Citrus Sinensis ID: 045140

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-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------47

MENAETNTEKLPSPSLSPRQEPDPKRLKMSATSTSDDERDLIPAAAGADSTTKRQLCKRRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGVSAVGQVVSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALDSSSHRDRESVMASLGSGNELVKCLECSERGRKVIGVMGKRTYQLGLPSNDENASLNSQVKVDTVVSTCNGDRHNTNLESVESNKTISESVMVENANSESVNETLVESRTSETVQNENTDLSLDLDSKNDSKVMAEERSVNGEEKLLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIFASYNKKWKDSHEE

cccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccEEEEEEEEccccccEEEEccccccHHHHHHHHHHHccccccccccccccccEEEEccccccccccccEEEEEEccccHHHHHHHHHcccccEEEEEEEEcccccccccccccEEEEEEEccccccccccHHHHHHHHccccHHHHHHHHcccccccccEEEcccccccccccccccccccccccEEEEEEEEcccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHccHHHHHHccccccccHHHHHHHHHHHHHcccccccccccccccccccccEEEEEEEEEEEEEEEcccEEEEEEEEEcHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHcccccccccccccccEEEccccccccccccccccc

cccccccHHccccccccHHHcHHHHHHHccccccccccccccccccccccccccccccccEEEEEEEEEcccccccccccccccHHHHHHHHHHHcccccHccccccccccHHHHcccccccccccEEEEEEEEcccHHHHHHHHHHccccEEEEEEEEcccccccHHHccccEEEEEcccHccccccccHHHHHHcccccHHHHHHHHHHHHcccccccHHHHHccccccccccccccccccccccccHHHHccccccccHHHHcccccccccccccccccHcccccccHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccccccccccccccccccEEEEEEEEccccEEEccEEEEEEEEEcHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHcccccccccccccccEEEEccccccHHHHHcccccc

menaetnteklpspslsprqepdpkrlkmsatstsdderdlipaaagadsttKRQLCKRRKIAIFFAYCgvgyqgmqknpgaktieGDLEEALfhsgavserdrgnprrydwarsartdkgvsavgqvvsgrfcidppglverlnsnlptqirIFGYKRVtasfnakkfcdqrryVYLLPvfaldssshrdrESVMASLGSGNELVKCLECSERGRKVIGVMgkrtyqlglpsndenaslnsqVKVDTVVStcngdrhntnlesvesnKTISESVMVenansesvNETLVESrtsetvqnentdlsldldskndskvmaeersvngeekllkgsgfcygeEEKKRFNRILKHYvgshnfhnfttrtkaedpsarRYIISfgadsvvnvegidFLKCEVVGQSFMLHQIRKMIGLAVAVVRncapqsliETALqkdvninvptapevglYLDECIFASYnkkwkdshee

menaetnteklpspslsprqepdpkrLKMSatstsdderdlipaaagadsttkrqlCKRRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFhsgavserdrgnprrydwarsartdkgvsavgqvvsgrfcidppglverlnsnlPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFaldssshrDRESVMAslgsgnelvkCLECSERGRKVIGVMGKRTYQLglpsndenaslnsQVKVDTVVSTcngdrhntnlesvesnkTISESVMVENANSESVNETLVEsrtsetvqnentdlsldldskndSKVMAeersvngeekllkgsgfcyGEEEKKRFNRILKHyvgshnfhnfttrtkaedpsARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIetalqkdvninVPTAPEVGLYLDECIFASYnkkwkdshee

MENAETNTEKLPSPSLSPRQEPDPKRLKMSATSTSDDERDLIPAAAGADSTTKRQLCKRRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGVSAVGQVVSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALDSSSHRDRESVMASLGSGNELVKCLECSERGRKVIGVMGKRTYQLGLPSNDENASLNSQVKVDTVVSTCNGDRHNTNLESVESNKTISESVMVENANSESVNETLVESRTSETVQNENTdlsldldskndskVMAEERSVNGEEKLLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIFASYNKKWKDSHEE

******************************************************QLCKRRKIAIFFAYCGVGYQGMQ**********************************W******DKGVSAVGQVVSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALD*****************NELVKCLECSERGRKVIGVMGKRTYQLG******************************************************************************************************GSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIFASYNKKW******

************************************************************KIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGVSAVGQVVSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALDSSSHRDRESVMASLGSGNELVKCLECSERGRKVIGVMGKRTYQLGLPSNDENASLNSQVKVDTVVSTCNGDRHNTNLESVESNKTISESVMVENANSESVNETLVESRTSETVQNENTDLSLDLDSKNDSKVMAEERSVNGEEKLLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTK***PSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIFASYNK*W******

*************************************ERDLIPAAAGADSTTKRQLCKRRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGA*********RRYDWARSARTDKGVSAVGQVVSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALDS***********SLGSGNELVKCLECSERGRKVIGVMGKRTYQLGLPSNDENASLNSQVKVDTVVSTCNGDRHNTNLESVESNKTISESVMV************************NTDLSLDLDSKNDSKVMAEERSVNGEEKLLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIFASYNK********

*******************************************************LCKRRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGVSAVGQVVSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALDSSSHRDRESVMASLGSGNELVKCLECSERGRKVIGVMGKRTYQLGLPS*D******************************************************************************DSKVMAEERSVNGEEKLLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIFASYNKKWK*****

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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
Query		468	2.2.26 [Sep-21-2011]
O94396		534	tRNA pseudouridine syntha	yes	no	0.816	0.715	0.325	4e-50
Q9Y606		427	tRNA pseudouridine syntha	yes	no	0.365	0.400	0.415	4e-30
Q6CC39		528	tRNA pseudouridine syntha	yes	no	0.256	0.227	0.436	2e-29
Q4KM92		423	tRNA pseudouridine syntha	yes	no	0.367	0.406	0.423	3e-29
Q9WU56		423	tRNA pseudouridine syntha	yes	no	0.371	0.411	0.425	4e-29
Q6CWQ8		553	tRNA pseudouridine syntha	yes	no	0.320	0.271	0.401	2e-27
Q755C8		528	tRNA pseudouridine syntha	yes	no	0.284	0.251	0.4	5e-27
Q6FV05		549	tRNA pseudouridine syntha	yes	no	0.262	0.224	0.420	5e-27
Q12211		544	tRNA pseudouridine syntha	yes	no	0.262	0.226	0.404	9e-25
Q59S63		450	tRNA pseudouridine syntha	N/A	no	0.264	0.275	0.416	1e-21

>sp\|O94396\|PUS1_SCHPO tRNA pseudouridine synthase 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pus1 PE=1 SV=1	Back alignment and function desciption

 Score =  199 bits (505), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 135/415 (32%), Positives = 201/415 (48%), Gaps = 33/415 (7%)

Query: 59  RRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSART 118
           +RK+A    YCG GY GMQ NP +KTIEGDL +A   +GAVS  +  +P++   AR+ART
Sbjct: 43  KRKVACLVGYCGSGYHGMQLNPPSKTIEGDLFDAFVKAGAVSSYNADDPKKVALARAART 102

Query: 119 DKGVSAVGQVVSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYL 178
           DKGV A G V+S +  ++   L+E++N +LP  IR++   R   SFN + +C+ R Y Y+
Sbjct: 103 DKGVHAAGNVISLKLIMEDEKLIEKVNEHLPPSIRLWDVIRTINSFNPRTYCESRIYEYM 162

Query: 179 LPVFAL--DSSSHRDRESVMASLGSGNELVKCLECSERGRKVIGVMGKRTYQ-------- 228
           +P +A      S      +M +     E +     ++  R +    GK  +         
Sbjct: 163 VPTYAFVPPKPSSILGNCIMKNSPMPAEPINKENINQLSRSLFYEEGKEFWDDYDIAAKE 222

Query: 229 -LGLPSNDENASLNSQVKVDTVVSTCNGDRHNTNLESVESNKTISESVMVE-NANSESVN 286
            L L   D    +N   K           R    L + E+NK     V  + N + +S +
Sbjct: 223 ILSLYEQDPEGFVNPYSK-----------RGAAALANSENNKGSEAGVSAKTNPDMDSDS 271

Query: 287 ETLV-ESRTSETVQNENTDLSLDLDSKNDSKVMAEERSVNGEEKLLKGSGFCYGEEEKKR 345
             +V E    ++V++E+    +D   +        ER++   E +LK   +    +    
Sbjct: 272 SAIVNEFLKPDSVEDESAGSKIDPSYR-------LERALKHIE-VLKLKNYRISADRLSV 323

Query: 346 FNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFML 405
               L  YVG HNFHNFT        ++ R I SF A     +   +++ C+V GQSFML
Sbjct: 324 IRETLNQYVGVHNFHNFTVGQAFHQKNSNRVIRSFTASDPFMIGDTEWISCKVHGQSFML 383

Query: 406 HQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIFASYNK 460
           HQIRKMI LA+ VVR   P   I+ A +K   IN+P  P  GL L+   F  YN+
Sbjct: 384 HQIRKMIALAILVVRTGCPVERIQDAFKK-TKINIPKGPGFGLLLESPFFKGYNE 437

Formation of pseudouridine at positions 27 and 28 in the anticodon stem and loop of transfer RNAs; at positions 34 and 36 of intron-containing precursor tRNA(Ile) and at position 35 in the intron-containing tRNA(Tyr).
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -

>sp\|Q9Y606\|TRUA_HUMAN tRNA pseudouridine synthase A, mitochondrial OS=Homo sapiens GN=PUS1 PE=1 SV=3	Back alignment and function description

>sp\|Q6CC39\|PUS1_YARLI tRNA pseudouridine synthase 1 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=PUS1 PE=3 SV=1	Back alignment and function description

>sp\|Q4KM92\|TRUA_RAT tRNA pseudouridine synthase A, mitochondrial OS=Rattus norvegicus GN=Pus1 PE=2 SV=2	Back alignment and function description

>sp\|Q9WU56\|TRUA_MOUSE tRNA pseudouridine synthase A, mitochondrial OS=Mus musculus GN=Pus1 PE=1 SV=2	Back alignment and function description

>sp\|Q6CWQ8\|PUS1_KLULA tRNA pseudouridine synthase 1 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=PUS1 PE=3 SV=1	Back alignment and function description

>sp\|Q755C8\|PUS1_ASHGO tRNA pseudouridine synthase 1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=PUS1 PE=3 SV=2	Back alignment and function description

>sp\|Q6FV05\|PUS1_CANGA tRNA pseudouridine synthase 1 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=PUS1 PE=3 SV=1	Back alignment and function description

>sp\|Q12211\|PUS1_YEAST tRNA pseudouridine synthase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PUS1 PE=1 SV=1	Back alignment and function description

>sp\|Q59S63\|PUS1_CANAL tRNA pseudouridine synthase 1 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=PUS1 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
Query		468
255539108		584	pseudouridylate synthase, putative [Rici	0.982	0.787	0.655	1e-173
359492954		503	PREDICTED: tRNA pseudouridine synthase A	0.893	0.831	0.650	1e-170
356500639		548	PREDICTED: tRNA pseudouridine synthase A	0.895	0.764	0.677	1e-169
307136307		519	tRNA pseudouridine synthase family prote	0.948	0.855	0.652	1e-168
449455575		519	PREDICTED: tRNA pseudouridine synthase A	0.952	0.859	0.648	1e-168
147780612		559	hypothetical protein VITISV_031845 [Viti	0.929	0.778	0.614	1e-167
449485147		519	PREDICTED: LOW QUALITY PROTEIN: tRNA pse	0.952	0.859	0.646	1e-167
224061937		429	predicted protein [Populus trichocarpa]	0.771	0.841	0.683	1e-162
357480141		530	tRNA pseudouridine synthase [Medicago tr	0.935	0.826	0.631	1e-161
357480149		530	tRNA pseudouridine synthase [Medicago tr	0.935	0.826	0.629	1e-160

>gi\|255539108\|ref\|XP_002510619.1\| pseudouridylate synthase, putative [Ricinus communis] gi\|223551320\|gb\|EEF52806.1\| pseudouridylate synthase, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  614 bits (1583), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 319/487 (65%), Positives = 375/487 (77%), Gaps = 27/487 (5%)

Query: 1   MENAETNTEKLPSPSLSPRQEPDPKRLKMSATSTSDDERDLIPAAAGADSTTKRQLCKRR 60
           MEN++    K+ SP   P++EP+ KR +MS T+TSD+E     A     +T K+Q  KRR
Sbjct: 1   MENSDL---KITSPP--PQEEPERKRPRMS-TTTSDEEEIATTAPGDEAATVKKQRYKRR 54

Query: 61  KIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDK 120
           K+AIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAV E+DRG P+RYDWARSARTDK
Sbjct: 55  KMAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVPEQDRGCPKRYDWARSARTDK 114

Query: 121 GVSAVGQVVSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLP 180
           GVSAVGQV+SGRF +DPPGLV+RLNS LP+QIRIFGYKRVTASFNAKKFCD+RRYVYL+P
Sbjct: 115 GVSAVGQVISGRFYVDPPGLVDRLNSILPSQIRIFGYKRVTASFNAKKFCDRRRYVYLIP 174

Query: 181 VFALDSSSHRDRESVMASLGSGNELVKCLECSERGRKVIGVMGKRT-------YQLGLPS 233
           VFALD SSHRDRESV+ASLGSG+ELVKCLECSERGRKVIG +GKR+       +Q  +  
Sbjct: 175 VFALDPSSHRDRESVLASLGSGDELVKCLECSERGRKVIGAVGKRSFESKSEAFQTDILL 234

Query: 234 NDENASLNSQVKVDTVVSTCNGDRHNTNLESVE-SNKTISESVMVENA--------NSES 284
           N   A  N ++K D  +S  N      + E VE +N + +E    E+A        NSE 
Sbjct: 235 NGGCAIANCEIKEDISMSMDNAHGVRMHSEFVEQTNVSHNEDSETESAMPRTDILSNSED 294

Query: 285 VNETLVESRTSETVQNENTDLSLDLDSKN---DSKVMAEERSVNGEEKLLKGSGFCYGEE 341
            N    +S+  E + +E+     + +S+    DSK    E  VNGEE ++KGS FCYGEE
Sbjct: 295 GN-VKSDSKQEEVMVSEDAADGGNKESETMEKDSKASVGEERVNGEEHVMKGSEFCYGEE 353

Query: 342 EKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQ 401
           EK++FNRILK+YVGSHNFHNFTTRTKAEDPSA+RYIISF A + V VEGI+F+KCEV+GQ
Sbjct: 354 EKEKFNRILKYYVGSHNFHNFTTRTKAEDPSAQRYIISFDARTTVTVEGIEFVKCEVIGQ 413

Query: 402 SFMLHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIFASYNKK 461
           SFMLHQIRKMIGLAVA++RNCAP+SLI TALQKDV INVPTAPEVGLYLDEC F SYN+K
Sbjct: 414 SFMLHQIRKMIGLAVAIMRNCAPESLISTALQKDVKINVPTAPEVGLYLDECFFTSYNQK 473

Query: 462 WKDSHEE 468
           WKD HEE
Sbjct: 474 WKD-HEE 479

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359492954\|ref\|XP_002284797.2\| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356500639\|ref\|XP_003519139.1\| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like [Glycine max]	Back alignment and taxonomy information

>gi\|307136307\|gb\|ADN34131.1\| tRNA pseudouridine synthase family protein [Cucumis melo subsp. melo]	Back alignment and taxonomy information

>gi\|449455575\|ref\|XP_004145528.1\| PREDICTED: tRNA pseudouridine synthase A, mitochondrial-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|147780612\|emb\|CAN69118.1\| hypothetical protein VITISV_031845 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449485147\|ref\|XP_004157082.1\| PREDICTED: LOW QUALITY PROTEIN: tRNA pseudouridine synthase A, mitochondrial-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|224061937\|ref\|XP_002300673.1\| predicted protein [Populus trichocarpa] gi\|222842399\|gb\|EEE79946.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|357480141\|ref\|XP_003610356.1\| tRNA pseudouridine synthase [Medicago truncatula] gi\|355511411\|gb\|AES92553.1\| tRNA pseudouridine synthase [Medicago truncatula]	Back alignment and taxonomy information

>gi\|357480149\|ref\|XP_003610360.1\| tRNA pseudouridine synthase [Medicago truncatula] gi\|355511415\|gb\|AES92557.1\| tRNA pseudouridine synthase [Medicago truncatula] gi\|388510220\|gb\|AFK43176.1\| unknown [Medicago truncatula]	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
Query		468
TAIR\|locus:2199726		463	AT1G76120 [Arabidopsis thalian	0.521	0.526	0.578	1e-124
TAIR\|locus:2012898		549	AT1G20370 [Arabidopsis thalian	0.608	0.519	0.532	1.4e-73
UNIPROTKB\|E1BDL3		433	PUS1 "tRNA pseudouridine synth	0.412	0.445	0.413	4.8e-58
RGD\|1311871		423	Pus1 "pseudouridylate synthase	0.371	0.411	0.430	1.6e-57
UNIPROTKB\|Q4KM92		423	Pus1 "tRNA pseudouridine synth	0.371	0.411	0.430	1.6e-57
UNIPROTKB\|G8JLB3		384	PUS1 "tRNA pseudouridine synth	0.324	0.395	0.469	2.6e-57
UNIPROTKB\|Q9Y606		427	PUS1 "tRNA pseudouridine synth	0.324	0.355	0.469	2.6e-57
MGI\|MGI:1929237		423	Pus1 "pseudouridine synthase 1	0.371	0.411	0.425	3.3e-57
UNIPROTKB\|F1RFR2		433	PUS1 "tRNA pseudouridine synth	0.373	0.404	0.428	6.9e-57
UNIPROTKB\|F1NZ90		405	PUS1 "tRNA pseudouridine synth	0.378	0.437	0.397	8.8e-57

TAIR\|locus:2199726 AT1G76120 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 697 (250.4 bits), Expect = 1.0e-124, Sum P(2) = 1.0e-124
 Identities = 158/273 (57%), Positives = 194/273 (71%)

Query:    32 TSTSDDERDLIPAAAGADSTTKRQLCKRRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEE 91
             T+T+D+E DL  +  G    T+ Q     K+AI FA+CGVGYQGMQKNPGAKTIEG+LEE
Sbjct:     3 TTTTDEEIDL--SCDGG--VTEPQ-----KVAIIFAFCGVGYQGMQKNPGAKTIEGELEE 53

Query:    92 ALFHSGAVSERDRGNPRRYDWARSARTDKGVSAVGQVVSGRFCIDPPGLVERLNSNLPTQ 151
             ALFH+GAV E  RG P+ YD+ARSARTDKGVSAVGQVVSGRF +DP G V RLNSNLP Q
Sbjct:    54 ALFHAGAVPESIRGKPKLYDFARSARTDKGVSAVGQVVSGRFIVDPLGFVNRLNSNLPNQ 113

Query:   152 IRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALDSSSHRDRESVMASLGSGNELVKCLEC 211
             IRIFGYK VT SF++KKFCD+RRYVYLLPVFALD  SHRDRE+VMASLG G E VKC EC
Sbjct:   114 IRIFGYKHVTPSFSSKKFCDRRRYVYLLPVFALDPISHRDRETVMASLGPGEEYVKCFEC 173

Query:   212 SERGRKVI-GVMGK----------RTYQLGLPSNDENASLNSQVKVDTVVSTCNGDRHNT 260
             SERGRK+  G++GK            +Q  + SN+ +A L S +K++ + S   G     
Sbjct:   174 SERGRKIPPGLVGKWKGTNFGTKSLDFQSDISSNNSSA-LRSDIKIEALSSNLAG---LC 229

Query:   261 NLESVESNKTISESVMVENANSESVNETLVESR 293
             +++ VE  +   +S  + N NS   +ET V+S+
Sbjct:   230 SVD-VEVGRIQEDSCKL-NTNS---SETKVKSK 257

GO:0001522 "pseudouridine synthesis" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0009451 "RNA modification" evidence=IEA

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

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

TAIR\|locus:2012898 AT1G20370 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BDL3 PUS1 "tRNA pseudouridine synthase" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

RGD\|1311871 Pus1 "pseudouridylate synthase 1" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q4KM92 Pus1 "tRNA pseudouridine synthase A, mitochondrial" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|G8JLB3 PUS1 "tRNA pseudouridine synthase" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9Y606 PUS1 "tRNA pseudouridine synthase A, mitochondrial" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:1929237 Pus1 "pseudouridine synthase 1" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RFR2 PUS1 "tRNA pseudouridine synthase" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NZ90 PUS1 "tRNA pseudouridine synthase" [Gallus gallus (taxid:9031)]	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 Level	EC number	Confidence of Prediction
4th Layer	5.4.99.12	0.737
3rd Layer	5.4.99	0.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		468
cd02568		245	cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine sy	5e-58
cd02568		245	cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine sy	2e-57
PLN03078		513	PLN03078, PLN03078, Putative tRNA pseudouridine sy	3e-39
COG0101		266	COG0101, TruA, Pseudouridylate synthase [Translati	1e-30
TIGR00071		227	TIGR00071, hisT_truA, tRNA pseudouridine(38-40) sy	3e-24
COG0101		266	COG0101, TruA, Pseudouridylate synthase [Translati	8e-22
PRK00021		244	PRK00021, truA, tRNA pseudouridine synthase A; Val	2e-20
cd00497		215	cd00497, PseudoU_synth_TruA_like, Pseudouridine sy	5e-20
TIGR00071		227	TIGR00071, hisT_truA, tRNA pseudouridine(38-40) sy	2e-17
pfam01416		103	pfam01416, PseudoU_synth_1, tRNA pseudouridine syn	3e-17
cd02569		256	cd02569, PseudoU_synth_ScPus3, Pseudouridine synth	6e-17
cd02570		239	cd02570, PseudoU_synth_EcTruA, Eukaryotic and bact	4e-16
cd00497		215	cd00497, PseudoU_synth_TruA_like, Pseudouridine sy	4e-12
cd02866		219	cd02866, PseudoU_synth_TruA_Archea, Archeal pseudo	9e-12
PRK14589		265	PRK14589, PRK14589, tRNA pseudouridine synthase AC	1e-11
PRK00021		244	PRK00021, truA, tRNA pseudouridine synthase A; Val	2e-09
PRK14586		245	PRK14586, PRK14586, tRNA pseudouridine synthase AC	2e-09
PRK14588		272	PRK14588, PRK14588, tRNA pseudouridine synthase AC	6e-09
cd02570		239	cd02570, PseudoU_synth_EcTruA, Eukaryotic and bact	1e-08
PRK14587		256	PRK14587, PRK14587, tRNA pseudouridine synthase AC	8e-07
cd02569		256	cd02569, PseudoU_synth_ScPus3, Pseudouridine synth	7e-06
pfam01416		103	pfam01416, PseudoU_synth_1, tRNA pseudouridine syn	1e-05
PRK12434		245	PRK12434, PRK12434, tRNA pseudouridine synthase A;	2e-05
cd02866		219	cd02866, PseudoU_synth_TruA_Archea, Archeal pseudo	4e-05
PRK14589		265	PRK14589, PRK14589, tRNA pseudouridine synthase AC	4e-05
PRK14586		245	PRK14586, PRK14586, tRNA pseudouridine synthase AC	0.004

>gnl\|CDD\|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/ PUS2 like	Back alignment and domain information

 Score =  191 bits (487), Expect = 5e-58
 Identities = 65/119 (54%), Positives = 83/119 (69%), Gaps = 1/119 (0%)

Query: 338 YGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSV-VNVEGIDFLKC 396
           +  E  +RFN ILK YVG+HNFHNFT + K EDPSA R+I SF      V  EG++++  
Sbjct: 127 FALETLQRFNEILKEYVGTHNFHNFTVKKKFEDPSANRFIKSFYVSEPFVIEEGLEWISI 186

Query: 397 EVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIF 455
           ++ GQSFMLHQIRKMIGLA+A+VR  AP+SLIE +  KD  I +P AP +GL L+   F
Sbjct: 187 KIHGQSFMLHQIRKMIGLAIAIVRGGAPESLIELSFNKDKIIIIPLAPGLGLLLERPHF 245

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

>gnl\|CDD\|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/ PUS2 like	Back alignment and domain information

>gnl\|CDD\|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase; Provisional	Back alignment and domain information

>gnl\|CDD\|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase	Back alignment and domain information

>gnl\|CDD\|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated	Back alignment and domain information

>gnl\|CDD\|211322 cd00497, PseudoU_synth_TruA_like, Pseudouridine synthase, TruA family	Back alignment and domain information

>gnl\|CDD\|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase	Back alignment and domain information

>gnl\|CDD\|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase	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\|211337 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial pseudouridine synthases similar to E	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\|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated	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\|211337 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial pseudouridine synthases similar to E	Back alignment and domain information

>gnl\|CDD\|173051 PRK14587, PRK14587, 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\|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase	Back alignment and domain information

>gnl\|CDD\|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed	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\|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		468
KOG2553		416	consensus Pseudouridylate synthase [Translation, r	100.0
PLN03078		513	Putative tRNA pseudouridine synthase; Provisional	100.0
COG0101		266	TruA Pseudouridylate synthase [Translation, riboso	100.0
PRK00021		244	truA tRNA pseudouridine synthase A; Validated	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
cd02570		239	PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudou	100.0
TIGR00071		227	hisT_truA pseudouridylate synthase I. universal so	100.0
cd02568		245	PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: P	100.0
PRK14589		265	tRNA pseudouridine synthase ACD; Provisional	100.0
cd00497		224	PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudo	100.0
cd02866		221	PseudoU_synth_TruA_Archea PseudoU_synth_archea: Ps	100.0
cd02569		256	PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Ps	100.0
PRK14587		256	tRNA pseudouridine synthase ACD; Provisional	100.0
KOG2554		425	consensus Pseudouridylate synthase [Translation, r	100.0
KOG4393		295	consensus Predicted pseudouridylate synthase [RNA	100.0
PF01416		105	PseudoU_synth_1: tRNA pseudouridine synthase; Inte	99.82
PF01416		105	PseudoU_synth_1: tRNA pseudouridine synthase; Inte	98.23
PF10105		187	DUF2344: Uncharacterized protein conserved in bact	96.34
COG5011		228	Uncharacterized protein conserved in bacteria [Fun	85.68

>KOG2553 consensus Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

Probab=100.00  E-value=5.5e-88  Score=685.26  Aligned_cols=309  Identities=49%  Similarity=0.775  Sum_probs=277.5

Q ss_pred             cccccCcceEEEEEEEeCCCccceeecCCCCCHHHHHHHHHHHcCCCCcccCCCCCceeeeecccCCccccccCCEEeeE
Q 045140           53 KRQLCKRRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGVSAVGQVVSGR  132 (468)
Q Consensus        53 ~~~~~~krkval~i~Y~Gt~Y~G~Q~qp~~~TIEg~LE~AL~k~g~i~e~n~~~~~ki~~~rasRTDkGVHA~~qVvs~~  132 (468)
                      ++++++|+||+|+|||||++|+|||+||+.+||||+|++||+++|+|++.|+++++++.|+|||||||||||++||||++
T Consensus        30 ~~~k~~KrKVail~gY~G~gY~GmQ~N~~~kTIEgeL~~al~~aGaI~e~n~~dpkk~~~~raARTDKGVhA~~nviSlK  109 (416)
T KOG2553|consen   30 KAPKPRKRKVAILLGYCGTGYHGMQYNPPLKTIEGELFEALFKAGAISESNAGDPKKIGFARAARTDKGVHAAGNVISLK  109 (416)
T ss_pred             ccccccceEEEEEEEeccCCccceecCCCCCchHHHHHHHHHHcCCcccccccChHHhhhHHhhccccchhhhhheeEEE
Confidence            45889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecChhHHHHHHhhcCCCCeEEEEEEEcCCCCcccccCCceEEEEEecccccCCCCccchhHHHhhhCCCcchhhhhhhh
Q 045140          133 FCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALDSSSHRDRESVMASLGSGNELVKCLECS  212 (468)
Q Consensus       133 ~~id~~~l~~~LN~~LP~dIrV~~i~~V~~sF~AR~~c~~R~Y~Yllp~~~l~p~~~~~~~~~~a~~~~~~e~~~~~~~~  212 (468)
                      +.++++.++..||.+||++||||+|.||+++||||..|++|+|+|+||+++|.|+.+...+.+..      .+.+|+ |+
T Consensus       110 ~~~~~~~lv~~lN~~Lp~~IRv~~v~r~~k~F~pr~~CdsR~YeYllPtfal~~p~~~~~~~~~~------~~~~e~-~~  182 (416)
T KOG2553|consen  110 LELDDPELVEKLNEILPEQIRVWGVKRVTKSFNPRKQCDSRTYEYLLPTFALAPPKPSSLLEVDI------QYDKEF-EK  182 (416)
T ss_pred             EeeCcHHHHHHHhhhCCcceEEEEEEecCCCCCccccccceeEEEecceeeecCCCCccHHHhhh------hhhhhh-hh
Confidence            99999999999999999999999999999999999999999999999999999876655443332      267777 66


Q ss_pred             ccccccc-cccccccccCCCCCCCccccccccccccccccccCCCCCCCcccccccccccchhhhhhccCcccccccccc
Q 045140          213 ERGRKVI-GVMGKRTYQLGLPSNDENASLNSQVKVDTVVSTCNGDRHNTNLESVESNKTISESVMVENANSESVNETLVE  291 (468)
Q Consensus       213 ~~~~k~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  291 (468)
                      +-+++++ +.+++.+.+                                                               
T Consensus       183 ~f~~~~~~~~~~~~s~~---------------------------------------------------------------  199 (416)
T KOG2553|consen  183 EFWNTYPLSAKERLSGQ---------------------------------------------------------------  199 (416)
T ss_pred             hhccccchhhhhhhccc---------------------------------------------------------------
Confidence            6555431 111111000                                                               


Q ss_pred             ccccccccccccccccccccccchhhhhhhhhccccccccccccccCChhhHHHHHHHHhhcccccccccccCCcCCCCC
Q 045140          292 SRTSETVQNENTDLSLDLDSKNDSKVMAEERSVNGEEKLLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDP  371 (468)
Q Consensus       292 ~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~e~~~~alk~f~GtHdFhnFt~~~~~~d~  371 (468)
                                                          + ......|+++++.++.++++|+.|+|||||||||+++...||
T Consensus       200 ------------------------------------~-~~~~~~yr~s~~~l~~~~~~ls~Y~GthnFHNfT~~~~~~dp  242 (416)
T KOG2553|consen  200 ------------------------------------D-RKTESGYRLSEEKLEVFNTILSKYVGTHNFHNFTTGKDFTDP  242 (416)
T ss_pred             ------------------------------------c-cccccceeeCHHHHHHHHHHHHHhhcccccceecccCCCCCc
Confidence                                                0 013467999999999999999999999999999999999999


Q ss_pred             CceEEEEEEEEeeeeee--cCceEEEEEEEeCchhhHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCCCCCCCCCCCCce
Q 045140          372 SARRYIISFGADSVVNV--EGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLY  449 (468)
Q Consensus       372 s~~R~I~s~~~~~~~~~--~g~~~v~i~I~GqSFL~hQIRkMVG~lv~V~rg~~p~~~i~~~l~~~~~~~ip~APa~GL~  449 (468)
                      ++.|+|.+|.+++++.+  +|.+||.|.|+|||||+||||||||+||+|+|+++|.++|+.+|.++.++++|+||++||+
T Consensus       243 ss~R~I~s~~~~~pfv~~~~~~e~V~i~i~GQSFMLHQIRKMVglav~i~R~~~p~~~i~~af~~~~ri~IP~AP~~gLl  322 (416)
T KOG2553|consen  243 SSNRFIKSFTVSEPFVINDEGVEFVKIKIHGQSFMLHQIRKMVGLAVLIVRSGAPASTIQRAFNKEHKINIPKAPGEGLL  322 (416)
T ss_pred             cccceeeEEEecCcceeccCCceEEEEEEEcchhHHHHHHHHHHHHHHHHhcCCCHHHHHHhhCCCccccccCCCcceEE
Confidence            99999999999988877  7899999999999999999999999999999999999999999998899999999999999


Q ss_pred             eeecccCCCCcccccc-cCC
Q 045140          450 LDECIFASYNKKWKDS-HEE  468 (468)
Q Consensus       450 L~~v~y~~yn~~~~~~-~~~  468 (468)
                      |++|.|++||++...+ ||+
T Consensus       323 L~~~~F~~yn~~~~~~~~e~  342 (416)
T KOG2553|consen  323 LEEPHFESYNRKFRPSGHEE  342 (416)
T ss_pred             eecccccccccccCCCCcCC
Confidence            9999999999999988 553

>PLN03078 Putative tRNA pseudouridine synthase; Provisional	Back alignment and domain information

>COG0101 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK00021 truA tRNA pseudouridine synthase A; Validated	Back alignment and domain information

>PRK12434 tRNA pseudouridine synthase A; Reviewed	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

>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

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

>cd02866 PseudoU_synth_TruA_Archea PseudoU_synth_archea: Pseudouridine synthase,	Back alignment and domain information

>cd02569 PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like	Back alignment and domain information

>PRK14587 tRNA pseudouridine synthase ACD; Provisional	Back alignment and domain information

>KOG2554 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

>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

>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]	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
Query		468
1vs3_A		249	Crystal Structure Of The Trna Pseudouridine Synthas		7e-05

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

Back alignment and structure

Iteration: 1

Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust. Identities = 35/121 (28%), Positives = 56/121 (46%), Gaps = 13/121 (10%) Query: 60 RKIAIFFAYCGVGYQGMQKNP-GAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSART 118 R++ + Y G + G+Q+ G +T++G+LE AL GA+ + + RT Sbjct: 2 RRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKA----------VAAGRT 51 Query: 119 DKGVSAVGQV--VSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYV 176 D GV A+ V I + E LN LP +++ G + V F+A+K R Y Sbjct: 52 DAGVHALAMPFHVDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYR 111 Query: 177 Y 177 Y Sbjct: 112 Y 112

PyMOL of 1vs3

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		468
1vs3_A		249	TRNA pseudouridine synthase A; TRUA, tRNA modifica	1e-14
1vs3_A		249	TRNA pseudouridine synthase A; TRUA, tRNA modifica	2e-06
1dj0_A		264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	2e-14
1dj0_A		264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	2e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07

>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

 Score = 72.9 bits (180), Expect = 1e-14
 Identities = 34/125 (27%), Positives = 55/125 (44%), Gaps = 17/125 (13%)

Query: 60  RKIAIFFAYCGVGYQGMQKNP-GAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSART 118
           R++ +   Y G  + G+Q+   G +T++G+LE AL   G         P+      + RT
Sbjct: 2   RRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIG-------ALPKAVA---AGRT 51

Query: 119 DKGVSAVGQVVSGRF----CIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRR 174
           D GV A+             I    + E LN  LP  +++ G + V   F+A+K    R 
Sbjct: 52  DAGVHALAMPFH--VDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRA 109

Query: 175 YVYLL 179
           Y Y +
Sbjct: 110 YRYRI 114

PyMOL of 1vs3

>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

>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

>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

>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
Query		468
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}	Back alignment and structure

Probab=100.00  E-value=3.3e-72  Score=550.20  Aligned_cols=244  Identities=25%  Similarity=0.360  Sum_probs=216.7

Q ss_pred             cceEEEEEEEeCCCccceeecCCC-CCHHHHHHHHHHHcCCCCcccCCCCCceeeeecccCCccccccCCEEeeEee--c
Q 045140           59 RRKIAIFFAYCGVGYQGMQKNPGA-KTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGVSAVGQVVSGRFC--I  135 (468)
Q Consensus        59 krkval~i~Y~Gt~Y~G~Q~qp~~-~TIEg~LE~AL~k~g~i~e~n~~~~~ki~~~rasRTDkGVHA~~qVvs~~~~--i  135 (468)
                      |+||+|.|+||||+|+|||+||+. +|||++||+||.++|          +++.|.+||||||||||+|||+||++.  +
T Consensus         1 M~r~~l~i~YdGt~y~GwQ~Q~~~~~TVq~~Le~AL~~~~----------~~v~~~~agRTDaGVHA~gqv~~f~~~~~~   70 (249)
T 1vs3_A            1 MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIG----------ALPKAVAAGRTDAGVHALAMPFHVDVESAI   70 (249)
T ss_dssp             CEEEEEEEEECGGGCSBSSCCCTTCCCHHHHHHHHGGGGT----------BCSCCEESSCCBTTCEEEEEEEEEEECSCC
T ss_pred             CcEEEEEEEEECCCceeEeECCCCCCCHHHHHHHHHHHcC----------CcceEEEeccCcCCcCccccEEEEEECCCC
Confidence            679999999999999999999999 999999999999983          468899999999999999999999985  5


Q ss_pred             ChhHHHHHHhhcCCCCeEEEEEEEcCCCCcccccCCceEEEEEecccccCCCCccchhHHHhhhCCCcchhhhhhhhccc
Q 045140          136 DPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALDSSSHRDRESVMASLGSGNELVKCLECSERG  215 (468)
Q Consensus       136 d~~~l~~~LN~~LP~dIrV~~i~~V~~sF~AR~~c~~R~Y~Yllp~~~l~p~~~~~~~~~~a~~~~~~e~~~~~~~~~~~  215 (468)
                      +++.|+.+||++||+||+|+++.+|+.+||||++|.+|+|+|+|+.....++           +.               
T Consensus        71 ~~~~~~~~lN~~LP~dI~V~~~~~v~~~FhARf~a~~R~Y~Y~i~~~~~~~~-----------~~---------------  124 (249)
T 1vs3_A           71 PVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHPSP-----------LL---------------  124 (249)
T ss_dssp             CGGGHHHHHHHHSCTTEEEEEEEEECTTCCTTTTCSEEEEEEEEEECSSCCT-----------TT---------------
T ss_pred             CHHHHHHHHHhcCCcCEEEEEEEECCCCCCcccccccEEEEEEEccCCCCCh-----------hh---------------
Confidence            7889999999999999999999999999999999999999999986432110           00               


Q ss_pred             cccccccccccccCCCCCCCccccccccccccccccccCCCCCCCcccccccccccchhhhhhccCcccccccccccccc
Q 045140          216 RKVIGVMGKRTYQLGLPSNDENASLNSQVKVDTVVSTCNGDRHNTNLESVESNKTISESVMVENANSESVNETLVESRTS  295 (468)
Q Consensus       216 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  295 (468)
                                                                                                      
T Consensus       125 --------------------------------------------------------------------------------  124 (249)
T 1vs3_A          125 --------------------------------------------------------------------------------  124 (249)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             ccccccccccccccccccchhhhhhhhhccccccccccccccCChhhHHHHHHHHhhcccccccccccCCcCCCCCCceE
Q 045140          296 ETVQNENTDLSLDLDSKNDSKVMAEERSVNGEEKLLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARR  375 (468)
Q Consensus       296 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~e~~~~alk~f~GtHdFhnFt~~~~~~d~s~~R  375 (468)
                                                         ..+.|+...++|+++|++|++.|+|+|||+|||+...   ++++|
T Consensus       125 -----------------------------------~~~~~~~~~~ldi~~m~~aa~~l~G~HDF~~F~~~~~---~~~vR  166 (249)
T 1vs3_A          125 -----------------------------------RHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEET---RPGER  166 (249)
T ss_dssp             -----------------------------------TTTSEEECSCCCHHHHHHHHHHHSEEEEGGGGCSSCC---SCCEE
T ss_pred             -----------------------------------CCeeEEeCCCCCHHHHHHHHHHhcCceeHHheecCCC---CCCCc
Confidence                                               1346677778999999999999999999999997543   78999


Q ss_pred             EEEEEEEeeeeeecCceEEEEEEEeCchhhHHHHHHHHHHHHHHcCCCCHHHHHHHhC-CCCCCCCCCCCCCCceeeecc
Q 045140          376 YIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQ-KDVNINVPTAPEVGLYLDECI  454 (468)
Q Consensus       376 ~I~s~~~~~~~~~~g~~~v~i~I~GqSFL~hQIRkMVG~lv~V~rg~~p~~~i~~~l~-~~~~~~ip~APa~GL~L~~v~  454 (468)
                      +|+++++.+++..+| ++|.|+|+|+|||+||||+|||+|++||+|+.+.+.++.+|. +++...+|+|||+||||.+|.
T Consensus       167 ~I~~~~v~~~~~~~~-~~i~~~i~g~~FL~~mVR~mvG~l~~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~v~  245 (249)
T 1vs3_A          167 ELLEARLQVAEGEAG-LEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLYFVEAA  245 (249)
T ss_dssp             EEEEEEEEEEECSSS-EEEEEEEEESCCCTTHHHHHHHHHHHHHHSSSCGGGHHHHHHHCCGGGSCCCCCGGGEEEEEEE
T ss_pred             EEEEEEEEeccccCC-CEEEEEEEEChHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhCCCcccCcCccCCCCcEEeeee
Confidence            999999875433344 899999999999999999999999999999999999988884 677789999999999999999


Q ss_pred             cCC
Q 045140          455 FAS  457 (468)
Q Consensus       455 y~~  457 (468)
                      |++
T Consensus       246 Y~~  248 (249)
T 1vs3_A          246 YPE  248 (249)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            963

PyMOL of 1vs3

>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

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		468
d1dj0a_		264	d.265.1.1 (A:) Pseudouridine synthase I TruA {Esch	2e-14
d1dj0a_		264	d.265.1.1 (A:) Pseudouridine synthase I TruA {Esch	6e-09

>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 = 70.8 bits (172), Expect = 2e-14
 Identities = 34/121 (28%), Positives = 47/121 (38%), Gaps = 11/121 (9%)

Query: 59  RRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSART 118
             KIA+   Y G  Y G Q+    ++++  LE+AL                     + RT
Sbjct: 3   VYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVA---------NEPITVFCAGRT 53

Query: 119 DKGVSAVGQVVSGRFC--IDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYV 176
           D GV   GQVV                +N+NLP  I +   K V   F+A+     RRY 
Sbjct: 54  DAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYR 113

Query: 177 Y 177
           Y
Sbjct: 114 Y 114

PyMOL of d1dj0a_

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		468
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=7.8e-67  Score=513.17  Aligned_cols=245  Identities=25%  Similarity=0.379  Sum_probs=214.5

Q ss_pred             cCcceEEEEEEEeCCCccceeecCCCCCHHHHHHHHHHHcCCCCcccCCCCCceeeeecccCCccccccCCEEeeEee--
Q 045140           57 CKRRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGVSAVGQVVSGRFC--  134 (468)
Q Consensus        57 ~~krkval~i~Y~Gt~Y~G~Q~qp~~~TIEg~LE~AL~k~g~i~e~n~~~~~ki~~~rasRTDkGVHA~~qVvs~~~~--  134 (468)
                      .+|+||||.|+|+||+|+|||+||+.+||||+||+||.+++.         +++.|.+||||||||||++|||||++.  
T Consensus         1 p~~~r~al~i~Y~Gt~f~G~Q~Q~~~~TVq~~Le~aL~~~~~---------~~~~~~~agRTD~GVhA~~qv~~~~~~~~   71 (264)
T d1dj0a_           1 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVAN---------EPITVFCAGRTDAGVHGTGQVVHFETTAL   71 (264)
T ss_dssp             CCCEEEEEEEEECCTTSSCSCCTTCSSCHHHHHHHHHHHHHT---------SCCCEEESSCCCTTCEEEEEEEEEEESCC
T ss_pred             CCcEEEEEEEEEECCCeeeEeECcCCCCHHHHHHHHHHHhhC---------CCeEEEEeecccCCcceeeEEEEEeeccc
Confidence            368999999999999999999999999999999999999864         568999999999999999999999985  


Q ss_pred             cChhHHHHHHhhcCCCCeEEEEEEEcCCCCcccccCCceEEEEEecccccCCCCccchhHHHhhhCCCcchhhhhhhhcc
Q 045140          135 IDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALDSSSHRDRESVMASLGSGNELVKCLECSER  214 (468)
Q Consensus       135 id~~~l~~~LN~~LP~dIrV~~i~~V~~sF~AR~~c~~R~Y~Yllp~~~l~p~~~~~~~~~~a~~~~~~e~~~~~~~~~~  214 (468)
                      .++..+...||++||+||+|+++.+|+.+||||++|.+|+|+|+|+.....+...                         
T Consensus        72 ~~~~~~~~~lN~~Lp~dI~i~~~~~v~~~F~aR~~a~~r~Y~Y~i~~~~~~~~~~-------------------------  126 (264)
T d1dj0a_          72 RKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVL-------------------------  126 (264)
T ss_dssp             CCHHHHHHHHHHTSCTTEEEEEEEECCTTCCTTTTCCEEEEEEEEECSSSCCCTT-------------------------
T ss_pred             hhhhhhhcccccccccccccccceeccccccchhhhhhcccceeecccccccccc-------------------------
Confidence            5678899999999999999999999999999999999999999998643211100                         


Q ss_pred             ccccccccccccccCCCCCCCccccccccccccccccccCCCCCCCcccccccccccchhhhhhccCccccccccccccc
Q 045140          215 GRKVIGVMGKRTYQLGLPSNDENASLNSQVKVDTVVSTCNGDRHNTNLESVESNKTISESVMVENANSESVNETLVESRT  294 (468)
Q Consensus       215 ~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  294 (468)
                                                                                                      
T Consensus       127 --------------------------------------------------------------------------------  126 (264)
T d1dj0a_         127 --------------------------------------------------------------------------------  126 (264)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             cccccccccccccccccccchhhhhhhhhccccccccccccccCChhhHHHHHHHHhhcccccccccccCCcCCCCCCce
Q 045140          295 SETVQNENTDLSLDLDSKNDSKVMAEERSVNGEEKLLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSAR  374 (468)
Q Consensus       295 ~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~e~~~~alk~f~GtHdFhnFt~~~~~~d~s~~  374 (468)
                                                          ..+.++....+|+++|++|++.|+|+|||+||++... ...+..
T Consensus       127 ------------------------------------~~~~~~~~~~ld~~~m~~a~~~~~G~hdF~~F~~~~~-~~~~~~  169 (264)
T d1dj0a_         127 ------------------------------------SKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQC-QSRTPW  169 (264)
T ss_dssp             ------------------------------------TTSSEECCSCCCHHHHHHHHGGGCEEEECGGGCCTTC-CCSCCE
T ss_pred             ------------------------------------ccccccccCCcchHHHHHHHhhccCcccccccccccc-cCCCcc
Confidence                                                0234556678899999999999999999999987543 345788


Q ss_pred             EEEEEEEEeeeeeecCceEEEEEEEeCchhhHHHHHHHHHHHHHHcCCCCHHHHHHHhC-CCCCCCCCCCCCCCceeeec
Q 045140          375 RYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQ-KDVNINVPTAPEVGLYLDEC  453 (468)
Q Consensus       375 R~I~s~~~~~~~~~~g~~~v~i~I~GqSFL~hQIRkMVG~lv~V~rg~~p~~~i~~~l~-~~~~~~ip~APa~GL~L~~v  453 (468)
                      |+|..+.+..    ++ ++|.|+|+|+|||+||||+|||+|++||+|+++++.|+.+|. +++...+|+|||+||||++|
T Consensus       170 r~i~~~~~~~----~~-~~i~i~i~g~sFL~~qVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V  244 (264)
T d1dj0a_         170 RNVMHINVTR----HG-PYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAV  244 (264)
T ss_dssp             EEEEEEEEEE----ET-TEEEEEEEESCCCTTHHHHHHHHHHHHHTTSSCTTHHHHHHHHCCGGGSCCCCCSTTEEEEEE
T ss_pred             ccccccccee----cC-cEEEEEechhHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhcCCcccCccccCCCCCEEccc
Confidence            9999888653    33 799999999999999999999999999999999988988885 66778899999999999999


Q ss_pred             ccCC
Q 045140          454 IFAS  457 (468)
Q Consensus       454 ~y~~  457 (468)
                      .|+.
T Consensus       245 ~Y~~  248 (264)
T d1dj0a_         245 DYPD  248 (264)
T ss_dssp             ECCG
T ss_pred             ccCc
Confidence            9953

PyMOL of d1dj0a_