NATREDGVPDPLKTISRFDVIQMGSLLQLEVEGSGFLYRQVRNMV 245

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	237
TAIR|locus:2077552	323	AT3G06950 [Arabidopsis thalian	0.936	0.687	0.693	1.9e-83
TIGR_CMR|GSU_2877	244	GSU_2877 "tRNA pseudouridine s	0.827	0.803	0.405	3.3e-31
TIGR_CMR|CHY_2276	246	CHY_2276 "tRNA pseudouridine s	0.822	0.792	0.395	3e-30
TIGR_CMR|DET_0504	248	DET_0504 "tRNA pseudouridine s	0.805	0.770	0.388	5.2e-26
UNIPROTKB|P07649	270	truA "tRNA pseudouridine synth	0.843	0.740	0.341	6.6e-26
TIGR_CMR|CBU_0892	261	CBU_0892 "tRNA pseudouridine s	0.814	0.739	0.356	8.4e-26
UNIPROTKB|Q9KTA4	264	truA "tRNA pseudouridine synth	0.822	0.738	0.339	1.4e-25
TIGR_CMR|VC_0999	264	VC_0999 "tRNA pseudouridine sy	0.822	0.738	0.339	1.4e-25
TIGR_CMR|ECH_0622	245	ECH_0622 "tRNA pseudouridine s	0.822	0.795	0.349	2e-24
TIGR_CMR|APH_0502	246	APH_0502 "tRNA pseudouridine s	0.827	0.796	0.330	1.4e-23

TAIR|locus:2077552 AT3G06950 [Arabidopsis thaliana (taxid:3702)]

 Score = 836 (299.3 bits), Expect = 1.9e-83, P = 1.9e-83
 Identities = 156/225 (69%), Positives = 185/225 (82%)

Query:     5 VGLEGTNNTVKPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKL 64
             + +   N++VK    DS   +KWRLVI YDGTR+AGWQ+Q SPPTIQ ++EKALI++T+L
Sbjct:    24 ISMTNLNSSVK--VSDS-GAYKWRLVIAYDGTRFAGWQYQESPPTIQSMLEKALIQITEL 80

Query:    65 EREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVP 124
              R++L+L+GA RTD GVHAWGQVAHF+TPF+Y  L+S HAALNGLLP DIRVRE+SAAVP
Sbjct:    81 GRKELQLIGAGRTDAGVHAWGQVAHFVTPFNYTSLDSFHAALNGLLPKDIRVRELSAAVP 140

Query:   125 EFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFV 184
             EFHARFSA SK+Y Y+IYND  MDPFQ H+AYH  YKLN + MREAA  FVGKHDFSAF 
Sbjct:   141 EFHARFSASSKVYRYQIYNDTFMDPFQRHWAYHCAYKLNASKMREAANLFVGKHDFSAFA 200

Query:   185 NIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMV 229
             N  R D   +P+K+I RFDVI+MG+LLQLEVEGSGFLYRQVRNMV
Sbjct:   201 NATREDGVPDPLKTISRFDVIQMGSLLQLEVEGSGFLYRQVRNMV 245

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

GO:0006730 "one-carbon metabolic process" evidence=RCA

TIGR_CMR|GSU_2877 GSU_2877 "tRNA pseudouridine synthase A" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 343 (125.8 bits), Expect = 3.3e-31, P = 3.3e-31
 Identities = 82/202 (40%), Positives = 111/202 (54%)

Query:    28 RLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQV 87
             +L++ YDGT YAGWQ Q +  +IQ +VE AL R+ K   E +RL  + RTD GVHA G V
Sbjct:     5 KLILEYDGTNYAGWQLQPNGLSIQEVVEGALARLLK---EPVRLRASGRTDAGVHARGMV 61

Query:    88 AHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVM 147
             A F T  S   L +    LN LLPPDI VR    A+P F+ RF+A  K Y Y I+     
Sbjct:    62 AAFDTDRSIP-LRAFSDGLNALLPPDIAVRSADEALPGFNPRFAATGKHYRYTIHRGERR 120

Query:   148 DPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEM 207
              P     ++H    LN   MREAA +  G+ DF++F        A   ++ +   ++ + 
Sbjct:   121 SPLVRLQSWHVRGALNLAAMREAARHLTGERDFASFRTA--GCAARTTIRRVDAVEISDD 178

Query:   208 GALLQLEVEGSGFLYRQVRNMV 229
             G +L ++V GSGFL   VR MV
Sbjct:   179 GEMLTVDVHGSGFLRNMVRIMV 200

GO:0006400 "tRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|CHY_2276 CHY_2276 "tRNA pseudouridine synthase A" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 334 (122.6 bits), Expect = 3.0e-30, P = 3.0e-30
 Identities = 81/205 (39%), Positives = 111/205 (54%)

Query:    23 PGFKWRLVIGYDGTRYAGWQFQ-TSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGV 81
             P FK  L I YDGT +AG+Q Q  +P TIQ I+E+ L ++ K   E ++++GA RTD GV
Sbjct:     5 PNFK--LTIAYDGTNFAGFQKQKNTPQTIQGILEEKLHKILK---EPVKVIGAGRTDAGV 59

Query:    82 HAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI 141
             HA GQV +F  P+    ++ I   LN  LP  IRV E      +FHAR+SA+ K Y Y +
Sbjct:    60 HALGQVVNFSAPWKAP-VDKIPEILNNTLPTAIRVLEAEIVPDDFHARYSARKKEYRYYL 118

Query:   142 YNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFR 201
             Y      PF   YA+    KL+   + +A EY +G HDFS F     + +  NP+K++F 
Sbjct:   119 YYGPP-SPFYERYAWALPQKLDREKVAKALEYLIGTHDFSGFGAAGSSGK--NPIKTMFE 175

Query:   202 FDVIEMGALLQLEVEGSGFLYRQVR 226
                 E G L         FLY+  R
Sbjct:   176 ASYREDGFLGYFTFVADSFLYKMAR 200

GO:0006400 "tRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|DET_0504 DET_0504 "tRNA pseudouridine synthase A" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 80/206 (38%), Positives = 108/206 (52%)

Query:    29 LVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 88
             LVI Y+GTRY+G+Q Q    TIQ  +E A IR  KL  E  R+ G+ RTD GVHA  QV 
Sbjct:     3 LVIEYEGTRYSGFQVQDKGATIQGELETA-IR--KLTSEQTRVSGSGRTDAGVHAAYQVV 59

Query:    89 HFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMD 148
              +++  S  GL+ I   LN  LPPDI V+E+      F  R  A S+ Y Y+I N     
Sbjct:    60 SYLSESSL-GLDKIKGGLNFYLPPDIAVKEVHFVAESFDVRRRAISREYSYQILNSKTRS 118

Query:   149 PFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPV--KSIFRFDVIE 206
             P     A+   YKL+  LM +A +   G+HDF AF +      +L P   K++ R +   
Sbjct:   119 PLARLQAWQVPYKLDIKLMEQAFKMLEGEHDFIAFAS------SLGPEIKKTVRRVNWTR 172

Query:   207 MGAL---LQLEVEGSGFLYRQVRNMV 229
             +G     L   +E + FL  QVRN +
Sbjct:   173 LGIREDRLIFNIEANSFLTHQVRNTI 198

GO:0006400 "tRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

UNIPROTKB|P07649 truA "tRNA pseudouridine synthase I" [Escherichia coli K-12 (taxid:83333)]

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 71/208 (34%), Positives = 109/208 (52%)

Query:    23 PGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 82
             P +K  L I YDG++Y GWQ Q    ++Q  +EKAL +V     E + +  A RTD GVH
Sbjct:     8 PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVH 64

Query:    83 AWGQVAHF-ITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI 141
               GQV HF  T    D   ++   +N  LP DI VR +     +FHARFSA ++ Y Y I
Sbjct:    65 GTGQVVHFETTALRKDAAWTL--GVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYII 122

Query:   142 YNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFR 201
             YN  +          H    L+   M  AA+  +G++DF++F  +Q   R   P +++  
Sbjct:   123 YNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRT--PWRNVMH 180

Query:   202 FDVIEMGALLQLEVEGSGFLYRQVRNMV 229
              +V   G  + ++++ + F++  VRN+V
Sbjct:   181 INVTRHGPYVVVDIKANAFVHHMVRNIV 208

GO:0000049 "tRNA binding" evidence=IDA

GO:0031119 "tRNA pseudouridine synthesis" evidence=IMP

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

TIGR_CMR|CBU_0892 CBU_0892 "tRNA pseudouridine synthase A" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 73/205 (35%), Positives = 109/205 (53%)

Query:    28 RLVIG--YDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 85
             R+ +G  YDG+ Y GWQ Q +  T+Q  VEKAL  V       + +  A RTD GVHA  
Sbjct:     3 RIALGIRYDGSAYHGWQVQEALKTVQGEVEKALSAVAN---HPVFVTCAGRTDAGVHASA 59

Query:    86 QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 145
             QVAHF T  +Y    +     N  LP DI +    A   +FHAR+SA ++ Y Y +YN  
Sbjct:    60 QVAHFDTT-AYRSDHAWVFGANSNLPHDISILWAKAVEEDFHARYSAMARRYRYIVYNHE 118

Query:   146 VMDPF-QHHYAYHSVYK-LNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFD 203
             +     +    +H  Y+ L+   M+  A+Y +G+HDFS+F       R   PV+ IF+ +
Sbjct:   119 IRPAILRKAIGWH--YRPLDEKRMQAGAQYLIGEHDFSSFQGAGCQSRT--PVRKIFQIE 174

Query:   204 VIEMGALLQLEVEGSGFLYRQVRNM 228
             +  +  ++ +EV+ + FL   VRN+
Sbjct:   175 IYRIRRMVVIEVQANAFLLHMVRNI 199

GO:0006400 "tRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

UNIPROTKB|Q9KTA4 truA "tRNA pseudouridine synthase A" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 290 (107.1 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 69/203 (33%), Positives = 107/203 (52%)

Query:    28 RLVIG--YDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 85
             R+ +G  YDGT Y GWQ Q    ++Q  +EKAL   +K+    + +  A RTD GVH  G
Sbjct:     2 RIALGIEYDGTHYYGWQRQREVKSVQEALEKAL---SKIANHPVEVQCAGRTDAGVHGTG 58

Query:    86 QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 145
             QV HF T      +     A N  LP DI VR   A   EFHARFSA ++ Y Y IYN  
Sbjct:    59 QVVHFDTTAERQMVAWTMGA-NANLPKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHV 117

Query:   146 VMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVI 205
                   +    H   +L+   M++A +Y +G++DF++F  +    R+  P +++   +V 
Sbjct:   118 YRPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRS--PWRNVMHLNVT 175

Query:   206 EMGALLQLEVEGSGFLYRQVRNM 228
               G  + ++++ + F++  VRN+
Sbjct:   176 RHGRYVVIDIKANAFVHHMVRNI 198

GO:0006400 "tRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|VC_0999 VC_0999 "tRNA pseudouridine synthase A" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 290 (107.1 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 69/203 (33%), Positives = 107/203 (52%)

Query:    28 RLVIG--YDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 85
             R+ +G  YDGT Y GWQ Q    ++Q  +EKAL   +K+    + +  A RTD GVH  G
Sbjct:     2 RIALGIEYDGTHYYGWQRQREVKSVQEALEKAL---SKIANHPVEVQCAGRTDAGVHGTG 58

Query:    86 QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 145
             QV HF T      +     A N  LP DI VR   A   EFHARFSA ++ Y Y IYN  
Sbjct:    59 QVVHFDTTAERQMVAWTMGA-NANLPKDIAVRWAMAVPDEFHARFSATARRYRYVIYNHV 117

Query:   146 VMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVI 205
                   +    H   +L+   M++A +Y +G++DF++F  +    R+  P +++   +V 
Sbjct:   118 YRPGILNSGVSHYHGELDVEKMQQAGQYLLGENDFTSFRAVHCQSRS--PWRNVMHLNVT 175

Query:   206 EMGALLQLEVEGSGFLYRQVRNM 228
               G  + ++++ + F++  VRN+
Sbjct:   176 RHGRYVVIDIKANAFVHHMVRNI 198

GO:0006400 "tRNA modification" evidence=ISS

GO:0009982 "pseudouridine synthase activity" evidence=ISS

TIGR_CMR|ECH_0622 ECH_0622 "tRNA pseudouridine synthase A" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 73/209 (34%), Positives = 113/209 (54%)

Query:    26 KWRLVIGYDGTRYAGWQFQT-SPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAW 84
             ++++ I Y+G+ + GWQ Q  S  +IQ I+E A++   K  ++   +  A RTD GVHA 
Sbjct:     2 RYKITIEYNGSNFIGWQKQKHSSNSIQEILENAIL---KFSQQHTTVYVAGRTDAGVHAL 58

Query:    85 GQVAHFITPFSYDGLESIHAALN-GLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI-- 141
             GQVAHF    + D    +  A+N  L+P  I +  +     +FHARFSAK + Y YKI  
Sbjct:    59 GQVAHFDLTTNLDTYV-VRNAINYHLIPHAIAILSVEKTDDKFHARFSAKKRHYLYKIIN 117

Query:   142 -YNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIF 200
              Y+   +D +   +  H+   LN   M +A EY  G HDFS+F    R+ ++ NP+K+I 
Sbjct:   118 RYSPLTID-YNRAWLIHN--PLNIENMIQAIEYIKGNHDFSSFR--ARHCQSKNPIKTID 172

Query:   201 RFDVIEMGALLQLEVEGSGFLYRQVRNMV 229
                +I     + + +    FL+ QVR +V
Sbjct:   173 DLKIIHNNQSINIHISAISFLHHQVRIIV 201

GO:0006400 "tRNA modification" evidence=ISS

TIGR_CMR|APH_0502 APH_0502 "tRNA pseudouridine synthase A" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 271 (100.5 bits), Expect = 1.4e-23, P = 1.4e-23
 Identities = 67/203 (33%), Positives = 109/203 (53%)

Query:    26 KWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIR-VTKLEREDLRLVGASRTDTGVHAW 84
             +++ V+ Y+GT + GWQ Q     +   V++++ R + +  ++ + +  A RTD GVHA 
Sbjct:     2 RYKAVVEYEGTSFIGWQRQHG--VVGKSVQESIERSIKEFCQQSVIVYAAGRTDAGVHAT 59

Query:    85 GQVAHFITPFSYDGLESIHAALNGLLPPD-IRVREISAAVPEFHARFSAKSKIYHYKIYN 143
             GQV HF    S +    I  ALN  L  + + + ++     EFHARFSAK + Y YKI N
Sbjct:    60 GQVVHFDLKVSREDYV-IKNALNHYLRNEKVSILQLERVDEEFHARFSAKKRHYTYKISN 118

Query:   144 DAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFD 203
                         +H   +LN   MREAA Y VGKHDF++F    ++ ++ + +K++   D
Sbjct:   119 REAPLCIDLMRMWHVPKRLNVENMREAASYIVGKHDFASFR--AKDCQSKSSIKTVDSID 176

Query:   204 VIEMGALLQLEVEGSGFLYRQVR 226
             +I     + + +    FL++QVR
Sbjct:   177 IIAAEEEININISAQSFLHKQVR 199

GO:0006400 "tRNA modification" 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)
Q813Z9	TRUA2_BACCR	5, ., 4, ., 9, 9, ., 1, 2	0.3627	0.8312	0.8040	yes	no
Q6I3T8	TRUA2_BACAN	5, ., 4, ., 9, 9, ., 1, 2	0.3725	0.8312	0.8040	yes	no
P70973	TRUA_BACSU	5, ., 4, ., 9, 9, ., 1, 2	0.4257	0.8354	0.8016	yes	no
C0ZIL2	TRUA_BREBN	5, ., 4, ., 9, 9, ., 1, 2	0.3872	0.8354	0.8114	yes	no
A8F9B7	TRUA_BACP2	5, ., 4, ., 9, 9, ., 1, 2	0.4059	0.8354	0.8016	yes	no
Q73E17	TRUA2_BACC1	5, ., 4, ., 9, 9, ., 1, 2	0.3725	0.8312	0.8040	yes	no
B2UYE4	TRUA_CLOBA	5, ., 4, ., 9, 9, ., 1, 2	0.3960	0.8270	0.8032	yes	no
A3DJK8	TRUA_CLOTH	5, ., 4, ., 9, 9, ., 1, 2	0.4207	0.8270	0.8032	yes	no
Q8R7Y7	TRUA_THETN	5, ., 4, ., 9, 9, ., 1, 2	0.4477	0.8227	0.8125	yes	no
B2TIK9	TRUA_CLOBB	5, ., 4, ., 9, 9, ., 1, 2	0.3910	0.8270	0.8032	yes	no
Q6HNW5	TRUA2_BACHK	5, ., 4, ., 9, 9, ., 1, 2	0.3725	0.8312	0.8040	yes	no
Q63GF1	TRUA2_BACCZ	5, ., 4, ., 9, 9, ., 1, 2	0.3627	0.8312	0.8040	yes	no
Q65P74	TRUA_BACLD	5, ., 4, ., 9, 9, ., 1, 2	0.4108	0.8354	0.8016	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
4th Layer	5.4.99.12	0.824
3rd Layer	5.4.99	0.766

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00019724001	RecName- Full=Pseudouridylate synthase; EC=5.4.99.-; (304 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00033342001	SubName- Full=Chromosome chr19 scaffold_66, whole genome shotgun sequence; (203 aa)	•			•			•		0.905
	GSVIVG00027910001	SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (235 aa)	•		•	•			•		0.902
	GSVIVG00019749001	SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_2, whole genome shotgu [...] (161 aa)	•			•			•		0.894
	GSVIVG00015501001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (385 aa)	•		•				•		0.890
	GSVIVG00016972001	SubName- Full=Chromosome chr11 scaffold_14, whole genome shotgun sequence; (489 aa)	•			•			•		0.887
	GSVIVG00035276001	SubName- Full=Chromosome chr10 scaffold_76, whole genome shotgun sequence;; DNA-dependent RNA p [...] (310 aa)	•						•		0.884
	rps8	RecName- Full=30S ribosomal protein S8, chloroplastic;; One of the primary rRNA binding protein [...] (134 aa)	•						•		0.873
	GSVIVG00015322001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (167 aa)	•			•			•		0.870
	GSVIVG00014289001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (195 aa)	•						•		0.867
	GSVIVG00020642001	SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (502 aa)			•	•		•	•		0.867

---

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	237
cd02570	239	cd02570, PseudoU_synth_EcTruA, Eukaryotic and bact	1e-86
PRK00021	244	PRK00021, truA, tRNA pseudouridine synthase A; Val	6e-85
COG0101	266	COG0101, TruA, Pseudouridylate synthase [Translati	1e-76
PRK12434	245	PRK12434, PRK12434, tRNA pseudouridine synthase A;	6e-58
TIGR00071	227	TIGR00071, hisT_truA, tRNA pseudouridine(38-40) sy	9e-54
PRK14586	245	PRK14586, PRK14586, tRNA pseudouridine synthase AC	2e-50
cd00497	215	cd00497, PseudoU_synth_TruA_like, Pseudouridine sy	6e-37
cd02866	219	cd02866, PseudoU_synth_TruA_Archea, Archeal pseudo	7e-37
PRK14588	272	PRK14588, PRK14588, tRNA pseudouridine synthase AC	2e-35
PRK14589	265	PRK14589, PRK14589, tRNA pseudouridine synthase AC	8e-34
cd02569	256	cd02569, PseudoU_synth_ScPus3, Pseudouridine synth	4e-30
cd02568	245	cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine sy	3e-22
pfam01416	103	pfam01416, PseudoU_synth_1, tRNA pseudouridine syn	8e-11
PRK14587	256	PRK14587, PRK14587, tRNA pseudouridine synthase AC	2e-10
pfam01416	103	pfam01416, PseudoU_synth_1, tRNA pseudouridine syn	1e-05
PLN03078	513	PLN03078, PLN03078, Putative tRNA pseudouridine sy	0.001

>gnl|CDD|211337 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial pseudouridine synthases similar to E

 Score =  256 bits (656), Expect = 1e-86
 Identities = 93/201 (46%), Positives = 122/201 (60%), Gaps = 6/201 (2%)

Query: 29  LVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 88
           L I YDGT ++GWQ Q +  T+Q  +EKAL ++     E +R++GA RTD GVHA GQVA
Sbjct: 1   LTIEYDGTNFSGWQRQPNGRTVQGELEKALSKIAG---EPVRVIGAGRTDAGVHALGQVA 57

Query: 89  HFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMD 148
           HF TP     LE +  ALN LLPPDIRV        +FHARFSAKS+ Y Y+I N  V  
Sbjct: 58  HFDTPSEIP-LEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRPVPS 116

Query: 149 PFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMG 208
           PF   Y +H    L+   M+EAA+  +G HDFS+F       +  + V++I+R DV   G
Sbjct: 117 PFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFRAAGCQSK--STVRTIYRADVYREG 174

Query: 209 ALLQLEVEGSGFLYRQVRNMV 229
            L+  E+  +GFLY  VRN+V
Sbjct: 175 DLIVFEIRANGFLYHMVRNIV 195

coli TruA. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA. psi38 and psi39 in tRNAs are highly phylogenetically conserved. P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators. Length = 239

>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated

 Score =  252 bits (646), Expect = 6e-85
 Identities = 87/204 (42%), Positives = 119/204 (58%), Gaps = 6/204 (2%)

Query: 26  KWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 85
           +  L I YDGT + GWQ Q +  T+Q  +EKAL ++     E +R++GA RTD GVHA G
Sbjct: 3   RIALTIEYDGTNFHGWQRQPNGRTVQGELEKALSKLAG---EPVRVIGAGRTDAGVHALG 59

Query: 86  QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 145
           QVAHF TP      E    ALN LLP DI V        +FHARFSAK++ Y Y+IYN  
Sbjct: 60  QVAHFDTPAPRP-PEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRYRYRIYNRP 118

Query: 146 VMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVI 205
              PF   Y +H  Y L+   M EAA+Y +G+HDF++F       +  +PV++I+  DV 
Sbjct: 119 ARPPFLRGYVWHYPYPLDVDAMNEAAQYLLGEHDFTSFRASGCQSK--SPVRTIYEADVT 176

Query: 206 EMGALLQLEVEGSGFLYRQVRNMV 229
             G  +  ++  +GFL+  VRN+V
Sbjct: 177 REGDFIVFDISANGFLHNMVRNIV 200

Length = 244

>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]

 Score =  231 bits (592), Expect = 1e-76
 Identities = 93/204 (45%), Positives = 131/204 (64%), Gaps = 6/204 (2%)

Query: 26  KWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 85
           +  L I YDGTR+ GWQ Q +  T+Q  +EKAL ++     E +R++GA RTD GVHA G
Sbjct: 3   RIALKIAYDGTRFHGWQRQPNVRTVQGELEKALSKIGG---ESVRVIGAGRTDAGVHALG 59

Query: 86  QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 145
           QV HF TP +   LE +  ALN LLPPDIRV +++    +FHARFSAKS+ Y Y IYN  
Sbjct: 60  QVVHFDTP-ADRPLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYRYIIYNAP 118

Query: 146 VMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVI 205
           +  PF  +Y +H  Y L+   MREAA+  +G HDF++F       ++ +PV++I+R DV 
Sbjct: 119 LRPPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFTSFRKAG--CQSKSPVRTIYRIDVS 176

Query: 206 EMGALLQLEVEGSGFLYRQVRNMV 229
             G L+ +++ G+ FL+  VRN+V
Sbjct: 177 RDGDLIVIDISGNSFLWHMVRNIV 200

Length = 266

>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed

 Score =  183 bits (467), Expect = 6e-58
 Identities = 79/203 (38%), Positives = 116/203 (57%), Gaps = 7/203 (3%)

Query: 28  RLVIGYDGTRYAGWQFQTSPP-TIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ 86
           +L I YDG+RY GWQ   +   TIQ  +E  L   +++  E++ ++G  RTD GVHA  Q
Sbjct: 5   KLTIQYDGSRYKGWQKLGNNDNTIQGKIESVL---SEMTGEEIEIIGCGRTDAGVHALNQ 61

Query: 87  VAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAV 146
           VA+F T       + I   LN  LP DI V  +      FHAR++ KSK Y YKI+N+  
Sbjct: 62  VANFQTDEK-LSEDKIKKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNEKF 120

Query: 147 MDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIE 206
            + F   Y+ H   KL+   M+EAA+Y VG HDF++F N +   ++   V+ I+  D++E
Sbjct: 121 HNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFTSFTNAKSKKKST--VREIYSIDIME 178

Query: 207 MGALLQLEVEGSGFLYRQVRNMV 229
               +Q+ V G+GFL+  VR +V
Sbjct: 179 EDGFVQIRVSGNGFLHNMVRIIV 201

Length = 245

>gnl|CDD|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase

 Score =  172 bits (438), Expect = 9e-54
 Identities = 79/204 (38%), Positives = 109/204 (53%), Gaps = 17/204 (8%)

Query: 26  KWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 85
           K  L I YDG+ Y GWQ Q +  T+Q  +EKAL  + K   + + ++ A RTD GVHA G
Sbjct: 2   KIALKIAYDGSNYHGWQRQPNKRTVQGELEKALEAIGK---KKITIMSAGRTDKGVHAMG 58

Query: 86  QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 145
           QV  F TP        ++A LN LLPPDIRV+ ++     FHARFSA  + Y Y +YN  
Sbjct: 59  QVISFDTP-KEIPDNKLNAKLNALLPPDIRVKALAPVNDNFHARFSASKRHYRYILYNHR 117

Query: 146 VMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVI 205
                      H    L+   MR AA+  +GKHDFS F   +   R  +P+++I    V 
Sbjct: 118 -----------HYYSPLDLEKMRAAAKQLLGKHDFSNFSKAKSKSR--SPIRTISDIKVS 164

Query: 206 EMGALLQLEVEGSGFLYRQVRNMV 229
           E G  +  ++ G+ FL+  VR +V
Sbjct: 165 ESGEYIIFDIIGNSFLWHMVRKIV 188

Members of this family are the tRNA modification enzyme TruA, tRNA pseudouridine(38-40) synthase. In a few species (e.g. Bacillus anthracis), TruA is represented by two paralogs [Protein synthesis, tRNA and rRNA base modification]. Length = 227

>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional

 Score =  164 bits (416), Expect = 2e-50
 Identities = 78/201 (38%), Positives = 111/201 (55%), Gaps = 7/201 (3%)

Query: 30  VIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAH 89
           V+ YDG+ + G+Q Q    T+Q + E AL R+ K   + +    A RTDTGVHA GQV  
Sbjct: 7   VVSYDGSNFFGYQGQPDVRTVQGVFEDALERIFK---QRIYTQAAGRTDTGVHANGQVIA 63

Query: 90  FITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDP 149
           F  P      E I  A+N  LP DI V+++      FH RF AK +IYHY I      + 
Sbjct: 64  FNCPNDRMTEEDIKNAMNANLPDDIYVKKVFEVPKNFHPRFDAKKRIYHYFILTSKEKNV 123

Query: 150 FQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEM-G 208
           F   Y +   Y+L+   MR+AA+Y  G+HDF++F   +      NPV++I+R  ++ +  
Sbjct: 124 FLRKYVWWFPYELDLEAMRKAAKYLEGEHDFTSF---KTGSDERNPVRTIYRIRILRLKK 180

Query: 209 ALLQLEVEGSGFLYRQVRNMV 229
            L+ + VEG  FL R VRN+V
Sbjct: 181 DLILIRVEGRSFLRRMVRNIV 201

Length = 245

>gnl|CDD|211322 cd00497, PseudoU_synth_TruA_like, Pseudouridine synthase, TruA family

 Score =  128 bits (324), Expect = 6e-37
 Identities = 62/199 (31%), Positives = 92/199 (46%), Gaps = 28/199 (14%)

Query: 31  IGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHF 90
            GYDGT+Y G+Q Q   PT++    + +I + K       +  A+RTD GV A GQV   
Sbjct: 1   FGYDGTKYHGFQRQNDVPTVE---GELIIALLKAGNIPYFIKAAARTDRGVSALGQVVAI 57

Query: 91  ITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPF 150
            T       E    ALNG+LP DIRV  + +  P+FHA      + Y Y I +       
Sbjct: 58  ETE-RRLTPE----ALNGILPGDIRVFAVHSVPPDFHAPRYCDHRTYRYYIPS------- 105

Query: 151 QHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGAL 210
                    + L+   ++ AA  F+G HDF+ F          N V++I   +  ++   
Sbjct: 106 ---------FPLDDERLKSAASRFLGTHDFTNF----SKKDTRNTVRTIISIECKDLNPF 152

Query: 211 LQLEVEGSGFLYRQVRNMV 229
           + +E +   FL+ QVR MV
Sbjct: 153 VVVEFKAKSFLWHQVRRMV 171

This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae PUS1 catalyzes the formation of psi34 and psi36 in the intron containing tRNAIle, psi35 in the intron containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44 in U2 snRNA and, psi38 and psi39 in tRNAs are highly phylogenetically conserved. Psi 26,27,28,34,35,36,65 and 67 in tRNAs are less highly conserved. Mouse Pus1p regulates nuclear receptor activity through pseudouridylation of Steroid Receptor RNA Activator. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA). Length = 215

>gnl|CDD|211343 cd02866, PseudoU_synth_TruA_Archea, Archeal pseudouridine synthases

 Score =  128 bits (324), Expect = 7e-37
 Identities = 62/203 (30%), Positives = 91/203 (44%), Gaps = 28/203 (13%)

Query: 29  LVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 88
           L I YDGT + G+Q Q    T++  + KAL     +     RL  A RTD GVHA G V 
Sbjct: 1   LKIAYDGTNFHGFQRQPDVRTVEGELIKAL-EELGIIESRARLYSAGRTDRGVHALGNVV 59

Query: 89  HFITPFSYDGLESIH-AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVM 147
                  ++  +      +N  LP DI V   +    +F  R  A  K Y Y + +D   
Sbjct: 60  ------VFETEKEPIPPMINAKLPKDIWVLAGAKVPEDFDPRRWAHRKYYRYNLGSD--- 110

Query: 148 DPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEM 207
                          +   M+EAA+  +G HDFS F    + D   +PV++I R ++ E 
Sbjct: 111 --------------YDVEAMKEAAKKLIGTHDFSNF---SKRDGRKDPVRTIERIEISEN 153

Query: 208 GALLQLEVEGSGFLYRQVRNMVN 230
           G  + ++V G  FL+  VR +V 
Sbjct: 154 GEFITIDVVGESFLWNMVRRIVG 176

This group consists of archeal pseudouridine synthases.Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. This group of proteins make Psedouridine in tRNAs. Length = 219

>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional

 Score =  126 bits (317), Expect = 2e-35
 Identities = 75/203 (36%), Positives = 99/203 (48%), Gaps = 7/203 (3%)

Query: 29  LVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 88
           L++ YDGT +AG Q+QT   T+Q  +E A   +T+  R   R+V A RTD GVHA GQVA
Sbjct: 6   LLLEYDGTDFAGSQWQTDGRTVQGALEAAWQALTQERR---RIVLAGRTDAGVHARGQVA 62

Query: 89  HFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMD 148
           H  T   +  L +I   LN  LP DI V+    A P+FHARFSA  + Y Y I       
Sbjct: 63  HVQTDTRHS-LATIWRGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREYRYVIDCAPAPS 121

Query: 149 PFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNI--QRNDRALNPVKSIFRFDVIE 206
           P   H   H    L+   M  A +  +G HDF+AF     + +             +   
Sbjct: 122 PQLRHQVLHYAGTLDVAAMDAALKLLIGTHDFAAFTTAPQEGSTVRTCYWARCTDTEWFG 181

Query: 207 MGALLQLEVEGSGFLYRQVRNMV 229
              LL +EV  + FL   VRN+V
Sbjct: 182 R-PLLAIEVAANAFLQHMVRNIV 203

Length = 272

>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional

 Score =  122 bits (307), Expect = 8e-34
 Identities = 67/199 (33%), Positives = 88/199 (44%), Gaps = 25/199 (12%)

Query: 31  IGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKL-EREDLRLVGASRTDTGVHAWGQVAH 89
           I Y GTR+ G Q+Q    T++     A  R+    +  +     A RTD GVHA GQV  
Sbjct: 7   ISYIGTRFFGSQYQPDQRTVEGEFIAACRRLGLFSDWREAGFALAGRTDRGVHARGQVLA 66

Query: 90  FITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDP 149
           F T      +E    ALNG LPPDI     +     FH R+ A S+ Y Y          
Sbjct: 67  FSTHKPERAVE----ALNGQLPPDIWCTGWAEVPESFHPRYDAISRTYRY---------- 112

Query: 150 FQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGA 209
                 Y S    +   MR+AA  F+G HDFS F  ++   +  +PV++I R  V   G 
Sbjct: 113 ------YFSRPPSDINAMRDAAGEFIGTHDFSCFARVE--GK--SPVRTILRIRVFSDGG 162

Query: 210 LLQLEVEGSGFLYRQVRNM 228
               EV    FL+  VR M
Sbjct: 163 FPVFEVTAQSFLWHMVRCM 181

Length = 265

>gnl|CDD|211336 cd02569, PseudoU_synth_ScPus3, Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like

 Score =  112 bits (282), Expect = 4e-30
 Identities = 64/227 (28%), Positives = 96/227 (42%), Gaps = 43/227 (18%)

Query: 29  LVIGYDGTRYAGWQFQ-TSPPTIQCIVEKALIRVTKL--EREDLRLVGASRTDTGVHAWG 85
           L   Y G  Y G+  Q  +  T++  + +AL + T+L  +R+        RTD GV A+G
Sbjct: 1   LRFAYLGWNYNGFAVQEETTNTVEETLFEALEK-TRLIEDRQTSNYSRCGRTDKGVSAFG 59

Query: 86  QVAHFIT------PFSYDGLESIHAA-----------LNGLLPPDIRVREISAAVPEFHA 128
           QV               D    + +            LN +LPPDIR+   +   P+F A
Sbjct: 60  QVISLDVRSNLKPEDGLDPSTDVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSA 119

Query: 129 RFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQR 188
           RFS  S+ Y Y                +     L+  LMR+AA+  +G+HDF  F  +  
Sbjct: 120 RFSCVSRTYRY----------------FFPKGDLDIELMRKAAKLLLGEHDFRNFCKMDV 163

Query: 189 NDRALNPVKSIFRFDVIE------MGALLQLEVEGSGFLYRQVRNMV 229
            ++  N V+ +   +V           L   EV GS FL+ QVR M+
Sbjct: 164 ANQVTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFLWHQVRCMM 210

This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya. Length = 256

>gnl|CDD|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/ PUS2 like

 Score = 91.1 bits (227), Expect = 3e-22
 Identities = 60/221 (27%), Positives = 96/221 (43%), Gaps = 39/221 (17%)

Query: 29  LVIGYDGTRYAGWQFQT-SPPTIQCIVEKALIR---VTKLEREDLRLVG---ASRTDTGV 81
           L+ GY GT Y G Q+   +  TI+  +E+AL +   +++    D + +G   A+RTD GV
Sbjct: 1   LLFGYCGTGYHGMQYNPGAYKTIEGELERALFKAGAISESNAGDPKKIGFSRAARTDKGV 60

Query: 82  HAWGQV--AHFIT--PFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIY 137
           HA   V     I   P     LE +   LN  LP DIRV  I+     F+AR +  S+ Y
Sbjct: 61  HAARNVVSLKVIIDDPEGLGILEDLVEKLNSHLPSDIRVFGITRVTKSFNARKACDSRTY 120

Query: 138 HYKIYNDAVMDPFQHHYAYHSVYKLNTT-LMREAAEYFVGKHDFSAFVNIQRNDRALNP- 195
            Y +                  + L T     E  + +VG H+F  F       +  +P 
Sbjct: 121 EYLL----------------PTFALETLQRFNEILKEYVGTHNFHNFTV---KKKFEDPS 161

Query: 196 ----VKSIFRFDVIEMGALLQ---LEVEGSGFLYRQVRNMV 229
               +KS +  +   +   L+   +++ G  F+  Q+R M+
Sbjct: 162 ANRFIKSFYVSEPFVIEEGLEWISIKIHGQSFMLHQIRKMI 202

This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle, psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are highly phylogenetically conserved. Psi 26,27,28,34,35,36,65 and 67 in tRNAs are less highly conserved. Mouse Pus1p regulates nuclear receptor activity through pseudouridylation of Steroid Receptor RNA Activator. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA). Length = 245

>gnl|CDD|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase

 Score = 57.1 bits (138), Expect = 8e-11
 Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 4/61 (6%)

Query: 170 AAEYFVGKHDFSAFVNIQRNDRAL-NPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNM 228
           AA+ + G HDFS F   Q+      + +++I    +   G LL  E++G+GFLY QVR M
Sbjct: 1   AAKLYDGTHDFSGF---QKQRTVQKSLIRTIESIGIERDGELLVFEIKGNGFLYHQVRIM 57

Query: 229 V 229
           V
Sbjct: 58  V 58

Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis. Length = 103

>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional

 Score = 59.1 bits (143), Expect = 2e-10
 Identities = 57/200 (28%), Positives = 86/200 (43%), Gaps = 40/200 (20%)

Query: 31  IGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHF 90
           I YDGT + G  F   P +++  + +    +         L   SRTD GV A G V   
Sbjct: 7   IAYDGTLFYG--FTGHPNSLEPALRRVFGEI---------LGRGSRTDPGVSAVGNVV-- 53

Query: 91  ITPFSYDGLESIH-AALNGLLPPDIRVREISAAVPE-FHARFSAKSKIYHYKIYNDAVMD 148
           +T       + +    +N  LP  +    + A VPE F+ R  AK + Y Y         
Sbjct: 54  MTS------QKLPLGYVNSKLPRGVWAWAV-AEVPEGFNPR-RAKRRRYLY--------- 96

Query: 149 PFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMG 208
                 A H  +  +   MREAAE   G HD+S+F+  +R ++A   V +++   V   G
Sbjct: 97  -----VAPH--WGEDVEAMREAAELLAGTHDYSSFIQ-RRGEKATPTVTTVYEIGVELRG 148

Query: 209 ALLQLEVEGSGFLYRQVRNM 228
            L+ L   G GF  + +R M
Sbjct: 149 DLIYLYFVGRGFRNKMIRKM 168

Length = 256

>gnl|CDD|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 27/121 (22%), Positives = 40/121 (33%), Gaps = 36/121 (29%)

Query: 29  LVIGYDGT-RYAGWQFQTSPPTIQCIVEKALIRVTKLEREDL----------------RL 71
               YDGT  ++G+Q Q    T+Q  + + +  +      +L                 +
Sbjct: 1   AAKLYDGTHDFSGFQKQ---RTVQKSLIRTIESIGIERDGELLVFEIKGNGFLYHQVRIM 57

Query: 72  VG-ASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARF 130
           VG   RT  GVHA  QV                  LN  L P       +  +  FH R+
Sbjct: 58  VGALLRTGKGVHALEQVVSL---------------LNSKLRPRAPPTAPAVGLYLFHVRY 102

Query: 131 S 131
            
Sbjct: 103 D 103

Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis. Length = 103

>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase; Provisional

 Score = 39.1 bits (91), Expect = 0.001
 Identities = 51/189 (26%), Positives = 77/189 (40%), Gaps = 46/189 (24%)

Query: 9   GTNNTVKPPTDDSF--------PGFKWR--------LVIGYDGTRYAGWQFQ---TSPPT 49
            ++ ++ PP+ D           G KW         L +GY GT Y G Q Q   +S  T
Sbjct: 39  PSSTSLSPPSSDPPLTDNSDQGGGMKWESARKKKVVLRVGYVGTDYRGLQKQRDLSSLST 98

Query: 50  IQCIVEKALIRVTKLERE----DLRLVG---ASRTDTGVHAWGQVAHFIT-----PFSY- 96
           I+  +E A+ +   + RE    +L  +G   +SRTD GVH+   +A  I+     P +  
Sbjct: 99  IEGELETAIFKAGGI-RESNYGNLHKIGWARSSRTDKGVHS---LATMISLKMEIPENAW 154

Query: 97  -DGLESIHAA--LNGLLPPDIRVREISAAVPEFHARFSAKSKIYHY-------KIYNDAV 146
            D  + I  A  +N  LP +IRV  I  A   F  R     + Y Y        I +   
Sbjct: 155 KDDPDGIALAKFINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFS 214

Query: 147 MDPFQHHYA 155
            +    H +
Sbjct: 215 SEEIDEHIS 223

Length = 513

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	237
COG0101	266	TruA Pseudouridylate synthase [Translation, riboso	100.0
PRK12434	245	tRNA pseudouridine synthase A; Reviewed	100.0
PRK14586	245	tRNA pseudouridine synthase ACD; Provisional	100.0
PRK00021	244	truA tRNA pseudouridine synthase A; Validated	100.0
PRK14588	272	tRNA pseudouridine synthase ACD; Provisional	100.0
cd02570	239	PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudou	100.0
TIGR00071	227	hisT_truA pseudouridylate synthase I. universal so	100.0
PRK14589	265	tRNA pseudouridine synthase ACD; Provisional	100.0
cd02569	256	PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Ps	100.0
cd00497	224	PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudo	100.0
cd02866	221	PseudoU_synth_TruA_Archea PseudoU_synth_archea: Ps	100.0
cd02568	245	PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: P	100.0
PRK14587	256	tRNA pseudouridine synthase ACD; Provisional	100.0
PLN03078	513	Putative tRNA pseudouridine synthase; Provisional	100.0
KOG2554	425	consensus Pseudouridylate synthase [Translation, r	100.0
KOG2553	416	consensus Pseudouridylate synthase [Translation, r	100.0
KOG4393	295	consensus Predicted pseudouridylate synthase [RNA	100.0
PF01416	105	PseudoU_synth_1: tRNA pseudouridine synthase; Inte	99.58
PF01416	105	PseudoU_synth_1: tRNA pseudouridine synthase; Inte	98.43
PF10105	187	DUF2344: Uncharacterized protein conserved in bact	97.37
TIGR01213	388	conserved hypothetical protein TIGR01213. Members	96.7
COG1258	398	Predicted pseudouridylate synthase [Translation, r	95.92
PRK14554	422	putative pseudouridylate synthase; Provisional	94.97
cd01291	87	PseudoU_synth PseudoU_synth: Pseudouridine synthas	92.93
COG5011	228	Uncharacterized protein conserved in bacteria [Fun	83.97

>COG0101 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.1e-73  Score=503.83  Aligned_cols=204  Identities=46%  Similarity=0.769  Sum_probs=193.0

Q ss_pred             ceeEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHH
Q 042710           24 GFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIH  103 (237)
Q Consensus        24 ~~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~  103 (237)
                      |+||+|.|+||||+|+|||+||+.+|||++||+||.+++.   .++.+.+|||||+||||.+||+||+++.+.. ++.|.
T Consensus         1 m~ri~l~iaYdGt~f~G~Q~Qp~~~TVQ~~le~aL~~i~~---~~~~i~~AGRTD~GVHA~gqv~hfd~~~~~~-~~~~~   76 (266)
T COG0101           1 MKRIALKIAYDGTRFHGWQRQPNVRTVQGELEKALSKIGG---ESVRVIGAGRTDAGVHALGQVVHFDTPADRP-LEKLV   76 (266)
T ss_pred             CceEEEEEEEcCCceeeeccCCCCCCHHHHHHHHHHHhcC---CcceeEEecCCCcCccccccEEEEEcCCccc-HHHHH
Confidence            4699999999999999999999999999999999999986   4679999999999999999999999987643 78999


Q ss_pred             HHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccccccccc
Q 042710          104 AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAF  183 (237)
Q Consensus       104 ~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F  183 (237)
                      .+||++||+||+|+++++||++|||||+|.+|+|+|+|++...++||..+++|+++.+||+++|++|++.|+|+|||+||
T Consensus        77 ~~lN~~Lp~dI~V~~~~~v~~~FhaRfsa~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~aa~~l~G~HDF~sF  156 (266)
T COG0101          77 RALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYRYIIYNAPLRPPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFTSF  156 (266)
T ss_pred             HHHHhcCCCCcEEEEEEECCCCCCCcccccceEEEEEEcCccCCChhhhcccccccCcCCHHHHHHHHHHccccccchhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccCCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHh
Q 042710          184 VNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSY  233 (237)
Q Consensus       184 ~~~~~~~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~  233 (237)
                      |+.++.  .++++|||+++++.+.++++.|+|+|+||||||||+|||+++
T Consensus       157 ~~~~~~--~~s~vRti~~~~v~~~~~~i~i~i~g~sFL~~mVR~iVg~l~  204 (266)
T COG0101         157 RKAGCQ--SKSPVRTIYRIDVSRDGDLIVIDISGNSFLWHMVRNIVGALL  204 (266)
T ss_pred             ccCCCc--cCCCeEEEEEEEEEecCCEEEEEEEeChhHHHHHHHHHHHHH
Confidence            998753  458999999999999999999999999999999999999554

>PRK12434 tRNA pseudouridine synthase A; Reviewed

Probab=100.00  E-value=2.7e-73  Score=498.15  Aligned_cols=205  Identities=39%  Similarity=0.641  Sum_probs=192.8

Q ss_pred             ceeEEEEEEEeCCCceeeeeCCC-CCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHH
Q 042710           24 GFKWRLVIGYDGTRYAGWQFQTS-PPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESI  102 (237)
Q Consensus        24 ~~~~~l~i~YdGt~y~G~Q~Q~~-~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l  102 (237)
                      |++|+|.|+||||+|+|||+||+ .+|||++||+||.++.+   +++++.+|||||+||||++||+||+++... +++.+
T Consensus         1 m~~~~l~i~YdGt~y~G~Q~Q~~~~~TVq~~le~aL~~~~~---~~~~~~~agRTD~GVHA~~qv~~f~~~~~~-~~~~l   76 (245)
T PRK12434          1 MRNIKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVLSEMTG---EEIEIIGCGRTDAGVHALNQVANFQTDEKL-SEDKI   76 (245)
T ss_pred             CceEEEEEEECCCccceEeeCCCCCCCHHHHHHHHHHHHhC---CCeEEEEeccCCCCcCccCcEEEEEcCCCC-CHHHH
Confidence            57999999999999999999996 89999999999999875   689999999999999999999999998654 57899


Q ss_pred             HHHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhccccccccc
Q 042710          103 HAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSA  182 (237)
Q Consensus       103 ~~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~  182 (237)
                      ..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|++....+||.++|+|+++.+||+++|++||+.|+|+|||++
T Consensus        77 ~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~  156 (245)
T PRK12434         77 KKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNEKFHNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFTS  156 (245)
T ss_pred             HHHHHccCCCCeEEEEEEECCCCcccccCCCcEEEEEEEccCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcCHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccCCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          183 FVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       183 F~~~~~~~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      ||+.++  +.++++|+|+++++.+.++++.|+|+|+||||||||+|||+++.
T Consensus       157 F~~~~~--~~~~~~R~I~~~~v~~~~~~~~i~i~g~~FL~~mVR~mvg~ll~  206 (245)
T PRK12434        157 FTNAKS--KKKSTVREIYSIDIMEEDGFVQIRVSGNGFLHNMVRIIVGALIE  206 (245)
T ss_pred             hcCCCC--CCCCCEEEEEEEEEEEeCCEEEEEEEecHHHHHHHHHHHHHHHH
Confidence            997643  35689999999999988899999999999999999999997764

>PRK14586 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=1.6e-72  Score=493.27  Aligned_cols=205  Identities=38%  Similarity=0.589  Sum_probs=191.4

Q ss_pred             ceeEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHH
Q 042710           24 GFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIH  103 (237)
Q Consensus        24 ~~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~  103 (237)
                      |++|+|.|+||||+|+|||+||+.+|||++||+||.++.+   +++.+++||||||||||++||+||+++.+..+++.|.
T Consensus         1 m~~~~l~i~YdGt~f~G~Q~Q~~~~TVq~~le~aL~~~~~---~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~   77 (245)
T PRK14586          1 MKRVAAVVSYDGSNFFGYQGQPDVRTVQGVFEDALERIFK---QRIYTQAAGRTDTGVHANGQVIAFNCPNDRMTEEDIK   77 (245)
T ss_pred             CeEEEEEEEEcCCceeeEEECCCCCCHHHHHHHHHHHHhC---CCeeEEEecCCccCCCccCcEEEEEecCCcCCHHHHH
Confidence            5799999999999999999999999999999999999975   6899999999999999999999999987634678999


Q ss_pred             HHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccccccccc
Q 042710          104 AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAF  183 (237)
Q Consensus       104 ~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F  183 (237)
                      .+||++||+||+|+++.+||++|||||+|++|+|+|+|++++.++||.++|+|+.+.+||+++|++||+.|+|+|||++|
T Consensus        78 ~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~~~l~G~HDF~~F  157 (245)
T PRK14586         78 NAMNANLPDDIYVKKVFEVPKNFHPRFDAKKRIYHYFILTSKEKNVFLRKYVWWFPYELDLEAMRKAAKYLEGEHDFTSF  157 (245)
T ss_pred             HHHHccCCCCeEEEEEEECCCCcCcccCCCcEEEEEEEecCCCCChhhCCceEEeCCCCCHHHHHHHHHHccCcchHHhh
Confidence            99999999999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             ccccccCCCCCCcEEEEEEEEEE-eCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          184 VNIQRNDRALNPVKSIFRFDVIE-MGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       184 ~~~~~~~~~~~~vR~I~~~~i~~-~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                       +..+  +.++++|+|+++++.+ .++++.|+|+|+||||||||+|||+++.
T Consensus       158 -~~~~--~~~~~vR~I~~~~~~~~~~~~i~~~i~g~~FL~~mVR~mvg~l~~  206 (245)
T PRK14586        158 -KTGS--DERNPVRTIYRIRILRLKKDLILIRVEGRSFLRRMVRNIVGALVK  206 (245)
T ss_pred             -cCCC--CCCCCcEEEEEEEEEEccCCEEEEEEEechhHHHHHHHHHHHHHH
Confidence             4432  3568999999999988 4789999999999999999999997765

>PRK00021 truA tRNA pseudouridine synthase A; Validated

Probab=100.00  E-value=7.9e-72  Score=488.71  Aligned_cols=205  Identities=42%  Similarity=0.693  Sum_probs=193.6

Q ss_pred             ceeEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHH
Q 042710           24 GFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIH  103 (237)
Q Consensus        24 ~~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~  103 (237)
                      |++|+|.|+||||+|+|||+||+.+|||++||+||.+++.   +++++.+||||||||||++||++|+++.. .+++.+.
T Consensus         1 m~~~~l~i~YdGt~y~G~q~q~~~~TVq~~le~aL~~~~~---~~~~~~~agRTD~GVHA~~qvv~~~~~~~-~~~~~~~   76 (244)
T PRK00021          1 MMRIALTIEYDGTNFHGWQRQPNGRTVQGELEKALSKLAG---EPVRVIGAGRTDAGVHALGQVAHFDTPAP-RPPEKWR   76 (244)
T ss_pred             CeEEEEEEEECCCccceeeeCCCCCCHHHHHHHHHHHHhC---CCeEEEEEccCCCcccccCcEEEEEeCCC-CCHHHHH
Confidence            6799999999999999999999999999999999999985   68999999999999999999999999875 3578999


Q ss_pred             HHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccccccccc
Q 042710          104 AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAF  183 (237)
Q Consensus       104 ~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F  183 (237)
                      .+||+.||+||+|+++.+||++|||||+|++|+|+|+|+....++||.++++|++..++|+++|++|++.|+|+|||+||
T Consensus        77 ~~lN~~Lp~dI~V~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~a~~~~~G~HdF~~F  156 (244)
T PRK00021         77 RALNALLPDDIAVLWAEEVPDDFHARFSAKARRYRYRIYNRPARPPFLRGYVWHYPYPLDVDAMNEAAQYLLGEHDFTSF  156 (244)
T ss_pred             HHHHhcCCCCEEEEEeEecCCCcCcCcCCCceEEEEEEecCCCCChhhCCcEEEeCCCCcHHHHHHHHHHhcCceeeeee
Confidence            99999999999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             ccccccCCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          184 VNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       184 ~~~~~~~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      |+.+.  +.++++|+|+++++.++++++.|+|+|+||||||||+|||+++.
T Consensus       157 ~~~~~--~~~~~~R~I~~~~v~~~~~~~~i~i~g~sFL~~qVR~mvg~l~~  205 (244)
T PRK00021        157 RASGC--QSKSPVRTIYEADVTREGDFIVFDISANGFLHNMVRNIVGTLLE  205 (244)
T ss_pred             eCCCC--CCCCCeEEEEEEEEEEcCCEEEEEEEEchhHHHHHHHHHHHHHH
Confidence            86542  35789999999999988899999999999999999999998875

>PRK14588 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=1.7e-71  Score=493.24  Aligned_cols=204  Identities=37%  Similarity=0.507  Sum_probs=190.8

Q ss_pred             ceeEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHH
Q 042710           24 GFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIH  103 (237)
Q Consensus        24 ~~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~  103 (237)
                      |++|+|.|+||||+|+|||+||+.+|||++||+||.++..   +++.+.+|||||+||||++||+||+++... +++.+.
T Consensus         1 m~~~~l~iaYdGt~f~G~Q~Q~~~~TVq~~Le~aL~~l~~---~~i~i~~AgRTDaGVHA~gQv~~f~~~~~~-~~~~l~   76 (272)
T PRK14588          1 MRTIALLLEYDGTDFAGSQWQTDGRTVQGALEAAWQALTQ---ERRRIVLAGRTDAGVHARGQVAHVQTDTRH-SLATIW   76 (272)
T ss_pred             CceEEEEEEEcCCceeeeEECCCCCCHHHHHHHHHHHhhC---CCceEEEecCCCcCcCccccEEEEEcCCCC-CHHHHH
Confidence            5799999999999999999999999999999999999874   689999999999999999999999998664 578999


Q ss_pred             HHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccccccccc
Q 042710          104 AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAF  183 (237)
Q Consensus       104 ~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F  183 (237)
                      .+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+++..++||.++|+|+++.++|+++|++||+.|+|+|||++|
T Consensus        77 ~~LN~~LP~dI~V~~v~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F  156 (272)
T PRK14588         77 RGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREYRYVIDCAPAPSPQLRHQVLHYAGTLDVAAMDAALKLLIGTHDFAAF  156 (272)
T ss_pred             HHHHhcCCCCeEEEEEEECCCCcCcccCCCcEEEEEEEcCCCCCChhhcCceEecCCCCCHHHHHHHHHHccCCcchHhh
Confidence            99999999999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             ccccccCCCCCCcEEEEEEEEEEe----CcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          184 VNIQRNDRALNPVKSIFRFDVIEM----GALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       184 ~~~~~~~~~~~~vR~I~~~~i~~~----~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      |+..   +.++++|+|+++++.+.    ++++.|+|+|+||||||||+|||+++.
T Consensus       157 ~~~~---~~~~~vRtI~~~~~~~~~~~~~~~i~~~i~g~~FL~~mVR~mVg~ll~  208 (272)
T PRK14588        157 TTAP---QEGSTVRTCYWARCTDTEWFGRPLLAIEVAANAFLQHMVRNIVGTLLL  208 (272)
T ss_pred             cCCC---CCCCCeEEEEEEEEEEcccCCCCEEEEEEEEchhHHHHHHHHHHHHHH
Confidence            9762   24689999999999874    378999999999999999999997764

>cd02570 PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like

Probab=100.00  E-value=9e-70  Score=474.27  Aligned_cols=200  Identities=47%  Similarity=0.752  Sum_probs=189.1

Q ss_pred             EEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHHHHHHc
Q 042710           29 LVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNG  108 (237)
Q Consensus        29 l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~~~lN~  108 (237)
                      |+|+||||+|+|||+||+.+|||++||+||.+++.   +++++.+|||||+||||++||+||+++.+. +++.+..+||+
T Consensus         1 l~i~Y~Gt~f~G~q~q~~~~TVq~~le~aL~~~~~---~~~~i~~agRTD~GVHA~~qvv~~~~~~~~-~~~~~~~~lN~   76 (239)
T cd02570           1 LTIEYDGTNFSGWQRQPNGRTVQGELEKALSKIAG---EPVRVIGAGRTDAGVHALGQVAHFDTPSEI-PLEKLIKALNS   76 (239)
T ss_pred             CEEEEeCCccceeeeCCCCCCHHHHHHHHHHHHhC---CCeEEEEECcCCCCcCccccEEEEEECCCC-CHHHHHHHHHc
Confidence            57999999999999999999999999999999975   689999999999999999999999998764 57899999999


Q ss_pred             cCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhccccccccccccccc
Q 042710          109 LLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQR  188 (237)
Q Consensus       109 ~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~~~~~  188 (237)
                      .||+||+|+++.+|+++|||||+|++|+|+|+|+....++||.++++|+++.++|+++|++|+++|+|+|||+|||+.+.
T Consensus        77 ~Lp~dI~v~~i~~v~~~F~aR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~d~~~m~~a~~~f~G~HdF~~F~~~~~  156 (239)
T cd02570          77 LLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRPVPSPFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFRAAGC  156 (239)
T ss_pred             cCCCCEEEEEEEECCCCcCcccCCCceEEEEEEccCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcchhhhCCCCC
Confidence            99999999999999999999999999999999999888899999999999999999999999999999999999998653


Q ss_pred             cCCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          189 NDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       189 ~~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                        ..++++|+|+++++.+.++++.|+|+|+||||||||+|||+++.
T Consensus       157 --~~~~~~R~I~~~~v~~~~~~~~i~i~g~sFL~~qVR~mvg~ll~  200 (239)
T cd02570         157 --QSKSTVRTIYRADVYREGDLIVFEIRANGFLYHMVRNIVGTLLE  200 (239)
T ss_pred             --CCCCCeEEEEEEEEEEeCCEEEEEEEEcHHHHHHHHHHHHHHHH
Confidence              24689999999999998899999999999999999999998876

This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA. psi38 and psi39 in tRNAs are highly phylogenetically conserved. P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators.

>TIGR00071 hisT_truA pseudouridylate synthase I

Probab=100.00  E-value=1.4e-69  Score=470.00  Aligned_cols=193  Identities=40%  Similarity=0.654  Sum_probs=178.3

Q ss_pred             eeEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHHH
Q 042710           25 FKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHA  104 (237)
Q Consensus        25 ~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~~  104 (237)
                      ++|+|.|+||||+|+|||+||+.+|||++||+||.+++.   +++++.+|||||+||||++||+||+++.+. +++.|..
T Consensus         1 ~~~~l~i~YdGt~f~G~Q~Q~~~~TVq~~le~aL~~~~~---~~i~~~~agRTD~GVHA~~qv~~f~~~~~~-~~~~~~~   76 (227)
T TIGR00071         1 RKIALKIAYDGSNYHGWQRQPNKRTVQGELEKALEAIGK---KKITIMSAGRTDKGVHAMGQVISFDTPKEI-PDNKLNA   76 (227)
T ss_pred             CeEEEEEEEcCCCeeEEeECcCCCCHHHHHHHHHHHHhC---CCeeEEeeccCcCCccccccEEEEEecCCC-CHHHHHH
Confidence            589999999999999999999999999999999999975   689999999999999999999999998764 5788999


Q ss_pred             HHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhccccccccccc
Q 042710          105 ALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFV  184 (237)
Q Consensus       105 ~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~  184 (237)
                      +||+.||+||+|+++.+|+++|||||+|++|+|+|+|+...           ++..++|+++|++|++.|+|+|||++||
T Consensus        77 ~lN~~Lp~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~-----------~~~~~ld~~~m~~a~~~~~G~HDF~~F~  145 (227)
T TIGR00071        77 KLNALLPPDIRVKALAPVNDNFHARFSASKRHYRYILYNHR-----------HYYSPLDLEKMRAAAKQLLGKHDFSNFS  145 (227)
T ss_pred             HHHccCCCCEEEEEEEeCCCCcCCCCCCCcEEEEEEEccCc-----------ccCCCCCHHHHHHHHHHccCcccHHHhc
Confidence            99999999999999999999999999999999999997643           3346799999999999999999999999


Q ss_pred             cccccCCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          185 NIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       185 ~~~~~~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      +..+  +.++++|+|+++++.+.++++.|+|+|+||||||||+|||+++.
T Consensus       146 ~~~~--~~~~~~R~i~~~~v~~~~~~~~i~i~g~~FL~~mVR~mvg~l~~  193 (227)
T TIGR00071       146 KAKS--KSRSPIRTISDIKVSESGEYIIFDIIGNSFLWHMVRKIVGALVL  193 (227)
T ss_pred             CCCC--CCCCCeEEEEEEEEEEcCCEEEEEEEecHHHHHHHHHHHHHHHH
Confidence            7642  35789999999999998899999999999999999999997763

universal so far, single copy in all prokaryotes, 3 in yeast. Trusted cutoff for orthology is about 100 based on 1 match only in complete prokaryote with length 200.

>PRK14589 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=1.5e-66  Score=459.64  Aligned_cols=186  Identities=35%  Similarity=0.513  Sum_probs=171.5

Q ss_pred             eeEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhcccc-ccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHH
Q 042710           25 FKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLE-REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIH  103 (237)
Q Consensus        25 ~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~-~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~  103 (237)
                      ++|+|.|+||||+|+|||+||+.+|||++||+||.+++.+. .+++.+.+|||||+||||++||+||+++.    ++.+.
T Consensus         1 ~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~Le~aL~~~~~~~~~~~~~i~~agRTDaGVHA~gqv~~f~~~~----~~~~~   76 (265)
T PRK14589          1 MRLAFRISYIGTRFFGSQYQPDQRTVEGEFIAACRRLGLFSDWREAGFALAGRTDRGVHARGQVLAFSTHK----PERAV   76 (265)
T ss_pred             CcEEEEEEEcCCCeeeeeeCCCCCCHHHHHHHHHHHhhCccCCceeeEEEeccCCcCccccccEEEEEeCC----hHHHH
Confidence            38999999999999999999999999999999999997542 25789999999999999999999999863    57799


Q ss_pred             HHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccccccccc
Q 042710          104 AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAF  183 (237)
Q Consensus       104 ~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F  183 (237)
                      .+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+.                .++|+++|++||+.|+|+|||+||
T Consensus        77 ~~lN~~LP~dI~V~~~~~v~~~FhAR~~a~~R~Y~Y~i~~----------------~~lD~~~m~~a~~~f~G~HDF~~F  140 (265)
T PRK14589         77 EALNGQLPPDIWCTGWAEVPESFHPRYDAISRTYRYYFSR----------------PPSDINAMRDAAGEFIGTHDFSCF  140 (265)
T ss_pred             HHHHhhCCCCeEEEEEEEcCCCCCcccCCceeEEEEEEec----------------CccHHHHHHHHHHHccCCccHHHH
Confidence            9999999999999999999999999999999999999852                358999999999999999999999


Q ss_pred             ccccccCCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          184 VNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       184 ~~~~~~~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      |+.+    .++++|+|+++++.+.++++.|+|+|+||||||||+|||+++.
T Consensus       141 ~~~~----~~~~vRtI~~i~v~~~~~~~~~~i~G~~FL~~mVR~mVG~ll~  187 (265)
T PRK14589        141 ARVE----GKSPVRTILRIRVFSDGGFPVFEVTAQSFLWHMVRCMAGALLQ  187 (265)
T ss_pred             hccC----CCCCeEEEEEEEEEEeCCEEEEEEEechhHHHHHHHHHHHHHH
Confidence            9763    3578999999999998899999999999999999999997765

>cd02569 PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like

Probab=100.00  E-value=1.5e-66  Score=457.99  Aligned_cols=190  Identities=33%  Similarity=0.513  Sum_probs=168.6

Q ss_pred             EEEEEeCCCceeeeeCCC-CCcHHHHHHHHHHHhcccc-ccceeeeecccCCCcccccCcEEEEEeCCCCCCH-------
Q 042710           29 LVIGYDGTRYAGWQFQTS-PPTIQCIVEKALIRVTKLE-REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGL-------   99 (237)
Q Consensus        29 l~i~YdGt~y~G~Q~Q~~-~~TVq~~le~aL~~~~~~~-~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~-------   99 (237)
                      |+|+||||+|+|||+||+ .+|||++||+||.+++.+. .+++.+.+|||||+||||++||+||+++.+..+.       
T Consensus         1 l~i~YdGt~y~G~Q~Q~~~~~TVq~~Le~aL~~~~~i~~~~~~~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~~~~~~   80 (256)
T cd02569           1 LRFAYLGWNYNGFAVQEETTNTVEETLFEALEKTRLIEDRQTSNYSRCGRTDKGVSAFGQVISLDVRSNLKPEDGLDPST   80 (256)
T ss_pred             CEEEEeCCcceeeeECCCCCCCHHHHHHHHHHHhcCCCCCCceeEEeecccCccccccCcEEEEEecCCCCccccccccc
Confidence            579999999999999997 5899999999999998543 3589999999999999999999999997543211       


Q ss_pred             ----------HHHHHHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHH
Q 042710          100 ----------ESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMRE  169 (237)
Q Consensus       100 ----------~~l~~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~  169 (237)
                                ..+..+||++||+||+|+++.+|+++|||||+|++|+|+|+|+..                ++|+++|++
T Consensus        81 ~~~~~~~~~~~~~~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~----------------~ldi~~m~~  144 (256)
T cd02569          81 DVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSARFSCVSRTYRYFFPKG----------------DLDIELMRK  144 (256)
T ss_pred             cccccccchHHHHHHHHHhhCCCCcEEEEEEECCCCcCCCccCCceEEEEEecCC----------------CCCHHHHHH
Confidence                      258899999999999999999999999999999999999999753                599999999


Q ss_pred             HHhhccccccccccccccccCCCCCCcEEEEEEEEEEeC------cEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          170 AAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMG------ALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       170 a~~~~~G~HDF~~F~~~~~~~~~~~~vR~I~~~~i~~~~------~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      ||++|+|+|||++||+.....+.++++|+|+++++.+.+      +++.|+|+|+||||||||+|||+++.
T Consensus       145 a~~~f~G~HDF~~F~~~~~~~~~~~~~RtI~~~~v~~~~~~~~~~~~~~~~i~g~~FL~~mVR~mvg~ll~  215 (256)
T cd02569         145 AAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFLWHQVRCMMAVLFL  215 (256)
T ss_pred             HHHHhhCCcchHHHhccCcccCCCCCceEEEEEEEEEccCCCCCCcEEEEEEEEcHHHHHHHHHHHHHHHH
Confidence            999999999999999764322357899999999998753      78999999999999999999997765

This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya.

>cd00497 PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudouridine synthase, TruA family

Probab=100.00  E-value=3.4e-66  Score=447.88  Aligned_cols=183  Identities=39%  Similarity=0.597  Sum_probs=167.7

Q ss_pred             EEEeCCCceeeeeCCCCCcHHHHHHHHHHHhcccc-ccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHHHHHHcc
Q 042710           31 IGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLE-REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGL  109 (237)
Q Consensus        31 i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~-~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~~~lN~~  109 (237)
                      |+||||+|+|||+||+.+|||++||+||.+++..+ .+++.+.+|||||+||||++||+||+++...   +.+..+||+.
T Consensus         1 i~YdGt~f~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~i~~agRTD~GVHA~~qv~~~~~~~~~---~~~~~~lN~~   77 (224)
T cd00497           1 IAYDGWKYHGFQRQPDVPTVEGELFKALLKTGLIESPKPSNYSRAGRTDKGVSALGQVVSLETRSKL---KPYPDILNGL   77 (224)
T ss_pred             CEEcCCceeeEeeCcCCCCHHHHHHHHHHHhhCcCCCcceeEEEeccccccccccccEEEEEECCCc---HHHHHHHHhh
Confidence            68999999999999999999999999999998631 1379999999999999999999999998653   2799999999


Q ss_pred             CCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccccccccccccccc
Q 042710          110 LPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRN  189 (237)
Q Consensus       110 LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~~~~~~  189 (237)
                      ||+||+|+++++|+++||||++|++|+|+|+|+..                ++|+++|++|++.|+|+|||+|||+.++ 
T Consensus        78 Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~----------------~~d~~~m~~a~~~f~G~HDF~~F~~~~~-  140 (224)
T cd00497          78 LPKDIRVLAWAPVPEDFHARFSCVSRTYRYYFPGG----------------DLDIEAMREAAKLLLGTHDFRNFCKKDG-  140 (224)
T ss_pred             CCCCcEEEEEEEeCCCCCCCcccCeEEEEEEECCC----------------CcCHHHHHHHHHHccCcccHHHhcCCCC-
Confidence            99999999999999999999999999999999753                5899999999999999999999997643 


Q ss_pred             CCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          190 DRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       190 ~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                       ..++++|||+++++.+.++++.|+|+|+||||||||+|||+++.
T Consensus       141 -~~~~~~RtI~~~~v~~~~~~~~i~i~g~sFL~~mVR~mvg~ll~  184 (224)
T cd00497         141 -RKKNPVRTIISAEVEEVDDFYVFEVKGKSFLWHQVRRIVAALFL  184 (224)
T ss_pred             -CCCCCeEEEEEEEEEecCCEEEEEEEEcHHHHHHHHHHHHHHHH
Confidence             24789999999999998899999999999999999999997764

This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae PUS1 catalyzes the formation of psi34 and psi36 in the intron containing tRNAIle, psi35 in the intron containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44 in U2 snRNA and, psi38 and psi39 in tRNAs are highly ph

>cd02866 PseudoU_synth_TruA_Archea PseudoU_synth_archea: Pseudouridine synthase,

Probab=100.00  E-value=1e-65  Score=444.07  Aligned_cols=181  Identities=36%  Similarity=0.550  Sum_probs=166.0

Q ss_pred             EEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhcccc-ccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHHHHHH
Q 042710           29 LVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLE-REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALN  107 (237)
Q Consensus        29 l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~-~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~~~lN  107 (237)
                      |.|+||||+|+|||+||+.+|||++||+||.+++.+. .+++.+++|||||+||||++||+||+++..     .+..+||
T Consensus         1 l~i~Y~Gt~y~G~q~q~~~~TVq~~le~aL~~~~~~~~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~-----~~~~~lN   75 (221)
T cd02866           1 LKVAYDGTPYHGFQRQPDVRTVEGELIKALRRLGIIESPKRPRLYSAGRTDAGVSALGNVVAFETEKE-----LTPPAIN   75 (221)
T ss_pred             CEEEEeCCceeeeeeCCCCCCHHHHHHHHHHHhhccccCCceEEEEEcCCccccCccccEEEEEeCcH-----HHHHHHH
Confidence            5799999999999999999999999999999997532 357999999999999999999999998743     2789999


Q ss_pred             ccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccccccccccccc
Q 042710          108 GLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQ  187 (237)
Q Consensus       108 ~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~~~~  187 (237)
                      ++||+||+|+++.+||++||||++|++|+|+|+|+..                ++|+++|++|++.|+|+|||++||+.+
T Consensus        76 ~~LP~dI~v~~~~~v~~~F~ar~~a~~r~Y~Y~i~~~----------------~ld~~~m~~a~~~~~G~HDF~~F~~~~  139 (221)
T cd02866          76 NALPKDIRVWAWAKVPEDFHPRRDARRRYYRYYLGAE----------------DYDVEAMAEAAKKLIGTHDFSNFSKRD  139 (221)
T ss_pred             hhCCCCEEEEEEEEeCCCCCCCccCCeEEEEEEECCC----------------cCCHHHHHHHHHHhcCCcCHHHhhCCC
Confidence            9999999999999999999999999999999998642                589999999999999999999999753


Q ss_pred             ccCCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          188 RNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       188 ~~~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      +    .+++|+|+++++.+.++++.|+|+|+||||||||+|||+++.
T Consensus       140 ~----~~~~R~I~~~~~~~~~~~~~~~i~g~~FL~~mVR~mvg~ll~  182 (221)
T cd02866         140 G----RDPVRTIERIEIRENGEFLVIDVVGESFLWNMVRRIVGALSL  182 (221)
T ss_pred             C----CCCcEEEEEEEEEEcCCEEEEEEEEcHHHHHHHHHHHHHHHH
Confidence            2    378999999999998899999999999999999999997764

This group consists of archealpseudouridine synthases.Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. This group of proteins make Psedouridine in tRNAs.

>cd02568 PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: Pseudouridine synthase, PUS1/ PUS2 like

Probab=100.00  E-value=5.7e-65  Score=445.59  Aligned_cols=190  Identities=29%  Similarity=0.442  Sum_probs=170.3

Q ss_pred             EEEEEeCCCceeeeeCCCC-CcHHHHHHHHHHHhcccc------ccceeeeecccCCCcccccCcEEEEEeCCCCCC---
Q 042710           29 LVIGYDGTRYAGWQFQTSP-PTIQCIVEKALIRVTKLE------REDLRLVGASRTDTGVHAWGQVAHFITPFSYDG---   98 (237)
Q Consensus        29 l~i~YdGt~y~G~Q~Q~~~-~TVq~~le~aL~~~~~~~------~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~---   98 (237)
                      |.|+||||+|+|||+||+. +|||++||+||.+++.++      .+++++++|||||+||||++||+||+++...++   
T Consensus         1 l~i~Y~Gt~f~G~Q~Q~~~~~TVq~~le~aL~~~~~~~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~   80 (245)
T cd02568           1 LLFGYCGTGYHGMQYNPGNYKTIEGELERALVKAGAISESNAGDPKKIGFSRAARTDKGVHAARNVVSLKVIIDDPEGLG   80 (245)
T ss_pred             CEEEEeCCCccccccCCCCCCChHHHHHHHHHHcCCcCccccCChhhcceeeecccccchhheeeEEEEEEecccccccc
Confidence            5799999999999999998 999999999999998642      257999999999999999999999999866432   


Q ss_pred             -HHHHHHHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccc
Q 042710           99 -LESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGK  177 (237)
Q Consensus        99 -~~~l~~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~  177 (237)
                       ++++..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+...    +           +|+++|++|++.|+|+
T Consensus        81 ~~~~~~~~lN~~Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~~----~-----------~d~~~m~~a~~~~~G~  145 (245)
T cd02568          81 IGEDLVEKLNSHLPEDIRVFGITRVTKSFNARKACDSRTYEYLLPTFA----L-----------ETLDRFNEILKLYVGT  145 (245)
T ss_pred             chHHHHHHHHccCCCceEEEEEEcCCCCCCcchhhhcceeEEECCccc----H-----------hHHHHHHHHHHHhhCc
Confidence             67899999999999999999999999999999999999999996532    1           8999999999999999


Q ss_pred             ccccccccccccCCCCCCcEEEEEEEEEEe------CcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          178 HDFSAFVNIQRNDRALNPVKSIFRFDVIEM------GALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       178 HDF~~F~~~~~~~~~~~~vR~I~~~~i~~~------~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      |||++||+... .+.++++|+|.++++.+.      .+++.|+|+|+||||||||+|||+++.
T Consensus       146 HdF~~F~~~~~-~~~~~~~R~i~~~~~~~~~~~~~~~~~i~i~i~g~~FL~~mVR~mvg~l~~  207 (245)
T cd02568         146 HNFHNFTVRKK-FEDPSANRFIISFYVSEPFVIEEGLEWVSIEIHGQSFMLHQIRKMIGLAIA  207 (245)
T ss_pred             cccccCccccc-ccCCCceeEEEEEEEecceeecCCccEEEEEEEechHHHHHHHHHHHHHHH
Confidence            99999998643 134689999999999864      378999999999999999999998765

This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle, psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal. Psi44 in U

>PRK14587 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=5.9e-61  Score=421.49  Aligned_cols=173  Identities=26%  Similarity=0.397  Sum_probs=154.3

Q ss_pred             eeEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHHH
Q 042710           25 FKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHA  104 (237)
Q Consensus        25 ~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~~  104 (237)
                      ++|+|.|+||||+|+|||+||+  |||++||+||.++..         .|||||+||||++||+||.  .+. +    ..
T Consensus         1 ~~~~l~i~YdGt~f~G~Q~Q~~--TVq~~Le~aL~~i~~---------~agRTDaGVHA~~qv~~~~--~~~-~----~~   62 (256)
T PRK14587          1 MPYLYRIAYDGTLFYGFTGHPN--SLEPALRRVFGEILG---------RGSRTDPGVSAVGNVVMTS--QKL-P----LG   62 (256)
T ss_pred             CcEEEEEEECCCcccceecCcc--hHHHHHHHHHHHhcc---------CccCCccCCCcccCEEEEC--CcC-C----HH
Confidence            4799999999999999999998  999999999998742         2999999999999999983  222 1    46


Q ss_pred             HHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhccccccccccc
Q 042710          105 ALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFV  184 (237)
Q Consensus       105 ~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~  184 (237)
                      +||+.||+||+|+++.+|+++||||+ |++|+|+|+|+                ..++|+++|++|++.|+|+|||++||
T Consensus        63 ~LN~~LP~dI~V~~~~~V~~~FhaR~-a~~R~Y~Y~i~----------------~~~lDi~~m~~aa~~l~G~HDF~~F~  125 (256)
T PRK14587         63 YVNSKLPRGVWAWAVAEVPEGFNPRR-AKRRRYLYVAP----------------HWGEDVEAMREAAELLAGTHDYSSFI  125 (256)
T ss_pred             HHHhcCCCCeEEEEEEECCCCcCcCc-ccceEEEEEEc----------------cCcchHHHHHHHHHHhcCCcChHHhc
Confidence            89999999999999999999999997 99999999983                12499999999999999999999999


Q ss_pred             cccccCCCCC-CcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          185 NIQRNDRALN-PVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       185 ~~~~~~~~~~-~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      +.++.  .++ ++|+|+++++.+.++++.|+|+|+||||||||+|||+++.
T Consensus       126 ~~~~~--~~~~~vRtI~~i~v~~~~~~i~i~i~g~sFL~~mVR~mVG~Ll~  174 (256)
T PRK14587        126 QRRGE--KATPTVTTVYEIGVELRGDLIYLYFVGRGFRNKMIRKMAWAILA  174 (256)
T ss_pred             cCCCC--CCCCCEEEEEEEEEEEeCCEEEEEEEechhHHHHHHHHHHHHHH
Confidence            76432  345 8999999999988899999999999999999999997764

>PLN03078 Putative tRNA pseudouridine synthase; Provisional

Probab=100.00  E-value=1.2e-60  Score=447.83  Aligned_cols=210  Identities=23%  Similarity=0.318  Sum_probs=176.5

Q ss_pred             CCCceeEEEEEEEeCCCceeeeeCCC---CCcHHHHHHHHHHHhcccc------ccceeeeecccCCCcccccCcEEEEE
Q 042710           21 SFPGFKWRLVIGYDGTRYAGWQFQTS---PPTIQCIVEKALIRVTKLE------REDLRLVGASRTDTGVHAWGQVAHFI   91 (237)
Q Consensus        21 ~~~~~~~~l~i~YdGt~y~G~Q~Q~~---~~TVq~~le~aL~~~~~~~------~~~~~~~~agRTD~GVHA~~qv~~~~   91 (237)
                      ..+|++|+|.|+||||+|+|||+|++   .+|||++||+||.+++++.      .+++.+.+||||||||||++||+||+
T Consensus        67 ~~~krrvaL~IaYdGt~Y~G~Q~Q~n~~~~~TVEg~LE~AL~k~~~I~e~n~~~~~ki~~~rAgRTDkGVHA~gQVvsf~  146 (513)
T PLN03078         67 SARKKKVVLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNYGNLHKIGWARSSRTDKGVHSLATMISLK  146 (513)
T ss_pred             cccceEEEEEEEEcCCCcceeeECCCCCCCCCHHHHHHHHHHHHhCccccccccccceeEEeeccCCcCccccccEEEEe
Confidence            36789999999999999999999987   4799999999999997642      25789999999999999999999999


Q ss_pred             eCCCC------CCHHHHHHHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeec--CCCCCccccccccccCCCCC
Q 042710           92 TPFSY------DGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYN--DAVMDPFQHHYAYHSVYKLN  163 (237)
Q Consensus        92 ~~~~~------~~~~~l~~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~--~~~~~p~~~~~~~~~~~~ld  163 (237)
                      ++.+.      .+...|..+||++||+||+|+++.+|+++|||||+|++|+|+|+|++  ....++|...+.|+     |
T Consensus       147 l~~p~~~~~~d~~~~~L~~~LN~~LP~DIRVl~v~~V~~~FhAR~sc~sRtY~Y~iP~~~~~~k~~f~~~~~~~-----d  221 (513)
T PLN03078        147 MEIPENAWKDDPDGIALAKFINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFSSEEIDE-----H  221 (513)
T ss_pred             ccCcchhccccchHHHHHHHHHhcCCCCeEEEEEEECCCCcCCCCCCCceEEEEEEccccccCCCccchhhhHH-----H
Confidence            85421      11236889999999999999999999999999999999999999988  44455666666554     8


Q ss_pred             HHHHHHHHhhccccccccccccccccCCC---------------------------------------------------
Q 042710          164 TTLMREAAEYFVGKHDFSAFVNIQRNDRA---------------------------------------------------  192 (237)
Q Consensus       164 ~~~m~~a~~~~~G~HDF~~F~~~~~~~~~---------------------------------------------------  192 (237)
                      +++|++|+++|+|+|||+|||...+-...                                                   
T Consensus       222 I~kMneAl~~fiGtHDFhNFT~r~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~  301 (513)
T PLN03078        222 ISEFNSILNGFEGEHPFHNYTARSKYRKKLPGKHKQRNGAVSRRAKSSKEMSSSESEENHGEISEEDEEDLSFSSIPSGS  301 (513)
T ss_pred             HHHHHHHHHhcccccCcccccCCCccCccccccccccccccccccccccccccccccccccccccchhhhhccccccccc
Confidence            99999999999999999999975421100                                                   


Q ss_pred             --------------------------------CCCcEEEEEEEEEE-----eCcEEEEEEEeCccchHhHHHHHHHHhhc
Q 042710          193 --------------------------------LNPVKSIFRFDVIE-----MGALLQLEVEGSGFLYRQVRNMVNHSYCS  235 (237)
Q Consensus       193 --------------------------------~~~vR~I~~~~i~~-----~~~~~~i~i~G~sFL~~qVR~mVG~~~a~  235 (237)
                                                      .+..|.|+++.+..     +.+++.|+|.|+|||+||||+|||+++|.
T Consensus       302 ~~~~~~~~~~~~~~~~~~~~wl~e~d~~d~i~~s~~R~I~~~~~~~~~~~~g~~fv~i~I~GqSFmlhQIRKMIG~~~aV  381 (513)
T PLN03078        302 SDENEDILKFQSSQVQIRARWLHEPDETDRISASHFRKIFRCSCGKLEKSLGFDFVELSIWGESFMLHQIRKMVGTAVAV  381 (513)
T ss_pred             cccccccccccccchhhhhhhccCCccccccchhheEEEEEeecCCccccCCceEEEEEEEehhHHHHHHHHHHHHHHHH
Confidence                                            02368899888632     34799999999999999999999999875

>KOG2554 consensus Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=4.4e-54  Score=383.72  Aligned_cols=198  Identities=31%  Similarity=0.470  Sum_probs=172.2

Q ss_pred             CCCCceeEEEEEEEeCCCceeeeeCC--CCCcHHHHHHHHHHHhccc-cccceeeeecccCCCcccccCcEEEEEeCCCC
Q 042710           20 DSFPGFKWRLVIGYDGTRYAGWQFQT--SPPTIQCIVEKALIRVTKL-EREDLRLVGASRTDTGVHAWGQVAHFITPFSY   96 (237)
Q Consensus        20 ~~~~~~~~~l~i~YdGt~y~G~Q~Q~--~~~TVq~~le~aL~~~~~~-~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~   96 (237)
                      ...+++.++|.|+|+|++|.|+..|+  +.+|||+.|++||.+...+ +.++..+++||||||||+|.|||+|+++.+..
T Consensus        61 s~~~kR~IAlkiaY~GW~Y~Gla~Qe~T~~~TIEg~l~eAL~kt~Lies~~~~~ysRCGRTDKGVSAfgQviSl~lRS~~  140 (425)
T KOG2554|consen   61 SAHSKRHIALKIAYLGWNYQGLAPQEHTNNPTIEGKLFEALKKTRLIESRQTCNYSRCGRTDKGVSAFGQVISLVLRSRI  140 (425)
T ss_pred             hcccceEEEEEEEEeccccCceecCCCCCCcchHHHHHHHHHhhhcccCcccccccccCCcccchhhhhheeeeeeeccC
Confidence            44788999999999999999999995  4579999999999998754 35567899999999999999999999875432


Q ss_pred             CCH--------------HHHHHHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCC
Q 042710           97 DGL--------------ESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKL  162 (237)
Q Consensus        97 ~~~--------------~~l~~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~l  162 (237)
                      +.+              -.....||++||+||||.+|.+||+.|+|||+|..|+|+|+++-                ..|
T Consensus       141 p~~~s~~~~~~~a~~~Ei~Y~~mLN~vLP~dIRi~awapvp~~FsARFsC~~RtYrY~F~k----------------~dL  204 (425)
T KOG2554|consen  141 PMPDSQRDAVATADSEEIPYVHMLNRVLPPDIRIVAWAPVPPTFSARFSCVQRTYRYYFPK----------------KDL  204 (425)
T ss_pred             CCchhhhccccccccccccHHHHHhccCCCcceEEEEecCCCCccceeehhhceeeEeccC----------------CCc
Confidence            211              13567899999999999999999999999999999999999863                479


Q ss_pred             CHHHHHHHHhhccccccccccccccccCCCCCCcEEEEEEEEEEeCc---EEEEEEEeCccchHhHHHHHHHHh
Q 042710          163 NTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGA---LLQLEVEGSGFLYRQVRNMVNHSY  233 (237)
Q Consensus       163 d~~~m~~a~~~~~G~HDF~~F~~~~~~~~~~~~vR~I~~~~i~~~~~---~~~i~i~G~sFL~~qVR~mVG~~~  233 (237)
                      |+++|.+||++|+|+|||+|||+-+...+..+..|+|.+++|...++   ++.|+|.|++|||||||+||++++
T Consensus       205 dI~~M~kAA~l~vGe~DFrNFCK~D~~n~vtny~Rti~s~kV~~~~~~~~my~ldi~g~AFLwHqVRcimaiL~  278 (425)
T KOG2554|consen  205 DIDRMSKAASLLVGEHDFRNFCKIDVSNGVTNYERTILSAKVEDVGQTPGMYYLDIQGSAFLWHQVRCIMAILF  278 (425)
T ss_pred             CHHHHHHHHHHHhcchhhhhhhhhcchhhhHHHHhhhheeeEEEcCCCCceEEEEeechhhHHHHHHHHHHHHH
Confidence            99999999999999999999999765444567899999999987654   699999999999999999999554

>KOG2553 consensus Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.2e-53  Score=388.28  Aligned_cols=216  Identities=26%  Similarity=0.397  Sum_probs=182.5

Q ss_pred             CCCCCCCCCceeEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhcccc------ccceeeeecccCCCcccccCcEE
Q 042710           15 KPPTDDSFPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLE------REDLRLVGASRTDTGVHAWGQVA   88 (237)
Q Consensus        15 ~~~~~~~~~~~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~------~~~~~~~~agRTD~GVHA~~qv~   88 (237)
                      +++...+.+++++++.++|+|++|+|+|+||+.+|||++|++||.+++.+.      .+++.+.+|+||||||||++||+
T Consensus        27 ~e~~~~k~~KrKVail~gY~G~gY~GmQ~N~~~kTIEgeL~~al~~aGaI~e~n~~dpkk~~~~raARTDKGVhA~~nvi  106 (416)
T KOG2553|consen   27 KESKAPKPRKRKVAILLGYCGTGYHGMQYNPPLKTIEGELFEALFKAGAISESNAGDPKKIGFARAARTDKGVHAAGNVI  106 (416)
T ss_pred             cccccccccceEEEEEEEeccCCccceecCCCCCchHHHHHHHHHHcCCcccccccChHHhhhHHhhccccchhhhhhee
Confidence            344556678999999999999999999999999999999999999998763      45788999999999999999999


Q ss_pred             EEEeCCCCCCHHHHHHHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCcccc----------------
Q 042710           89 HFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQH----------------  152 (237)
Q Consensus        89 ~~~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~----------------  152 (237)
                      |++++.+.   ..+...||..||++|||+++.+|++.||||..|.+|+|+|.||+..+.+|-..                
T Consensus       107 SlK~~~~~---~~lv~~lN~~Lp~~IRv~~v~r~~k~F~pr~~CdsR~YeYllPtfal~~p~~~~~~~~~~~~~~e~~~~  183 (416)
T KOG2553|consen  107 SLKLELDD---PELVEKLNEILPEQIRVWGVKRVTKSFNPRKQCDSRTYEYLLPTFALAPPKPSSLLEVDIQYDKEFEKE  183 (416)
T ss_pred             EEEEeeCc---HHHHHHHhhhCCcceEEEEEEecCCCCCccccccceeEEEecceeeecCCCCccHHHhhhhhhhhhhhh
Confidence            99998652   67999999999999999999999999999999999999999998765433111                


Q ss_pred             ---cc-------------ccccCCCCC---HHHHHHHHhhccccccccccccccccCCCCCCcEEEEEEEEE-------E
Q 042710          153 ---HY-------------AYHSVYKLN---TTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVI-------E  206 (237)
Q Consensus       153 ---~~-------------~~~~~~~ld---~~~m~~a~~~~~G~HDF~~F~~~~~~~~~~~~vR~I~~~~i~-------~  206 (237)
                         .+             .....+.++   ++.++++++.++|+||||||+.... ...++..|.|.++.+.       +
T Consensus       184 f~~~~~~~~~~~~s~~~~~~~~~yr~s~~~l~~~~~~ls~Y~GthnFHNfT~~~~-~~dpss~R~I~s~~~~~pfv~~~~  262 (416)
T KOG2553|consen  184 FWNTYPLSAKERLSGQDRKTESGYRLSEEKLEVFNTILSKYVGTHNFHNFTTGKD-FTDPSSNRFIKSFTVSEPFVINDE  262 (416)
T ss_pred             hccccchhhhhhhcccccccccceeeCHHHHHHHHHHHHHhhcccccceecccCC-CCCccccceeeEEEecCcceeccC
Confidence               00             011223344   4578899999999999999998653 2356788999999887       3


Q ss_pred             eCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          207 MGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       207 ~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      +-+++.+.|+|+|||.||||+|||+|++
T Consensus       263 ~~e~V~i~i~GQSFMLHQIRKMVglav~  290 (416)
T KOG2553|consen  263 GVEFVKIKIHGQSFMLHQIRKMVGLAVL  290 (416)
T ss_pred             CceEEEEEEEcchhHHHHHHHHHHHHHH
Confidence            4579999999999999999999998886

>KOG4393 consensus Predicted pseudouridylate synthase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=4.4e-47  Score=327.03  Aligned_cols=209  Identities=35%  Similarity=0.486  Sum_probs=181.3

Q ss_pred             ceeEEEEEEEeCCCceeeeeCCCCC--cHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCC-CHH
Q 042710           24 GFKWRLVIGYDGTRYAGWQFQTSPP--TIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYD-GLE  100 (237)
Q Consensus        24 ~~~~~l~i~YdGt~y~G~Q~Q~~~~--TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~-~~~  100 (237)
                      .+||+|+|+||||+|.|||.+....  |||+-||+|.+..+..  +++++..|||||+||||+.|+++++++.... ...
T Consensus         4 ~~ryll~i~ydgT~f~e~a~~~s~~~~tIq~~leea~eeqt~l--~~l~l~~ssrtDa~Vha~~naa~~~vpr~sg~~~~   81 (295)
T KOG4393|consen    4 IMRYLLKIPYDGTAFEESAERLSKVARTIQGFLEEASEEQTGL--DRLDLESSSRTDAGVHAYLNAAHYIVPRFSGSQQQ   81 (295)
T ss_pred             hheeEEEecccccccHHHHhccCCcceehhhhhhhhHHhhcCC--cceeecccCCCchhhheeeeeEEEEeecccCCcHH
Confidence            5799999999999999999998765  9999999999999875  6799999999999999999999999987621 244


Q ss_pred             HHHHHHHccC-CC--CeEEeeeeecCCCCcccccccceEEEEEeecC-CCCCccccccccccCCCCCHHHHHHHHhhccc
Q 042710          101 SIHAALNGLL-PP--DIRVREISAAVPEFHARFSAKSKIYHYKIYND-AVMDPFQHHYAYHSVYKLNTTLMREAAEYFVG  176 (237)
Q Consensus       101 ~l~~~lN~~L-P~--dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~-~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G  176 (237)
                      ....++|..| ++  ||+|.++..||.+|||||+|.+|+|.|++.++ ...++|+++++|++++.||..+|++|+++|+|
T Consensus        82 ~~~~a~nt~l~~k~gdirV~dv~~Vps~FhaR~sassRtY~YRla~g~d~l~~fERd~cW~lp~~lna~kmqeaa~lf~G  161 (295)
T KOG4393|consen   82 AKDRAVNTVLQRKDGDIRVIDVRCVPSNFHARYSASSRTYFYRLASGSDPLSIFERDRCWHLPEELNARKMQEAAPLFEG  161 (295)
T ss_pred             HHHHHHhccccCCCCceEEEEeeecCcchhheecccceeEEEEeecCCCccChhhhcccccCCcccCHHHHHhhhhhhcc
Confidence            5666777766 44  99999999999999999999999999999984 45578999999999999999999999999999


Q ss_pred             cccccccccccccCCCCCCcEEEEEEEEE----------------EeCcEEEEEEEeCccchHhHHHHHHHHhhcc
Q 042710          177 KHDFSAFVNIQRNDRALNPVKSIFRFDVI----------------EMGALLQLEVEGSGFLYRQVRNMVNHSYCSR  236 (237)
Q Consensus       177 ~HDF~~F~~~~~~~~~~~~vR~I~~~~i~----------------~~~~~~~i~i~G~sFL~~qVR~mVG~~~a~~  236 (237)
                      +|||.+|++...  ....+++|+-...+.                ...+++.++++++||||.|||+|+..+++.+
T Consensus       162 ~hdfsaf~~ats--~~y~P~~t~rr~sv~~~g~~~a~~~~~~~e~~~~~~~nve~e~~gflyrQvRrm~a~LV~~g  235 (295)
T KOG4393|consen  162 SHDFSAFTEATS--TVYFPSITERRLSVLNNGDPLACSNQPETEGVTTNVGNVEGETEGFLYRQVRRMRAYLVTAG  235 (295)
T ss_pred             chhhhhhhcCCC--CCCCCcccceeeeecccCCccccccCCccccceeeeEEEEEEecchHHHHHHhhheeeeeec
Confidence            999999998752  355677777666652                1346899999999999999999999877643

>PF01416 PseudoU_synth_1: tRNA pseudouridine synthase; InterPro: IPR020097 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones

Probab=99.58  E-value=9.1e-17  Score=122.76  Aligned_cols=61  Identities=41%  Similarity=0.690  Sum_probs=50.7

Q ss_pred             HHhhccccccccccccccccCCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHh
Q 042710          170 AAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSY  233 (237)
Q Consensus       170 a~~~~~G~HDF~~F~~~~~~~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~  233 (237)
                      |++.|+|+|||++|++..+.  .++++|+|.++++.+.++++. +|+|+|||+||||+|||.++
T Consensus         1 A~~~~~G~HdF~~f~~~~~~--~~~~~r~i~~~~~~~~~~~~~-~i~g~~Fl~~~vR~~vg~~~   61 (105)
T PF01416_consen    1 AAKLYVGTHDFSGFQKQKTV--EKNTIRTIFSIDIIEEGDVVV-EIHGNSFLRHQVRIMVGTLL   61 (105)
T ss_dssp             -CCEETCEEECCGCSSCS-H--HHHHCCCEEEEECCCCCCEEE-EEEESS--TTHHHHHHCCCC
T ss_pred             CcceeEecCCCcCCEECCcc--cccHHHHHHHHhhhcCCCEEE-EEEecccccccchhhhHHHH
Confidence            67899999999999987432  257899999999999899999 99999999999999999654

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 pseudouridine synthase I (TruA). TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA [, ]. TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis []. These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1VS3_B 2NR0_B 2NQP_D 1DJ0_A 2NRE_A.

>PF01416 PseudoU_synth_1: tRNA pseudouridine synthase; InterPro: IPR020097 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones

Probab=98.43  E-value=1.4e-08  Score=77.35  Aligned_cols=82  Identities=29%  Similarity=0.424  Sum_probs=62.4

Q ss_pred             EEEeCC-CceeeeeCCCCCcHHHHHHHHHHHhcccccc----------------ceeeeecccCCCcccccCcEEEEEeC
Q 042710           31 IGYDGT-RYAGWQFQTSPPTIQCIVEKALIRVTKLERE----------------DLRLVGASRTDTGVHAWGQVAHFITP   93 (237)
Q Consensus        31 i~YdGt-~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~----------------~~~~~~agRTD~GVHA~~qv~~~~~~   93 (237)
                      ..|+|+ +|+|||+|   +|++...+++|..+......                ..-+..++|||+|||+..|+..+   
T Consensus         3 ~~~~G~HdF~~f~~~---~~~~~~~~r~i~~~~~~~~~~~~~~i~g~~Fl~~~vR~~vg~~~~~~~G~~~~~~i~~~---   76 (105)
T PF01416_consen    3 KLYVGTHDFSGFQKQ---KTVEKNTIRTIFSIDIIEEGDVVVEIHGNSFLRHQVRIMVGTLLRTGRGVHSLEQIAEL---   76 (105)
T ss_dssp             CEETCEEECCGCSSC---S-HHHHHCCCEEEEECCCCCCEEEEEEESS--TTHHHHHHCCCCHHHTTSCEEECCCCC---
T ss_pred             ceeEecCCCcCCEEC---CcccccHHHHHHHHhhhcCCCEEEEEEecccccccchhhhHHHHHHhcCCCCHHHHHHH---
Confidence            579999 99999999   56776666666665432111                22356799999999999987765   


Q ss_pred             CCCCCHHHHHHHHHccCCC---CeEEeeeeecC-CCCccccc
Q 042710           94 FSYDGLESIHAALNGLLPP---DIRVREISAAV-PEFHARFS  131 (237)
Q Consensus        94 ~~~~~~~~l~~~lN~~LP~---dIrV~~~~~v~-~~FhaR~~  131 (237)
                                  ||..+|+   + +|+.+.+++ -.||++|+
T Consensus        77 ------------L~~~~~~~~~~-ri~~ap~~gL~L~~v~y~  105 (105)
T PF01416_consen   77 ------------LNSKLRPKAPP-RILTAPAVGLYLFHVRYD  105 (105)
T ss_dssp             ------------HHHHSCTTS-T-EEEEEEECCECCEECCTT
T ss_pred             ------------HhccCccccCC-CcceeeCCCCCceEeeCc
Confidence                        7888855   6 999999999 89999985

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 pseudouridine synthase I (TruA). TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA [, ]. TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis []. These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1VS3_B 2NR0_B 2NQP_D 1DJ0_A 2NRE_A.

>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function

Probab=97.37  E-value=0.0061  Score=51.60  Aligned_cols=113  Identities=19%  Similarity=0.249  Sum_probs=82.1

Q ss_pred             cHHHHHHHHHHHhccc---c---ccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHHHHHHccCCCCeEEeeeeec
Q 042710           49 TIQCIVEKALIRVTKL---E---REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAA  122 (237)
Q Consensus        49 TVq~~le~aL~~~~~~---~---~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~v  122 (237)
                      -+...+|.||.+++.-   +   ....+++.+.=.=-||.+.+-++.+.+..+. +++.+.+.||+.||++|+|.++.++
T Consensus        19 dl~r~~eRa~rRA~lp~a~SqGFnP~Pkisf~~aLpvGv~S~~E~~di~l~~~~-~~~~~~~rLn~~lP~Gl~i~~~~~i   97 (187)
T PF10105_consen   19 DLMRVFERALRRAGLPVAYSQGFNPHPKISFAPALPVGVESLAEYMDIELEEDI-DPEEVLERLNAVLPEGLRILEAEEI   97 (187)
T ss_pred             HHHHHHHHHhhhcCCCeeecCCCCCCcceeecccccCceeeccEEEEEEEecCC-CHHHHHHHHHHhCCCCCEEEEEEEc
Confidence            3466889999987631   0   1246788888888999999999999997654 5889999999999999999999999


Q ss_pred             CCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccccc
Q 042710          123 VPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHD  179 (237)
Q Consensus       123 ~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HD  179 (237)
                      +....+ ..+.-..+.|.+...                ..+.+.+.++++.|.-..+
T Consensus        98 ~~~~~s-l~~~i~~~~Y~i~~~----------------~~~~~~~~~~~~~~~~~~~  137 (187)
T PF10105_consen   98 PPKAPS-LMALINAAEYRITLP----------------EIDEEELEEAIEAFLAAEE  137 (187)
T ss_pred             cCCCcc-hhhhcceEEEEEEec----------------CCCHHHHHHHHHHHHCCCC
Confidence            854422 233345677776421                3456677777776654433

>TIGR01213 conserved hypothetical protein TIGR01213

Probab=96.70  E-value=0.056  Score=50.64  Aligned_cols=155  Identities=17%  Similarity=0.251  Sum_probs=103.2

Q ss_pred             CCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCc----EEEEEeCCC-CCCHHHHHHHHHccCCCCeEEeeeee
Q 042710           47 PPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ----VAHFITPFS-YDGLESIHAALNGLLPPDIRVREISA  121 (237)
Q Consensus        47 ~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~q----v~~~~~~~~-~~~~~~l~~~lN~~LP~dIrV~~~~~  121 (237)
                      ..|||+.|...+..+.+  ..+..+++|||-|.-|--+|.    |+-+.-|.. ..+++.+.+.+|+.....|.|.+..-
T Consensus       184 ~~SVeelI~~~v~~~~~--~~~~~Fh~aGREDvDvRMLG~GRPFvlEi~~P~rr~~dl~~le~~IN~~~~g~V~v~~L~~  261 (388)
T TIGR01213       184 PESVEELIASPFLKATG--GTDAYFHGAGREDVDVRMLGTGRPFVLEVKEPRYRKIDLDPLEEEINTSGKGKVEVEGLKF  261 (388)
T ss_pred             CchHHHHHHHHHHHHhC--CceeEEeccCccccceeeccCCCceEEEecCCccCCCCHHHHHHHHhhccCCCEEEEEeEE
Confidence            46999999998888765  357999999999999998863    333332321 23577899999999999999999886


Q ss_pred             cCCCCc--ccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccc--ccccccccccccCCCCCCcE
Q 042710          122 AVPEFH--ARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGK--HDFSAFVNIQRNDRALNPVK  197 (237)
Q Consensus       122 v~~~Fh--aR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~--HDF~~F~~~~~~~~~~~~vR  197 (237)
                      ++..=-  -......|+|+=.+..               ..+++.+.++++++.|.|.  +-.+--...-. .....-.|
T Consensus       262 ~~~~~v~~ik~~~~~K~Y~alV~~---------------~~~v~~e~L~~~~~~l~g~~I~QrTP~RV~hR-Ra~~~R~R  325 (388)
T TIGR01213       262 ATREEVEEVKEEKHRKVYRALVEV---------------DGPVSDEDLEELCKELEGATIYQRTPLRVLHR-RADLVRER  325 (388)
T ss_pred             EcHHHHHHHhccCCceEEEEEEEE---------------CCCCCHHHHHHHHHhccCCEEEccCCceEEEe-cCCCceEE
Confidence            654210  1122336888866643               3468889999999998883  11111111100 11123469


Q ss_pred             EEEEEEEEEe-CcEEEEEEEeCc
Q 042710          198 SIFRFDVIEM-GALLQLEVEGSG  219 (237)
Q Consensus       198 ~I~~~~i~~~-~~~~~i~i~G~s  219 (237)
                      +|+++++... +..+.+.|.+++
T Consensus       326 ~I~~i~~~~i~~~~~~l~v~~qa  348 (388)
T TIGR01213       326 RVYQVDLSGLDGNHAELIIEAEG  348 (388)
T ss_pred             EEEEEEEEEEcCCEEEEEEEecC
Confidence            9999998764 446677777665

Members of this family show twilight-zone similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.

>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]

Probab=95.92  E-value=0.26  Score=45.94  Aligned_cols=156  Identities=17%  Similarity=0.240  Sum_probs=104.3

Q ss_pred             CCcHHHHHHHHHHHhccccccceeeeecccCCCcccccC----cEEEEEeCC-CCCCHHHHHHHHHccCCCCeEEeeeee
Q 042710           47 PPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG----QVAHFITPF-SYDGLESIHAALNGLLPPDIRVREISA  121 (237)
Q Consensus        47 ~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~----qv~~~~~~~-~~~~~~~l~~~lN~~LP~dIrV~~~~~  121 (237)
                      ..||++.|-..+..+.+  ..+..+++|||-|--|--+|    -|+-+.-|. ...+++.+...+|.-.  .+.|..+.-
T Consensus       190 ~~sve~~i~~~~~~~f~--g~~~~fhgAGREDvDvRMLG~GRPfVlEvk~Pr~R~~dl~~l~~~in~~~--~vev~~l~f  265 (398)
T COG1258         190 PESVEELIKQPIKEAFG--GLDAKFHGAGREDVDVRMLGTGRPFVLEVKEPRRRNVDLDELEEEINRGG--KVEVFDLEF  265 (398)
T ss_pred             cccHHHHHHHHHHHhcc--CceeEEEccCCCccceeeecCCCceEEEecCcccccCChHHHHHHhccCC--cEEEEEEEe
Confidence            46888888886666654  35789999999999998888    455555552 2246889999999988  889998887


Q ss_pred             cCCCCcccc---cccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccc-ccccccccccccCCCCCCcE
Q 042710          122 AVPEFHARF---SAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGK-HDFSAFVNIQRNDRALNPVK  197 (237)
Q Consensus       122 v~~~FhaR~---~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~-HDF~~F~~~~~~~~~~~~vR  197 (237)
                      +...=-.+.   .-..|+|+=.+.               +..+++.+++.+++.-|.|. =.=+.+..........-.+|
T Consensus       266 ~~~e~v~~ik~~~~~rK~YrAlV~---------------~~~~v~~e~l~~~~~~L~g~~I~QrTP~RV~hrRadlvR~R  330 (398)
T COG1258         266 VGREEVEEIKETERHRKVYRALVY---------------SDRPVSDEKLEEVLGSLEGKTIRQRTPRRVLHRRADLVRIR  330 (398)
T ss_pred             cCHHHHHHHHhccccceeEEEEEE---------------ECCCcCHHHHHHHHhhccCcEEeecChHHHhhhhcccceEE
Confidence            764322221   233566766553               24578999999999999994 33333332211111223478


Q ss_pred             EEEEEEEEEe-CcEEEEEEEeCccc
Q 042710          198 SIFRFDVIEM-GALLQLEVEGSGFL  221 (237)
Q Consensus       198 ~I~~~~i~~~-~~~~~i~i~G~sFL  221 (237)
                      .|+.+.+... +....+.|.+.+=|
T Consensus       331 ~V~~l~~~~~~~~~~~~~i~~egGl  355 (398)
T COG1258         331 RVYELSLDLIDDRHAELEIEAEGGL  355 (398)
T ss_pred             EEEEeeeeeccCceEEEEEEecccc
Confidence            8999888764 45667777666533

>PRK14554 putative pseudouridylate synthase; Provisional

Probab=94.97  E-value=0.97  Score=42.96  Aligned_cols=153  Identities=15%  Similarity=0.186  Sum_probs=94.3

Q ss_pred             CcHHHHHHHHHHHhccccccceeeeecccCCCcccccCc----EEEEEeCCC-CCCHHHHHHHHHccCCCCeEEeeeeec
Q 042710           48 PTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ----VAHFITPFS-YDGLESIHAALNGLLPPDIRVREISAA  122 (237)
Q Consensus        48 ~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~q----v~~~~~~~~-~~~~~~l~~~lN~~LP~dIrV~~~~~v  122 (237)
                      .|||+.|...+.....  ..+..+++|||-|.-|--+|.    |+-+.-|.. ..+++.+.  +|..-...|.|.....+
T Consensus       220 ~SVeelI~~~i~~~f~--~~~~~fh~aGREDvDVRmLG~GRPFViEi~~p~r~~~~~~~l~--~~~~~~g~V~v~~l~~~  295 (422)
T PRK14554        220 ESVEELIAKPVIEAFG--GEDAVFHGAGREDVDARMLGTGRPFVIEVKEPRKRKVDLEALE--EEINADGKVEVENLRFA  295 (422)
T ss_pred             CCHHHHHHHHHHHHhC--CCceEEecCCCCCcceEecCCCCceEEEecCcccccCCHHHHH--HhhccCCCEEEEEEEEE
Confidence            6999999988877654  368999999999999999986    444433321 12345555  44444688999998877


Q ss_pred             CCCCcc--cccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhccccc-cccccccccccCCCCCCcEEE
Q 042710          123 VPEFHA--RFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKH-DFSAFVNIQRNDRALNPVKSI  199 (237)
Q Consensus       123 ~~~Fha--R~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~H-DF~~F~~~~~~~~~~~~vR~I  199 (237)
                      +..--.  ......|+|+=.++.               ..+++.+.++++++.|.|.- .=+.............-+|+|
T Consensus       296 ~~~~~~~ik~~~~~K~YralV~~---------------~~~v~~e~l~~~~~~l~~~~I~QrTP~RV~hRR~~~~R~R~I  360 (422)
T PRK14554        296 TRKEVERIKEEKASKTYRALVES---------------DEPVSEEELEKLLDELSGATIEQRTPRRVKHRRADLVRVRKV  360 (422)
T ss_pred             cHHHHHHHhcCCCceEEEEEEEE---------------CCCCCHHHHHHHHHhccCcEeeccCcHhhhhhccccceeeEE
Confidence            654211  112233788765543               34678888999998887651 101111110001112346899


Q ss_pred             EEEEEEEe-CcEEEEEEEeCc
Q 042710          200 FRFDVIEM-GALLQLEVEGSG  219 (237)
Q Consensus       200 ~~~~i~~~-~~~~~i~i~G~s  219 (237)
                      +++++... +..+.+.|.+++
T Consensus       361 ~~i~~~~i~~~~~~l~i~~ea  381 (422)
T PRK14554        361 YDISGELIDDKHFELRIKCEG  381 (422)
T ss_pred             EEEEEEEEcCcEEEEEEEEec
Confidence            99988764 344555555543

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

Probab=92.93  E-value=1.2  Score=32.42  Aligned_cols=21  Identities=24%  Similarity=0.120  Sum_probs=18.4

Q ss_pred             ceeeeecccCCCcccccCcEEE
Q 042710           68 DLRLVGASRTDTGVHAWGQVAH   89 (237)
Q Consensus        68 ~~~~~~agRTD~GVHA~~qv~~   89 (237)
                      .-++..||+.|+..... |+++
T Consensus        23 ~~~i~~aG~kDk~a~t~-q~v~   43 (87)
T cd01291          23 PKRVGYAGRKDKRAVTT-QLVS   43 (87)
T ss_pred             hheEEECccCCCCeeEE-EEEc
Confidence            45789999999999999 8777

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).

>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.97  E-value=1.2  Score=38.22  Aligned_cols=73  Identities=15%  Similarity=0.207  Sum_probs=55.8

Q ss_pred             HHHHHHHHHhccc------cccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHHHHHHHccCCCCeEEeeeeecCCC
Q 042710           52 CIVEKALIRVTKL------EREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPE  125 (237)
Q Consensus        52 ~~le~aL~~~~~~------~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~v~~~  125 (237)
                      ..+++++.+++.-      -....+++.|.=---|+...|-.+-|++.... +++++.+.||+.||+|+.+.+++.+++.
T Consensus        23 RlidR~iRRAglpiayT~GFhP~prmsia~alpvG~~ssge~fd~eL~e~v-~~dk~~etl~~~lp~Dl~~~~v~~iD~k  101 (228)
T COG5011          23 RLIDRTIRRAGLPIAYTGGFHPHPRMSIAQALPVGIYSSGEIFDFELTEEV-SEDKFKETLNKALPNDLPAYDVEKIDKK  101 (228)
T ss_pred             HHHHHHHHhcCCceeecCCCCCCCceeeccccccccccCceEEEEEeeeec-CcHHHHHHHHHhCCCCcchhheeeecCC
Confidence            3466777775421      01245677777777899999999999886543 5789999999999999999999999763

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	237
1dj0_A	264	The Crystal Structure Of E. Coli Pseudouridine Synt		3e-26
2nqp_A	270	Crystal Structure Of Pseudoudirinde Synthase Trua I		3e-26
1vs3_A	249	Crystal Structure Of The Trna Pseudouridine Synthas		5e-18

>pdb|1DJ0|A Chain A, The Crystal Structure Of E. Coli Pseudouridine Synthase I At 1.5 Angstrom Resolution Length = 264

Iteration: 1
 Score =  115 bits (287), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 71/208 (34%), Positives = 109/208 (52%), Gaps = 8/208 (3%)
Query: 23  PGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 82
           P +K  L I YDG++Y GWQ Q    ++Q  +EKAL +V     E + +  A RTD GVH
Sbjct: 2   PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVH 58
Query: 83  AWGQVAHF-ITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI 141
             GQV HF  T    D   ++   +N  LP DI VR +     +FHARFSA ++ Y Y I
Sbjct: 59  GTGQVVHFETTALRKDAAWTL--GVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYII 116
Query: 142 YNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFR 201
           YN  +          H    L+   M  AA+  +G++DF++F  +Q   R   P +++  
Sbjct: 117 YNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSR--TPWRNVMH 174
Query: 202 FDVIEMGALLQLEVEGSGFLYRQVRNMV 229
            +V   G  + ++++ + F++  VRN+V
Sbjct: 175 INVTRHGPYVVVDIKANAFVHHMVRNIV 202

>pdb|2NQP|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In Complex With Leucyl Trna Length = 270

Iteration: 1
 Score =  114 bits (286), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 71/208 (34%), Positives = 109/208 (52%), Gaps = 8/208 (3%)
Query: 23  PGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 82
           P +K  L I YDG++Y GWQ Q    ++Q  +EKAL +V     E + +  A RTD GVH
Sbjct: 8   PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVH 64
Query: 83  AWGQVAHF-ITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI 141
             GQV HF  T    D   ++   +N  LP DI VR +     +FHARFSA ++ Y Y I
Sbjct: 65  GTGQVVHFETTALRKDAAWTL--GVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYII 122
Query: 142 YNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFR 201
           YN  +          H    L+   M  AA+  +G++DF++F  +Q   R   P +++  
Sbjct: 123 YNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSR--TPWRNVMH 180
Query: 202 FDVIEMGALLQLEVEGSGFLYRQVRNMV 229
            +V   G  + ++++ + F++  VRN+V
Sbjct: 181 INVTRHGPYVVVDIKANAFVHHMVRNIV 208

>pdb|1VS3|A Chain A, Crystal Structure Of The Trna Pseudouridine Synthase Trua From Thermus Thermophilus Hb8 Length = 249

Iteration: 1
 Score = 87.8 bits (216), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 66/203 (32%), Positives = 92/203 (45%), Gaps = 6/203 (2%)
Query: 29  LVIGYDGTRYAGWQFQ-TSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQV 87
           L+  YDGT +AG Q Q     T+Q  +E+AL  +  L +     V A RTD GVHA    
Sbjct: 6   LLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKA----VAAGRTDAGVHALAMP 61
Query: 88  AHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVM 147
            H +   S   +E +  ALN LLP D++V       P+FHAR  A  + Y Y+I      
Sbjct: 62  FH-VDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHP 120
Query: 148 DPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVIEM 207
            P   H A      L+   M EA    +G+H+F  F   +        +++  +    E 
Sbjct: 121 SPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGERELLEARLQVAEGEA 180
Query: 208 GALLQLEVEGSGFLYRQVRNMVN 230
           G  ++L   G  FL  QVR MV 
Sbjct: 181 GLEVRLYFRGKSFLRGQVRGMVG 203

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	237
1dj0_A	264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	5e-88
1vs3_A	249	TRNA pseudouridine synthase A; TRUA, tRNA modifica	4e-84

>1dj0_A Pseudouridine synthase I; alpha/beta fold, RNA-binding motif, RNA-modifying enzyme, lyase; 1.50A {Escherichia coli} SCOP: d.265.1.1 PDB: 2nqp_A 2nr0_A 2nre_A Length = 264

 Score =  260 bits (667), Expect = 5e-88
 Identities = 69/207 (33%), Positives = 107/207 (51%), Gaps = 6/207 (2%)

Query: 23  PGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 82
           P +K  L I YDG++Y GWQ Q    ++Q  +EKAL +V     E + +  A RTD GVH
Sbjct: 2   PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVH 58

Query: 83  AWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIY 142
             GQV HF T        +    +N  LP DI VR +     +FHARFSA ++ Y Y IY
Sbjct: 59  GTGQVVHFETTALRK-DAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIY 117

Query: 143 NDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRF 202
           N  +          H    L+   M  AA+  +G++DF++F  +Q    +  P +++   
Sbjct: 118 NHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQ--SRTPWRNVMHI 175

Query: 203 DVIEMGALLQLEVEGSGFLYRQVRNMV 229
           +V   G  + ++++ + F++  VRN+V
Sbjct: 176 NVTRHGPYVVVDIKANAFVHHMVRNIV 202

>1vs3_A TRNA pseudouridine synthase A; TRUA, tRNA modification, structural NPPSFA, national project on protein structural and function analyses; 2.25A {Thermus thermophilus} Length = 249

 Score =  249 bits (639), Expect = 4e-84
 Identities = 67/206 (32%), Positives = 89/206 (43%), Gaps = 10/206 (4%)

Query: 27  WRLVIGYDGTRYAGWQFQTS-PPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 85
             L+  YDGT +AG Q Q     T+Q  +E+AL  +        + V A RTD GVHA  
Sbjct: 4   LLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIG----ALPKAVAAGRTDAGVHALA 59

Query: 86  QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 145
              H     +   +E +  ALN LLP D++V       P+FHAR  A  + Y Y+I    
Sbjct: 60  MPFHVDVESAIP-VEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRP 118

Query: 146 VMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRFDVI 205
              P   H A      L+   M EA    +G+H+F  F   +   R         R  V 
Sbjct: 119 HPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEE--TRPGERELLEARLQVA 176

Query: 206 --EMGALLQLEVEGSGFLYRQVRNMV 229
             E G  ++L   G  FL  QVR MV
Sbjct: 177 EGEAGLEVRLYFRGKSFLRGQVRGMV 202

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	237
1dj0_A	264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	100.0
1vs3_A	249	TRNA pseudouridine synthase A; TRUA, tRNA modifica	100.0
2v9k_A	530	Uncharacterized protein FLJ32312; pseudouridine sy	96.63

>1dj0_A Pseudouridine synthase I; alpha/beta fold, RNA-binding motif, RNA-modifying enzyme, lyase; 1.50A {Escherichia coli} SCOP: d.265.1.1 PDB: 2nqp_A 2nr0_A 2nre_A

Probab=100.00  E-value=1.6e-75  Score=515.69  Aligned_cols=207  Identities=33%  Similarity=0.515  Sum_probs=196.3

Q ss_pred             CCceeEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHH
Q 042710           22 FPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLES  101 (237)
Q Consensus        22 ~~~~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~  101 (237)
                      .||+||+|.|+||||+|+|||+||+.+|||++||+||.++.+   +++.+++||||||||||++||+||+++... +++.
T Consensus         1 ~Pm~r~~l~i~YdGt~y~GwQ~Q~~~~TVq~~Le~AL~~~~~---~~v~~~~agRTDaGVHA~gqv~~f~~~~~~-~~~~   76 (264)
T 1dj0_A            1 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVHGTGQVVHFETTALR-KDAA   76 (264)
T ss_dssp             CCCEEEEEEEEECCTTSSCSCCTTCSSCHHHHHHHHHHHHHT---SCCCEEESSCCCTTCEEEEEEEEEEESCCC-CHHH
T ss_pred             CCccEEEEEEEEeCCCceeEEECcCCCCHHHHHHHHHHHHhC---CCeEEEEeccCCCCCchhhEEEEEEECCCC-CHHH
Confidence            378999999999999999999999999999999999999974   589999999999999999999999998764 5889


Q ss_pred             HHHHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccccccc
Q 042710          102 IHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFS  181 (237)
Q Consensus       102 l~~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~  181 (237)
                      |..+||++||+||+|+++.+|+++|||||+|++|+|+|+|++....+||.++|+|++..+||+++|++|++.|+|+|||+
T Consensus        77 ~~~~lN~~LP~dI~V~~~~~V~~~FhARf~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~M~~aa~~l~G~HDF~  156 (264)
T 1dj0_A           77 WTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFT  156 (264)
T ss_dssp             HHHHHHHTSCTTEEEEEEEECCTTCCTTTTCCEEEEEEEEECSSSCCCTTTTSSEECCSCCCHHHHHHHHGGGCEEEECG
T ss_pred             HHHHHHhhCCcCeEEEEEEeCCCCCCcccccccEEEEEEEccCCCCChhHcCceEeeCCCCCHHHHHHHHHHhcCcccHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccccCCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          182 AFVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       182 ~F~~~~~~~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      |||+.++  +.++++|+|++++|.+.++++.|+|+|+||||||||+|||+++.
T Consensus       157 ~F~~~~~--~~~s~vR~I~~~~v~~~~~~i~~~i~g~~FL~~mVR~mvG~L~~  207 (264)
T 1dj0_A          157 SFRAVQC--QSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLME  207 (264)
T ss_dssp             GGCCTTC--CCSCCEEEEEEEEEEEETTEEEEEEEESCCCTTHHHHHHHHHHH
T ss_pred             HhccCCC--CCCCcEEEEEEEEEEECCCEEEEEEEEchHHHHHHHHHHHHHHH
Confidence            9998754  35789999999999999999999999999999999999997764

>1vs3_A TRNA pseudouridine synthase A; TRUA, tRNA modification, structural NPPSFA, national project on protein structural and function analyses; 2.25A {Thermus thermophilus}

Probab=100.00  E-value=6.3e-75  Score=508.16  Aligned_cols=202  Identities=32%  Similarity=0.413  Sum_probs=191.5

Q ss_pred             ceeEEEEEEEeCCCceeeeeCCCC-CcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHHH
Q 042710           24 GFKWRLVIGYDGTRYAGWQFQTSP-PTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESI  102 (237)
Q Consensus        24 ~~~~~l~i~YdGt~y~G~Q~Q~~~-~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~l  102 (237)
                      |+||+|.|+||||+|+|||+||+. +|||++||+||.++ +   +++++++||||||||||++||+||+++.+. +++.|
T Consensus         1 M~r~~l~i~YdGt~y~GwQ~Q~~~~~TVq~~Le~AL~~~-~---~~v~~~~agRTDaGVHA~gqv~~f~~~~~~-~~~~~   75 (249)
T 1vs3_A            1 MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGI-G---ALPKAVAAGRTDAGVHALAMPFHVDVESAI-PVEKV   75 (249)
T ss_dssp             CEEEEEEEEECGGGCSBSSCCCTTCCCHHHHHHHHGGGG-T---BCSCCEESSCCBTTCEEEEEEEEEEECSCC-CGGGH
T ss_pred             CcEEEEEEEEECCCceeEeECCCCCCCHHHHHHHHHHHc-C---CcceEEEeccCcCCcCccccEEEEEECCCC-CHHHH
Confidence            679999999999999999999999 99999999999999 3   589999999999999999999999998764 57889


Q ss_pred             HHHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhccccccccc
Q 042710          103 HAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSA  182 (237)
Q Consensus       103 ~~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~  182 (237)
                      ..+||++||+||+|+++.+|+++|||||+|++|+|+|+|++...++||.++|+|+++.+||+++|++|++.|+|+|||+|
T Consensus        76 ~~~lN~~LP~dI~V~~~~~v~~~FhARf~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~ldi~~m~~aa~~l~G~HDF~~  155 (249)
T 1vs3_A           76 PEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLG  155 (249)
T ss_dssp             HHHHHHHSCTTEEEEEEEEECTTCCTTTTCSEEEEEEEEEECSSCCTTTTTTSEEECSCCCHHHHHHHHHHHSEEEEGGG
T ss_pred             HHHHHhcCCcCEEEEEEEECCCCCCcccccccEEEEEEEccCCCCChhhCCeeEEeCCCCCHHHHHHHHHHhcCceeHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccCCCCCCcEEEEEEEEE----EeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          183 FVNIQRNDRALNPVKSIFRFDVI----EMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       183 F~~~~~~~~~~~~vR~I~~~~i~----~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      ||+..+    ++++|+|++++|.    +.++++.|+|+|+||||||||+|||+++.
T Consensus       156 F~~~~~----~~~vR~I~~~~v~~~~~~~~~~i~~~i~g~~FL~~mVR~mvG~l~~  207 (249)
T 1vs3_A          156 FAKEET----RPGERELLEARLQVAEGEAGLEVRLYFRGKSFLRGQVRGMVGTLLE  207 (249)
T ss_dssp             GCSSCC----SCCEEEEEEEEEEEEECSSSEEEEEEEEESCCCTTHHHHHHHHHHH
T ss_pred             eecCCC----CCCCcEEEEEEEEeccccCCCEEEEEEEEChHHHHHHHHHHHHHHH
Confidence            998643    6899999999998    67789999999999999999999997765

>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domai; HET: EPE; 2.0A {Homo sapiens}

Probab=96.63  E-value=0.023  Score=53.91  Aligned_cols=156  Identities=13%  Similarity=0.183  Sum_probs=102.0

Q ss_pred             CcHHHHHHHHHHHhccccccceeeeecccCCCcccccCc----EEEEEeCCCC----CCHHHHHHHHHccCCCCeEEeee
Q 042710           48 PTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ----VAHFITPFSY----DGLESIHAALNGLLPPDIRVREI  119 (237)
Q Consensus        48 ~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~q----v~~~~~~~~~----~~~~~l~~~lN~~LP~dIrV~~~  119 (237)
                      .|||+.|...+.....  .....+++|||-|.-|--+|.    |+.+.-|...    .+.+.+...+|+ .-..|.|.+.
T Consensus       317 ~SVee~I~~~i~~~f~--~~~~~Fh~sGREDvDVRmLG~GRPFvlEi~~P~r~~~~~~dl~~le~~IN~-~~~~V~V~~L  393 (530)
T 2v9k_A          317 SSVEELISDHLLAVFK--AESFNFSSSGREDVDVRTLGNGRPFAIELVNPHRVHFTSQEIKELQQKINN-SSNKIQVRDL  393 (530)
T ss_dssp             CCHHHHHHTTHHHHHT--CSEEEEEESSCCCTTCEEEEEEEEEEEEEESCSCCCCCHHHHHHHHHHHHT-TCSSEEEEEE
T ss_pred             CCHHHHHHHHHHHhcC--CCeEEEeecCCCCCceeecCCCCcEEEEecCccccccchhHHHHHHHHHhc-cCCcEEEEee
Confidence            6999999988887765  467999999999999999997    5555444322    135667889998 3456999999


Q ss_pred             eecCCCCcccc----cccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhccccccccccccccc-cCCCCC
Q 042710          120 SAAVPEFHARF----SAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQR-NDRALN  194 (237)
Q Consensus       120 ~~v~~~FhaR~----~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~~~~~-~~~~~~  194 (237)
                      ..++..=-.+.    .-+.|+|.=.++.               ..+++.+.++++.. |.|---+.---.... ......
T Consensus       394 ~~v~~~~~~~ik~ge~~~~K~Y~alv~~---------------~~~v~~e~l~~~~~-l~~l~I~QrtP~RV~hRR~~~~  457 (530)
T 2v9k_A          394 QLVTREAIGHMKEGEEEKTKTYSALIWT---------------NKAIQKKDIEFLND-IKDLKIDQKTPLRVLHRRPLAV  457 (530)
T ss_dssp             EEECTHHHHHHHHHHHHCCEEEEEEEEE---------------SSCCCHHHHGGGGG-CCSEEEEEECCGGGTTTSCCCE
T ss_pred             EEEcHHHHHHHhcccccCCeEEEEEEEE---------------cCCCCHHHHHHHHh-cCCceeeccCCeEEEEecCCCc
Confidence            98874321111    1245788866543               34577777777655 655222111000000 011112


Q ss_pred             CcEEEEEEEEEE-eCcEEEEEEEeCccch
Q 042710          195 PVKSIFRFDVIE-MGALLQLEVEGSGFLY  222 (237)
Q Consensus       195 ~vR~I~~~~i~~-~~~~~~i~i~G~sFL~  222 (237)
                      -.|+|+++++.+ .+..+.+.|..++=+|
T Consensus       458 R~R~I~~i~~~~~~~~~~~l~i~~eaGtY  486 (530)
T 2v9k_A          458 RARVIHFMETQYVDEHHFRLHLKTQAGTY  486 (530)
T ss_dssp             EEEEEEEEEEEEEETTEEEEEEEECTTCC
T ss_pred             cceEEEEEEEEEecCCEEEEEEEecCCCE
Confidence            479999999876 5678899999887555

---

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	237
d1dj0a_	264	d.265.1.1 (A:) Pseudouridine synthase I TruA {Esch	7e-29

>d1dj0a_ d.265.1.1 (A:) Pseudouridine synthase I TruA {Escherichia coli [TaxId: 562]} Length = 264

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

 Score =  107 bits (267), Expect = 7e-29
 Identities = 69/207 (33%), Positives = 108/207 (52%), Gaps = 6/207 (2%)

Query: 23  PGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 82
           P +K  L I YDG++Y GWQ Q    ++Q  +EKAL   +++  E + +  A RTD GVH
Sbjct: 2   PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKAL---SQVANEPITVFCAGRTDAGVH 58

Query: 83  AWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIY 142
             GQV HF T        +    +N  LP DI VR +     +FHARFSA ++ Y Y IY
Sbjct: 59  GTGQVVHFETTALRKD-AAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIY 117

Query: 143 NDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFSAFVNIQRNDRALNPVKSIFRF 202
           N  +          H    L+   M  AA+  +G++DF++F  +Q   R   P +++   
Sbjct: 118 NHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSR--TPWRNVMHI 175

Query: 203 DVIEMGALLQLEVEGSGFLYRQVRNMV 229
           +V   G  + ++++ + F++  VRN+V
Sbjct: 176 NVTRHGPYVVVDIKANAFVHHMVRNIV 202

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	237
d1dj0a_	264	Pseudouridine synthase I TruA {Escherichia coli [T	100.0

>d1dj0a_ d.265.1.1 (A:) Pseudouridine synthase I TruA {Escherichia coli [TaxId: 562]}

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

Probab=100.00  E-value=2e-69  Score=474.59  Aligned_cols=207  Identities=33%  Similarity=0.514  Sum_probs=196.0

Q ss_pred             CCceeEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhccccccceeeeecccCCCcccccCcEEEEEeCCCCCCHHH
Q 042710           22 FPGFKWRLVIGYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLES  101 (237)
Q Consensus        22 ~~~~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~  101 (237)
                      +||+||+|.|+||||+|+|||+||+.+|||++||+||.+++.   +++.+.+||||||||||++||++|+++... +.+.
T Consensus         1 p~~~r~al~i~Y~Gt~f~G~Q~Q~~~~TVq~~Le~aL~~~~~---~~~~~~~agRTD~GVhA~~qv~~~~~~~~~-~~~~   76 (264)
T d1dj0a_           1 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVHGTGQVVHFETTALR-KDAA   76 (264)
T ss_dssp             CCCEEEEEEEEECCTTSSCSCCTTCSSCHHHHHHHHHHHHHT---SCCCEEESSCCCTTCEEEEEEEEEEESCCC-CHHH
T ss_pred             CCcEEEEEEEEEECCCeeeEeECcCCCCHHHHHHHHHHHhhC---CCeEEEEeecccCCcceeeEEEEEeeccch-hhhh
Confidence            579999999999999999999999999999999999999875   689999999999999999999999998764 5789


Q ss_pred             HHHHHHccCCCCeEEeeeeecCCCCcccccccceEEEEEeecCCCCCccccccccccCCCCCHHHHHHHHhhcccccccc
Q 042710          102 IHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQHHYAYHSVYKLNTTLMREAAEYFVGKHDFS  181 (237)
Q Consensus       102 l~~~lN~~LP~dIrV~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~  181 (237)
                      +...||+.||+||+|+++.+|+++|||||+|++|+|+|+|.+...++++.+.+.|+....+|+++|++|++.|+|+|||+
T Consensus        77 ~~~~lN~~Lp~dI~i~~~~~v~~~F~aR~~a~~r~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~a~~~~~G~hdF~  156 (264)
T d1dj0a_          77 WTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFT  156 (264)
T ss_dssp             HHHHHHHTSCTTEEEEEEEECCTTCCTTTTCCEEEEEEEEECSSSCCCTTTTSSEECCSCCCHHHHHHHHGGGCEEEECG
T ss_pred             hhcccccccccccccccceeccccccchhhhhhcccceeeccccccccccccccccccCCcchHHHHHHHhhccCccccc
Confidence            99999999999999999999999999999999999999999999899999999999999999999999999999999999


Q ss_pred             ccccccccCCCCCCcEEEEEEEEEEeCcEEEEEEEeCccchHhHHHHHHHHhh
Q 042710          182 AFVNIQRNDRALNPVKSIFRFDVIEMGALLQLEVEGSGFLYRQVRNMVNHSYC  234 (237)
Q Consensus       182 ~F~~~~~~~~~~~~vR~I~~~~i~~~~~~~~i~i~G~sFL~~qVR~mVG~~~a  234 (237)
                      +||+.+..  ..+++|+|..+++.+.++++.|+|+|+||||||||+|||++++
T Consensus       157 ~F~~~~~~--~~~~~r~i~~~~~~~~~~~i~i~i~g~sFL~~qVR~mvg~ll~  207 (264)
T d1dj0a_         157 SFRAVQCQ--SRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLME  207 (264)
T ss_dssp             GGCCTTCC--CSCCEEEEEEEEEEEETTEEEEEEEESCCCTTHHHHHHHHHHH
T ss_pred             cccccccc--CCCcccccccccceecCcEEEEEechhHHHHHHHHHHHHHHHH
Confidence            99987543  4678999999999999999999999999999999999998875