Citrus Sinensis ID: 043662

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------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-------260-------270-------280-------290-------300-------310-------320-------330
MSYGVVGLPSPLYSNGLLPSTNKQGVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEHLRLPAACPLSSFGRHHSVRKCKLPFY
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEccccccccccccccccHHHHHHHHHHHHHccccccEEEEEcccccccccccccEEEEEcccccccHHHHHHHHHcccccccEEEEEEEccccccccccccccEEEEEEEcccccccccccEEEEEcccccHHHHHHHHHHccccccHHHccccccccccccccEEEEEEEEEEEccEEEEEEEEccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccc
cccEEccccccccccccccccccccccccEEcccccccccccccccccEEEEEEEEEccccccccEEccccccHHHHHHHHHHHHHHHccccEEEEEEcccccccccccEEEEEccccccccHHHHHHHHHHHccccEEEEEEEEccccccccccccEEEEEEEEEEccccccccccccEEEcccccHHHHHHHHHHHcEEEEcHHHcccccccccccccEEEEEEEEEEcccEEEEEEEHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHccccHcccccccEEEEEEEccHHHcccccccccccccccccccEcEEEcc
msygvvglpsplysngllpstnkqgvgvvglegtnntvkpptddsfpgfkWRLVIAYDgtryagwqfqtspptIQCIVEKALIRVTKLEREdlrlvgasrtdtgvhawgqvahfitpfsydGLESIHAALngllppdirVREISAAVPEFHARFSAKSKIYHYKiyndavmdpfqrhyaYHSVYKLNTTLMRQAAEYFvgkhdfsafvnvqrndrllnpvksvfrFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIgkeaippdivpkilATQDRKELAKYalsapphglcLVEVKYneehlrlpaacplssfgrhhsvrkcklpfy
MSYGVVGLPSPLYSNGLLPSTNKQGVGVVGLEgtnntvkpptddsfpgfKWRLVIAYDGTRYAGWqfqtspptiQCIVEKALIRVTKLEREDLrlvgasrtdtgvhawGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIgkeaippdiVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEHLRLPaacplssfgrhhsvrkcklpfy
MSYGVVGLPSPLYSNGLLPSTNKQGVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEHLRLPAACPLSSFGRHHSVRKCKLPFY
************************GVGVVGLEG**********DSFPGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEHLRLPAACPLSSFGRHH**********
******GLPSPLYSNGLL******************************FKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQR**RLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEHLRLPAACPLSSFGRHHSVRKCKLPFY
MSYGVVGLPSPLYSNGLLPSTNKQGVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEHLRLPAACPLSSFGRHHSVRKCKLPFY
*SYGVVGLPSPLYSNGLLPSTNKQGVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEHLRLPAACPLSSFGRHHSVRKCKLPFY
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSYGVVGLPSPLYSNGLLPSTNKQGVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEHLRLPAACPLSSFGRHHSVRKCKLPFY
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query330 2.2.26 [Sep-21-2011]
Q6MEE7256 tRNA pseudouridine syntha yes no 0.751 0.968 0.419 1e-53
B1I1B5250 tRNA pseudouridine syntha yes no 0.733 0.968 0.428 5e-47
Q8R7Y7240 tRNA pseudouridine syntha yes no 0.724 0.995 0.427 1e-46
A8F526245 tRNA pseudouridine syntha yes no 0.721 0.971 0.407 1e-45
Q8XLQ0248 tRNA pseudouridine syntha yes no 0.727 0.967 0.391 1e-45
A3DJK8244 tRNA pseudouridine syntha yes no 0.727 0.983 0.405 8e-45
P70973247 tRNA pseudouridine syntha yes no 0.745 0.995 0.407 2e-44
Q9PJT0267 tRNA pseudouridine syntha yes no 0.721 0.891 0.416 4e-44
C4KZL4246 tRNA pseudouridine syntha yes no 0.727 0.975 0.396 4e-44
B8I814245 tRNA pseudouridine syntha yes no 0.733 0.987 0.400 9e-44
>sp|Q6MEE7|TRUA1_PARUW tRNA pseudouridine synthase A 1 OS=Protochlamydia amoebophila (strain UWE25) GN=truA1 PE=3 SV=1 Back     alignment and function desciption
 Score =  210 bits (534), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 107/255 (41%), Positives = 163/255 (63%), Gaps = 7/255 (2%)

Query: 51  WRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ 110
           ++L IAYDGT Y+GWQ Q +  +IQ  +++AL  +  L++E + LVG+ RTD GVHA GQ
Sbjct: 4   YKLTIAYDGTNYSGWQIQPNASSIQQKIQEALCIL--LKKEKVVLVGSGRTDAGVHAKGQ 61

Query: 111 VAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAV 170
           VAHF     Y  L  +H +LNGLLP DIR++ +    P FH+++SA  K YHY ++ + V
Sbjct: 62  VAHFHFQ-DYIDLSRLHVSLNGLLPRDIRIKAVEPVSPRFHSQYSAIRKEYHYYLHLNKV 120

Query: 171 MDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVN-VQRNDRLLNPVKSVFRFDVI 229
           MDPFQR Y++H   K++  ++++AA  F G HDF++F N   R     NPV++++R D+ 
Sbjct: 121 MDPFQRLYSWHFQRKIDVNILKKAAILFTGTHDFTSFANEAHRGTAAKNPVRTLYRLDIK 180

Query: 230 EMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAP 289
                L+LE EG GFLY+ VRN+V  L+ +       + + +I A ++R++    +L+AP
Sbjct: 181 PNEGGLRLEFEGDGFLYKMVRNIVGTLMDVASHKRAIEEINQIFAAKNRRQA---SLAAP 237

Query: 290 PHGLCLVEVKYNEEH 304
           P GL L++V Y  E+
Sbjct: 238 PEGLFLIQVFYENEN 252
Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs.
Protochlamydia amoebophila (strain UWE25) (taxid: 264201)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: 1EC: 2
>sp|B1I1B5|TRUA_DESAP tRNA pseudouridine synthase A OS=Desulforudis audaxviator (strain MP104C) GN=truA PE=3 SV=1 Back     alignment and function description
>sp|Q8R7Y7|TRUA_THETN tRNA pseudouridine synthase A OS=Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) GN=truA PE=3 SV=1 Back     alignment and function description
>sp|A8F526|TRUA_THELT tRNA pseudouridine synthase A OS=Thermotoga lettingae (strain ATCC BAA-301 / DSM 14385 / TMO) GN=truA PE=3 SV=1 Back     alignment and function description
>sp|Q8XLQ0|TRUA1_CLOPE tRNA pseudouridine synthase A 1 OS=Clostridium perfringens (strain 13 / Type A) GN=truA1 PE=3 SV=1 Back     alignment and function description
>sp|A3DJK8|TRUA_CLOTH tRNA pseudouridine synthase A OS=Clostridium thermocellum (strain ATCC 27405 / DSM 1237) GN=truA PE=3 SV=1 Back     alignment and function description
>sp|P70973|TRUA_BACSU tRNA pseudouridine synthase A OS=Bacillus subtilis (strain 168) GN=truA PE=3 SV=2 Back     alignment and function description
>sp|Q9PJT0|TRUA_CHLMU tRNA pseudouridine synthase A OS=Chlamydia muridarum (strain MoPn / Nigg) GN=truA PE=3 SV=1 Back     alignment and function description
>sp|C4KZL4|TRUA_EXISA tRNA pseudouridine synthase A OS=Exiguobacterium sp. (strain ATCC BAA-1283 / AT1b) GN=truA PE=3 SV=1 Back     alignment and function description
>sp|B8I814|TRUA_CLOCE tRNA pseudouridine synthase A OS=Clostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10) GN=truA PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query330
225432191336 PREDICTED: tRNA pseudouridine synthase A 0.872 0.857 0.843 1e-144
297736816326 unnamed protein product [Vitis vinifera] 0.872 0.883 0.843 1e-144
255556594344 pseudouridylate synthase, putative [Rici 0.878 0.843 0.776 1e-132
147865780403 hypothetical protein VITISV_020811 [Viti 0.809 0.662 0.817 1e-131
356564676309 PREDICTED: tRNA pseudouridine synthase A 0.875 0.935 0.758 1e-131
356545824327 PREDICTED: tRNA pseudouridine synthase A 0.969 0.978 0.695 1e-131
357479187322 tRNA pseudouridine synthase family prote 0.936 0.959 0.7 1e-131
357479185350 tRNA pseudouridine synthase family prote 0.872 0.822 0.743 1e-130
449441496335 PREDICTED: tRNA pseudouridine synthase A 0.942 0.928 0.698 1e-130
297829238323 tRNA pseudouridine synthase family prote 0.975 0.996 0.658 1e-126
>gi|225432191|ref|XP_002275097.1| PREDICTED: tRNA pseudouridine synthase A 1-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  517 bits (1331), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 243/288 (84%), Positives = 263/288 (91%)

Query: 43  DDSFPGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTD 102
           + S  G+KWRLVIAY+GTRY+GWQ+Q SPPTIQCIVEKAL R TKLEREDL LVGASRTD
Sbjct: 49  NTSASGYKWRLVIAYEGTRYSGWQYQQSPPTIQCIVEKALTRATKLEREDLYLVGASRTD 108

Query: 103 TGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYH 162
           TGVHAWGQVAHF+TPF+YDGLESIHAALNGLLPPDIRVREIS AVPEFHARFS KSKIYH
Sbjct: 109 TGVHAWGQVAHFLTPFNYDGLESIHAALNGLLPPDIRVREISPAVPEFHARFSVKSKIYH 168

Query: 163 YKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKS 222
           YKIYNDAVMDPF RHY YHSVYKLNT  MR+AA++F GKHDFSAFVN   NDR  NPVK+
Sbjct: 169 YKIYNDAVMDPFLRHYVYHSVYKLNTLAMREAAKHFTGKHDFSAFVNASHNDRSPNPVKN 228

Query: 223 VFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELA 282
           +FRFDV EMGALLQLEVEGSGFLYRQVRNMVALLLQIG+EAIPP+IVP ILAT+DRKELA
Sbjct: 229 IFRFDVNEMGALLQLEVEGSGFLYRQVRNMVALLLQIGREAIPPNIVPWILATRDRKELA 288

Query: 283 KYALSAPPHGLCLVEVKYNEEHLRLPAACPLSSFGRHHSVRKCKLPFY 330
           KYALSAPPHGLCL+ VKYNEEHL+LP+ CP +S GRHH+VRKCKLPFY
Sbjct: 289 KYALSAPPHGLCLMSVKYNEEHLQLPSGCPATSHGRHHTVRKCKLPFY 336

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297736816|emb|CBI26017.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255556594|ref|XP_002519331.1| pseudouridylate synthase, putative [Ricinus communis] gi|223541646|gb|EEF43195.1| pseudouridylate synthase, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|147865780|emb|CAN81146.1| hypothetical protein VITISV_020811 [Vitis vinifera] Back     alignment and taxonomy information
>gi|356564676|ref|XP_003550576.1| PREDICTED: tRNA pseudouridine synthase A 1-like [Glycine max] Back     alignment and taxonomy information
>gi|356545824|ref|XP_003541334.1| PREDICTED: tRNA pseudouridine synthase A 1-like [Glycine max] Back     alignment and taxonomy information
>gi|357479187|ref|XP_003609879.1| tRNA pseudouridine synthase family protein [Medicago truncatula] gi|355510934|gb|AES92076.1| tRNA pseudouridine synthase family protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|357479185|ref|XP_003609878.1| tRNA pseudouridine synthase family protein [Medicago truncatula] gi|355510933|gb|AES92075.1| tRNA pseudouridine synthase family protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|449441496|ref|XP_004138518.1| PREDICTED: tRNA pseudouridine synthase A 1-like [Cucumis sativus] gi|449518841|ref|XP_004166444.1| PREDICTED: tRNA pseudouridine synthase A 1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297829238|ref|XP_002882501.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] gi|297328341|gb|EFH58760.1| tRNA pseudouridine synthase family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query330
TAIR|locus:2077552323 AT3G06950 [Arabidopsis thalian 0.975 0.996 0.664 1e-116
TIGR_CMR|GSU_2877244 GSU_2877 "tRNA pseudouridine s 0.727 0.983 0.381 1.9e-37
TIGR_CMR|CHY_2276246 CHY_2276 "tRNA pseudouridine s 0.730 0.979 0.396 2.4e-37
TIGR_CMR|CBU_0892261 CBU_0892 "tRNA pseudouridine s 0.760 0.961 0.357 1.3e-34
UNIPROTKB|P07649270 truA "tRNA pseudouridine synth 0.778 0.951 0.349 8.5e-33
UNIPROTKB|Q9KTA4264 truA "tRNA pseudouridine synth 0.745 0.931 0.359 3.7e-32
TIGR_CMR|ECH_0622245 ECH_0622 "tRNA pseudouridine s 0.721 0.971 0.354 3.7e-32
TIGR_CMR|VC_0999264 VC_0999 "tRNA pseudouridine sy 0.745 0.931 0.359 3.7e-32
TIGR_CMR|DET_0504248 DET_0504 "tRNA pseudouridine s 0.718 0.955 0.376 1.8e-30
TIGR_CMR|APH_0502246 APH_0502 "tRNA pseudouridine s 0.736 0.987 0.335 7.9e-30
TAIR|locus:2077552 AT3G06950 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1150 (409.9 bits), Expect = 1.0e-116, P = 1.0e-116
 Identities = 220/331 (66%), Positives = 265/331 (80%)

Query:     1 MSYGVVGLPSPLYSNGLLPSTNKQGVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIAYDGT 60
             MS     LP  L++NG L S   Q + +  L   N++VK    DS   +KWRLVIAYDGT
Sbjct:     1 MSCVTPALPPSLFTNGYLSSP--QNISMTNL---NSSVK--VSDS-GAYKWRLVIAYDGT 52

Query:    61 RYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSY 120
             R+AGWQ+Q SPPTIQ ++EKALI++T+L R++L+L+GA RTD GVHAWGQVAHF+TPF+Y
Sbjct:    53 RFAGWQYQESPPTIQSMLEKALIQITELGRKELQLIGAGRTDAGVHAWGQVAHFVTPFNY 112

Query:   121 DGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAY 180
               L+S HAALNGLLP DIRVRE+SAAVPEFHARFSA SK+Y Y+IYND  MDPFQRH+AY
Sbjct:   113 TSLDSFHAALNGLLPKDIRVRELSAAVPEFHARFSASSKVYRYQIYNDTFMDPFQRHWAY 172

Query:   181 HSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVE 240
             H  YKLN + MR+AA  FVGKHDFSAF N  R D + +P+K++ RFDVI+MG+LLQLEVE
Sbjct:   173 HCAYKLNASKMREAANLFVGKHDFSAFANATREDGVPDPLKTISRFDVIQMGSLLQLEVE 232

Query:   241 GSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKY-ALSAPPHGLCLVEVK 299
             GSGFLYRQVRNMVALL+QIGKEA+  DIVP IL T+DR+ LAKY +L A PHGLCLV VK
Sbjct:   233 GSGFLYRQVRNMVALLIQIGKEALDSDIVPMILETKDRRVLAKYTSLPASPHGLCLVSVK 292

Query:   300 YNEEHLRLPAACPLSSFGRHHSVRKCKLPFY 330
             Y E+HL+LP  CP++S GRHH++ KCKLPFY
Sbjct:   293 YKEDHLKLPLDCPVTSSGRHHTITKCKLPFY 323
GO:0001522 "pseudouridine synthesis" evidence=IEA
GO:0003723 "RNA binding" evidence=IEA
GO:0009451 "RNA modification" evidence=IEA
GO:0009507 "chloroplast" evidence=ISM
GO:0009982 "pseudouridine synthase activity" evidence=IEA;ISS;TAS
GO:0006730 "one-carbon metabolic process" evidence=RCA
TIGR_CMR|GSU_2877 GSU_2877 "tRNA pseudouridine synthase A" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_2276 CHY_2276 "tRNA pseudouridine synthase A" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_0892 CBU_0892 "tRNA pseudouridine synthase A" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
UNIPROTKB|P07649 truA "tRNA pseudouridine synthase I" [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
UNIPROTKB|Q9KTA4 truA "tRNA pseudouridine synthase A" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|ECH_0622 ECH_0622 "tRNA pseudouridine synthase A" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] Back     alignment and assigned GO terms
TIGR_CMR|VC_0999 VC_0999 "tRNA pseudouridine synthase A" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
TIGR_CMR|DET_0504 DET_0504 "tRNA pseudouridine synthase A" [Dehalococcoides ethenogenes 195 (taxid:243164)] Back     alignment and assigned GO terms
TIGR_CMR|APH_0502 APH_0502 "tRNA pseudouridine synthase A" [Anaplasma phagocytophilum HZ (taxid:212042)] Back     alignment and assigned GO terms

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 LevelEC numberConfidence of Prediction
4th Layer5.4.99.120.824
3rd Layer5.4.990.766

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query330
cd02570239 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bact 1e-107
PRK00021244 PRK00021, truA, tRNA pseudouridine synthase A; Val 1e-105
COG0101266 COG0101, TruA, Pseudouridylate synthase [Translati 2e-91
PRK12434245 PRK12434, PRK12434, tRNA pseudouridine synthase A; 1e-73
TIGR00071227 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) sy 5e-66
PRK14586245 PRK14586, PRK14586, tRNA pseudouridine synthase AC 2e-62
PRK14588272 PRK14588, PRK14588, tRNA pseudouridine synthase AC 9e-48
cd00497215 cd00497, PseudoU_synth_TruA_like, Pseudouridine sy 2e-46
cd02866219 cd02866, PseudoU_synth_TruA_Archea, Archeal pseudo 4e-46
PRK14589265 PRK14589, PRK14589, tRNA pseudouridine synthase AC 5e-39
cd02569256 cd02569, PseudoU_synth_ScPus3, Pseudouridine synth 4e-38
cd02568245 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine sy 3e-27
pfam01416103 pfam01416, PseudoU_synth_1, tRNA pseudouridine syn 5e-22
PRK14587256 PRK14587, PRK14587, tRNA pseudouridine synthase AC 8e-13
pfam01416103 pfam01416, PseudoU_synth_1, tRNA pseudouridine syn 6e-06
>gnl|CDD|211337 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial pseudouridine synthases similar to E Back     alignment and domain information 
 Score =  312 bits (803), Expect = e-107
 Identities = 109/248 (43%), Positives = 151/248 (60%), Gaps = 9/248 (3%)

Query: 53  LVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 112
           L I YDGT ++GWQ Q +  T+Q  +EKAL ++     E +R++GA RTD GVHA GQVA
Sbjct: 1   LTIEYDGTNFSGWQRQPNGRTVQGELEKALSKIAG---EPVRVIGAGRTDAGVHALGQVA 57

Query: 113 HFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMD 172
           HF TP     LE +  ALN LLPPDIRV        +FHARFSAKS+ Y Y+I N  V  
Sbjct: 58  HFDTPSEIP-LEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRPVPS 116

Query: 173 PFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMG 232
           PF R Y +H    L+   M++AA+  +G HDFS+F       +  + V++++R DV   G
Sbjct: 117 PFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFRAAGCQSK--STVRTIYRADVYREG 174

Query: 233 ALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHG 292
            L+  E+  +GFLY  VRN+V  LL++G+  + P+ + +IL  +DR        +AP HG
Sbjct: 175 DLIVFEIRANGFLYHMVRNIVGTLLEVGRGKLSPEDIKEILEAKDRTAAGP---TAPAHG 231

Query: 293 LCLVEVKY 300
           L LV+V+Y
Sbjct: 232 LYLVKVEY 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|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated Back     alignment and domain information
>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed Back     alignment and domain information
>gnl|CDD|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase Back     alignment and domain information
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional Back     alignment and domain information
>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional Back     alignment and domain information
>gnl|CDD|211322 cd00497, PseudoU_synth_TruA_like, Pseudouridine synthase, TruA family Back     alignment and domain information
>gnl|CDD|211343 cd02866, PseudoU_synth_TruA_Archea, Archeal pseudouridine synthases Back     alignment and domain information
>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional Back     alignment and domain information
>gnl|CDD|211336 cd02569, PseudoU_synth_ScPus3, Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like Back     alignment and domain information
>gnl|CDD|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/ PUS2 like Back     alignment and domain information
>gnl|CDD|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase Back     alignment and domain information
>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional Back     alignment and domain information
>gnl|CDD|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 330
PRK12434245 tRNA pseudouridine synthase A; Reviewed 100.0
COG0101266 TruA Pseudouridylate synthase [Translation, riboso 100.0
PRK14588272 tRNA pseudouridine synthase ACD; Provisional 100.0
PRK14586245 tRNA pseudouridine synthase ACD; Provisional 100.0
PRK00021244 truA tRNA pseudouridine synthase A; Validated 100.0
cd02570239 PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudou 100.0
TIGR00071227 hisT_truA pseudouridylate synthase I. universal so 100.0
PRK14589265 tRNA pseudouridine synthase ACD; Provisional 100.0
cd00497224 PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudo 100.0
cd02569256 PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Ps 100.0
cd02866221 PseudoU_synth_TruA_Archea PseudoU_synth_archea: Ps 100.0
cd02568245 PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: P 100.0
PRK14587256 tRNA pseudouridine synthase ACD; Provisional 100.0
PLN03078513 Putative tRNA pseudouridine synthase; Provisional 100.0
KOG2553416 consensus Pseudouridylate synthase [Translation, r 100.0
KOG4393295 consensus Predicted pseudouridylate synthase [RNA 100.0
KOG2554425 consensus Pseudouridylate synthase [Translation, r 100.0
PF01416105 PseudoU_synth_1: tRNA pseudouridine synthase; Inte 99.88
PF01416105 PseudoU_synth_1: tRNA pseudouridine synthase; Inte 98.16
PF10105187 DUF2344: Uncharacterized protein conserved in bact 97.17
TIGR01213388 conserved hypothetical protein TIGR01213. Members 95.73
PRK14554422 putative pseudouridylate synthase; Provisional 94.2
COG1258398 Predicted pseudouridylate synthase [Translation, r 92.63
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 91.16
>PRK12434 tRNA pseudouridine synthase A; Reviewed Back     alignment and domain information 
Probab=100.00  E-value=5.5e-79  Score=567.87  Aligned_cols=244  Identities=38%  Similarity=0.652  Sum_probs=229.2

Q ss_pred             cceEEEEEEEeCCCceeeeeCCC-CCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHHH
Q 043662           48 GFKWRLVIAYDGTRYAGWQFQTS-PPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESI  126 (330)
Q Consensus        48 ~~r~~l~v~YdGt~y~G~Q~Q~~-~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l  126 (330)
                      |.+|+|.|+||||+|+|||+|++ .+|||++||+||.+++.   +++++.+|||||+||||++||+||+++... +++.+
T Consensus         1 m~~~~l~i~YdGt~y~G~Q~Q~~~~~TVq~~le~aL~~~~~---~~~~~~~agRTD~GVHA~~qv~~f~~~~~~-~~~~l   76 (245)
T PRK12434          1 MRNIKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVLSEMTG---EEIEIIGCGRTDAGVHALNQVANFQTDEKL-SEDKI   76 (245)
T ss_pred             CceEEEEEEECCCccceEeeCCCCCCCHHHHHHHHHHHHhC---CCeEEEEeccCCCCcCccCcEEEEEcCCCC-CHHHH
Confidence            46899999999999999999996 89999999999999875   689999999999999999999999998664 57889


Q ss_pred             HHHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhccccccccc
Q 043662          127 HAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSA  206 (330)
Q Consensus       127 ~~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~  206 (330)
                      ..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|++....+||.++|.|++...+|+++|++||+.|+|+|||++
T Consensus        77 ~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~  156 (245)
T PRK12434         77 KKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNEKFHNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFTS  156 (245)
T ss_pred             HHHHHccCCCCeEEEEEEECCCCcccccCCCcEEEEEEEccCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcCHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccCCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCC
Q 043662          207 FVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYAL  286 (330)
Q Consensus       207 F~~~~~~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~  286 (330)
                      ||+...  +.++++|+|++++|.+.++++.|+|+|+||||||||+|||+|++||+|++++++|+++|+.+++...   .+
T Consensus       157 F~~~~~--~~~~~~R~I~~~~v~~~~~~~~i~i~g~~FL~~mVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r~~~---~~  231 (245)
T PRK12434        157 FTNAKS--KKKSTVREIYSIDIMEEDGFVQIRVSGNGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDRNQA---NC  231 (245)
T ss_pred             hcCCCC--CCCCCEEEEEEEEEEEeCCEEEEEEEecHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcccC---CC
Confidence            997643  3578999999999998888999999999999999999999999999999999999999999877643   36


Q ss_pred             CcCCCCceEeeeec
Q 043662          287 SAPPHGLCLVEVKY  300 (330)
Q Consensus       287 ~APa~GL~L~~V~Y  300 (330)
                      +|||+||||++|.|
T Consensus       232 ~APa~GL~L~~V~Y  245 (245)
T PRK12434        232 TAPASGLYLENVEY  245 (245)
T ss_pred             ccCCCCCEEeEeEC
Confidence            99999999999998

>COG0101 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK14588 tRNA pseudouridine synthase ACD; Provisional Back     alignment and domain information
>PRK14586 tRNA pseudouridine synthase ACD; Provisional Back     alignment and domain information
>PRK00021 truA tRNA pseudouridine synthase A; Validated Back     alignment and domain information
>cd02570 PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like Back     alignment and domain information
>TIGR00071 hisT_truA pseudouridylate synthase I Back     alignment and domain information
>PRK14589 tRNA pseudouridine synthase ACD; Provisional Back     alignment and domain information
>cd00497 PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudouridine synthase, TruA family Back     alignment and domain information
>cd02569 PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like Back     alignment and domain information
>cd02866 PseudoU_synth_TruA_Archea PseudoU_synth_archea: Pseudouridine synthase, Back     alignment and domain information
>cd02568 PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: Pseudouridine synthase, PUS1/ PUS2 like Back     alignment and domain information
>PRK14587 tRNA pseudouridine synthase ACD; Provisional Back     alignment and domain information
>PLN03078 Putative tRNA pseudouridine synthase; Provisional Back     alignment and domain information
>KOG2553 consensus Pseudouridylate synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG4393 consensus Predicted pseudouridylate synthase [RNA processing and modification; Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG2554 consensus Pseudouridylate synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>TIGR01213 conserved hypothetical protein TIGR01213 Back     alignment and domain information
>PRK14554 putative pseudouridylate synthase; Provisional Back     alignment and domain information
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query330
1dj0_A264 The Crystal Structure Of E. Coli Pseudouridine Synt 4e-33
2nqp_A270 Crystal Structure Of Pseudoudirinde Synthase Trua I 4e-33
1vs3_A249 Crystal Structure Of The Trna Pseudouridine Synthas 8e-27
>pdb|1DJ0|A Chain A, The Crystal Structure Of E. Coli Pseudouridine Synthase I At 1.5 Angstrom Resolution Length = 264 Back     alignment and structure 
Iteration: 1

 Score =  138 bits (348), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 93/269 (34%), Positives = 142/269 (52%), Gaps = 12/269 (4%)
Query: 47  PGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 106
           P +K  L I YDG++Y GWQ Q    ++Q  +EKAL   +++  E + +  A RTD GVH
Sbjct: 2   PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKAL---SQVANEPITVFCAGRTDAGVH 58
Query: 107 AWGQVAHF-ITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI 165
             GQV HF  T    D   ++   +N  LP DI VR +     +FHARFSA ++ Y Y I
Sbjct: 59  GTGQVVHFETTALRKDAAWTL--GVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYII 116
Query: 166 YNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFR 225
           YN  +          H    L+   M +AA+  +G++DF++F  VQ   R   P ++V  
Sbjct: 117 YNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSR--TPWRNVMH 174
Query: 226 FDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYA 285
            +V   G  + ++++ + F++  VRN+V  L+++G    P   + ++LA +DR  LA  A
Sbjct: 175 INVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRT-LA--A 231
Query: 286 LSAPPHGLCLVEVKYNEEH-LRLPAACPL 313
            +A   GL LV V Y + + L  P   PL
Sbjct: 232 ATAKAEGLYLVAVDYPDRYDLPKPPMGPL 260
>pdb|2NQP|A Chain A, Crystal Structure Of Pseudoudirinde Synthase Trua In Complex With Leucyl Trna Length = 270 Back     alignment and structure
>pdb|1VS3|A Chain A, Crystal Structure Of The Trna Pseudouridine Synthase Trua From Thermus Thermophilus Hb8 Length = 249 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query330
1dj0_A264 Pseudouridine synthase I; alpha/beta fold, RNA-bin 1e-109
1vs3_A249 TRNA pseudouridine synthase A; TRUA, tRNA modifica 1e-105
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-05
>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 Back     alignment and structure
 Score =  317 bits (815), Expect = e-109
 Identities = 90/270 (33%), Positives = 135/270 (50%), Gaps = 10/270 (3%)

Query: 47  PGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 106
           P +K  L I YDG++Y GWQ Q    ++Q  +EKAL +V     E + +  A RTD GVH
Sbjct: 2   PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVH 58

Query: 107 AWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIY 166
             GQV HF T        +    +N  LP DI VR +     +FHARFSA ++ Y Y IY
Sbjct: 59  GTGQVVHFETTALRK-DAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIY 117

Query: 167 NDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRF 226
           N  +          H    L+   M +AA+  +G++DF++F  VQ   R   P ++V   
Sbjct: 118 NHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSR--TPWRNVMHI 175

Query: 227 DVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYAL 286
           +V   G  + ++++ + F++  VRN+V  L+++G    P   + ++LA +DR   A    
Sbjct: 176 NVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAA--- 232

Query: 287 SAPPHGLCLVEVKYNEEHLRLPAACPLSSF 316
           +A   GL LV V Y  +   LP       F
Sbjct: 233 TAKAEGLYLVAVDY-PDRYDLPKPPMGPLF 261
>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 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query330
1dj0_A264 Pseudouridine synthase I; alpha/beta fold, RNA-bin 100.0
1vs3_A249 TRNA pseudouridine synthase A; TRUA, tRNA modifica 100.0
2v9k_A530 Uncharacterized protein FLJ32312; pseudouridine sy 95.67
>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 Back     alignment and structure
Probab=100.00  E-value=2.1e-81  Score=588.26  Aligned_cols=254  Identities=35%  Similarity=0.543  Sum_probs=237.3

Q ss_pred             CCcceEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHH
Q 043662           46 FPGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLES  125 (330)
Q Consensus        46 ~~~~r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~  125 (330)
                      +||+||+|.|+||||+|+|||+||+.+|||++||+||.++++   +++.+++||||||||||++||+||+++... +.+.
T Consensus         1 ~Pm~r~~l~i~YdGt~y~GwQ~Q~~~~TVq~~Le~AL~~~~~---~~v~~~~agRTDaGVHA~gqv~~f~~~~~~-~~~~   76 (264)
T 1dj0_A            1 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVHGTGQVVHFETTALR-KDAA   76 (264)
T ss_dssp             CCCEEEEEEEEECCTTSSCSCCTTCSSCHHHHHHHHHHHHHT---SCCCEEESSCCCTTCEEEEEEEEEEESCCC-CHHH
T ss_pred             CCccEEEEEEEEeCCCceeEEECcCCCCHHHHHHHHHHHHhC---CCeEEEEeccCCCCCchhhEEEEEEECCCC-CHHH
Confidence            368899999999999999999999999999999999999975   689999999999999999999999998764 5788


Q ss_pred             HHHHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccc
Q 043662          126 IHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFS  205 (330)
Q Consensus       126 l~~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~  205 (330)
                      +..+||+.||+||+|+++++|+++|||||+|++|+|+|+|++....+||.++|.|++..+||+++|++|++.|+|+|||+
T Consensus        77 ~~~~lN~~LP~dI~V~~~~~V~~~FhARf~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~M~~aa~~l~G~HDF~  156 (264)
T 1dj0_A           77 WTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFT  156 (264)
T ss_dssp             HHHHHHHTSCTTEEEEEEEECCTTCCTTTTCCEEEEEEEEECSSSCCCTTTTSSEECCSCCCHHHHHHHHGGGCEEEECG
T ss_pred             HHHHHHhhCCcCeEEEEEEeCCCCCCcccccccEEEEEEEccCCCCChhHcCceEeeCCCCCHHHHHHHHHHhcCcccHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccCCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCC
Q 043662          206 AFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYA  285 (330)
Q Consensus       206 ~F~~~~~~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~  285 (330)
                      |||+..+  +.++++|+|++++|.+.++++.|+|+|+||||||||+|||+|++||+|++++++|+++|+.++|...   .
T Consensus       157 ~F~~~~~--~~~s~vR~I~~~~v~~~~~~i~~~i~g~~FL~~mVR~mvG~L~~vG~G~~~~~~i~~~L~~~~r~~~---~  231 (264)
T 1dj0_A          157 SFRAVQC--QSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLA---A  231 (264)
T ss_dssp             GGCCTTC--CCSCCEEEEEEEEEEEETTEEEEEEEESCCCTTHHHHHHHHHHHHHTTSSCTTHHHHHHHHCCGGGS---C
T ss_pred             HhccCCC--CCCCcEEEEEEEEEEECCCEEEEEEEEchHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhCCCcccC---c
Confidence            9997754  4578999999999999999999999999999999999999999999999999999999999988654   3


Q ss_pred             CCcCCCCceEeeeecCCCCCCCCC
Q 043662          286 LSAPPHGLCLVEVKYNEEHLRLPA  309 (330)
Q Consensus       286 ~~APa~GL~L~~V~Y~~~~~~~~~  309 (330)
                      ++|||+||||++|.|++. +.++.
T Consensus       232 ~~APa~GL~L~~V~Y~~~-~~~~~  254 (264)
T 1dj0_A          232 ATAKAEGLYLVAVDYPDR-YDLPK  254 (264)
T ss_dssp             CCCCSTTEEEEEEECCGG-GCCCC
T ss_pred             CccCCCCcEEeeeccCch-hcccc
Confidence            699999999999999754 34443
>1vs3_A TRNA pseudouridine synthase A; TRUA, tRNA modification, structural NPPSFA, national project on protein structural and function analyses; 2.25A {Thermus thermophilus} Back     alignment and structure
>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domai; HET: EPE; 2.0A {Homo sapiens} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 330
d1dj0a_264 d.265.1.1 (A:) Pseudouridine synthase I TruA {Esch 3e-46
>d1dj0a_ d.265.1.1 (A:) Pseudouridine synthase I TruA {Escherichia coli [TaxId: 562]} Length = 264 Back     information, alignment and structure

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 =  155 bits (393), Expect = 3e-46
 Identities = 90/268 (33%), Positives = 138/268 (51%), Gaps = 10/268 (3%)

Query: 47  PGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVH 106
           P +K  L I YDG++Y GWQ Q    ++Q  +EKAL   +++  E + +  A RTD GVH
Sbjct: 2   PVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKAL---SQVANEPITVFCAGRTDAGVH 58

Query: 107 AWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIY 166
             GQV HF T        +    +N  LP DI VR +     +FHARFSA ++ Y Y IY
Sbjct: 59  GTGQVVHFETTALRKD-AAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIY 117

Query: 167 NDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRF 226
           N  +          H    L+   M +AA+  +G++DF++F  VQ   R   P ++V   
Sbjct: 118 NHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSR--TPWRNVMHI 175

Query: 227 DVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYAL 286
           +V   G  + ++++ + F++  VRN+V  L+++G    P   + ++LA +DR   A    
Sbjct: 176 NVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAA--- 232

Query: 287 SAPPHGLCLVEVKYNEEH-LRLPAACPL 313
           +A   GL LV V Y + + L  P   PL
Sbjct: 233 TAKAEGLYLVAVDYPDRYDLPKPPMGPL 260

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query330
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]} Back     information, alignment and structure
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=2.4e-76  Score=551.37  Aligned_cols=257  Identities=34%  Similarity=0.527  Sum_probs=237.6

Q ss_pred             CCcceEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHH
Q 043662           46 FPGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLES  125 (330)
Q Consensus        46 ~~~~r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~  125 (330)
                      |+++||+|.|+||||+|+|||+|++.+|||++||+||.+++.   +++.+.+||||||||||++||+||+++... +.+.
T Consensus         1 p~~~r~al~i~Y~Gt~f~G~Q~Q~~~~TVq~~Le~aL~~~~~---~~~~~~~agRTD~GVhA~~qv~~~~~~~~~-~~~~   76 (264)
T d1dj0a_           1 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---EPITVFCAGRTDAGVHGTGQVVHFETTALR-KDAA   76 (264)
T ss_dssp             CCCEEEEEEEEECCTTSSCSCCTTCSSCHHHHHHHHHHHHHT---SCCCEEESSCCCTTCEEEEEEEEEEESCCC-CHHH
T ss_pred             CCcEEEEEEEEEECCCeeeEeECcCCCCHHHHHHHHHHHhhC---CCeEEEEeecccCCcceeeEEEEEeeccch-hhhh
Confidence            579999999999999999999999999999999999999976   789999999999999999999999998764 5788


Q ss_pred             HHHHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccc
Q 043662          126 IHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFS  205 (330)
Q Consensus       126 l~~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~  205 (330)
                      +...||+.||+||+|+++.+|+++||||++|++|+|+|++.++...+++.+.+.|+....+|+++|++|++.|+|+|||+
T Consensus        77 ~~~~lN~~Lp~dI~i~~~~~v~~~F~aR~~a~~r~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~a~~~~~G~hdF~  156 (264)
T d1dj0a_          77 WTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFT  156 (264)
T ss_dssp             HHHHHHHTSCTTEEEEEEEECCTTCCTTTTCCEEEEEEEEECSSSCCCTTTTSSEECCSCCCHHHHHHHHGGGCEEEECG
T ss_pred             hhcccccccccccccccceeccccccchhhhhhcccceeeccccccccccccccccccCCcchHHHHHHHhhccCccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccCCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCC
Q 043662          206 AFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYA  285 (330)
Q Consensus       206 ~F~~~~~~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~  285 (330)
                      +|++...  ...+++|+|..+++.+.++++.|+|+|+||||||||+|||+|++||+|++++++|+++|+.+++...   .
T Consensus       157 ~F~~~~~--~~~~~~r~i~~~~~~~~~~~i~i~i~g~sFL~~qVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r~~~---~  231 (264)
T d1dj0a_         157 SFRAVQC--QSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLA---A  231 (264)
T ss_dssp             GGCCTTC--CCSCCEEEEEEEEEEEETTEEEEEEEESCCCTTHHHHHHHHHHHHHTTSSCTTHHHHHHHHCCGGGS---C
T ss_pred             ccccccc--cCCCcccccccccceecCcEEEEEechhHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhcCCcccC---c
Confidence            9987754  3567899999999999999999999999999999999999999999999999999999998876543   3


Q ss_pred             CCcCCCCceEeeeecCCCCCCCCCCCC
Q 043662          286 LSAPPHGLCLVEVKYNEEHLRLPAACP  312 (330)
Q Consensus       286 ~~APa~GL~L~~V~Y~~~~~~~~~~~~  312 (330)
                      ++|||+||||++|.|++.. .+|..+.
T Consensus       232 ~~APa~GL~L~~V~Y~~~~-~~p~~~~  257 (264)
T d1dj0a_         232 ATAKAEGLYLVAVDYPDRY-DLPKPPM  257 (264)
T ss_dssp             CCCCSTTEEEEEEECCGGG-CCCCCCC
T ss_pred             cccCCCCCEEcccccCccc-cCCCCCC
Confidence            6899999999999997543 5554443