Citrus Sinensis ID: 044732

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250
Protein Sequence
MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNFDPQNSLIP
Secondary Structure (PSIPRED)
cEEEccccccccHHHHHHHHHHccccccEEEEEEEccccccccccccccEEEEEcccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccEEEEEEEEEEEEEEccccccccccccEEEEEEEEEcHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccccccEEEEEEcccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEccccccccHHHHHHHHHHHcccccEEEEEEEccHHccccHcHHHEEEEEEEEccccccccccccccccHHHHHHHHcHHHHccHHHHHHHHHEcccccccccccccccccHHHHHHHHHHHccccccHHHHccccccccccccccEEEEEEEHHEEEEccccccccccccEEEEEEEEHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHccccccccccccccEEEEEcccccccccccccc
Coil and Loop (DISEMBL)
miildtwrkdvkpsdiedainsaapgkiRVISVSQVsrvfhpnfsakWRRYLYIfplndgenreqsiDSEVEVEnfhtsnnvgkqsngcyeNIENLlindeggfgshekprnfTICRVNLLLQRLEGKLLSYKtfardtkasrnigpptecfIYHArateailpcpvndhgegrkVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATcrratappappeglclvdvgytnfdpqnslip
Flexible Loop (DISEMBL)
miildtwrkdvkpsdiedainsaapgkIRVISVSQVSRvfhpnfsakwrRYLYIFPLNDGENREQSIDSEVEVENFhtsnnvgkqsnGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKtfardtkasrnigpPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVReaaagadedALLKLMDATCRRATAPPAPPEGLCLVDVGYTNFDPQNSLIP
Low Complexity Region (SEG)
MIILDTWRKDVKPSDIEDAINSAAPGKirvisvsqvsrvFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVReaaagadedallKLMDatcrratappappEGLCLVDVGYTNFDPQNSLIP
Disordered region (IsUnstruct)
******W************INSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLN****************************NGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMD**********************************
Disordered Region (DISOPRED)
MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDT******GPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNFDPQNSLIP
Disordered Region (DISEMBL)
MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNFDPQNSLIP
Disordered Region (DISPRO)
MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNFDPQNSLIP
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNFDPQNSLIP
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	250	2.2.26 [Sep-21-2011]
Q7TU07	276	tRNA pseudouridine syntha	yes	no	0.768	0.695	0.240	1e-07
Q2S4S9	265	tRNA pseudouridine syntha	yes	no	0.288	0.271	0.460	2e-06
P57861	264	tRNA pseudouridine syntha	yes	no	0.304	0.287	0.397	6e-06
Q5FPX3	275	tRNA pseudouridine syntha	yes	no	0.42	0.381	0.324	1e-05
A4J151	247	tRNA pseudouridine syntha	yes	no	0.668	0.676	0.248	2e-05
Q73KE3	268	tRNA pseudouridine syntha	yes	no	0.684	0.638	0.236	2e-05
Q8U2C1	266	tRNA pseudouridine syntha	yes	no	0.28	0.263	0.352	3e-05
A8FTU0	261	tRNA pseudouridine syntha	yes	no	0.252	0.241	0.396	3e-05
Q4QL79	269	tRNA pseudouridine syntha	yes	no	0.288	0.267	0.368	5e-05
A5UIY2	269	tRNA pseudouridine syntha	yes	no	0.288	0.267	0.368	5e-05

>sp|Q7TU07|TRUA_RHOBA tRNA pseudouridine synthase A OS=Rhodopirellula baltica (strain SH1) GN=truA PE=3 SV=1

 Score = 57.0 bits (136), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 58/241 (24%), Positives = 87/241 (36%), Gaps = 49/241 (20%)

Query: 3   ILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGEN 62
           +L  W+ D     ++ AINS  P  IRV +V +    FHP   A  ++Y Y+        
Sbjct: 71  VLPVWKADT--VALQRAINSKLPNDIRVKAVRETRERFHPIADATGKQYQYLV------- 121

Query: 63  REQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLL 122
                                 Q  G  +   N  +N  GG   H              +
Sbjct: 122 ----------------------QVGGSRDPFANRFVNRVGGPIDHSA------------M 147

Query: 123 QRLEGKLLSYKTFA--RDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVE 180
           Q    K +    F   + T A R   P T   I+ AR    +   P     EG    C E
Sbjct: 148 QSAAAKFVGRHDFKAFQGTGAER---PSTVRTIHSARWIPRVATGPTGAELEGEH-WCFE 203

Query: 181 LVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYT 240
           +    FL  MVR L+ T++         + + +++ +  R+   P APP+GL L  V Y 
Sbjct: 204 IDGEGFLYNMVRNLMGTMLEVGRGKKSPNWIDEVLASRDRKMAGPTAPPQGLFLCRVDYP 263

Query: 241 N 241
           +
Sbjct: 264 D 264

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.
Rhodopirellula baltica (strain SH1) (taxid: 243090)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: 1EC: 2

>sp|Q2S4S9|TRUA_SALRD tRNA pseudouridine synthase A OS=Salinibacter ruber (strain DSM 13855 / M31) GN=truA PE=3 SV=1

 Score = 53.1 bits (126), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 179 VELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVG 238
           VE+V  RFL  MVR LV TLV         DAL  ++ A  RRA  P  PPEGL L  V 
Sbjct: 184 VEVVGTRFLHGMVRALVGTLVEIGHEKRAADALPAVLAARDRRAAGPSMPPEGLVLEAVR 243

Query: 239 YTN--FD--PQNSLIP 250
           Y    FD  P + L+P
Sbjct: 244 YEQPLFDDGPGDPLVP 259

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

Salinibacter ruber (strain DSM 13855 / M31) (taxid: 309807)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|P57861|TRUA_PASMU tRNA pseudouridine synthase A OS=Pasteurella multocida (strain Pm70) GN=truA PE=3 SV=1

 Score = 51.6 bits (122), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 175 KVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCL 234
           + + V++ AN F+  MVR +V +L+   A     + +  L+    RR  AP A PEGL L
Sbjct: 179 QYIIVDIQANAFVHHMVRNIVGSLIEVGAGHQPVEWIGWLLAQKDRRLAAPTAKPEGLYL 238

Query: 235 VDVGY-TNFD-PQNSLIP 250
           V+V Y T F  PQN+L P
Sbjct: 239 VNVSYPTQFQLPQNALGP 256

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

Pasteurella multocida (strain Pm70) (taxid: 272843)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|Q5FPX3|TRUA_GLUOX tRNA pseudouridine synthase A OS=Gluconobacter oxydans (strain 621H) GN=truA PE=3 SV=1

 Score = 50.4 bits (119), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 59/111 (53%), Gaps = 6/111 (5%)

Query: 140 KASRNIGPPTECFIYHARATEAILPCP----VNDHGEGRKVMCVELVANRFLRKMVRVLV 195
           +A+ ++  P +   + A A +A  P      +N H +G  VM ++  A  FL   VR + 
Sbjct: 165 QAANHLLGPHDFTSFRAVACQARSPIRTLDVLNIHRDGELVM-IDTKARSFLHHQVRNMA 223

Query: 196 ATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNFDPQN 246
            TL+   +     + ++++++A  R A    APPEGLCL+DVGY + DP N
Sbjct: 224 GTLMMIGSRQWPVEKIIEILEAKDRCAAGQTAPPEGLCLMDVGYPD-DPFN 273

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

Gluconobacter oxydans (strain 621H) (taxid: 290633)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|A4J151|TRUA_DESRM tRNA pseudouridine synthase A OS=Desulfotomaculum reducens (strain MI-1) GN=truA PE=3 SV=1

 Score = 49.7 bits (117), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/221 (24%), Positives = 83/221 (37%), Gaps = 54/221 (24%)

Query: 19  AINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHT 78
           A+N   PG I+V+   +V   FH  FSA  + Y Y            SI     +  FH 
Sbjct: 81  ALNVLLPGDIKVVKAEEVPMDFHARFSAVAKTYRY------------SIYHHRVMSPFHR 128

Query: 79  SNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARD 138
                     CY                HE PR   +  +       EG      T+  D
Sbjct: 129 YY--------CY----------------HE-PRRLDVNAMQ------EGAAYLLGTY--D 155

Query: 139 TKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATL 198
            K+ +  G P +  I      + I   PV         + + L  N FL  MVR++  TL
Sbjct: 156 FKSFQAQGTPVKDTIRTIYRADIIEDAPV---------INLYLRGNGFLYNMVRIITGTL 206

Query: 199 VREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
           +         + ++K++++  R      APP+GLCL++V Y
Sbjct: 207 LNIGFGKIKPEDMVKIIESKNRTLAGTTAPPQGLCLMEVEY 247

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

Desulfotomaculum reducens (strain MI-1) (taxid: 349161)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|Q73KE3|TRUA_TREDE tRNA pseudouridine synthase A OS=Treponema denticola (strain ATCC 35405 / CIP 103919 / DSM 14222) GN=truA PE=3 SV=1

 Score = 49.7 bits (117), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 56/237 (23%), Positives = 90/237 (37%), Gaps = 66/237 (27%)

Query: 9   KDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSID 68
           K ++ S+   A+NS  P  IRV+  ++VS + H  F+A  R   Y + +  G+       
Sbjct: 80  KSMRASNFLPALNSILPKDIRVMDAAEVSPLLHARFNALSRT--YRYKIKCGKT------ 131

Query: 69  SEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICR------VNLLL 122
                                                +HE+P  + I R      +N + 
Sbjct: 132 -----------------------------------IFAHEQPYTWHIRRYPDIAALNEMA 156

Query: 123 QRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELV 182
             L G+L        D  A    G  +   I  +R  +  +    ND+      +  E+ 
Sbjct: 157 SCLSGEL--------DCTAFSAAGDQS---ISKSRYIKKAVFFIENDY------LIFEIC 199

Query: 183 ANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
           AN FL KMVR +V TL+     GA +     ++++  R    P APP+GL L  + Y
Sbjct: 200 ANAFLWKMVRSIVGTLLHLDEIGASKKDFKDILESKMREKAGPTAPPQGLFLWSIEY 256

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

Treponema denticola (strain ATCC 35405 / CIP 103919 / DSM 14222) (taxid: 243275)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|Q8U2C1|TRUA_PYRFU tRNA pseudouridine synthase A OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=truA PE=3 SV=1

 Score = 49.3 bits (116), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 176 VMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRA-TAPPAPPEGLCL 234
           V+ VE+    FL +MVR +V+ LV  +     E+ ++++++    ++   PPAPPEGL L
Sbjct: 159 VVVVEIEGKSFLWEMVRRIVSALVLCSQGVLAEERIVEMLNGKFEKSRKVPPAPPEGLLL 218

Query: 235 VDVGYTNFDPQ 245
            D+ Y N + Q
Sbjct: 219 WDIKYENVEFQ 229

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

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (taxid: 186497)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|A8FTU0|TRUA_SHESH tRNA pseudouridine synthase A OS=Shewanella sediminis (strain HAW-EB3) GN=truA PE=3 SV=1

 Score = 48.9 bits (115), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/63 (39%), Positives = 35/63 (55%)

Query: 177 MCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVD 236
           +CV++ AN FL  MVR +V TL+         + + +L+D   R   AP A P GL +VD
Sbjct: 181 ICVDIKANAFLHHMVRNIVGTLLEIGLGNQRPEWIPQLLDLKDRSQAAPTAKPNGLYMVD 240

Query: 237 VGY 239
           V Y
Sbjct: 241 VTY 243

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

Shewanella sediminis (strain HAW-EB3) (taxid: 425104)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|Q4QL79|TRUA_HAEI8 tRNA pseudouridine synthase A OS=Haemophilus influenzae (strain 86-028NP) GN=truA PE=3 SV=1

 Score = 48.5 bits (114), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 4/76 (5%)

Query: 175 KVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCL 234
           K + V++ AN F+  MVR +V +L+   A     + +  L++   R+  AP A P+GL L
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 235 VDVGYTNFDPQNSLIP 250
           VDV Y    PQ   IP
Sbjct: 239 VDVIY----PQKFDIP 250

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

Haemophilus influenzae (strain 86-028NP) (taxid: 281310)

EC: 5

EC: .

EC: 4

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 2

>sp|A5UIY2|TRUA_HAEIG tRNA pseudouridine synthase A OS=Haemophilus influenzae (strain PittGG) GN=truA PE=3 SV=1

 Score = 48.1 bits (113), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 4/76 (5%)

Query: 175 KVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCL 234
           K + V++ AN F+  MVR +V +L+   A     + +  L++   R+  AP A P+GL L
Sbjct: 179 KYIIVDIQANAFVHHMVRNIVGSLIEVGAGNQPIEWMQWLLEQKNRQLAAPTAKPDGLYL 238

Query: 235 VDVGYTNFDPQNSLIP 250
           VDV Y    PQ   IP
Sbjct: 239 VDVIY----PQKFDIP 250

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

Haemophilus influenzae (strain PittGG) (taxid: 374931)

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	250
255566350	443	pseudouridylate synthase, putative [Rici	0.968	0.546	0.74	2e-98
224118612	428	predicted protein [Populus trichocarpa]	0.968	0.565	0.72	5e-96
359474454	433	PREDICTED: tRNA pseudouridine synthase A	0.968	0.558	0.684	6e-96
297742024	402	unnamed protein product [Vitis vinifera]	0.868	0.539	0.655	7e-87
297805092	420	tRNA pseudouridine synthase family prote	0.956	0.569	0.627	2e-84
356527708	404	PREDICTED: tRNA pseudouridine synthase A	0.912	0.564	0.676	4e-81
449518731	444	PREDICTED: tRNA pseudouridine synthase A	0.964	0.542	0.7	7e-81
449439176	444	PREDICTED: tRNA pseudouridine synthase A	0.964	0.542	0.696	1e-80
356511427	387	PREDICTED: tRNA pseudouridine synthase A	0.908	0.586	0.673	8e-79
294461715	448	unknown [Picea sitchensis]	0.976	0.544	0.608	1e-76

>gi|255566350|ref|XP_002524161.1| pseudouridylate synthase, putative [Ricinus communis] gi|223536579|gb|EEF38224.1| pseudouridylate synthase, putative [Ricinus communis]

 Score =  364 bits (934), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 185/250 (74%), Positives = 212/250 (84%), Gaps = 8/250 (3%)

Query: 6   TWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQ 65
           TWRKDV+P +IEDAINS+APGKIRVISVS+VSRVFHPNFSAKWRRYLYIFP+NDGE+ EQ
Sbjct: 197 TWRKDVRPHEIEDAINSSAPGKIRVISVSEVSRVFHPNFSAKWRRYLYIFPINDGEDSEQ 256

Query: 66  SIDSEVEVENFHTSNNVGKQSNGCYE-----NIENLLINDEGGFGSHEKPRNFTICRVNL 120
           S DSE ++EN  +     +Q NGC E     ++E L+ +D+      +KPR F+ICRVN 
Sbjct: 257 SFDSE-DLENLRSYEKYDEQRNGCAELTSEEHVEELITSDKDELEGAKKPRIFSICRVNQ 315

Query: 121 LLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVE 180
           LLQ+LEGKLLSYK FARDTKASRN+GPPTECFIYHARATEA LPCP  DHGEGRKVMCVE
Sbjct: 316 LLQQLEGKLLSYKIFARDTKASRNVGPPTECFIYHARATEARLPCP--DHGEGRKVMCVE 373

Query: 181 LVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYT 240
           LVANRFLRKMVRVLVAT +REAAAGA++DALLKLMDA+CRRA+APPAPP+GLCL DVGYT
Sbjct: 374 LVANRFLRKMVRVLVATSIREAAAGAEDDALLKLMDASCRRASAPPAPPDGLCLFDVGYT 433

Query: 241 NFDPQNSLIP 250
            FD Q  ++P
Sbjct: 434 EFDAQICIVP 443

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118612|ref|XP_002331405.1| predicted protein [Populus trichocarpa] gi|222873619|gb|EEF10750.1| predicted protein [Populus trichocarpa]

 Score =  356 bits (913), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 180/250 (72%), Positives = 203/250 (81%), Gaps = 8/250 (3%)

Query: 6   TWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQ 65
           TWRKDVKP +IEDAIN  APGK+RV S+S+VSR FHPNFSAKWRRYLYIFPLND     +
Sbjct: 182 TWRKDVKPHEIEDAINDVAPGKVRVESISEVSRAFHPNFSAKWRRYLYIFPLND-GENRE 240

Query: 66  SIDSEVEVENFHTSNNVGKQSNGC-----YENIENLLINDEGGFGSHEKPRNFTICRVNL 120
            I+ E  +ENF +  N  KQ N C      EN+EN +I+DE      +KPR+F++CRVN 
Sbjct: 241 EIEGEGGIENFSSHENCEKQRNECGELASEENVENSIISDEDELQGAKKPRSFSVCRVNQ 300

Query: 121 LLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVE 180
           LLQ+LEGKLLSYK FARDTKASRN+GPPTECF+YHARATE  LP P  DH +G +VMCVE
Sbjct: 301 LLQQLEGKLLSYKMFARDTKASRNVGPPTECFLYHARATETRLPSP--DHEKGIRVMCVE 358

Query: 181 LVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYT 240
           L+ANRFLRKMVRVLVAT VREAAAGA EDALLKLMDATCRRATAPPAPP+GLCLVDVGYT
Sbjct: 359 LIANRFLRKMVRVLVATSVREAAAGAQEDALLKLMDATCRRATAPPAPPDGLCLVDVGYT 418

Query: 241 NFDPQNSLIP 250
            FDP+N LIP
Sbjct: 419 EFDPRNCLIP 428

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359474454|ref|XP_002275354.2| PREDICTED: tRNA pseudouridine synthase A-like [Vitis vinifera]

 Score =  356 bits (913), Expect = 6e-96,   Method: Compositional matrix adjust.
 Identities = 171/250 (68%), Positives = 204/250 (81%), Gaps = 8/250 (3%)

Query: 6   TWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQ 65
           TW+KDVK  DIEDAIN AAPGK+RVISVS+VSR+FHPNFSAKWR Y YIFPLNDG++ EQ
Sbjct: 185 TWKKDVKVQDIEDAINGAAPGKLRVISVSEVSRIFHPNFSAKWRHYFYIFPLNDGDDGEQ 244

Query: 66  SIDSEVEVENFHTSNNVGKQSNGC------YENIENLLINDEGGFGSHEKPRNFTICRVN 119
             ++E++++    +   G+Q + C       EN ENL+ +D+G F S +KP  F+I RV+
Sbjct: 245 ISENEMDIQKISFNEKYGEQGSECPAQYNGGENTENLIFDDDGEFESRKKPSTFSISRVD 304

Query: 120 LLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCV 179
            LL++LEGKLLSYK FARDTKASRNIGPPTECF++HARATEA L    +D GEG KVMC+
Sbjct: 305 QLLRQLEGKLLSYKIFARDTKASRNIGPPTECFVFHARATEARLQ--FSDDGEGTKVMCI 362

Query: 180 ELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
           ELVANRFLRKMVRVLVAT +REAAAGA++DALLKLMDATCRRATAPPAPP+GLCL+DVG+
Sbjct: 363 ELVANRFLRKMVRVLVATSIREAAAGAEQDALLKLMDATCRRATAPPAPPDGLCLIDVGF 422

Query: 240 TNFDPQNSLI 249
           T FDPQ   I
Sbjct: 423 TEFDPQICFI 432

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742024|emb|CBI33811.3| unnamed protein product [Vitis vinifera]

 Score =  325 bits (834), Expect = 7e-87,   Method: Compositional matrix adjust.
 Identities = 160/244 (65%), Positives = 188/244 (77%), Gaps = 27/244 (11%)

Query: 6   TWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQ 65
           TW+KDVK  DIEDAIN AAPGK+RVISVS+VSR+FHPNFSAKWR Y YIFPLNDG++ EQ
Sbjct: 185 TWKKDVKVQDIEDAINGAAPGKLRVISVSEVSRIFHPNFSAKWRHYFYIFPLNDGDDGEQ 244

Query: 66  SIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRL 125
             ++E++++    + N                          +KP  F+I RV+ LL++L
Sbjct: 245 ISENEMDIQKISFNEN-------------------------RKKPSTFSISRVDQLLRQL 279

Query: 126 EGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANR 185
           EGKLLSYK FARDTKASRNIGPPTECF++HARATEA L    +D GEG KVMC+ELVANR
Sbjct: 280 EGKLLSYKIFARDTKASRNIGPPTECFVFHARATEARLQ--FSDDGEGTKVMCIELVANR 337

Query: 186 FLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNFDPQ 245
           FLRKMVRVLVAT +REAAAGA++DALLKLMDATCRRATAPPAPP+GLCL+DVG+T FDPQ
Sbjct: 338 FLRKMVRVLVATSIREAAAGAEQDALLKLMDATCRRATAPPAPPDGLCLIDVGFTEFDPQ 397

Query: 246 NSLI 249
              I
Sbjct: 398 ICFI 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297805092|ref|XP_002870430.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] gi|297316266|gb|EFH46689.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  317 bits (813), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 160/255 (62%), Positives = 195/255 (76%), Gaps = 16/255 (6%)

Query: 6   TWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQ 65
           TWRKD++P  IEDAIN  A GK+RV+S+S+VSR FHPNFSAKWRRYLYIFPL+D E+  +
Sbjct: 170 TWRKDIEPIAIEDAINKDASGKLRVVSISKVSRSFHPNFSAKWRRYLYIFPLDDAESLHE 229

Query: 66  SIDSEVEVENFHTSNNVGKQSNGCY--ENIENLLINDE---------GGFGSHEKPRNFT 114
           S ++    ENF    N  KQ NG    EN E ++++++          G    EKP +F+
Sbjct: 230 SGENH---ENFIFDENHEKQRNGLLSEENTEEVILSEDDELEIEETSNGLEVVEKPSDFS 286

Query: 115 ICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGR 174
           + +V+ LLQ+L+GK+LSYK FARDTKA+RN GPPTECF+YHARA E  L C  +D  EGR
Sbjct: 287 VIKVDQLLQQLQGKVLSYKMFARDTKAARNEGPPTECFMYHARAAEIRLSC--SDCVEGR 344

Query: 175 KVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCL 234
           +VMCVELVANRFLRKMVRVLVAT +REAAAGA+ DALLKL++A+CRRATAPPAP EGLCL
Sbjct: 345 RVMCVELVANRFLRKMVRVLVATSIREAAAGAENDALLKLLEASCRRATAPPAPSEGLCL 404

Query: 235 VDVGYTNFDPQNSLI 249
            DVGY +FDPQ SLI
Sbjct: 405 FDVGYADFDPQTSLI 419

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356527708|ref|XP_003532450.1| PREDICTED: tRNA pseudouridine synthase A-like [Glycine max]

 Score =  306 bits (785), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 165/244 (67%), Positives = 187/244 (76%), Gaps = 16/244 (6%)

Query: 6   TWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQ 65
           TW+KDVKP DIEDAIN AAPGK+RVISVS+VSRVFHPNFSAKWRRYLYIFPL +G   +Q
Sbjct: 174 TWKKDVKPRDIEDAINHAAPGKLRVISVSEVSRVFHPNFSAKWRRYLYIFPLTNGGYTDQ 233

Query: 66  SIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRL 125
           S D+    ++F             Y  I +    DE    + +K   F+I +VN LL++L
Sbjct: 234 SSDNGEFYDSFK------------YNEIHDSASKDE--LENEKKSYAFSISKVNRLLRKL 279

Query: 126 EGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANR 185
           EGKLLSYK FARDTKASRN GPPTECF+YHARA E  LP    DHGE  KVMCVELVANR
Sbjct: 280 EGKLLSYKMFARDTKASRNDGPPTECFVYHARAMEVKLPA--TDHGEETKVMCVELVANR 337

Query: 186 FLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNFDPQ 245
           FLRKMVRVLVAT +REAAAGA++DAL+KLMDATCRRATAPPAPP+GLCLVDVGYT F+PQ
Sbjct: 338 FLRKMVRVLVATSIREAAAGAEDDALIKLMDATCRRATAPPAPPDGLCLVDVGYTEFEPQ 397

Query: 246 NSLI 249
              I
Sbjct: 398 KCFI 401

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449518731|ref|XP_004166389.1| PREDICTED: tRNA pseudouridine synthase A-like [Cucumis sativus]

 Score =  306 bits (783), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 175/250 (70%), Positives = 194/250 (77%), Gaps = 9/250 (3%)

Query: 6   TWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQ 65
           TWR DVKP DIED+INSAAPGK+R  SVSQVSR+FHPNFSAKWRRYLYI PLNDGEN E 
Sbjct: 195 TWRTDVKPQDIEDSINSAAPGKLRTSSVSQVSRIFHPNFSAKWRRYLYILPLNDGENMEP 254

Query: 66  SIDSEVEVENFHTSNNVG-KQSNG--CYENIENLLI---NDEGGFGSHEKPRNFTICRVN 119
              +   VEN    N V  + SNG  C + I + L+   NDE    S +KP+ F+I RVN
Sbjct: 255 DSTTWENVENREEENFVKIEASNGEKCVDGIHDNLVLSPNDEE-LVSADKPQTFSITRVN 313

Query: 120 LLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCV 179
            LL++LEGKLLSYK FARDTKASRN GPPTECF+YHARA E  LPC   + G GR VMCV
Sbjct: 314 QLLRKLEGKLLSYKMFARDTKASRNEGPPTECFVYHARAAETRLPCL--EQGVGRSVMCV 371

Query: 180 ELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
           ELVANRFLRKMVRVLVAT +REAAAGA EDALL+LMDATCRRATAPPAPP+GL LVDVGY
Sbjct: 372 ELVANRFLRKMVRVLVATAIREAAAGAGEDALLELMDATCRRATAPPAPPDGLSLVDVGY 431

Query: 240 TNFDPQNSLI 249
           T+FD Q   I
Sbjct: 432 TDFDSQICFI 441

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439176|ref|XP_004137363.1| PREDICTED: tRNA pseudouridine synthase A-like [Cucumis sativus]

 Score =  305 bits (781), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 174/250 (69%), Positives = 194/250 (77%), Gaps = 9/250 (3%)

Query: 6   TWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQ 65
           TWR DVKP DIED+INSAAPGK+R  SVSQVSR+FHPNFSAKWRRYLYI PLNDGEN E 
Sbjct: 195 TWRTDVKPQDIEDSINSAAPGKLRTSSVSQVSRIFHPNFSAKWRRYLYILPLNDGENMEP 254

Query: 66  SIDSEVEVENFHTSNNVG-KQSNG--CYENIENLLI---NDEGGFGSHEKPRNFTICRVN 119
              +   VEN    N V  + SNG  C + I + L+   ND+    S +KP+ F+I RVN
Sbjct: 255 DSTTWENVENREEENFVKIEASNGEKCVDGIHDNLVLSPNDQE-LVSADKPQTFSITRVN 313

Query: 120 LLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCV 179
            LL++LEGKLLSYK FARDTKASRN GPPTECF+YHARA E  LPC   + G GR VMCV
Sbjct: 314 QLLRKLEGKLLSYKMFARDTKASRNEGPPTECFVYHARAAETRLPCL--EQGVGRSVMCV 371

Query: 180 ELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
           ELVANRFLRKMVRVLVAT +REAAAGA EDALL+LMDATCRRATAPPAPP+GL LVDVGY
Sbjct: 372 ELVANRFLRKMVRVLVATAIREAAAGAGEDALLELMDATCRRATAPPAPPDGLSLVDVGY 431

Query: 240 TNFDPQNSLI 249
           T+FD Q   I
Sbjct: 432 TDFDSQICFI 441

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356511427|ref|XP_003524428.1| PREDICTED: tRNA pseudouridine synthase A-like [Glycine max]

 Score =  299 bits (765), Expect = 8e-79,   Method: Compositional matrix adjust.
 Identities = 165/245 (67%), Positives = 185/245 (75%), Gaps = 18/245 (7%)

Query: 6   TWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQ 65
           TW+KDVKP DIEDAIN A PGK RVISVS+VSRVFHPNFSAKWRRYLYIFPL +G   +Q
Sbjct: 157 TWKKDVKPRDIEDAINHATPGKFRVISVSEVSRVFHPNFSAKWRRYLYIFPLTNGRYTDQ 216

Query: 66  SIDSEVEVENFHTSNNVGKQSNGC-YENIENLLINDEGGFGSHEKPRNFTICRVNLLLQR 124
           S             N+ G   N C Y  I +    DE   G  +K   F+  +VN LL++
Sbjct: 217 S-------------NDNGHFYNSCKYNEIHDSASKDELENG--KKSYMFSTSKVNRLLRK 261

Query: 125 LEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVAN 184
           LEGKLLSYK FARDTKASRN GPPTECF+YHARA E + P P  DHGE  KVMCVELVA+
Sbjct: 262 LEGKLLSYKMFARDTKASRNDGPPTECFVYHARAME-VKP-PTTDHGEETKVMCVELVAD 319

Query: 185 RFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNFDP 244
           RFLRKMVRVLVAT +REAAAGA++DAL+KLMDATCRRATAPPAPP+GLCLVDVGYT FDP
Sbjct: 320 RFLRKMVRVLVATSIREAAAGAEDDALIKLMDATCRRATAPPAPPDGLCLVDVGYTEFDP 379

Query: 245 QNSLI 249
           +   I
Sbjct: 380 KKCFI 384

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294461715|gb|ADE76416.1| unknown [Picea sitchensis]

 Score =  291 bits (746), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 151/248 (60%), Positives = 181/248 (72%), Gaps = 4/248 (1%)

Query: 6   TWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQ 65
           TWRKD    DIE  IN+AA GK++V+S+S+VSR FHPNFSAKWRRYLYI PL DGE  + 
Sbjct: 201 TWRKDTSLEDIESEINAAALGKLKVVSISEVSREFHPNFSAKWRRYLYILPLKDGEGNKT 260

Query: 66  SID--SEVEVENFHTSNNVGKQSNGC-YENIENLLINDEGGFGSHEKPRNFTICRVNLLL 122
            +D  S V  ++   ++  G QS      N+E + I+  G   +  KP NF +  VN LL
Sbjct: 261 VVDGGSPVTYDSLCLADEGGNQSTDMNVINMEAMNISATGKHQASVKPHNFNVDTVNQLL 320

Query: 123 QRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDH-GEGRKVMCVEL 181
           Q+LEG+ LSY+ FARDT+ASR+ GP TECF++HARA  A LP    DH  +GR VMCVEL
Sbjct: 321 QQLEGQSLSYRIFARDTQASRSRGPATECFMHHARAAVATLPYMGQDHTSKGRTVMCVEL 380

Query: 182 VANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTN 241
           VANRFLRKMVRVLVAT VREAAAGA  D LLKLM ATCRRA+APPAPPEGLCLVD+GYT+
Sbjct: 381 VANRFLRKMVRVLVATAVREAAAGATPDNLLKLMHATCRRASAPPAPPEGLCLVDIGYTD 440

Query: 242 FDPQNSLI 249
            + +N LI
Sbjct: 441 INQENFLI 448

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

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)

No hits with e-value below 0.001 by BLAST

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	0.737
3rd Layer	5.4.99	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_scaffold_164000053 hypothetical protein (428 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	250
PRK00021	244	PRK00021, truA, tRNA pseudouridine synthase A; Val	2e-22
COG0101	266	COG0101, TruA, Pseudouridylate synthase [Translati	7e-20
cd02570	239	cd02570, PseudoU_synth_EcTruA, Eukaryotic and bact	3e-14
pfam01416	103	pfam01416, PseudoU_synth_1, tRNA pseudouridine syn	1e-09
PRK14588	272	PRK14588, PRK14588, tRNA pseudouridine synthase AC	4e-09
cd02570	239	cd02570, PseudoU_synth_EcTruA, Eukaryotic and bact	2e-07
PRK14586	245	PRK14586, PRK14586, tRNA pseudouridine synthase AC	5e-07
cd02866	219	cd02866, PseudoU_synth_TruA_Archea, Archeal pseudo	1e-06
PRK12434	245	PRK12434, PRK12434, tRNA pseudouridine synthase A;	4e-06
cd00497	215	cd00497, PseudoU_synth_TruA_like, Pseudouridine sy	6e-06
TIGR00071	227	TIGR00071, hisT_truA, tRNA pseudouridine(38-40) sy	1e-05
PRK14589	265	PRK14589, PRK14589, tRNA pseudouridine synthase AC	3e-05
TIGR00071	227	TIGR00071, hisT_truA, tRNA pseudouridine(38-40) sy	9e-05
cd00497	215	cd00497, PseudoU_synth_TruA_like, Pseudouridine sy	2e-04
cd02568	245	cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine sy	8e-04

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

 Score = 92.1 bits (230), Expect = 2e-22
 Identities = 57/232 (24%), Positives = 82/232 (35%), Gaps = 56/232 (24%)

Query: 9   KDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSID 68
               P     A+N+  P  I V+   +V   FH  FSAK RRY Y   + +   R     
Sbjct: 68  APRPPEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRYRYR--IYNRPAR----- 120

Query: 69  SEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGK 128
                        V       Y                   P    +  +N   Q L G+
Sbjct: 121 ------PPFLRGYVW-----HY-------------------PYPLDVDAMNEAAQYLLGE 150

Query: 129 LLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLR 188
              + +F      S++        IY A          V   G+    +  ++ AN FL 
Sbjct: 151 H-DFTSFRASGCQSKS----PVRTIYEAD---------VTREGD---FIVFDISANGFLH 193

Query: 189 KMVRVLVATLVREAAAGA-DEDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
            MVR +V TL+ E   G    + + +L++A  R    P AP EGL LV+V Y
Sbjct: 194 NMVRNIVGTLL-EVGKGKRPPEDIKELLEAKDRTLAGPTAPAEGLYLVEVDY 244

Length = 244

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

 Score = 85.4 bits (212), Expect = 7e-20
 Identities = 51/242 (21%), Positives = 79/242 (32%), Gaps = 57/242 (23%)

Query: 4   LDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENR 63
            DT   D     +  A+N+  P  IRV+ V++V   FH  FSAK R Y YI       N 
Sbjct: 64  FDT-PADRPLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYRYIIY-----NA 117

Query: 64  EQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQ 123
                                                         P    +  +    +
Sbjct: 118 PLRPPFLANYVWHV--------------------------------PYPLDLDAMREAAK 145

Query: 124 RLEGKLLSYKTFAR-DTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELV 182
            L G    + +F +   ++   +       IY            V+  G+   +   ++ 
Sbjct: 146 LLLGTH-DFTSFRKAGCQSKSPVR-----TIYRID---------VSRDGDLIVI---DIS 187

Query: 183 ANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNF 242
            N FL  MVR +V  L+         + + +L++A  R+   P AP EGL LV V Y   
Sbjct: 188 GNSFLWHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRKLAGPTAPAEGLYLVRVDYPED 247

Query: 243 DP 244
             
Sbjct: 248 FE 249

Length = 266

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

 Score = 69.4 bits (171), Expect = 3e-14
 Identities = 31/92 (33%), Positives = 41/92 (44%), Gaps = 14/92 (15%)

Query: 149 TECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGA-D 207
           T   IY A               EG  +   E+ AN FL  MVR +V TL+ E   G   
Sbjct: 161 TVRTIYRADVYR-----------EGDLI-VFEIRANGFLYHMVRNIVGTLL-EVGRGKLS 207

Query: 208 EDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
            + + ++++A  R A  P AP  GL LV V Y
Sbjct: 208 PEDIKEILEAKDRTAAGPTAPAHGLYLVKVEY 239

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|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase

 Score = 54.0 bits (130), Expect = 1e-09
 Identities = 19/68 (27%), Positives = 32/68 (47%)

Query: 172 EGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEG 231
              +++  E+  N FL   VR++V  L+R        + ++ L+++  R    P AP  G
Sbjct: 35  RDGELLVFEIKGNGFLYHQVRIMVGALLRTGKGVHALEQVVSLLNSKLRPRAPPTAPAVG 94

Query: 232 LCLVDVGY 239
           L L  V Y
Sbjct: 95  LYLFHVRY 102

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|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional

 Score = 55.3 bits (133), Expect = 4e-09
 Identities = 24/67 (35%), Positives = 34/67 (50%)

Query: 173 GRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGL 232
           GR ++ +E+ AN FL+ MVR +V TL+         D    ++ +  RR   P AP  GL
Sbjct: 181 GRPLLAIEVAANAFLQHMVRNIVGTLLLVGRGRMTVDQFGAVLASRDRRLAGPTAPAHGL 240

Query: 233 CLVDVGY 239
            L  V Y
Sbjct: 241 YLTAVRY 247

Length = 272

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

 Score = 49.8 bits (120), Expect = 2e-07
 Identities = 18/47 (38%), Positives = 24/47 (51%)

Query: 9   KDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIF 55
            ++    +  A+NS  P  IRV+S  +V   FH  FSAK R Y Y  
Sbjct: 63  SEIPLEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRI 109

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|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional

 Score = 49.0 bits (117), Expect = 5e-07
 Identities = 55/228 (24%), Positives = 88/228 (38%), Gaps = 60/228 (26%)

Query: 13  PSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVE 72
             DI++A+N+  P  I V  V +V + FHP F AK +R  + F L    ++E+++     
Sbjct: 73  EEDIKNAMNANLPDDIYVKKVFEVPKNFHPRFDAK-KRIYHYFILT---SKEKNVFLRKY 128

Query: 73  VENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGK--LL 130
           V  F                                 P    +  +    + LEG+    
Sbjct: 129 VWWF---------------------------------PYELDLEAMRKAAKYLEGEHDFT 155

Query: 131 SYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANR-FLRK 189
           S+KT + +    R I        Y  R    IL          +K + +  V  R FLR+
Sbjct: 156 SFKTGSDERNPVRTI--------YRIR----IL--------RLKKDLILIRVEGRSFLRR 195

Query: 190 MVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDV 237
           MVR +V  LV+      + + + ++++A  R   A  AP  GL L  V
Sbjct: 196 MVRNIVGALVKVGLGQWEPEKIKEVLEARDRSKAAGTAPAHGLYLYKV 243

Length = 245

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

 Score = 47.8 bits (114), Expect = 1e-06
 Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 172 EGRKVMCVELVANRFLRKMVRVLVATLVREAAAGA-DEDALLKLMDATCRRATAPPAPPE 230
           E  + + +++V   FL  MVR +V   + E   G  + + + KL+D   R    PPAPPE
Sbjct: 152 ENGEFITIDVVGESFLWNMVRRIV-GALSEVGKGKRENEWVEKLLDGEFRPEGVPPAPPE 210

Query: 231 GLCLVDVGY 239
           GL LVDV Y
Sbjct: 211 GLILVDVKY 219

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|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed

 Score = 46.3 bits (110), Expect = 4e-06
 Identities = 17/61 (27%), Positives = 29/61 (47%)

Query: 179 VELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVG 238
           + +  N FL  MVR++V  L+         + + ++++A  R      AP  GL L +V 
Sbjct: 185 IRVSGNGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDRNQANCTAPASGLYLENVE 244

Query: 239 Y 239
           Y
Sbjct: 245 Y 245

Length = 245

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

 Score = 45.5 bits (108), Expect = 6e-06
 Identities = 21/68 (30%), Positives = 29/68 (42%)

Query: 172 EGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEG 231
           +    + VE  A  FL   VR +V  L+          ++ +L+          PAP EG
Sbjct: 148 DLNPFVVVEFKAKSFLWHQVRRMVGFLMLVGEGLHSPSSVSRLLAGPAPPIPMVPAPAEG 207

Query: 232 LCLVDVGY 239
           L LVDV Y
Sbjct: 208 LLLVDVKY 215

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

 Score = 44.6 bits (106), Expect = 1e-05
 Identities = 20/63 (31%), Positives = 29/63 (46%)

Query: 172 EGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEG 231
           E  + +  +++ N FL  MVR +V  LV         + + KL+DA  R      AP  G
Sbjct: 165 ESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLAPTTAPANG 224

Query: 232 LCL 234
           L L
Sbjct: 225 LYL 227

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|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional

 Score = 44.0 bits (104), Expect = 3e-05
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 180 ELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
           E+ A  FL  MVR +   L++      + D + +L+   C+R    PAP EGL L DV  
Sbjct: 167 EVTAQSFLWHMVRCMAGALLQIGEGEMEPDDIERLLSGPCKR-KVKPAPAEGLVLWDVDC 225

Query: 240 -TNFDP 244
              F P
Sbjct: 226 GLTFTP 231

Length = 265

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

 Score = 42.3 bits (100), Expect = 9e-05
 Identities = 16/53 (30%), Positives = 27/53 (50%)

Query: 8   RKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDG 60
            K++  + +   +N+  P  IRV +++ V+  FH  FSA  R Y YI   +  
Sbjct: 66  PKEIPDNKLNAKLNALLPPDIRVKALAPVNDNFHARFSASKRHYRYILYNHRH 118

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|211322 cd00497, PseudoU_synth_TruA_like, Pseudouridine synthase, TruA family

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 24/90 (26%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 18  DAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYI---FPLNDGENREQSIDSEVEVE 74
           +A+N   PG IRV +V  V   FH       R Y Y    FPL+D   +  +    +   
Sbjct: 66  EALNGILPGDIRVFAVHSVPPDFHAPRYCDHRTYRYYIPSFPLDDERLKS-AASRFLGTH 124

Query: 75  NFHTSNNVGKQSNGCYENIENLLINDEGGF 104
           +F   N   K +      I ++   D   F
Sbjct: 125 DFT--NFSKKDTRNTVRTIISIECKDLNPF 152

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|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/ PUS2 like

 Score = 39.5 bits (93), Expect = 8e-04
 Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 6/105 (5%)

Query: 2   IILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFP--LND 59
           +I+D         D+ + +NS  P  IRV  +++V++ F+   +   R Y Y+ P    +
Sbjct: 71  VIIDDPEGLGILEDLVEKLNSHLPSDIRVFGITRVTKSFNARKACDSRTYEYLLPTFALE 130

Query: 60  GENREQSIDSEVE-VENFH--TSNNVGKQSNGCYENIENLLINDE 101
              R   I  E     NFH  T      +       I++  +++ 
Sbjct: 131 TLQRFNEILKEYVGTHNFHNFTVKK-KFEDPSANRFIKSFYVSEP 174

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	250
COG0101	266	TruA Pseudouridylate synthase [Translation, riboso	100.0
PRK12434	245	tRNA pseudouridine synthase A; Reviewed	100.0
PRK14588	272	tRNA pseudouridine synthase ACD; Provisional	100.0
PRK14586	245	tRNA pseudouridine synthase ACD; Provisional	100.0
PRK00021	244	truA tRNA pseudouridine synthase A; Validated	100.0
cd02570	239	PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudou	100.0
TIGR00071	227	hisT_truA pseudouridylate synthase I. universal so	100.0
cd02569	256	PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Ps	100.0
cd02866	221	PseudoU_synth_TruA_Archea PseudoU_synth_archea: Ps	100.0
cd00497	224	PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudo	100.0
PRK14589	265	tRNA pseudouridine synthase ACD; Provisional	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
KOG2553	416	consensus Pseudouridylate synthase [Translation, r	100.0
KOG4393	295	consensus Predicted pseudouridylate synthase [RNA	100.0
KOG2554	425	consensus Pseudouridylate synthase [Translation, r	100.0
PF01416	105	PseudoU_synth_1: tRNA pseudouridine synthase; Inte	99.9
PF10105	187	DUF2344: Uncharacterized protein conserved in bact	95.23

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

Probab=100.00  E-value=2.2e-53  Score=370.53  Aligned_cols=187  Identities=27%  Similarity=0.382  Sum_probs=162.1

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      |+|||+ +.+..++.|..+||+.||+||+|+++++||++|||||+|++|+|+|+|++..  .++      ||...     
T Consensus        61 v~hfd~-~~~~~~~~~~~~lN~~Lp~dI~V~~~~~v~~~FhaRfsa~~R~Y~Y~i~~~~--~~~------~~~~~-----  126 (266)
T COG0101          61 VVHFDT-PADRPLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYRYIIYNAP--LRP------PFLAN-----  126 (266)
T ss_pred             EEEEEc-CCcccHHHHHHHHHhcCCCCcEEEEEEECCCCCCCcccccceEEEEEEcCcc--CCC------hhhhc-----
Confidence            799999 6677799999999999999999999999999999999999999999999877  432      22232     


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                              ++|+.+.++|+++|++|++.|+||| ||+|||+..    ...+++.|+|++++.. 
T Consensus       127 ------------------------~~~~~~~~ld~~~m~~aa~~l~G~H-DF~sF~~~~----~~~~s~vRti~~~~v~-  176 (266)
T COG0101         127 ------------------------YVWHVPYPLDLDAMREAAKLLLGTH-DFTSFRKAG----CQSKSPVRTIYRIDVS-  176 (266)
T ss_pred             ------------------------ccccccCcCCHHHHHHHHHHccccc-cchhhccCC----CccCCCeEEEEEEEEE-
Confidence                                    4678888999999999999999999 999999852    2223456666655432 


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecCC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYT  240 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~  240 (250)
                                 ..++++.|+|+|+||||||||+|||+|++||+|+++++++.++|++++|..++|+|||+||||++|.|+
T Consensus       177 -----------~~~~~i~i~i~g~sFL~~mVR~iVg~l~~vg~g~~~~~~i~~ll~~~~r~~~~~~Apa~GL~L~~v~Y~  245 (266)
T COG0101         177 -----------RDGDLIVIDISGNSFLWHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRKLAGPTAPAEGLYLVRVDYP  245 (266)
T ss_pred             -----------ecCCEEEEEEEeChhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhccCcccCCCCCCCCccEEEeeccC
Confidence                       224688999999999999999999999999999999999999999999989999999999999999997


Q ss_pred             CC
Q 044732          241 NF  242 (250)
Q Consensus       241 ~~  242 (250)
                      +.
T Consensus       246 ~~  247 (266)
T COG0101         246 ED  247 (266)
T ss_pred             Cc
Confidence            63

>PRK12434 tRNA pseudouridine synthase A; Reviewed

Probab=100.00  E-value=2.3e-53  Score=369.13  Aligned_cols=184  Identities=22%  Similarity=0.341  Sum_probs=160.1

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      |+||++ +..++++.+..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+++.  .++      ||..+     
T Consensus        62 v~~f~~-~~~~~~~~l~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~--~~~------~f~~~-----  127 (245)
T PRK12434         62 VANFQT-DEKLSEDKIKKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNEK--FHN------VFMRK-----  127 (245)
T ss_pred             EEEEEc-CCCCCHHHHHHHHHccCCCCeEEEEEEECCCCcccccCCCcEEEEEEEccCC--CCC------hhhCC-----
Confidence            689999 6789999999999999999999999999999999999999999999999876  432      23333     


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                              ++|+...++|+++|++||+.|+|+| ||++||+.    +.+.+++.|+|.++... 
T Consensus       128 ------------------------~~~~~~~~ld~~~m~~a~~~~~G~H-DF~~F~~~----~~~~~~~~R~I~~~~v~-  177 (245)
T PRK12434        128 ------------------------YSMHVNEKLDVKAMKEAAKYLVGSH-DFTSFTNA----KSKKKSTVREIYSIDIM-  177 (245)
T ss_pred             ------------------------eEEEeCCCCCHHHHHHHHHHccCCc-CHHhhcCC----CCCCCCCEEEEEEEEEE-
Confidence                                    3566778899999999999999999 99999974    22334566777665432 


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY  239 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y  239 (250)
                                 ++.+++.|+|+|+||||||||+|||+|++||+|++++++|.++|++++|...+++|||+||||++|.|
T Consensus       178 -----------~~~~~~~i~i~g~~FL~~mVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y  245 (245)
T PRK12434        178 -----------EEDGFVQIRVSGNGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDRNQANCTAPASGLYLENVEY  245 (245)
T ss_pred             -----------EeCCEEEEEEEecHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcccCCCccCCCCCEEeEeEC
Confidence                       22358999999999999999999999999999999999999999999988889999999999999998

>PRK14588 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=1.6e-52  Score=368.53  Aligned_cols=189  Identities=25%  Similarity=0.350  Sum_probs=162.7

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      ||||++ +..++++.+..+||+.||+||+|+++++|+++|||||+|++|+|+|+|+++.  .++      ||..+     
T Consensus        61 v~~f~~-~~~~~~~~l~~~LN~~LP~dI~V~~v~~v~~~FhaR~~a~~R~Y~Y~i~~~~--~~~------p~~~~-----  126 (272)
T PRK14588         61 VAHVQT-DTRHSLATIWRGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREYRYVIDCAP--APS------PQLRH-----  126 (272)
T ss_pred             EEEEEc-CCCCCHHHHHHHHHhcCCCCeEEEEEEECCCCcCcccCCCcEEEEEEEcCCC--CCC------hhhcC-----
Confidence            689999 6788999999999999999999999999999999999999999999998776  433      23333     


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                              ++|+.+.++|+++|++||+.|+||| ||++||+.     .+.+++.|+|.++....
T Consensus       127 ------------------------~~~~~~~~lDi~~m~~a~~~f~G~H-DF~~F~~~-----~~~~~~vRtI~~~~~~~  176 (272)
T PRK14588        127 ------------------------QVLHYAGTLDVAAMDAALKLLIGTH-DFAAFTTA-----PQEGSTVRTCYWARCTD  176 (272)
T ss_pred             ------------------------ceEecCCCCCHHHHHHHHHHccCCc-chHhhcCC-----CCCCCCeEEEEEEEEEE
Confidence                                    3566778899999999999999999 99999974     12345778887765432


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecCC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYT  240 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~  240 (250)
                      ..       . .+.+++.|+|+|+||||||||+|||+|++||+|++++++|.++|++++|..++++|||+||||++|.|+
T Consensus       177 ~~-------~-~~~~~i~~~i~g~~FL~~mVR~mVg~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~  248 (272)
T PRK14588        177 TE-------W-FGRPLLAIEVAANAFLQHMVRNIVGTLLLVGRGRMTVDQFGAVLASRDRRLAGPTAPAHGLYLTAVRYP  248 (272)
T ss_pred             cc-------c-CCCCEEEEEEEEchhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccCCCCCCCCCcEEeeEecC
Confidence            10       1 133689999999999999999999999999999999999999999999988999999999999999997


Q ss_pred             C
Q 044732          241 N  241 (250)
Q Consensus       241 ~  241 (250)
                      +
T Consensus       249 ~  249 (272)
T PRK14588        249 P  249 (272)
T ss_pred             c
Confidence            5

>PRK14586 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=6.9e-52  Score=359.89  Aligned_cols=184  Identities=26%  Similarity=0.402  Sum_probs=157.7

Q ss_pred             CeEEecCCCC-CChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhccccc
Q 044732            1 MIILDTWRKD-VKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTS   79 (250)
Q Consensus         1 ~~~f~~~~~~-~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~   79 (250)
                      |+||++ +.. ++++.|..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+.+.  .++      ||..+    
T Consensus        61 v~~f~~-~~~~~~~~~l~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~--~~~------~f~~~----  127 (245)
T PRK14586         61 VIAFNC-PNDRMTEEDIKNAMNANLPDDIYVKKVFEVPKNFHPRFDAKKRIYHYFILTSK--EKN------VFLRK----  127 (245)
T ss_pred             EEEEEe-cCCcCCHHHHHHHHHccCCCCeEEEEEEECCCCcCcccCCCcEEEEEEEecCC--CCC------hhhCC----
Confidence            689999 555 8999999999999999999999999999999999999999999998766  332      33343    


Q ss_pred             cccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeee
Q 044732           80 NNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARAT  159 (250)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~  159 (250)
                                               ++|+.+.++|+++|++||+.|+||| ||++| +.    +.+.+++.|+|+++...
T Consensus       128 -------------------------~~~~~~~~ld~~~m~~a~~~l~G~H-DF~~F-~~----~~~~~~~vR~I~~~~~~  176 (245)
T PRK14586        128 -------------------------YVWWFPYELDLEAMRKAAKYLEGEH-DFTSF-KT----GSDERNPVRTIYRIRIL  176 (245)
T ss_pred             -------------------------ceEEeCCCCCHHHHHHHHHHccCcc-hHHhh-cC----CCCCCCCcEEEEEEEEE
Confidence                                     3566677899999999999999999 99999 42    22334567777665431


Q ss_pred             ccccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecC
Q 044732          160 EAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY  239 (250)
Q Consensus       160 vr~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y  239 (250)
                                 ....+++.|+|+|+||||||||+|||+|++||+|++++++|.++|++++|..++++|||+||||++|.|
T Consensus       177 -----------~~~~~~i~~~i~g~~FL~~mVR~mvg~l~~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~v~f  245 (245)
T PRK14586        177 -----------RLKKDLILIRVEGRSFLRRMVRNIVGALVKVGLGQWEPEKIKEVLEARDRSKAAGTAPAHGLYLYKVLF  245 (245)
T ss_pred             -----------EccCCEEEEEEEechhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcccCCCccCCCCCEEeEeEC
Confidence                       112358999999999999999999999999999999999999999999998889999999999999986

>PRK00021 truA tRNA pseudouridine synthase A; Validated

Probab=100.00  E-value=1.7e-51  Score=357.70  Aligned_cols=184  Identities=29%  Similarity=0.395  Sum_probs=159.5

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      |+||++ +..++++.+..+||+.||+||+|+++.+||++|||||+|++|+|+|+|+.+.  .++      ||..+     
T Consensus        61 vv~~~~-~~~~~~~~~~~~lN~~Lp~dI~V~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~~--~~~------~~~~~-----  126 (244)
T PRK00021         61 VAHFDT-PAPRPPEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRYRYRIYNRP--ARP------PFLRG-----  126 (244)
T ss_pred             EEEEEe-CCCCCHHHHHHHHHhcCCCCEEEEEeEecCCCcCcCcCCCceEEEEEEecCC--CCC------hhhCC-----
Confidence            689999 6789999999999999999999999999999999999999999999999876  332      22333     


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                              ++|+....+|+++|++|++.|+||| ||+|||+.    +.+.+++.|+|.++... 
T Consensus       127 ------------------------~~~~~~~~ld~~~m~~a~~~~~G~H-dF~~F~~~----~~~~~~~~R~I~~~~v~-  176 (244)
T PRK00021        127 ------------------------YVWHYPYPLDVDAMNEAAQYLLGEH-DFTSFRAS----GCQSKSPVRTIYEADVT-  176 (244)
T ss_pred             ------------------------cEEEeCCCCcHHHHHHHHHHhcCce-eeeeeeCC----CCCCCCCeEEEEEEEEE-
Confidence                                    3566777899999999999999999 99999863    23345567777665432 


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY  239 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y  239 (250)
                                 ++.+++.|+|+|+||||||||+|||+|+++|+|++++++|+++|+++++...+++|||+||+|++|.|
T Consensus       177 -----------~~~~~~~i~i~g~sFL~~qVR~mvg~l~~vg~g~~~~~~i~~~L~~~~~~~~~~~APa~GL~L~~v~Y  244 (244)
T PRK00021        177 -----------REGDFIVFDISANGFLHNMVRNIVGTLLEVGKGKRPPEDIKELLEAKDRTLAGPTAPAEGLYLVEVDY  244 (244)
T ss_pred             -----------EcCCEEEEEEEEchhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccCCCccCCCCCEEeeeEC
Confidence                       22368999999999999999999999999999999999999999998887789999999999999998

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

Probab=100.00  E-value=6.4e-51  Score=353.19  Aligned_cols=184  Identities=29%  Similarity=0.388  Sum_probs=158.9

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      |+||++ +..++++.++.+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+.+.  .++      ||..+     
T Consensus        56 vv~~~~-~~~~~~~~~~~~lN~~Lp~dI~v~~i~~v~~~F~aR~~a~~R~Y~Y~i~~~~--~~~------~~~~~-----  121 (239)
T cd02570          56 VAHFDT-PSEIPLEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRP--VPS------PFLRR-----  121 (239)
T ss_pred             EEEEEE-CCCCCHHHHHHHHHccCCCCEEEEEEEECCCCcCcccCCCceEEEEEEccCC--CCC------hhhCC-----
Confidence            689999 6788999999999999999999999999999999999999999999999875  322      23333     


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                              ++|+...++|+++|++||+.|+|+| ||+|||+..    ...+++.|+|.++... 
T Consensus       122 ------------------------~~~~~~~~~d~~~m~~a~~~f~G~H-dF~~F~~~~----~~~~~~~R~I~~~~v~-  171 (239)
T cd02570         122 ------------------------YVWHVPRPLDIEAMQEAAKLLLGTH-DFSSFRAAG----CQSKSTVRTIYRADVY-  171 (239)
T ss_pred             ------------------------eEEEeCCCCCHHHHHHHHHHccCCc-chhhhCCCC----CCCCCCeEEEEEEEEE-
Confidence                                    3556677899999999999999999 999999742    2234566777665432 


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY  239 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y  239 (250)
                                 ++.+++.|+|+|+||||||||+|||+|+++|+|++++++|+++|+++++...+++|||+||||++|.|
T Consensus       172 -----------~~~~~~~i~i~g~sFL~~qVR~mvg~ll~vg~g~~~~~~i~~~l~~~~~~~~~~~APa~GL~L~~v~Y  239 (239)
T cd02570         172 -----------REGDLIVFEIRANGFLYHMVRNIVGTLLEVGRGKLSPEDIKEILEAKDRTAAGPTAPAHGLYLVKVEY  239 (239)
T ss_pred             -----------EeCCEEEEEEEEcHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccCCCCcCCCCCEEeeeEC
Confidence                       23368999999999999999999999999999999999999999998887779999999999999998

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=1e-49  Score=342.75  Aligned_cols=168  Identities=26%  Similarity=0.413  Sum_probs=146.9

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      |+||++ +..++++.|..+||+.||+||+|+++++|+++|||||+|++|+|+|+|+.+.                     
T Consensus        60 v~~f~~-~~~~~~~~~~~~lN~~Lp~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~---------------------  117 (227)
T TIGR00071        60 VISFDT-PKEIPDNKLNAKLNALLPPDIRVKALAPVNDNFHARFSASKRHYRYILYNHR---------------------  117 (227)
T ss_pred             EEEEEe-cCCCCHHHHHHHHHccCCCCEEEEEEEeCCCCcCCCCCCCcEEEEEEEccCc---------------------
Confidence            689999 6789999999999999999999999999999999999999999999998432                     


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                                 +...++|+++|++|++.|+||| ||++||+.    +.+.+++.|+|.++..  
T Consensus       118 ---------------------------~~~~~ld~~~m~~a~~~~~G~H-DF~~F~~~----~~~~~~~~R~i~~~~v--  163 (227)
T TIGR00071       118 ---------------------------HYYSPLDLEKMRAAAKQLLGKH-DFSNFSKA----KSKSRSPIRTISDIKV--  163 (227)
T ss_pred             ---------------------------ccCCCCCHHHHHHHHHHccCcc-cHHHhcCC----CCCCCCCeEEEEEEEE--
Confidence                                       0123589999999999999999 99999974    2233456666665443  


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeee
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCL  234 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L  234 (250)
                                .++.+++.|+|+|+||||||||+|||+|++||+|++++++|+++|++++|..++++|||+||||
T Consensus       164 ----------~~~~~~~~i~i~g~~FL~~mVR~mvg~l~~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L  227 (227)
T TIGR00071       164 ----------SESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLAPTTAPANGLYL  227 (227)
T ss_pred             ----------EEcCCEEEEEEEecHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccCCCCCCCCCCcC
Confidence                      2344689999999999999999999999999999999999999999998888899999999998

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.

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

Probab=100.00  E-value=3e-49  Score=344.98  Aligned_cols=176  Identities=23%  Similarity=0.333  Sum_probs=147.0

Q ss_pred             CeEEecCCCCCChh------------------HHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCC
Q 044732            1 MIILDTWRKDVKPS------------------DIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGEN   62 (250)
Q Consensus         1 ~~~f~~~~~~~~~~------------------~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~   62 (250)
                      |+||++ .+.++++                  .+..+||+.||+||+|+++++|+++|||||+|++|+|+|+|+.+    
T Consensus        61 v~~f~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~----  135 (256)
T cd02569          61 VISLDV-RSNLKPEDGLDPSTDVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSARFSCVSRTYRYFFPKG----  135 (256)
T ss_pred             EEEEEe-cCCCCccccccccccccccccchHHHHHHHHHhhCCCCcEEEEEEECCCCcCCCccCCceEEEEEecCC----
Confidence            689999 5556554                  68999999999999999999999999999999999999999632    


Q ss_pred             CccccchhhhhhccccccccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhcccccccccccccccccc
Q 044732           63 REQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKAS  142 (250)
Q Consensus        63 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~  142 (250)
                                                                       ++|+++|++||+.|+||| ||++||+...  
T Consensus       136 -------------------------------------------------~ldi~~m~~a~~~f~G~H-DF~~F~~~~~--  163 (256)
T cd02569         136 -------------------------------------------------DLDIELMRKAAKLLLGEH-DFRNFCKMDV--  163 (256)
T ss_pred             -------------------------------------------------CCCHHHHHHHHHHhhCCc-chHHHhccCc--
Confidence                                                             278999999999999999 9999997421  


Q ss_pred             ccCCCCceeEEEeeeeeccccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCC
Q 044732          143 RNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRA  222 (250)
Q Consensus       143 ~~~~~~~~r~i~~~~~~vr~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~  222 (250)
                      ..+.+++.|+|.++......      ....+.+++.|+|+|+||||||||+|||+|++||+|++++++|+++|++++|..
T Consensus       164 ~~~~~~~~RtI~~~~v~~~~------~~~~~~~~~~~~i~g~~FL~~mVR~mvg~ll~vg~G~~~~~~i~~~L~~~~r~~  237 (256)
T cd02569         164 ANQVTNYVRRVLSAEVEPVD------QHPDGDGLYYFEVRGSAFLWHQVRCMMAVLFLIGQGLEPPSVISQLLDVEKNPR  237 (256)
T ss_pred             ccCCCCCceEEEEEEEEEcc------CCCCCCcEEEEEEEEcHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhCccccC
Confidence            11234566777665542100      000123689999999999999999999999999999999999999999998887


Q ss_pred             CCC--CCCCCCeeeeeecC
Q 044732          223 TAP--PAPPEGLCLVDVGY  239 (250)
Q Consensus       223 ~~~--~APa~GL~L~~V~Y  239 (250)
                      +++  +|||+||+|++|.|
T Consensus       238 ~~~~~~Ap~~GL~L~~v~~  256 (256)
T cd02569         238 KPQYTMASEVPLVLYDCGF  256 (256)
T ss_pred             CCCcCcCCCCCcEEEEeeC
Confidence            777  99999999999987

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.

>cd02866 PseudoU_synth_TruA_Archea PseudoU_synth_archea: Pseudouridine synthase,

Probab=100.00  E-value=3.3e-49  Score=338.17  Aligned_cols=162  Identities=29%  Similarity=0.486  Sum_probs=142.0

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      |+||++ +..+    +..+||+.||+||+|+++.+||++||||++|++|+|+|+|+..                      
T Consensus        60 v~~f~~-~~~~----~~~~lN~~LP~dI~v~~~~~v~~~F~ar~~a~~r~Y~Y~i~~~----------------------  112 (221)
T cd02866          60 VVAFET-EKEL----TPPAINNALPKDIRVWAWAKVPEDFHPRRDARRRYYRYYLGAE----------------------  112 (221)
T ss_pred             EEEEEe-CcHH----HHHHHHhhCCCCEEEEEEEEeCCCCCCCccCCeEEEEEEECCC----------------------
Confidence            689999 4333    8999999999999999999999999999999999999999632                      


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                                     ++|+++|++||+.|+|+| ||++||+..    .  .++.|+|.++... 
T Consensus       113 -------------------------------~ld~~~m~~a~~~~~G~H-DF~~F~~~~----~--~~~~R~I~~~~~~-  153 (221)
T cd02866         113 -------------------------------DYDVEAMAEAAKKLIGTH-DFSNFSKRD----G--RDPVRTIERIEIR-  153 (221)
T ss_pred             -------------------------------cCCHHHHHHHHHHhcCCc-CHHHhhCCC----C--CCCcEEEEEEEEE-
Confidence                                           268999999999999999 999999741    1  2456766655432 


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY  239 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y  239 (250)
                                 ++.+++.|+|+|+||||||||+|||+|++||+|++++++|+++|+++++...+++|||+||||++|.|
T Consensus       154 -----------~~~~~~~~~i~g~~FL~~mVR~mvg~ll~vg~g~~~~~~i~~~l~~~~~~~~~~~APa~GL~L~~v~Y  221 (221)
T cd02866         154 -----------ENGEFLVIDVVGESFLWNMVRRIVGALSLVGKGKRENEWVDKLLDGEFRKKDGVPAPPEGLILVDVKY  221 (221)
T ss_pred             -----------EcCCEEEEEEEEcHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhCCCcccCCCCCCCCCcEEEEeeC
Confidence                       23468999999999999999999999999999999999999999999887778899999999999998

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.

>cd00497 PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudouridine synthase, TruA family

Probab=100.00  E-value=4.9e-49  Score=337.85  Aligned_cols=166  Identities=28%  Similarity=0.412  Sum_probs=143.6

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      |+||++ +..++  .+..+||+.||+||+|+++++|+++||||++|++|+|+|+|+.+                      
T Consensus        58 v~~~~~-~~~~~--~~~~~lN~~Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~----------------------  112 (224)
T cd00497          58 VVSLET-RSKLK--PYPDILNGLLPKDIRVLAWAPVPEDFHARFSCVSRTYRYYFPGG----------------------  112 (224)
T ss_pred             EEEEEE-CCCcH--HHHHHHHhhCCCCcEEEEEEEeCCCCCCCcccCeEEEEEEECCC----------------------
Confidence            689999 55544  89999999999999999999999999999999999999999632                      


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                                     ++|+++|++||+.|+||| ||+|||+..    ...+++.|+|.++... 
T Consensus       113 -------------------------------~~d~~~m~~a~~~f~G~H-DF~~F~~~~----~~~~~~~RtI~~~~v~-  155 (224)
T cd00497         113 -------------------------------DLDIEAMREAAKLLLGTH-DFRNFCKKD----GRKKNPVRTIISAEVE-  155 (224)
T ss_pred             -------------------------------CcCHHHHHHHHHHccCcc-cHHHhcCCC----CCCCCCeEEEEEEEEE-
Confidence                                           268999999999999999 999999742    2224566776655432 


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCC-CCCCCCeeeeeecC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAP-PAPPEGLCLVDVGY  239 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~-~APa~GL~L~~V~Y  239 (250)
                                 +..+++.|+|+|+||||||||+|||+|++||+|++++++|.++|+++++...++ +|||+||||++|.|
T Consensus       156 -----------~~~~~~~i~i~g~sFL~~mVR~mvg~ll~vg~g~~~~~~i~~~l~~~~~~~~~~~~APa~GL~L~~V~Y  224 (224)
T cd00497         156 -----------EVDDFYVFEVKGKSFLWHQVRRIVAALFLVGQGLEPPSIISRLLDEEKRPSKPQYPAPPEPLVLWDCKY  224 (224)
T ss_pred             -----------ecCCEEEEEEEEcHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcccCCCCcCCCCCcEEeeeeC
Confidence                       223689999999999999999999999999999999999999999988776544 99999999999998

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

>PRK14589 tRNA pseudouridine synthase ACD; Provisional

Probab=100.00  E-value=1.7e-48  Score=341.20  Aligned_cols=164  Identities=27%  Similarity=0.434  Sum_probs=143.8

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      |+||++ +.   ++.+..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+..                      
T Consensus        64 v~~f~~-~~---~~~~~~~lN~~LP~dI~V~~~~~v~~~FhAR~~a~~R~Y~Y~i~~~----------------------  117 (265)
T PRK14589         64 VLAFST-HK---PERAVEALNGQLPPDIWCTGWAEVPESFHPRYDAISRTYRYYFSRP----------------------  117 (265)
T ss_pred             EEEEEe-CC---hHHHHHHHHhhCCCCeEEEEEEEcCCCCCcccCCceeEEEEEEecC----------------------
Confidence            689999 43   7889999999999999999999999999999999999999999521                      


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                                     ++|+++|++||+.|+||| ||+|||+.    .  .+++.|+|.++... 
T Consensus       118 -------------------------------~lD~~~m~~a~~~f~G~H-DF~~F~~~----~--~~~~vRtI~~i~v~-  158 (265)
T PRK14589        118 -------------------------------PSDINAMRDAAGEFIGTH-DFSCFARV----E--GKSPVRTILRIRVF-  158 (265)
T ss_pred             -------------------------------ccHHHHHHHHHHHccCCc-cHHHHhcc----C--CCCCeEEEEEEEEE-
Confidence                                           268999999999999999 99999974    1  34566777665432 


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecCC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYT  240 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~  240 (250)
                                 .+.+++.|+|+|+||||||||+|||+|++||+|++++++|+++|+++++. .+++|||+||||++|.|+
T Consensus       159 -----------~~~~~~~~~i~G~~FL~~mVR~mVG~ll~vg~G~~~~~~i~~~L~~~~r~-~~~~APa~GL~L~~V~Y~  226 (265)
T PRK14589        159 -----------SDGGFPVFEVTAQSFLWHMVRCMAGALLQIGEGEMEPDDIERLLSGPCKR-KVKPAPAEGLVLWDVDCG  226 (265)
T ss_pred             -----------EeCCEEEEEEEechhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhCcCCC-CCCccCCCCcEEeeeecC
Confidence                       22368899999999999999999999999999999999999999998875 478999999999999997


Q ss_pred             C
Q 044732          241 N  241 (250)
Q Consensus       241 ~  241 (250)
                      .
T Consensus       227 ~  227 (265)
T PRK14589        227 L  227 (265)
T ss_pred             C
Confidence            4

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

Probab=100.00  E-value=1.9e-47  Score=332.48  Aligned_cols=175  Identities=23%  Similarity=0.360  Sum_probs=146.4

Q ss_pred             CeEEecCCCCCC-----hhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhc
Q 044732            1 MIILDTWRKDVK-----PSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVEN   75 (250)
Q Consensus         1 ~~~f~~~~~~~~-----~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~   75 (250)
                      |+||++ +..++     ++++..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+...                
T Consensus        66 v~~~~~-~~~~~~~~~~~~~~~~~lN~~Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~~----------------  128 (245)
T cd02568          66 VVSLKV-IIDDPEGLGIGEDLVEKLNSHLPEDIRVFGITRVTKSFNARKACDSRTYEYLLPTFA----------------  128 (245)
T ss_pred             EEEEEE-eccccccccchHHHHHHHHccCCCceEEEEEEcCCCCCCcchhhhcceeEEECCccc----------------
Confidence            689999 56676     89999999999999999999999999999999999999999996322                


Q ss_pred             cccccccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEe
Q 044732           76 FHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYH  155 (250)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~  155 (250)
                                                      .    +|+++|++|++.|+|+| ||++||+..   ....+++.|+|.+
T Consensus       129 --------------------------------~----~d~~~m~~a~~~~~G~H-dF~~F~~~~---~~~~~~~~R~i~~  168 (245)
T cd02568         129 --------------------------------L----ETLDRFNEILKLYVGTH-NFHNFTVRK---KFEDPSANRFIIS  168 (245)
T ss_pred             --------------------------------H----hHHHHHHHHHHHhhCcc-ccccCcccc---cccCCCceeEEEE
Confidence                                            0    58999999999999999 999999742   1123456677766


Q ss_pred             eeeeccccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeee
Q 044732          156 ARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLV  235 (250)
Q Consensus       156 ~~~~vr~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~  235 (250)
                      +.......      ...+.+++.|+|+|+||||||||+|||+|++||+|++++++|+++|+.+ +...+|+|||+||||+
T Consensus       169 ~~~~~~~~------~~~~~~~i~i~i~g~~FL~~mVR~mvg~l~~vg~g~~~~~~i~~~L~~~-~~~~~~~APa~GL~L~  241 (245)
T cd02568         169 FYVSEPFV------IEEGLEWVSIEIHGQSFMLHQIRKMIGLAIAIVRGGAPESLIDLSFNKA-KRIIIPLAPGLGLLLE  241 (245)
T ss_pred             EEEeccee------ecCCccEEEEEEEechHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhccc-ccccccCCCCcceeEe
Confidence            54321000      0013468999999999999999999999999999999999999999964 4457899999999999


Q ss_pred             eecC
Q 044732          236 DVGY  239 (250)
Q Consensus       236 ~V~Y  239 (250)
                      +|.|
T Consensus       242 ~v~y  245 (245)
T cd02568         242 YPHF  245 (245)
T ss_pred             cccC
Confidence            9988

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=6.9e-46  Score=322.58  Aligned_cols=153  Identities=24%  Similarity=0.388  Sum_probs=131.4

Q ss_pred             HHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhccccccccCccCCCcccccccc
Q 044732           17 EDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSNNVGKQSNGCYENIENL   96 (250)
Q Consensus        17 ~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (250)
                      ..+||+.||+||+|+++.+|+++||||+ |++|+|+|+|+..                                      
T Consensus        61 ~~~LN~~LP~dI~V~~~~~V~~~FhaR~-a~~R~Y~Y~i~~~--------------------------------------  101 (256)
T PRK14587         61 LGYVNSKLPRGVWAWAVAEVPEGFNPRR-AKRRRYLYVAPHW--------------------------------------  101 (256)
T ss_pred             HHHHHhcCCCCeEEEEEEECCCCcCcCc-ccceEEEEEEccC--------------------------------------
Confidence            5799999999999999999999999997 9999999998410                                      


Q ss_pred             ccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCC-ceeEEEeeeeeccccCCCcccCCCCce
Q 044732           97 LINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPP-TECFIYHARATEAILPCPVNDHGEGRK  175 (250)
Q Consensus        97 ~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~-~~r~i~~~~~~vr~i~~~~~~~~~~~~  175 (250)
                                     ++|+++|++|++.|+|+| ||++||+..    .+.++ +.|+|.++...            ..++
T Consensus       102 ---------------~lDi~~m~~aa~~l~G~H-DF~~F~~~~----~~~~~~~vRtI~~i~v~------------~~~~  149 (256)
T PRK14587        102 ---------------GEDVEAMREAAELLAGTH-DYSSFIQRR----GEKATPTVTTVYEIGVE------------LRGD  149 (256)
T ss_pred             ---------------cchHHHHHHHHHHhcCCc-ChHHhccCC----CCCCCCCEEEEEEEEEE------------EeCC
Confidence                           279999999999999999 999999742    22233 56666655432            1235


Q ss_pred             EEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecCCC
Q 044732          176 VMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTN  241 (250)
Q Consensus       176 ~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~~  241 (250)
                      ++.|+|+|+||||||||+|||+|++||+|++++++|.++|+.+ +..++++|||+||||++|.|++
T Consensus       150 ~i~i~i~g~sFL~~mVR~mVG~Ll~Vg~G~~~~~~i~~~L~~~-r~~~~~~APa~GL~L~~V~Y~~  214 (256)
T PRK14587        150 LIYLYFVGRGFRNKMIRKMAWAILAAGRGVLSRRDIAELLERP-RPGAVPSAPAEGLVLLDIEYDV  214 (256)
T ss_pred             EEEEEEEechhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcC-cccCCCCCCCCCCEEeeeccCc
Confidence            8899999999999999999999999999999999999999954 6678999999999999999974

>PLN03078 Putative tRNA pseudouridine synthase; Provisional

Probab=100.00  E-value=4.5e-41  Score=311.90  Aligned_cols=200  Identities=20%  Similarity=0.260  Sum_probs=144.8

Q ss_pred             CeEEecCCCC-----CC--hhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhh
Q 044732            1 MIILDTWRKD-----VK--PSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEV   73 (250)
Q Consensus         1 ~~~f~~~~~~-----~~--~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~   73 (250)
                      ||||+++ .+     .+  ...|..+||++||+||||+++.+|+++|||||+|++|+|+|+|++......          
T Consensus       142 Vvsf~l~-~p~~~~~~d~~~~~L~~~LN~~LP~DIRVl~v~~V~~~FhAR~sc~sRtY~Y~iP~~~~~~k----------  210 (513)
T PLN03078        142 MISLKME-IPENAWKDDPDGIALAKFINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSYLLPAEVIGIK----------  210 (513)
T ss_pred             EEEEecc-CcchhccccchHHHHHHHHHhcCCCCeEEEEEEECCCCcCCCCCCCceEEEEEEccccccCC----------
Confidence            6899973 21     12  236889999999999999999999999999999999999999997431011          


Q ss_pred             hccccccccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccC-CC-----
Q 044732           74 ENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNI-GP-----  147 (250)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~-~~-----  147 (250)
                      ..+..                         .+.|     .|+++|++|++.|+||| ||||||...+..... ++     
T Consensus       211 ~~f~~-------------------------~~~~-----~dI~kMneAl~~fiGtH-DFhNFT~r~~y~~~~~~~~~~~~  259 (513)
T PLN03078        211 SGFSS-------------------------EEID-----EHISEFNSILNGFEGEH-PFHNYTARSKYRKKLPGKHKQRN  259 (513)
T ss_pred             Cccch-------------------------hhhH-----HHHHHHHHHHHhccccc-CcccccCCCccCccccccccccc
Confidence            11110                         0111     28999999999999999 999999864321110 00     


Q ss_pred             -Cce---------------------------------------------------------eEEEee-------eeeccc
Q 044732          148 -PTE---------------------------------------------------------CFIYHA-------RATEAI  162 (250)
Q Consensus       148 -~~~---------------------------------------------------------r~i~~~-------~~~vr~  162 (250)
                       ...                                                         |.+...       ....|.
T Consensus       260 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wl~e~d~~d~i~~s~~R~  339 (513)
T PLN03078        260 GAVSRRAKSSKEMSSSESEENHGEISEEDEEDLSFSSIPSGSSDENEDILKFQSSQVQIRARWLHEPDETDRISASHFRK  339 (513)
T ss_pred             cccccccccccccccccccccccccccchhhhhccccccccccccccccccccccchhhhhhhccCCccccccchhheEE
Confidence             000                                                         000000       011223


Q ss_pred             cCCCcc---cCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecC
Q 044732          163 LPCPVN---DHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY  239 (250)
Q Consensus       163 i~~~~~---~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y  239 (250)
                      |..++.   ....|.+++.|+|.|+|||+||||+|||++++|++|.++++.|...|....+ ...|+||+.||+|++|.|
T Consensus       340 I~~~~~~~~~~~~g~~fv~i~I~GqSFmlhQIRKMIG~~~aV~rg~~~~~~i~~~L~~~~r-~~~P~AP~~GL~L~~~~F  418 (513)
T PLN03078        340 IFRCSCGKLEKSLGFDFVELSIWGESFMLHQIRKMVGTAVAVKRELLPRDIIRLSLTKFSR-IVLPLAPSEVLILRGNSF  418 (513)
T ss_pred             EEEeecCCccccCCceEEEEEEEehhHHHHHHHHHHHHHHHHHhccCCHHHHHHHhccccc-cccccCCCcceEEEeeec
Confidence            332221   1224678999999999999999999999999999999999999999987655 469999999999999999


Q ss_pred             CCCC
Q 044732          240 TNFD  243 (250)
Q Consensus       240 ~~~~  243 (250)
                      +.+.
T Consensus       419 ~~yn  422 (513)
T PLN03078        419 SVRK  422 (513)
T ss_pred             cccc
Confidence            8653

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

Probab=100.00  E-value=4.7e-38  Score=282.37  Aligned_cols=221  Identities=19%  Similarity=0.285  Sum_probs=156.4

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchh-------hhh
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSE-------VEV   73 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~-------~~~   73 (250)
                      ||+..+   .++...++..||..||++||||++.+|+++|++|..|.+|+|+|.||+..+..+.|...-.       -+.
T Consensus       105 viSlK~---~~~~~~lv~~lN~~Lp~~IRv~~v~r~~k~F~pr~~CdsR~YeYllPtfal~~p~~~~~~~~~~~~~~e~~  181 (416)
T KOG2553|consen  105 VISLKL---ELDDPELVEKLNEILPEQIRVWGVKRVTKSFNPRKQCDSRTYEYLLPTFALAPPKPSSLLEVDIQYDKEFE  181 (416)
T ss_pred             eeEEEE---eeCcHHHHHHHhhhCCcceEEEEEEecCCCCCccccccceeEEEecceeeecCCCCccHHHhhhhhhhhhh
Confidence            344554   3455889999999999999999999999999999999999999999998854443320000       000


Q ss_pred             hccccccccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEE
Q 044732           74 ENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFI  153 (250)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i  153 (250)
                      ..++..  +...   +.+.-+..|- .   -..-..-.+-+++.++++++.++||| ||||||...   ....++..|+|
T Consensus       182 ~~f~~~--~~~~---~~~~~s~~~~-~---~~~~yr~s~~~l~~~~~~ls~Y~Gth-nFHNfT~~~---~~~dpss~R~I  248 (416)
T KOG2553|consen  182 KEFWNT--YPLS---AKERLSGQDR-K---TESGYRLSEEKLEVFNTILSKYVGTH-NFHNFTTGK---DFTDPSSNRFI  248 (416)
T ss_pred             hhhccc--cchh---hhhhhccccc-c---cccceeeCHHHHHHHHHHHHHhhccc-ccceecccC---CCCCcccccee
Confidence            111100  0000   0000000000 0   00001123346789999999999999 999999852   23456788999


Q ss_pred             EeeeeeccccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCee
Q 044732          154 YHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLC  233 (250)
Q Consensus       154 ~~~~~~vr~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~  233 (250)
                      .++...  +...++   .+|.+||.+.|+|+|||.||||+|||.+|.|.++.++.+.|+..+++. ....+|.||+.||+
T Consensus       249 ~s~~~~--~pfv~~---~~~~e~V~i~i~GQSFMLHQIRKMVglav~i~R~~~p~~~i~~af~~~-~ri~IP~AP~~gLl  322 (416)
T KOG2553|consen  249 KSFTVS--EPFVIN---DEGVEFVKIKIHGQSFMLHQIRKMVGLAVLIVRSGAPASTIQRAFNKE-HKINIPKAPGEGLL  322 (416)
T ss_pred             eEEEec--Ccceec---cCCceEEEEEEEcchhHHHHHHHHHHHHHHHHhcCCCHHHHHHhhCCC-ccccccCCCcceEE
Confidence            876432  221110   257799999999999999999999999999999999999999999844 45679999999999


Q ss_pred             eeeecCCCCC
Q 044732          234 LVDVGYTNFD  243 (250)
Q Consensus       234 L~~V~Y~~~~  243 (250)
                      |.++.|+.++
T Consensus       323 L~~~~F~~yn  332 (416)
T KOG2553|consen  323 LEEPHFESYN  332 (416)
T ss_pred             eecccccccc
Confidence            9999998654

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

Probab=100.00  E-value=3e-34  Score=243.35  Aligned_cols=193  Identities=24%  Similarity=0.282  Sum_probs=151.8

Q ss_pred             CeEEecC-CCCCChhHHHHHHHhhC---CCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcc
Q 044732            1 MIILDTW-RKDVKPSDIEDAINSAA---PGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENF   76 (250)
Q Consensus         1 ~~~f~~~-~~~~~~~~l~~~lN~~L---P~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~   76 (250)
                      ++|++++ .+-........++|..|   |.||+|+++..||.+|||||+|.+|+|.|+|.++.  .+.+         .+
T Consensus        67 aa~~~vpr~sg~~~~~~~~a~nt~l~~k~gdirV~dv~~Vps~FhaR~sassRtY~YRla~g~--d~l~---------~f  135 (295)
T KOG4393|consen   67 AAHYIVPRFSGSQQQAKDRAVNTVLQRKDGDIRVIDVRCVPSNFHARYSASSRTYFYRLASGS--DPLS---------IF  135 (295)
T ss_pred             eEEEEeecccCCcHHHHHHHHhccccCCCCceEEEEeeecCcchhheecccceeEEEEeecCC--CccC---------hh
Confidence            4788884 22366778888999988   34999999999999999999999999999999865  3221         22


Q ss_pred             ccccccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEee
Q 044732           77 HTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHA  156 (250)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~  156 (250)
                      ..                         .++|+.+..|+.-+|++|+++|+|+| ||.+|++..    +....+.      
T Consensus       136 ER-------------------------d~cW~lp~~lna~kmqeaa~lf~G~h-dfsaf~~at----s~~y~P~------  179 (295)
T KOG4393|consen  136 ER-------------------------DRCWHLPEELNARKMQEAAPLFEGSH-DFSAFTEAT----STVYFPS------  179 (295)
T ss_pred             hh-------------------------cccccCCcccCHHHHHhhhhhhccch-hhhhhhcCC----CCCCCCc------
Confidence            11                         25888899999999999999999999 999998853    1111222      


Q ss_pred             eeeccccCCCcc-----------cCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCc----C
Q 044732          157 RATEAILPCPVN-----------DHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCR----R  221 (250)
Q Consensus       157 ~~~vr~i~~~~~-----------~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r----~  221 (250)
                       .|.|.++...+           .-..-.+++.++++++||||.|||+|++.||.+|.+.++..++..+|+.+++    +
T Consensus       180 -~t~rr~sv~~~g~~~a~~~~~~~e~~~~~~~nve~e~~gflyrQvRrm~a~LV~~g~~al~~~qv~~iLe~~~~~~l~k  258 (295)
T KOG4393|consen  180 -ITERRLSVLNNGDPLACSNQPETEGVTTNVGNVEGETEGFLYRQVRRMRAYLVTAGSRALLYHQVLYILEVRDIVGLLK  258 (295)
T ss_pred             -ccceeeeecccCCccccccCCccccceeeeEEEEEEecchHHHHHHhhheeeeeecccccchhhhhhhhhccchhhhhh
Confidence             22233332210           0011236889999999999999999999999999999999999999999987    3


Q ss_pred             CCCCCCCCCCeeeeeecCCC
Q 044732          222 ATAPPAPPEGLCLVDVGYTN  241 (250)
Q Consensus       222 ~~~~~APa~GL~L~~V~Y~~  241 (250)
                      ..++.|||+||+|..|.|.+
T Consensus       259 ~~~~vapphglfL~sv~Y~n  278 (295)
T KOG4393|consen  259 CVGTVAPPHGLFLSSVEYVN  278 (295)
T ss_pred             ccCCCCCCccceeeeEEech
Confidence            56899999999999999986

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

Probab=100.00  E-value=2.7e-34  Score=252.70  Aligned_cols=160  Identities=21%  Similarity=0.281  Sum_probs=129.3

Q ss_pred             hHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhccccccccCccCCCccccc
Q 044732           14 SDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSNNVGKQSNGCYENI   93 (250)
Q Consensus        14 ~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (250)
                      -.....||+.||+||||.++..||++|+|||+|..|+|+|+++-+                                   
T Consensus       158 i~Y~~mLN~vLP~dIRi~awapvp~~FsARFsC~~RtYrY~F~k~-----------------------------------  202 (425)
T KOG2554|consen  158 IPYVHMLNRVLPPDIRIVAWAPVPPTFSARFSCVQRTYRYYFPKK-----------------------------------  202 (425)
T ss_pred             ccHHHHHhccCCCcceEEEEecCCCCccceeehhhceeeEeccCC-----------------------------------
Confidence            346789999999999999999999999999999999999999722                                   


Q ss_pred             cccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeeccccCCCccc-CCC
Q 044732           94 ENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVND-HGE  172 (250)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~vr~i~~~~~~-~~~  172 (250)
                                        +|||++|++||..|+|+| ||+|||+.+.  .+...+.          +|+|.+..+. +.+
T Consensus       203 ------------------dLdI~~M~kAA~l~vGe~-DFrNFCK~D~--~n~vtny----------~Rti~s~kV~~~~~  251 (425)
T KOG2554|consen  203 ------------------DLDIDRMSKAASLLVGEH-DFRNFCKIDV--SNGVTNY----------ERTILSAKVEDVGQ  251 (425)
T ss_pred             ------------------CcCHHHHHHHHHHHhcch-hhhhhhhhcc--hhhhHHH----------HhhhheeeEEEcCC
Confidence                              389999999999999999 9999998632  1111223          3444443221 222


Q ss_pred             CceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcC--CCCCCCCCCCeeeeeecC
Q 044732          173 GRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRR--ATAPPAPPEGLCLVDVGY  239 (250)
Q Consensus       173 ~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~--~~~~~APa~GL~L~~V~Y  239 (250)
                      ..+++.|+|.|++|||||||+||+.|..||+|...|+-|.++|+-+...  ....+|-...|.|.++.|
T Consensus       252 ~~~my~ldi~g~AFLwHqVRcimaiL~liGq~~E~p~lI~dLldIek~P~kPqY~mA~~~PL~LydC~f  320 (425)
T KOG2554|consen  252 TPGMYYLDIQGSAFLWHQVRCIMAILFLIGQGLEQPSLISDLLDIEKNPQKPQYTMASDYPLELYDCDF  320 (425)
T ss_pred             CCceEEEEeechhhHHHHHHHHHHHHHHhccccCCchHHHHHHhcccCCCCceeeeccCCceEEEecCC
Confidence            3348999999999999999999999999999999999999999866432  234467778899999999

>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=99.90  E-value=3.2e-26  Score=174.14  Aligned_cols=102  Identities=25%  Similarity=0.378  Sum_probs=79.1

Q ss_pred             HHHhccccccccccccccccccccCCCCceeEEEeeeeeccccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHH
Q 044732          121 LLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVR  200 (250)
Q Consensus       121 a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~vr~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~  200 (250)
                      |++.|+|+| ||++|++..    ...+++.|          +|..+.  +..+.+++. +|+|+|||+||||+|||++++
T Consensus         1 A~~~~~G~H-dF~~f~~~~----~~~~~~~r----------~i~~~~--~~~~~~~~~-~i~g~~Fl~~~vR~~vg~~~~   62 (105)
T PF01416_consen    1 AAKLYVGTH-DFSGFQKQK----TVEKNTIR----------TIFSID--IIEEGDVVV-EIHGNSFLRHQVRIMVGTLLR   62 (105)
T ss_dssp             -CCEETCEE-ECCGCSSCS-----HHHHHCC----------CEEEEE--CCCCCCEEE-EEEESS--TTHHHHHHCCCCH
T ss_pred             CcceeEecC-CCcCCEECC----cccccHHH----------HHHHHh--hhcCCCEEE-EEEecccccccchhhhHHHHH
Confidence            578899999 999999851    11122334          444432  234456888 999999999999999999999


Q ss_pred             HHhCCCCHHHHHHHHHccCcCCCCC---CCCCCCeeeeeecCC
Q 044732          201 EAAAGADEDALLKLMDATCRRATAP---PAPPEGLCLVDVGYT  240 (250)
Q Consensus       201 vg~g~~~~~~i~~~L~~~~r~~~~~---~APa~GL~L~~V~Y~  240 (250)
                      +++|..+++++.++|++..+....+   +|||+||+|.+|.||
T Consensus        63 ~~~G~~~~~~i~~~L~~~~~~~~~~ri~~ap~~gL~L~~v~y~  105 (105)
T PF01416_consen   63 TGRGVHSLEQIAELLNSKLRPKAPPRILTAPAVGLYLFHVRYD  105 (105)
T ss_dssp             HHTTSCEEECCCCCHHHHSCTTS-TEEEEEEECCECCEECCTT
T ss_pred             HhcCCCCHHHHHHHHhccCccccCCCcceeeCCCCCceEeeCc
Confidence            9999999999999999998766666   999999999999996

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=95.23  E-value=0.053  Score=45.43  Aligned_cols=53  Identities=15%  Similarity=0.305  Sum_probs=41.1

Q ss_pred             EEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeec
Q 044732            3 ILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPL   57 (250)
Q Consensus         3 ~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~   57 (250)
                      -+.+ ..+++++.+.+.||+.||++|+|.++..++....+= .+.-..+.|.+..
T Consensus        65 di~l-~~~~~~~~~~~rLn~~lP~Gl~i~~~~~i~~~~~sl-~~~i~~~~Y~i~~  117 (187)
T PF10105_consen   65 DIEL-EEDIDPEEVLERLNAVLPEGLRILEAEEIPPKAPSL-MALINAAEYRITL  117 (187)
T ss_pred             EEEE-ecCCCHHHHHHHHHHhCCCCCEEEEEEEccCCCcch-hhhcceEEEEEEe
Confidence            3445 568999999999999999999999999998554432 3445667888864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	250
1vs3_A	249	TRNA pseudouridine synthase A; TRUA, tRNA modifica	2e-12
1vs3_A	249	TRNA pseudouridine synthase A; TRUA, tRNA modifica	3e-07
1dj0_A	264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	4e-11
1dj0_A	264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	2e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05

>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 = 63.6 bits (156), Expect = 2e-12
 Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 167 VNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGA-DEDALLKLMDATCRRATAP 225
           V +   G +V  +      FLR  VR +V TL+ E   G    ++L  ++    RR   P
Sbjct: 175 VAEGEAGLEV-RLYFRGKSFLRGQVRGMVGTLL-EVGLGKRPPESLKAILKTADRRLAGP 232

Query: 226 PAPPEGLCLVDVGY 239
            AP  GL  V+  Y
Sbjct: 233 TAPAHGLYFVEAAY 246

>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 = 49.0 bits (118), Expect = 3e-07
 Identities = 12/46 (26%), Positives = 21/46 (45%)

Query: 9   KDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYI 54
             +    + +A+N   P  ++V+   +V+  FH    A WR Y Y 
Sbjct: 68  SAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYR 113

>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 = 60.2 bits (147), Expect = 4e-11
 Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 179 VELVANRFLRKMVRVLVATLVREAAAGA-DEDALLKLMDATCRRATAPPAPPEGLCLVDV 237
           V++ AN F+  MVR +V +L+ E  A    E  + +L+ A  R   A  A  EGL LV V
Sbjct: 186 VDIKANAFVHHMVRNIVGSLM-EVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAV 244

Query: 238 GY-TNFD-PQNSLIP 250
            Y   +D P+  + P
Sbjct: 245 DYPDRYDLPKPPMGP 259

>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 = 49.8 bits (120), Expect = 2e-07
 Identities = 18/46 (39%), Positives = 21/46 (45%)

Query: 9   KDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYI 54
              K +     +N+  PG I V  V  V   FH  FSA  RRY YI
Sbjct: 70  ALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYI 115

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.8 bits (105), Expect = 1e-05
 Identities = 41/261 (15%), Positives = 75/261 (28%), Gaps = 59/261 (22%)

Query: 2   IILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFH-PNFSAKWRRYLYIFPLNDG 60
           +  D +  +    D++D   S       ++S  ++  +    +  +   R  +   L+  
Sbjct: 24  VFEDAFVDNFDCKDVQDMPKS-------ILSKEEIDHIIMSKDAVSGTLRLFWTL-LSKQ 75

Query: 61  ENREQSIDSEVEVENF-------HTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNF 113
           E   Q    EV   N+        T           Y    + L ND   F  +   R  
Sbjct: 76  EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ 135

Query: 114 TICRVNLLLQRL--EGKLLSY------KT-FARDTKASRNIGPPTECFIY-----HARAT 159
              ++   L  L     +L        KT  A D   S  +    +  I+     +  + 
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP 195

Query: 160 EAIL-------------PCPVNDHGEGRKVMCVELVA--NRFL--RKMVRVLVATLVREA 202
           E +L                 +DH    K+    + A   R L  +     L   LV   
Sbjct: 196 ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL---LV--- 249

Query: 203 AAGADE--DA-LLKLMDATCR 220
                   +A      + +C+
Sbjct: 250 ---LLNVQNAKAWNAFNLSCK 267

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	250
1vs3_A	249	TRNA pseudouridine synthase A; TRUA, tRNA modifica	100.0
1dj0_A	264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	100.0

>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=5e-55  Score=378.85  Aligned_cols=188  Identities=22%  Similarity=0.357  Sum_probs=162.4

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      ||||++ +..++++.|..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+++.  .++|      |...     
T Consensus        61 v~~f~~-~~~~~~~~~~~~lN~~LP~dI~V~~~~~v~~~FhARf~a~~R~Y~Y~i~~~~--~~~~------~~~~-----  126 (249)
T 1vs3_A           61 PFHVDV-ESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRP--HPSP------LLRH-----  126 (249)
T ss_dssp             EEEEEE-CSCCCGGGHHHHHHHHSCTTEEEEEEEEECTTCCTTTTCSEEEEEEEEEECS--SCCT------TTTT-----
T ss_pred             EEEEEE-CCCCCHHHHHHHHHhcCCcCEEEEEEEECCCCCCcccccccEEEEEEEccCC--CCCh------hhCC-----
Confidence            699999 6789999999999999999999999999999999999999999999999876  4332      2233     


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                              ++|+.+.++|+++|++||+.|+||| ||+|||+..    .  +++.|+|.++....
T Consensus       127 ------------------------~~~~~~~~ldi~~m~~aa~~l~G~H-DF~~F~~~~----~--~~~vR~I~~~~v~~  175 (249)
T 1vs3_A          127 ------------------------RALWVRRPLDLEAMEEALSLLLGRH-NFLGFAKEE----T--RPGERELLEARLQV  175 (249)
T ss_dssp             ------------------------TSEEECSCCCHHHHHHHHHHHSEEE-EGGGGCSSC----C--SCCEEEEEEEEEEE
T ss_pred             ------------------------eeEEeCCCCCHHHHHHHHHHhcCce-eHHheecCC----C--CCCCcEEEEEEEEe
Confidence                                    3566677899999999999999999 999999742    1  56777777654321


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecCC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYT  240 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~  240 (250)
                        .     ...+ ++++.|+|+|+||||||||+|||+|++||+|++++++|+++|++++|..++++|||+||||++|.|+
T Consensus       176 --~-----~~~~-~~~i~~~i~g~~FL~~mVR~mvG~l~~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~v~Y~  247 (249)
T 1vs3_A          176 --A-----EGEA-GLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLYFVEAAYP  247 (249)
T ss_dssp             --E-----ECSS-SEEEEEEEEESCCCTTHHHHHHHHHHHHHHSSSCGGGHHHHHHHCCGGGSCCCCCGGGEEEEEEECC
T ss_pred             --c-----cccC-CCEEEEEEEEChHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhCCCcccCcCccCCCCcEEeeeeCC
Confidence              0     0023 3799999999999999999999999999999999999999999999989999999999999999996


Q ss_pred             C
Q 044732          241 N  241 (250)
Q Consensus       241 ~  241 (250)
                      +
T Consensus       248 ~  248 (249)
T 1vs3_A          248 E  248 (249)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=7.7e-55  Score=380.43  Aligned_cols=186  Identities=27%  Similarity=0.335  Sum_probs=162.3

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      ||||++ +..++++.|..+||+.||+||+|+++++|+++|||||+|++|+|+|+|+++.  .++|      |...     
T Consensus        63 v~~f~~-~~~~~~~~~~~~lN~~LP~dI~V~~~~~V~~~FhARf~a~~R~Y~Y~i~~~~--~~~~------~~~~-----  128 (264)
T 1dj0_A           63 VVHFET-TALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHR--LRPA------VLSK-----  128 (264)
T ss_dssp             EEEEEE-SCCCCHHHHHHHHHHTSCTTEEEEEEEECCTTCCTTTTCCEEEEEEEEECSS--SCCC------TTTT-----
T ss_pred             EEEEEE-CCCCCHHHHHHHHHhhCCcCeEEEEEEeCCCCCCcccccccEEEEEEEccCC--CCCh------hHcC-----
Confidence            799999 6789999999999999999999999999999999999999999999999876  4332      2222     


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                              ++|+...++|+++|++||+.|+||| ||+|||+.    +.+.+++.|+|.++... 
T Consensus       129 ------------------------~~~~~~~~lD~~~M~~aa~~l~G~H-DF~~F~~~----~~~~~s~vR~I~~~~v~-  178 (264)
T 1dj0_A          129 ------------------------GVTHFYEPLDAERMHRAAQCLLGEN-DFTSFRAV----QCQSRTPWRNVMHINVT-  178 (264)
T ss_dssp             ------------------------SSEECCSCCCHHHHHHHHGGGCEEE-ECGGGCCT----TCCCSCCEEEEEEEEEE-
T ss_pred             ------------------------ceEeeCCCCCHHHHHHHHHHhcCcc-cHHHhccC----CCCCCCcEEEEEEEEEE-
Confidence                                    4566778899999999999999999 99999974    22345567777665432 


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecCC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYT  240 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~  240 (250)
                                 +.++++.|+|+|+||||||||+|||+|++||+|++++++|.++|++++|..++++|||+||||++|.|+
T Consensus       179 -----------~~~~~i~~~i~g~~FL~~mVR~mvG~L~~vG~G~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~  247 (264)
T 1dj0_A          179 -----------RHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYP  247 (264)
T ss_dssp             -----------EETTEEEEEEEESCCCTTHHHHHHHHHHHHHTTSSCTTHHHHHHHHCCGGGSCCCCCSTTEEEEEEECC
T ss_pred             -----------ECCCEEEEEEEEchHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhCCCcccCcCccCCCCcEEeeeccC
Confidence                       123689999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 044732          241 N  241 (250)
Q Consensus       241 ~  241 (250)
                      +
T Consensus       248 ~  248 (264)
T 1dj0_A          248 D  248 (264)
T ss_dssp             G
T ss_pred             c
Confidence            4

---

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	250
d1dj0a_	264	d.265.1.1 (A:) Pseudouridine synthase I TruA {Esch	3e-11

>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 = 59.6 bits (143), Expect = 3e-11
 Identities = 45/244 (18%), Positives = 78/244 (31%), Gaps = 26/244 (10%)

Query: 16  IEDAINSAAPGKIRVI-------SVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSID 68
           +E A++  A   I V         V    +V H   +A  +   +   +N     + ++ 
Sbjct: 33  LEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVR 92

Query: 69  SEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGK 128
               V +   +          Y    + L       G           R++   Q L G+
Sbjct: 93  WVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGE 152

Query: 129 LLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLR 188
                  A   ++           +                       + V++ AN F+ 
Sbjct: 153 NDFTSFRAVQCQSRTPWRNVMHINVT-----------------RHGPYVVVDIKANAFVH 195

Query: 189 KMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY-TNFD-PQN 246
            MVR +V +L+   A    E  + +L+ A  R   A  A  EGL LV V Y   +D P+ 
Sbjct: 196 HMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKP 255

Query: 247 SLIP 250
            + P
Sbjct: 256 PMGP 259

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	250
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=8.2e-49  Score=341.33  Aligned_cols=186  Identities=27%  Similarity=0.326  Sum_probs=158.7

Q ss_pred             CeEEecCCCCCChhHHHHHHHhhCCCCeEEEEEEecCCCCcccccCCceeEEEEeecCCCCCCccccchhhhhhcccccc
Q 044732            1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVEVENFHTSN   80 (250)
Q Consensus         1 ~~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~~~~V~~~FhAR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (250)
                      ||||++ ....+.+.+...||+.||+||+|+++.+|+++||||++|++|+|+|+|..+.  .+.+.      ..      
T Consensus        63 v~~~~~-~~~~~~~~~~~~lN~~Lp~dI~i~~~~~v~~~F~aR~~a~~r~Y~Y~i~~~~--~~~~~------~~------  127 (264)
T d1dj0a_          63 VVHFET-TALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHR--LRPAV------LS------  127 (264)
T ss_dssp             EEEEEE-SCCCCHHHHHHHHHHTSCTTEEEEEEEECCTTCCTTTTCCEEEEEEEEECSS--SCCCT------TT------
T ss_pred             EEEEee-ccchhhhhhhcccccccccccccccceeccccccchhhhhhcccceeecccc--ccccc------cc------
Confidence            689999 7889999999999999999999999999999999999999999999999776  32211      11      


Q ss_pred             ccCccCCCccccccccccccCCCCccccCCCCCCHHHHHHHHHhccccccccccccccccccccCCCCceeEEEeeeeec
Q 044732           81 NVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGKLLSYKTFARDTKASRNIGPPTECFIYHARATE  160 (250)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~m~~a~~~f~GtH~dF~~F~~~~~~~~~~~~~~~r~i~~~~~~v  160 (250)
                                             ...|+...++|+++|++|++.|+||| ||++|++..    ....+..|++...... 
T Consensus       128 -----------------------~~~~~~~~~ld~~~m~~a~~~~~G~h-dF~~F~~~~----~~~~~~~r~i~~~~~~-  178 (264)
T d1dj0a_         128 -----------------------KGVTHFYEPLDAERMHRAAQCLLGEN-DFTSFRAVQ----CQSRTPWRNVMHINVT-  178 (264)
T ss_dssp             -----------------------TSSEECCSCCCHHHHHHHHGGGCEEE-ECGGGCCTT----CCCSCCEEEEEEEEEE-
T ss_pred             -----------------------cccccccCCcchHHHHHHHhhccCcc-ccccccccc----ccCCCcccccccccce-
Confidence                                   13556778899999999999999999 999998742    2223455555544321 


Q ss_pred             cccCCCcccCCCCceEEEEEEEcchHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHccCcCCCCCCCCCCCeeeeeecCC
Q 044732          161 AILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYT  240 (250)
Q Consensus       161 r~i~~~~~~~~~~~~~i~~~i~G~sFL~~qVR~mVG~lv~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~  240 (250)
                                 ...+++.|+|+|+||||||||+|||+|++||+|++++++|+++|+++++...+++|||+||||++|.|+
T Consensus       179 -----------~~~~~i~i~i~g~sFL~~qVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~  247 (264)
T d1dj0a_         179 -----------RHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYP  247 (264)
T ss_dssp             -----------EETTEEEEEEEESCCCTTHHHHHHHHHHHHHTTSSCTTHHHHHHHHCCGGGSCCCCCSTTEEEEEEECC
T ss_pred             -----------ecCcEEEEEechhHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhcCCcccCccccCCCCCEEcccccC
Confidence                       233689999999999999999999999999999999999999999998888899999999999999997


Q ss_pred             C
Q 044732          241 N  241 (250)
Q Consensus       241 ~  241 (250)
                      +
T Consensus       248 ~  248 (264)
T d1dj0a_         248 D  248 (264)
T ss_dssp             G
T ss_pred             c
Confidence            5