Citrus Sinensis ID: 009530

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-------470-------480-------490-------500-------510-------520-------530--

MGRNSKKRKERGDNPFDSRGSENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKIAKAKLVNIVKEEEAVCGNKEKDPSDCMKQSESLSKDIKLSTENNEAACAKEVKQPHVESVCGADSQGKQMALKLGLTLPSSCYATMAIRELLKTSTSVAFHKTLN

ccccccccccccccccccccccccccccccEEEEEEEEccccHHHHHHHHHHHHccccccccccccccccEEEEEEEEEEcccHHHHHHHHcccccEEEEEEEEEccccccccccccEEEEEEcccccccHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHcccHHHHHHHHccccccccHHHHHHHHHHcccccHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEccEEEEccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccEEcEEcccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccEEccccEEEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHcccccHHcccccccHHHHHHHcccccccccccccccccccEEEEEEEEccccHHHHHHHHHHHcccccHHHHHccc

ccccccccccccccccccccccccccccccEEEEEEEEcccHHHHHHHHHHHHcccccccEEEcccccccEEEEEEEEEEEccHHHHHHHHHHccccEEEEEEEEccccEcccccccEEEEEEEcccccHHHHHHHHHHHHHHcccEEEcccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHccHHHHHHHHHHHHHHcccccHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEcccEEEEccccccccccccccHHccccccccccccccccccccccHHHccccEEEEcHHHHHcccEEEEEEEcccccccEEccccHHHHHHHHHHHHccccHHHHcccccccccccccccHHHHEEcccccEEEEEEEccccccccccHHHHHHccccccccccHHHHHHHHHHccccccccHHHHHHHHHHccccccccHHHHcccccHHHcccccccccEEEEEEEEEccHHHHHHHHHHHHHcccccHHHHHccc

mgrnskkrkergdnpfdsrgsenwpeQLGKFLRFHLYKENKDTQEALGLISKMLgilprsfgfagtkdkrsvsTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASAnslgrngfinyfglqrfgsgsvpthlVGATLLRGEWKSAVKMILDPREGERNEISKAREYYketddidgtlrklpRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLvfckgddtekelgcvnpefeyessndaddsshldevpetdhpdgrhnlVKTVtaadinsgkytiddvvlplpgsrviypmndVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWELLTyidgnkplaetdlDKIAKAKLVNIVKEEEavcgnkekdpsdcmkqseslskdiklsteNNEAACAkevkqphvesvcgadsQGKQMALKLgltlpsscyATMAIRELLKTSTSVAFHKTLN

mgrnskkrkergdnpfdsrgsenwpeQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFgfagtkdkrsvstQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASanslgrngFINYFGLQRFGSGSVPTHLVGAtllrgewksAVKMildpregerneiskareyyketddidgtlrKLPRHLVAERAILqclkkcpgnyLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVpetdhpdgrhnlvktvtaadinsgkytiddvvlplPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKIAKAKLVNIVKEeeavcgnkekdpsdcmkqseSLSKDIKLSTENNEAACAKEVKQPHVESVCGADSQGKQMALKLGLTLPSSCYATMAIRELLktstsvafhktln

**************************QLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILD**************YYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCV********************************LVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKIAKAKLVNIVKEE*********************************************************MALKLGLTLPSSCYATMAIRELLKTST*V*******

*************************EQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDE**********HNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHN***F*ITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKIA****************************************************************QGKQMALKLGLTLPSSCYATMAIRELLKTSTSV***K***

********************SENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAG**********RVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEY********************PDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKIAKAKLVNIVKEEEAV*****************LSKDIKLSTENNEAACAKEVKQPHVESVCGADSQGKQMALKLGLTLPSSCYATMAIRELLKTSTSVAFHKTLN

**********************NWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKG***********************************HPDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKIAKAK*****************D*SDCMKQSESLSKDIKLST************************QGKQMALKLGLTLPSSCYATMAIRELLKTST*********

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		532	2.2.26 [Sep-21-2011]
Q96PZ0		661	Pseudouridylate synthase	yes	no	0.763	0.614	0.343	7e-78
Q08647		676	Multisubstrate pseudourid	yes	no	0.859	0.676	0.348	1e-76
O74343		680	Putative pseudouridine sy	yes	no	0.804	0.629	0.341	1e-74
Q08DI8		659	Pseudouridylate synthase	yes	no	0.669	0.540	0.358	2e-71
Q9H0K6		701	Pseudouridylate synthase	no	no	0.684	0.519	0.296	2e-46
Q8CE46		702	Pseudouridylate synthase	no	no	0.657	0.498	0.311	1e-43
Q17426		577	Putative pseudouridine sy	yes	no	0.473	0.436	0.376	1e-38
Q1L8I0		643	Pseudouridylate synthase	no	no	0.635	0.525	0.289	1e-36
Q466V2		438	Probable tRNA pseudouridi	yes	no	0.481	0.584	0.344	2e-35
C5A1W0		415	Probable tRNA pseudouridi	yes	no	0.453	0.580	0.368	1e-33

>sp\|Q96PZ0\|PUS7_HUMAN Pseudouridylate synthase 7 homolog OS=Homo sapiens GN=PUS7 PE=1 SV=2	Back alignment and function desciption

 Score =  291 bits (746), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 176/512 (34%), Positives = 261/512 (50%), Gaps = 106/512 (20%)

Query: 23  NWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQ 82
           +WP+  G +  F LYKENKDT +A+ ++SK L + P  F + GTKDKR+++ Q + V K 
Sbjct: 249 SWPKSRGSYCHFVLYKENKDTMDAINVLSKYLRVKPNIFSYMGTKDKRAITVQEIAVLKI 308

Query: 83  RASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLG 142
            A +LA LNK L+  +LG+F Y K  L LG+L GN FT+ LR  +  ++D ++ + NSL 
Sbjct: 309 TAQRLAHLNKCLMNFKLGNFSYQKNPLKLGELQGNHFTVVLRN-ITGTDDQVQQAMNSLK 367

Query: 143 RNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREG-ERNEISKAREYYKE 201
             GFINY+G+QRFG+ +VPT+ VG  +L+  W   + +IL PR G E+  + K RE + +
Sbjct: 368 EIGFINYYGMQRFGTTAVPTYQVGRAILQNSWTEVMDLILKPRSGAEKGYLVKCREEWAK 427

Query: 202 TDDIDGTLRKLPRHLVAERAILQCLKKCP-GNYLQALKAIPRTLRMMYVHSYQSFLWNHA 260
           T D    LRKLP     E  +L+ L K    N + A   IPR  R+MY+HSYQS++WN+ 
Sbjct: 428 TKDPTAALRKLPVKRCVEGQLLRGLSKYGMKNIVSAFGIIPRNNRLMYIHSYQSYVWNNM 487

Query: 261 ASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHP 320
            S R++ +G +  V GDLV  KG                        +++++E       
Sbjct: 488 VSKRIEDYGLKP-VPGDLVL-KG----------------------ATATYIEE------- 516

Query: 321 DGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESL 380
                        D+N+  Y+I DVV+PLPG  VIYP + + E Y  +   D +++    
Sbjct: 517 ------------DDVNN--YSIHDVVMPLPGFDVIYPKHKIQEAYREMLTADNLDIDNMR 562

Query: 381 HNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKIAKAKLVNIVKEEE 440
           H ++++   S++G YR++  +P +  WE++ Y D   PL  TD+D +             
Sbjct: 563 HKIRDY---SLSGAYRKIIIRPQNVSWEVVAYDDPKIPLFNTDVDNL------------- 606

Query: 441 AVCGNKEKDPSDCMKQSESLSKDIKLSTENNEAACAKEVKQPHVESVCGADSQGKQMALK 500
                                                E K P V +     S+GK  ALK
Sbjct: 607 -------------------------------------EGKTPPVFA-----SEGKYRALK 624

Query: 501 LGLTLPSSCYATMAIRELLKTSTSVAFHKTLN 532
           +  +LP S YATMAIRE+LK  TS+     LN
Sbjct: 625 MDFSLPPSTYATMAIREVLKMDTSIKNQTQLN 656

Homo sapiens (taxid: 9606)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -

>sp\|Q08647\|PUS7_YEAST Multisubstrate pseudouridine synthase 7 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PUS7 PE=1 SV=1	Back alignment and function description

>sp\|O74343\|YH2X_SCHPO Putative pseudouridine synthase C1A4.09 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC1A4.09 PE=3 SV=1	Back alignment and function description

>sp\|Q08DI8\|PUS7_BOVIN Pseudouridylate synthase 7 homolog OS=Bos taurus GN=PUS7 PE=2 SV=1	Back alignment and function description

>sp\|Q9H0K6\|PUS7L_HUMAN Pseudouridylate synthase 7 homolog-like protein OS=Homo sapiens GN=PUS7L PE=1 SV=1	Back alignment and function description

>sp\|Q8CE46\|PUS7L_MOUSE Pseudouridylate synthase 7 homolog-like protein OS=Mus musculus GN=Pus7l PE=1 SV=1	Back alignment and function description

>sp\|Q17426\|YQ4B_CAEEL Putative pseudouridine synthase B0024.11 OS=Caenorhabditis elegans GN=B0024.11 PE=3 SV=1	Back alignment and function description

>sp\|Q1L8I0\|PUS7L_DANRE Pseudouridylate synthase 7 homolog-like protein OS=Danio rerio GN=pus7l PE=2 SV=1	Back alignment and function description

>sp\|Q466V2\|TRUD_METBF Probable tRNA pseudouridine synthase D OS=Methanosarcina barkeri (strain Fusaro / DSM 804) GN=truD PE=3 SV=1	Back alignment and function description

>sp\|C5A1W0\|TRUD_THEGJ Probable tRNA pseudouridine synthase D OS=Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) GN=truD 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		532
225451285		694	PREDICTED: multisubstrate pseudouridine	0.998	0.765	0.723	0.0
298204887		693	unnamed protein product [Vitis vinifera]	0.996	0.764	0.717	0.0
255542334		753	tRNA pseudouridine synthase d, putative	0.992	0.701	0.716	0.0
145338120		715	pseudouridine synthase [Arabidopsis thal	0.971	0.723	0.694	0.0
356571176		687	PREDICTED: multisubstrate pseudouridine	0.986	0.764	0.685	0.0
449449641		719	PREDICTED: putative pseudouridine syntha	0.973	0.720	0.705	0.0
356504097		687	PREDICTED: multisubstrate pseudouridine	0.986	0.764	0.676	0.0
297833180		710	pseudouridylate synthase [Arabidopsis ly	0.960	0.719	0.674	0.0
357512259		669	Pseudouridylate synthase-like protein [M	0.934	0.742	0.645	0.0
357133066		693	PREDICTED: pseudouridylate synthase 7 ho	0.951	0.730	0.603	1e-180

>gi\|225451285\|ref\|XP_002272750.1\| PREDICTED: multisubstrate pseudouridine synthase 7-like [Vitis vinifera]	Back alignment and taxonomy information

 Score =  807 bits (2084), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 384/531 (72%), Positives = 448/531 (84%)

Query: 2   GRNSKKRKERGDNPFDSRGSENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSF 61
           GRNS+KRK+R D PFDSRGS+NW E +GKFLRFHLYKENKDTQEA+GLI KMLGI PRSF
Sbjct: 161 GRNSRKRKDRRDKPFDSRGSDNWSEHVGKFLRFHLYKENKDTQEAIGLIGKMLGIQPRSF 220

Query: 62  GFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTI 121
           GFAGTKDKRSVSTQRVTVFKQ A++LAALN+RLIGI++GDFC+V+EGL+LGQLLGNRFTI
Sbjct: 221 GFAGTKDKRSVSTQRVTVFKQHANRLAALNERLIGIKVGDFCHVREGLVLGQLLGNRFTI 280

Query: 122 TLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMI 181
           TLRGVV DSE+ IKASA++LGR GFINYFGLQRFGSGSVPTHL+GA LLRGEW++AV +I
Sbjct: 281 TLRGVVADSEETIKASADALGRLGFINYFGLQRFGSGSVPTHLIGAALLRGEWETAVSLI 340

Query: 182 LDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIP 241
           LDPREGER+ I KAREYYKE+DDI+GTLR+ PRHLVAERAILQCLKK PGNYLQALKAIP
Sbjct: 341 LDPREGERDAIRKAREYYKESDDIEGTLRQFPRHLVAERAILQCLKKYPGNYLQALKAIP 400

Query: 242 RTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYES 301
           RTLRMMYVHSYQS+LWNHAAS RVQ +GT+ VV+GDLV+CKGD+ EK    VN EF+ + 
Sbjct: 401 RTLRMMYVHSYQSYLWNHAASMRVQNYGTKQVVLGDLVYCKGDNAEKVTRVVNSEFDDDG 460

Query: 302 SNDADDSSHLDEVPETDHPDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDV 361
            +DA DSSH DE+ ETD P+ R++ VK + A D+ +G YTIDDVVLPLPGSR IYP ND+
Sbjct: 461 CSDAFDSSHFDEISETDLPEERNDPVKALDAEDLLTGNYTIDDVVLPLPGSRAIYPTNDI 520

Query: 362 AEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAE 421
           A+VYH  A+KD I+LTES H+VKEFSIT+MTG +RRVFQKP+DFEWELLTY +GN PLAE
Sbjct: 521 AQVYHDFAKKDAISLTESAHSVKEFSITNMTGGFRRVFQKPIDFEWELLTYTEGNIPLAE 580

Query: 422 TDLDKIAKAKLVNIVKEEEAVCGNKEKDPSDCMKQSESLSKDIKLSTENNEAACAKEVKQ 481
           TD DKI K+K  NI+  E++  GN++++   CMKQSES   ++ LST+NNE     E+  
Sbjct: 581 TDWDKITKSKPSNIIGGEDSRNGNEKENSFQCMKQSESFEHNVNLSTDNNEPNGVTEIGL 640

Query: 482 PHVESVCGADSQGKQMALKLGLTLPSSCYATMAIRELLKTSTSVAFHKTLN 532
           P VE    + +   Q ALKL  TLP+SCYATMAIRELLKTSTSVAF KTLN
Sbjct: 641 PQVEPQFESGAPEAQRALKLSFTLPASCYATMAIRELLKTSTSVAFQKTLN 691

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|298204887\|emb\|CBI34194.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255542334\|ref\|XP_002512230.1\| tRNA pseudouridine synthase d, putative [Ricinus communis] gi\|223548191\|gb\|EEF49682.1\| tRNA pseudouridine synthase d, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|145338120\|ref\|NP_187133.3\| pseudouridine synthase [Arabidopsis thaliana] gi\|52354299\|gb\|AAU44470.1\| hypothetical protein AT3G04820 [Arabidopsis thaliana] gi\|61742699\|gb\|AAX55170.1\| hypothetical protein At3g04820 [Arabidopsis thaliana] gi\|332640619\|gb\|AEE74140.1\| pseudouridine synthase [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|356571176\|ref\|XP_003553755.1\| PREDICTED: multisubstrate pseudouridine synthase 7-like [Glycine max]	Back alignment and taxonomy information

>gi\|449449641\|ref\|XP_004142573.1\| PREDICTED: putative pseudouridine synthase C1A4.09-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356504097\|ref\|XP_003520835.1\| PREDICTED: multisubstrate pseudouridine synthase 7-like [Glycine max]	Back alignment and taxonomy information

>gi\|297833180\|ref\|XP_002884472.1\| pseudouridylate synthase [Arabidopsis lyrata subsp. lyrata] gi\|297330312\|gb\|EFH60731.1\| pseudouridylate synthase [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|357512259\|ref\|XP_003626418.1\| Pseudouridylate synthase-like protein [Medicago truncatula] gi\|355501433\|gb\|AES82636.1\| Pseudouridylate synthase-like protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|357133066\|ref\|XP_003568149.1\| PREDICTED: pseudouridylate synthase 7 homolog [Brachypodium distachyon]	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		532
TAIR\|locus:2114870		715	AT3G04820 [Arabidopsis thalian	0.971	0.723	0.694	1.1e-190
ZFIN\|ZDB-GENE-060620-1		627	pus7 "pseudouridylate synthase	0.486	0.413	0.456	4.6e-86
DICTYBASE\|DDB_G0271632		729	pus7 "tRNA pseudouridine synth	0.834	0.609	0.371	6.5e-83
UNIPROTKB\|F1ML88		659	PUS7 "Pseudouridylate synthase	0.484	0.391	0.437	4.5e-82
UNIPROTKB\|E2RAX2		764	EFCAB10 "Uncharacterized prote	0.484	0.337	0.433	4.5e-82
UNIPROTKB\|F1NCJ9		656	PUS7 "Uncharacterized protein"	0.484	0.393	0.422	9.4e-82
UNIPROTKB\|Q08DI8		659	PUS7 "Pseudouridylate synthase	0.484	0.391	0.433	1.2e-81
UNIPROTKB\|G3N0P5		731	PUS7 "Pseudouridylate synthase	0.484	0.352	0.432	3.1e-81
RGD\|1307054		660	Pus7 "pseudouridylate synthase	0.484	0.390	0.437	6.5e-81
SGD\|S000005769		676	PUS7 "Pseudouridine synthase"	0.753	0.593	0.390	1.8e-76

TAIR\|locus:2114870 AT3G04820 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1848 (655.6 bits), Expect = 1.1e-190, P = 1.1e-190
 Identities = 369/531 (69%), Positives = 422/531 (79%)

Query:     2 GRNSKKRKERGDNPFDSRGSENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSF 61
             G  SKKRKERGD PFDSRGSE+WPE +GKFLRFHLYKENKDTQEALGLI KMLG+ P+SF
Sbjct:   199 GNRSKKRKERGDKPFDSRGSEHWPEHVGKFLRFHLYKENKDTQEALGLIGKMLGVQPKSF 258

Query:    62 GFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTI 121
             GF+GTKDKRSVSTQRVTVFKQ+ASKLAALNKRL GI++GDFC VKEGLLLGQL+GNRFTI
Sbjct:   259 GFSGTKDKRSVSTQRVTVFKQQASKLAALNKRLFGIKVGDFCNVKEGLLLGQLMGNRFTI 318

Query:   122 TLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMI 181
             TLRGVV DSE+ IK SA SLG++GFINYFGLQRFGSGSVPTH VGA LL+GEWK AV MI
Sbjct:   319 TLRGVVADSEETIKQSAESLGKDGFINYFGLQRFGSGSVPTHHVGAALLKGEWKDAVDMI 378

Query:   182 LDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIP 241
             LDPRE ER+ ++ AREYYKET DIDGTLR+LPR+LVAERAILQCLKKCPGNYLQALK IP
Sbjct:   379 LDPRETERHVVNDAREYYKETGDIDGTLRQLPRYLVAERAILQCLKKCPGNYLQALKGIP 438

Query:   242 RTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYES 301
             RTLRMMYVHSYQS+LWN+AAS RV+ +GT  VV+GDLV  K D  ++ +  +  E   ES
Sbjct:   439 RTLRMMYVHSYQSYLWNNAASLRVKNYGTSQVVLGDLVSTKVDAAKRMVDSLTSEHN-ES 497

Query:   302 SNDADDSSHLDEVPETDHPDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDV 361
             S +A D   +D+    D P  R +LVK V+  D+ +G Y+  D+VLPLPGSRVIYP ND+
Sbjct:   498 SEEALDCDQVDDTAVVDLPAERSDLVKVVSIEDLEAGTYSTSDIVLPLPGSRVIYPSNDI 557

Query:   362 AEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAE 421
             AE+YH LA+KDGI+LTES+H VKEFSITSMTG YRRVFQKP+DFEWELLTY D NKPLAE
Sbjct:   558 AEIYHDLAKKDGISLTESIHGVKEFSITSMTGGYRRVFQKPIDFEWELLTYTDSNKPLAE 617

Query:   422 TDLDKIAKAKLVNIVKEEEAVCGNKEKDPSDCMKQSESLSKDIKLSTENNEAACAKEVKQ 481
             TDLD+I   K V  V   E +     K  ++     E+  KD    T++NEA   K+   
Sbjct:   618 TDLDRIPMNKPVEKVGSTEEIEDESMKSDTNPHDSGETNLKD---QTDSNEAE--KDTGN 672

Query:   482 PHVESVCGADSQGKQMALKLGLTLPSSCYATMAIRELLKTSTSVAFHKTLN 532
             P        DS+  QMALK+ LTLPSSCYATMAIRELLKTSTSVA+HKTLN
Sbjct:   673 P--------DSEQTQMALKMALTLPSSCYATMAIRELLKTSTSVAYHKTLN 715

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;TAS

GO:0000741 "karyogamy" evidence=RCA

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

ZFIN\|ZDB-GENE-060620-1 pus7 "pseudouridylate synthase 7 homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0271632 pus7 "tRNA pseudouridine synthase D" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

UNIPROTKB\|F1ML88 PUS7 "Pseudouridylate synthase 7 homolog" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RAX2 EFCAB10 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NCJ9 PUS7 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|Q08DI8 PUS7 "Pseudouridylate synthase 7 homolog" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|G3N0P5 PUS7 "Pseudouridylate synthase 7 homolog" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

RGD\|1307054 Pus7 "pseudouridylate synthase 7 homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

SGD\|S000005769 PUS7 "Pseudouridine synthase" [Saccharomyces cerevisiae (taxid:4932)]	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
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		532
cd02576		371	cd02576, PseudoU_synth_ScPUS7, Pseudouridine synth	1e-127
COG0585		406	COG0585, COG0585, Uncharacterized conserved protei	1e-71
cd02552		232	cd02552, PseudoU_synth_TruD_like, Pseudouridine sy	4e-60
TIGR00094		387	TIGR00094, tRNA_TruD_broad, tRNA pseudouridine syn	4e-59
cd02577		319	cd02577, PSTD1, Pseudouridine synthase, a subgroup	6e-57
pfam01142		336	pfam01142, TruD, tRNA pseudouridine synthase D (Tr	3e-43
PRK00984		341	PRK00984, truD, tRNA pseudouridine synthase D; Rev	1e-31
cd02575		253	cd02575, PseudoU_synth_EcTruD, Pseudouridine synth	2e-21
cd02576		371	cd02576, PseudoU_synth_ScPUS7, Pseudouridine synth	2e-13
cd01291		87	cd01291, PseudoU_synth, Pseudouridine synthases ca	3e-13
cd02552		232	cd02552, PseudoU_synth_TruD_like, Pseudouridine sy	3e-08
cd02576		371	cd02576, PseudoU_synth_ScPUS7, Pseudouridine synth	9e-06
cd02552		232	cd02552, PseudoU_synth_TruD_like, Pseudouridine sy	1e-05
cd01291		87	cd01291, PseudoU_synth, Pseudouridine synthases ca	0.002

>gnl\|CDD\|211341 cd02576, PseudoU_synth_ScPUS7, Pseudouridine synthase, TruD family	Back alignment and domain information

 Score =  377 bits (970), Expect = e-127
 Identities = 141/293 (48%), Positives = 188/293 (64%), Gaps = 13/293 (4%)

Query: 31  FLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAAL 90
           +L F LYKENKDT EA+  I+K+L + P  F +AGTKDKR+V+ QRV+V K  AS+L AL
Sbjct: 30  YLHFTLYKENKDTMEAINKIAKLLRVKPSDFSYAGTKDKRAVTVQRVSVKKVTASRLKAL 89

Query: 91  NKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYF 150
           N +L GIR+G+F Y  E L LG L GN FTI +R V  DSE++IK +  SL   GFINY+
Sbjct: 90  NSKLRGIRVGNFEYKDEPLKLGDLKGNEFTIVIRNVKADSEELIKQALESLKEKGFINYY 149

Query: 151 GLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPR-EGERNEISKAREYYKETDDIDGTL 209
           GLQRFG+ S+PTH +G  +L+  WK AV +IL PR E E  ++ +ARE +KET D    L
Sbjct: 150 GLQRFGTFSIPTHEIGIAILKENWKEAVDLILKPRSELEEGDLVEAREIWKETGDAKAAL 209

Query: 210 RKLPRHLVAERAILQCLKK---CPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQ 266
           +KLPR  VAE+A+L+ L K    P +YL A+ +IPR LR MYVH+YQS++WN A S R++
Sbjct: 210 KKLPRKKVAEKALLRGLSKYGNGPNDYLGAIGSIPRNLRSMYVHAYQSYVWNLAVSKRIK 269

Query: 267 KHGTEHVVVGDLVF--------CKGDDTEKELGCVNPEFEYESSNDADDSSHL 311
            +G + VV GDLV           G D       +   ++   S D  D  ++
Sbjct: 270 LYGLK-VVEGDLVIVIYDVVLPLPGHDVIYPSNEIGEWYKEVLSKDGLDPDNM 321

This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Saccharomyces cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in yeast U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35. Length = 371

>gnl\|CDD\|223658 COG0585, COG0585, Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>gnl\|CDD\|211326 cd02552, PseudoU_synth_TruD_like, Pseudouridine synthase, TruD family	Back alignment and domain information

>gnl\|CDD\|232822 TIGR00094, tRNA_TruD_broad, tRNA pseudouridine synthase, TruD family	Back alignment and domain information

>gnl\|CDD\|211342 cd02577, PSTD1, Pseudouridine synthase, a subgroup of the TruD family	Back alignment and domain information

>gnl\|CDD\|216326 pfam01142, TruD, tRNA pseudouridine synthase D (TruD)	Back alignment and domain information

>gnl\|CDD\|234884 PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	Back alignment and domain information

>gnl\|CDD\|211340 cd02575, PseudoU_synth_EcTruD, Pseudouridine synthase, similar to Escherichia coli TruD	Back alignment and domain information

>gnl\|CDD\|211341 cd02576, PseudoU_synth_ScPUS7, Pseudouridine synthase, TruD family	Back alignment and domain information

>gnl\|CDD\|211324 cd01291, PseudoU_synth, Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)	Back alignment and domain information

>gnl\|CDD\|211326 cd02552, PseudoU_synth_TruD_like, Pseudouridine synthase, TruD family	Back alignment and domain information

>gnl\|CDD\|211341 cd02576, PseudoU_synth_ScPUS7, Pseudouridine synthase, TruD family	Back alignment and domain information

>gnl\|CDD\|211326 cd02552, PseudoU_synth_TruD_like, Pseudouridine synthase, TruD family	Back alignment and domain information

>gnl\|CDD\|211324 cd01291, PseudoU_synth, Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi)	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		532
KOG2339		624	consensus Uncharacterized conserved protein [Funct	100.0
cd02576		371	PseudoU_synth_ScPUS7 PseudoU_synth_ScPUS7: Pseudou	100.0
PF01142		378	TruD: tRNA pseudouridine synthase D (TruD); InterP	100.0
COG0585		406	Uncharacterized conserved protein [Function unknow	100.0
cd02577		319	PSTD1 PSTD1: Pseudouridine synthase, a subgroup of	100.0
TIGR00094		387	tRNA_TruD_broad tRNA pseudouridine synthase, TruD	100.0
PRK00984		341	truD tRNA pseudouridine synthase D; Reviewed	100.0
cd02552		232	PseudoU_synth_TruD_like PseudoU_synth_TruD_like: P	100.0
cd02575		253	PseudoU_synth_EcTruD PseudoU_synth_EcTruD: Pseudou	100.0
cd01291		87	PseudoU_synth PseudoU_synth: Pseudouridine synthas	99.21
cd01291		87	PseudoU_synth PseudoU_synth: Pseudouridine synthas	97.13

>KOG2339 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

Probab=100.00  E-value=6.5e-114  Score=915.60  Aligned_cols=429  Identities=50%  Similarity=0.841  Sum_probs=400.4

Q ss_pred             cCCCCCCCCCCCcCCCCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHH
Q 009530           10 ERGDNPFDSRGSENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAA   89 (532)
Q Consensus        10 ~~~~~~~~~~~~~~wp~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~   89 (532)
                      ...+.++|.|+.+.|+.+.+.|+||+|+|+|++|++|++.||+.|+++++.|+|+|+|||||||+|+++|+++.++++..
T Consensus       189 ~K~~~~~d~r~~~~~~~~~~~~~~F~l~kenk~t~ea~g~ia~~L~v~p~~~~~~g~Kdkravt~Qrvsv~k~~~~~l~~  268 (624)
T KOG2339|consen  189 EKPDKPRDARGAEHWSRETADYCHFTLYKENKDTSEALGLIAKLLNVPPSGVRYAGTKDKRAVTTQRVSVRKVTPERLLA  268 (624)
T ss_pred             cccCcchhhhcccccccccccEEEEEEecccCCcHHHHHHHHHHhcCCCCCcChhhhhhhhhccceeeeEEEechhHHHH
Confidence            34668999999999998888899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHHHHH
Q 009530           90 LNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATL  169 (532)
Q Consensus        90 ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG~~l  169 (532)
                      +|..++++.+|+|.|.+..|+||+|+||||+|+||++....++.|.+++++++++|||||||+||||+.++.||.||.+|
T Consensus       269 ln~~lk~~~v~n~~~~~~~l~LGdL~GNrF~IvLR~~~~~~~e~i~~~l~sl~e~GFiNYfG~QRFG~~sv~t~~IG~~l  348 (624)
T KOG2339|consen  269 LNRKLKGIIVGNFIYKDDSLKLGDLKGNRFSIVLRGVRDDSEELIHQALESLKEKGFINYFGLQRFGSNSVRTHEIGLAL  348 (624)
T ss_pred             HHHhhhheeeeeeecccchhhhccccCceEEEEeccccccHHHHHHHHHHHHHhccchhhhchhhccccccccchhhHHH
Confidence            99999999999999999999999999999999999999878899999999999999999999999999999999999999


Q ss_pred             HhhcHHHHHHHhcCCCCCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhC--CCChHHhhhcCChhHHHH
Q 009530          170 LRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKC--PGNYLQALKAIPRTLRMM  247 (532)
Q Consensus       170 L~g~~~~Av~liL~p~~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~--~~~~~~Al~~iPr~lr~m  247 (532)
                      |+++|+.|+++||.|.....+ +.+|++.|.+++|+++++..+|+.+.+|++||.+|++.  ..||.+|+..|||++|+|
T Consensus       349 l~~~~~~A~~lil~p~~~~~~-v~~a~~~~~~t~da~~~l~~~p~~~~~E~~iL~~ls~~~~~~dy~~A~~~IPRnlRmm  427 (624)
T KOG2339|consen  349 LKRDWEKAIKLILTPRDLDYG-VGEARELWVQTRDAEAALSQLPRFKVAEKAILKCLSKGGKEKDYLQALYGIPRNLRML  427 (624)
T ss_pred             HHhHHHHHHhhcccccccccc-chHHHHHHHhcchhhhchhhCchHHHHHHHHHHHHHhcCCcccHHHHHHhcchhhhhh
Confidence            999999999999999988888 99999999999999999999999999999999999764  468999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCccccCcEEEecCCCCcccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCccce
Q 009530          248 YVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDGRHNLV  327 (532)
Q Consensus       248 yvhAYQSylwN~~~S~Ri~~~G~~~vv~GDLV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~v  327 (532)
                      |+|||||||||.+||+||+.||. +||+||||+..+..               |                +.+.+. ..+
T Consensus       428 YvHAYQS~iWN~~aS~RIe~yG~-rvV~GDLV~~~e~~---------------d----------------d~~~~~-~~~  474 (624)
T KOG2339|consen  428 YVHAYQSLIWNEAASRRIEEYGL-RVVEGDLVCVGEDE---------------D----------------DEPFEG-SKI  474 (624)
T ss_pred             hhhhhHHHHHHHHHHHHHHHcCc-cccccceeeccCCc---------------c----------------cccccc-cee
Confidence            99999999999999999999998 58999999986321               1                111111 468


Q ss_pred             eeehhhhhcCCCccccceeeecCCCCCCCCcchHHHHHHHHHhhcCCChhhhhhhhhhccccccccccccccccccceeE
Q 009530          328 KTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEW  407 (532)
Q Consensus       328 ~~lt~edi~~~~yti~DVvLPLPG~~v~yP~n~~~~~y~eiL~edGl~~~~~~~~~k~~~~~~l~G~YR~li~~P~dl~~  407 (532)
                      ++||+||++  +|+|+||||||||++++||.|++++||.++|.++|+++..|++..++|+   ++|+||+++++|.|++|
T Consensus       475 k~vt~ee~~--~Ysi~DVVLPLPG~dv~YPkn~~~~~Y~e~l~~d~ld~~nmr~k~r~~s---l~G~YRk~i~rp~nl~w  549 (624)
T KOG2339|consen  475 KVVTEEEIA--KYSIYDVVLPLPGFDVIYPKNEIAQWYVELLKEDGLDEFNMRHKVRDFS---LSGCYRKMIVRPKNLEW  549 (624)
T ss_pred             eEeeccccc--cceeeeEeecCCCcCccccCcHHHHHHHHHHHhcCCChhhccchhhhcc---cchhhHhHhcccccceE
Confidence            999999997  9999999999999999999999999999999999999999999999999   99999999999999999


Q ss_pred             EEEEecCCCCccccchHHHHhhcccchhhhhhhhhcCCCCCCCCccccccccchhhhcccccchhhhhhhhccCCccccc
Q 009530          408 ELLTYIDGNKPLAETDLDKIAKAKLVNIVKEEEAVCGNKEKDPSDCMKQSESLSKDIKLSTENNEAACAKEVKQPHVESV  487 (532)
Q Consensus       408 ~~~~y~d~~~~l~~tDld~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  487 (532)
                      ++++|+||++||+.||+|+|++..++...                                                   
T Consensus       550 ~li~Y~d~~~~l~~tD~D~L~~~~~p~~~---------------------------------------------------  578 (624)
T KOG2339|consen  550 ELIKYDDPEQPLILTDLDRLENRAIPESA---------------------------------------------------  578 (624)
T ss_pred             EEEecCCcccchhhchhhhhcCCCCCccc---------------------------------------------------
Confidence            99999999999999999999875443311                                                   


Q ss_pred             cCCCCccceeEEEEEEecCCcchhhHHHHHHhccCccHhhhhccC
Q 009530          488 CGADSQGKQMALKLGLTLPSSCYATMAIRELLKTSTSVAFHKTLN  532 (532)
Q Consensus       488 ~~~~~~~~~~al~l~f~Lp~ssYATmalREl~k~~ts~~~q~~l~  532 (532)
                          ..|+++||.|+|+||+|||||||||||||+|||+.-|+.||
T Consensus       579 ----e~g~~~Al~l~FsLpss~YATmalRE~lk~dts~~~q~~l~  619 (624)
T KOG2339|consen  579 ----EKGTYLALLLKFSLPSSAYATMALRELLKTDTSSGDQEMLN  619 (624)
T ss_pred             ----cccceeEEEEEeccCchHHHHHHHHHHHhhccccccHhhhh
Confidence                23679999999999999999999999999999999999886

>cd02576 PseudoU_synth_ScPUS7 PseudoU_synth_ScPUS7: Pseudouridine synthase, TruD family	Back alignment and domain information

>PF01142 TruD: tRNA pseudouridine synthase D (TruD); InterPro: IPR001656 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

>COG0585 Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family	Back alignment and domain information

>TIGR00094 tRNA_TruD_broad tRNA pseudouridine synthase, TruD family	Back alignment and domain information

>PRK00984 truD tRNA pseudouridine synthase D; Reviewed	Back alignment and domain information

>cd02552 PseudoU_synth_TruD_like PseudoU_synth_TruD_like: Pseudouridine synthase, TruD family	Back alignment and domain information

>cd02575 PseudoU_synth_EcTruD PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family	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

>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
Query		532
1z2z_A		446	Crystal Structure Of The Putative Trna Pseudouridin		4e-28
1sb7_A		368	Crystal Structure Of The E.Coli Pseudouridine Synth		5e-08
1szw_A		379	Crystal Structure Of E. Coli Trna Pseudouridine Syn		5e-08
1si7_A		369	Structure Of E. Coli Trna Psi 13 Pseudouridine Synt		5e-08

>pdb|1Z2Z|A Chain A, Crystal Structure Of The Putative Trna Pseudouridine Synthase D (Trud) From Methanosarcina Mazei, Northeast Structural Genomics Target Mar1 Length = 446

Back alignment and structure

Iteration: 1

Score = 122 bits (307), Expect = 4e-28, Method: Compositional matrix adjust. Identities = 84/257 (32%), Positives = 138/257 (53%), Gaps = 8/257 (3%) Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88 GK+L L K + DT +S++L + + AGTKDKR+++TQ++++F AS++ Sbjct: 47 GKYLIVELTKRDWDTHHLTRTLSRILQVSQKRISVAGTKDKRALTTQKISIFDTDASEIE 106 Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGV---VVDSEDVIKASANS-LGRN 144 ++ L I L ++ + LG L GN F IT+R + ++E ++K + + L + Sbjct: 107 KIH--LKDIELKVLGRSRKSVELGDLWGNDFRITVRNIENSPEETEALLKKTTDEILAQG 164 Query: 145 GFINYFGLQRFGSGSVPTHLVGATLLRGEW-KSAVKMILDPREGERNEISKAREYYKETD 203 G N+FG+QRFGS THLVG ++ G + K+A+ I +P E E AR++ K+T Sbjct: 165 GVPNFFGIQRFGSVRPVTHLVGKAIVEGNFEKAALLYIAEPFPEEPEETKNARQFVKDTL 224 Query: 204 DIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASA 263 D L+ P L ERA L P +Y + + +P+ L +VH YQS+++N Sbjct: 225 DFKEGLKTYPLRLGHERAXXNHLIANPEDYSGSFRVLPQNLYRXFVHGYQSYIYNIILCR 284 Query: 264 RVQKH-GTEHVVVGDLV 279 R++ V GD+V Sbjct: 285 RIEAGIPLNRAVEGDIV 301

PyMOL of 1z2z

>pdb|1SB7|A Chain A, Crystal Structure Of The E.Coli Pseudouridine Synthase Trud Length = 368

Back alignment and structure

>pdb|1SZW|A Chain A, Crystal Structure Of E. Coli Trna Pseudouridine Synthase Trud Length = 379

Back alignment and structure

>pdb|1SI7|A Chain A, Structure Of E. Coli Trna Psi 13 Pseudouridine Synthase Trud Length = 369

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
Query		532
1z2z_A		446	Probable tRNA pseudouridine synthase D; alpha-beta	2e-80
1z2z_A		446	Probable tRNA pseudouridine synthase D; alpha-beta	7e-05
1szw_A		379	TRNA pseudouridine synthase D; novel fold, RNA mod	3e-35
1szw_A		379	TRNA pseudouridine synthase D; novel fold, RNA mod	9e-11
1szw_A		379	TRNA pseudouridine synthase D; novel fold, RNA mod	2e-04

>1z2z_A Probable tRNA pseudouridine synthase D; alpha-beta protein., structural genomics, PSI, protein structure initiative; 2.60A {Methanosarcina mazei} Length = 446	Back alignment and structure

 Score =  257 bits (657), Expect = 2e-80
 Identities = 106/411 (25%), Positives = 180/411 (43%), Gaps = 42/411 (10%)

Query: 24  WPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQR 83
              + GK+L   L K + DT      +S++L +  +    AGTKDKR+++TQ++++F   
Sbjct: 42  EEGEEGKYLIVELTKRDWDTHHLTRTLSRILQVSQKRISVAGTKDKRALTTQKISIFDTD 101

Query: 84  ASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDV----IKASAN 139
           AS++  ++ +   I L      ++ + LG L GN F IT+R +    E+      K +  
Sbjct: 102 ASEIEKIHLK--DIELKVLGRSRKSVELGDLWGNDFRITVRNIENSPEETEALLKKTTDE 159

Query: 140 SLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMIL-DPREGERNEISKAREY 198
            L + G  N+FG+QRFGS    THLVG  ++ G ++ A  + + +P   E  E   AR++
Sbjct: 160 ILAQGGVPNFFGIQRFGSVRPVTHLVGKAIVEGNFEKAALLYIAEPFPEEPEETKNARQF 219

Query: 199 YKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWN 258
            K+T D    L+  P  L  ERA++  L   P +Y  + + +P+ L  M+VH YQS+++N
Sbjct: 220 VKDTLDFKEGLKTYPLRLGHERAMMNHLIANPEDYSGSFRVLPQNLYRMFVHGYQSYIYN 279

Query: 259 HAASARVQKHGT-EHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPET 317
                R++        V GD+V  + +                      DSS  ++V   
Sbjct: 280 IILCRRIEAGIPLNRAVEGDIVCFRNEVGL------------------PDSSKTEKVTSE 321

Query: 318 DHPDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLT 377
                   L            K     +  PLPG    +      E+ + + ++ G++L 
Sbjct: 322 TVNAMNRLL------------KLGRAFITAPLPGYNTEFASGIPGEIENGVLKELGVSLE 369

Query: 378 ESLHNVKEFSITSMTGNYRRVFQKPMD--FEWELLTYIDGNKPLAETDLDK 426
               N+++F   S  G  R V  +        E       +K + E  L K
Sbjct: 370 G--FNIEKFPEMSSKGTRREVLLEVKPKFEAGEDELNPGKSKAVLEFMLPK 418

PyMOL of 1z2z

>1z2z_A Probable tRNA pseudouridine synthase D; alpha-beta protein., structural genomics, PSI, protein structure initiative; 2.60A {Methanosarcina mazei} Length = 446	Back alignment and structure

>1szw_A TRNA pseudouridine synthase D; novel fold, RNA modification, TRUD, structural proteomics in europe, spine, structural genomics; 2.00A {Escherichia coli} SCOP: d.265.1.4 PDB: 1si7_A 1sb7_A Length = 379	Back alignment and structure

>1szw_A TRNA pseudouridine synthase D; novel fold, RNA modification, TRUD, structural proteomics in europe, spine, structural genomics; 2.00A {Escherichia coli} SCOP: d.265.1.4 PDB: 1si7_A 1sb7_A Length = 379	Back alignment and structure

>1szw_A TRNA pseudouridine synthase D; novel fold, RNA modification, TRUD, structural proteomics in europe, spine, structural genomics; 2.00A {Escherichia coli} SCOP: d.265.1.4 PDB: 1si7_A 1sb7_A Length = 379	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		532
1z2z_A		446	Probable tRNA pseudouridine synthase D; alpha-beta	100.0
1szw_A		379	TRNA pseudouridine synthase D; novel fold, RNA mod	100.0

>1z2z_A Probable tRNA pseudouridine synthase D; alpha-beta protein., structural genomics, PSI, protein structure initiative; 2.60A {Methanosarcina mazei}	Back alignment and structure

Probab=100.00  E-value=2.2e-96  Score=789.56  Aligned_cols=397  Identities=28%  Similarity=0.436  Sum_probs=342.5

Q ss_pred             CCCCCCCCCCcCC---CCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHH
Q 009530           12 GDNPFDSRGSENW---PEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA   88 (532)
Q Consensus        12 ~~~~~~~~~~~~w---p~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~   88 (532)
                      ...|.|+...+..   |.+.|+|++|+|+|+|+||++|++.||+.|||++++|+|||||||||||+|||||++..++++.
T Consensus        27 k~~peDF~V~Ei~~~~~~g~G~~l~f~l~K~n~dT~~a~~~Lak~lgi~~~~i~yAG~KDk~AvT~Q~~sv~~~~~~~l~  106 (446)
T 1z2z_A           27 RQEIEDFIVKEITNREEGEEGKYLIVELTKRDWDTHHLTRTLSRILQVSQKRISVAGTKDKRALTTQKISIFDTDASEIE  106 (446)
T ss_dssp             CSSGGGEEEEEEECCCCBSCSSEEEEEEEEESCCHHHHHHHHHHHHTCCGGGEEESSCCCSSSEEEEEEEEETCCHHHHT
T ss_pred             EecCCCceEEeeecCCCCCCCCEEEEEEEEcCCCHHHHHHHHHHHhCcChHhEeECccccCCeeEEEEEEEECCCHHHHh
Confidence            4557777766543   3678999999999999999999999999999999999999999999999999999999988887


Q ss_pred             HHhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCCCCHH---HHHHHHHhhcccc-ccccccCCCcCCCCCChHH
Q 009530           89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSED---VIKASANSLGRNG-FINYFGLQRFGSGSVPTHL  164 (532)
Q Consensus        89 ~ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~---~i~~~l~~l~~~G-FiNYFG~QRFGs~~~~th~  164 (532)
                      .+|  +.+++|++++|++++|++|+|.||+|+|+||+|...+.+   .|+++++.|+++| ||||||+||||+.+.+||+
T Consensus       107 ~l~--~~~i~i~~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~~~~i~~~l~~l~~~G~fpNYFG~QRFG~~~~~t~~  184 (446)
T 1z2z_A          107 KIH--LKDIELKVLGRSRKSVELGDLWGNDFRITVRNIENSPEETEALLKKTTDEILAQGGVPNFFGIQRFGSVRPVTHL  184 (446)
T ss_dssp             SCC--CTTEEEEEEEEESSCCCTTCEEEEEEEEEEEEESSCHHHHHHHHHHHHHHHHHHTEEECCCCTTTTCSSSCCHHH
T ss_pred             hcc--cCCeEEEEEEEecCCCCCCcCCCCEEEEEEecCCccchhhHHHHHHHHHHHHhcCCcceeccccccCCCCCCcHH
Confidence            776  789999999999999999999999999999999865433   8999999999999 9999999999999889999


Q ss_pred             HHHHHHhhcHHHHHHHhcC-CCCCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhCCCChHHhhhcCChh
Q 009530          165 VGATLLRGEWKSAVKMILD-PREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRT  243 (532)
Q Consensus       165 iG~~lL~g~~~~Av~liL~-p~~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~~~~~~~Al~~iPr~  243 (532)
                      ||++||+|+|++|+++||. |.+.+.+...+||+.|.++||+++||+.||+++.+||.||++|.+++++|.+|++.||++
T Consensus       185 iG~~ll~g~~~~Av~lil~~~~~~e~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~~~~~~~A~~~ipr~  264 (446)
T 1z2z_A          185 VGKAIVEGNFEKAALLYIAEPFPEEPEETKNARQFVKDTLDFKEGLKTYPLRLGHERAMMNHLIANPEDYSGSFRVLPQN  264 (446)
T ss_dssp             HHHHHHHTCHHHHHHHHHSCCCTTSCTTHHHHHHHHHHHCCHHHHHHHSCTTCHHHHHHHHHHHHSTTCGGGGGTTSCHH
T ss_pred             HHHHHHcCCHHHHHHHHhcCCCcccCHHHHHHHHHHHHcCCHHHHHHHCcchhHHHHHHHHHHHhccccHHHHHHhCCHH
Confidence            9999999999999999996 778888899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh-cCCCccccCcEEEecCCCCcccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCC
Q 009530          244 LRMMYVHSYQSFLWNHAASARVQK-HGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDG  322 (532)
Q Consensus       244 lr~myvhAYQSylwN~~~S~Ri~~-~G~~~vv~GDLV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~  322 (532)
                      +|+||||||||||||++||+||+. +++++|++||+|+..+.....       .    + .                   
T Consensus       265 lr~myv~AyQS~lfN~~lS~Ri~~~~~~~~~~~GDlv~~~~~~~~p-------~----~-~-------------------  313 (446)
T 1z2z_A          265 LYRMFVHGYQSYIYNIILCRRIEAGIPLNRAVEGDIVCFRNEVGLP-------D----S-S-------------------  313 (446)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCCSSSCCTTCCEECBCSSSCB-------C----S-S-------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCcCcccccceEeeccccCCc-------c----c-C-------------------
Confidence            999999999999999999999998 477789999999986542100       0    0 0                   


Q ss_pred             CccceeeehhhhhcC----CCccccceeeecCCCCCCCCcchHHHHHHHHHhhcCCChhhhh-hhhhhcccccccccccc
Q 009530          323 RHNLVKTVTAADINS----GKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESL-HNVKEFSITSMTGNYRR  397 (532)
Q Consensus       323 ~~~~v~~lt~edi~~----~~yti~DVvLPLPG~~v~yP~n~~~~~y~eiL~edGl~~~~~~-~~~k~~~~~~l~G~YR~  397 (532)
                         .+..+|+++++.    -.+.+.|||+||||+++.||.|+++++|+++|+++|+++++|. ..++.++   ++|+||+
T Consensus       314 ---~~~~~~~~~~~~~~~~~~~~~~~v~lPLpG~~~~~p~~~~~~~~~~il~~~gl~~~~f~~~~~~~~~---~~g~~R~  387 (446)
T 1z2z_A          314 ---KTEKVTSETVNAMNRLLKLGRAFITAPLPGYNTEFASGIPGEIENGVLKELGVSLEGFNIEKFPEMS---SKGTRRE  387 (446)
T ss_dssp             ---SCCCCCTTTHHHHHHHHTTTSCEEBCCBCSSSCCCCCSHHHHHHHHHHHHTTCCGGGSSCSSCGGGC---CCCBCCB
T ss_pred             ---ceeeechhhHHHHHHHHhcCCceEEEeecCCCCCCCchHHHHHHHHHHHHcCCChHHcccccccccC---cCCCcce
Confidence               011112222110    1235789999999999999999999999999999999998885 3455666   9999999


Q ss_pred             ccccccceeEEEEEecCCCCccccchHHHHhhcccchhhhhhhhhcCCCCCCCCccccccccchhhhcccccchhhhhhh
Q 009530          398 VFQKPMDFEWELLTYIDGNKPLAETDLDKIAKAKLVNIVKEEEAVCGNKEKDPSDCMKQSESLSKDIKLSTENNEAACAK  477 (532)
Q Consensus       398 li~~P~dl~~~~~~y~d~~~~l~~tDld~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  477 (532)
                      ++++|.|++ .+           .+|  .+                                          .       
T Consensus       388 l~~~p~~l~-~~-----------~~d--~~------------------------------------------~-------  404 (446)
T 1z2z_A          388 VLLEVKPKF-EA-----------GED--EL------------------------------------------N-------  404 (446)
T ss_dssp             SEEECCCBC-CE-----------EEC--TT------------------------------------------S-------
T ss_pred             eeecccccc-cc-----------ccc--ee------------------------------------------e-------
Confidence            999999998 11           011  00                                          0       


Q ss_pred             hccCCccccccCCCCccceeEEEEEEecCCcchhhHHHHHHhccCccHh
Q 009530          478 EVKQPHVESVCGADSQGKQMALKLGLTLPSSCYATMAIRELLKTSTSVA  526 (532)
Q Consensus       478 ~~~~~~~~~~~~~~~~~~~~al~l~f~Lp~ssYATmalREl~k~~ts~~  526 (532)
                                 .     ...+|+|+|+||+||||||+||||||.+||..
T Consensus       405 -----------~-----~~~~l~L~F~Lp~GsYAT~~LREl~k~~~~~~  437 (446)
T 1z2z_A          405 -----------P-----GKSKAVLEFMLPKGSYATTVLREYMKVNPLQM  437 (446)
T ss_dssp             -----------T-----TCEEEEEBCEEETTCCTHHHHHHHHCCCTTTC
T ss_pred             -----------c-----CCCEEEEEEEcCCccHHHHHHHHHhCCCcchh
Confidence                       0     13589999999999999999999999999864

PyMOL of 1z2z

>1szw_A TRNA pseudouridine synthase D; novel fold, RNA modification, TRUD, structural proteomics in europe, spine, structural genomics; 2.00A {Escherichia coli} SCOP: d.265.1.4 PDB: 1si7_A 1sb7_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		532
d1szwa_		341	d.265.1.4 (A:) tRNA pseudouridine synthase TruD {E	1e-40
d1szwa_		341	d.265.1.4 (A:) tRNA pseudouridine synthase TruD {E	9e-18
d1szwa_		341	d.265.1.4 (A:) tRNA pseudouridine synthase TruD {E	6e-06

>d1szwa_ d.265.1.4 (A:) tRNA pseudouridine synthase TruD {Escherichia coli [TaxId: 562]} Length = 341	Back information, alignment and structure


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

 Score =  147 bits (373), Expect = 1e-40
 Identities = 41/157 (26%), Positives = 62/157 (39%), Gaps = 2/157 (1%)

Query: 24  WPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQR 83
            P+  G+ +   + K   +T+     ++K L I  R   FAG KDK +V+ Q +      
Sbjct: 36  EPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPG 95

Query: 84  ASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGR 143
                    +L G ++ ++   K  L LG L GN FT+ LR   V + D ++     +  
Sbjct: 96  KEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLRE--VSNRDDVEQRLIDICV 153

Query: 144 NGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKM 180
            G  NYFG QRFG G                      
Sbjct: 154 KGVPNYFGAQRFGIGGSNLQGAQRWAQTNTPVRDRNK 190

PyMOL of d1szwa_

>d1szwa_ d.265.1.4 (A:) tRNA pseudouridine synthase TruD {Escherichia coli [TaxId: 562]} Length = 341	Back information, alignment and structure

>d1szwa_ d.265.1.4 (A:) tRNA pseudouridine synthase TruD {Escherichia coli [TaxId: 562]} Length = 341	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		532
d1szwa_		341	tRNA pseudouridine synthase TruD {Escherichia coli	100.0

>d1szwa_ d.265.1.4 (A:) tRNA pseudouridine synthase TruD {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

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

Probab=100.00  E-value=3.3e-73  Score=588.64  Aligned_cols=289  Identities=24%  Similarity=0.320  Sum_probs=228.1

Q ss_pred             CCCCCCCCCCcCC---CCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHH
Q 009530           12 GDNPFDSRGSENW---PEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA   88 (532)
Q Consensus        12 ~~~~~~~~~~~~w---p~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~   88 (532)
                      ...|.|+...+.+   |.+.|+|++|+|+|+|+||++|++.||+.|||++++|+|||+|||||||+|||||+.+......
T Consensus        21 k~~peDF~V~E~~~~~~~~~G~~~~~~l~K~~~dT~~ai~~Lar~l~v~~~~i~yAG~KDk~AvT~Q~vSv~~~~~~~~~  100 (341)
T d1szwa_          21 KANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGKEMPD  100 (341)
T ss_dssp             SSSGGGEEEEEECSSCCCSCSSEEEEEEEESSSCHHHHHHHHHHHTTCCGGGEEESCCCCTTSEEEEEEEEECCSSCCCC
T ss_pred             eCCCCCceEEeccCCCCCCCcCEEEEEEEECCCCHHHHHHHHHHHhCCChhheeecccccCceeeeeeeeeeccchhhhh
Confidence            5678888887654   6778999999999999999999999999999999999999999999999999999876543322


Q ss_pred             HHhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHHHH
Q 009530           89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGAT  168 (532)
Q Consensus        89 ~ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG~~  168 (532)
                      ..|..+.+++++++.|++++|++|+|.||+|+|+||+|.  ..+.+.++++.+++.|||||||+||||+.+         
T Consensus       101 ~~~~~~~~i~i~~~~~~~~~l~lG~l~GNrF~I~lR~v~--~~~~~~~~l~~i~~~GfpNYfG~QRFG~~~---------  169 (341)
T d1szwa_         101 LSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVS--NRDDVEQRLIDICVKGVPNYFGAQRFGIGG---------  169 (341)
T ss_dssp             GGGCCCTTEEEEEEEEESSCCCTTCCCEEEEEEEEBSCS--CHHHHHHHHHHHHHHCEECCCCGGGGCGGG---------
T ss_pred             hhhcccCCceEEEEeecCCCccCCccCCCeEEEEECCCC--chHHHHHHHHHHHhcCCcccccccccCCCC---------
Confidence            234457899999999999999999999999999999997  467899999999999999999999999764         


Q ss_pred             HHhhcHHHHHHHhcCCCCCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhCCCChHHhhhcCChhHHHHH
Q 009530          169 LLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMY  248 (532)
Q Consensus       169 lL~g~~~~Av~liL~p~~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~~~~~~~Al~~iPr~lr~my  248 (532)
                         ++|++|.++++.                                                    +...+|+++|+||
T Consensus       170 ---~~~~~a~~~~~~----------------------------------------------------~~~~~~r~lr~ly  194 (341)
T d1szwa_         170 ---SNLQGAQRWAQT----------------------------------------------------NTPVRDRNKRSFW  194 (341)
T ss_dssp             ---HHHHHHHHHHC-----------------------------------------------------------CHHHHHH
T ss_pred             ---ccHHHHHHHHhc----------------------------------------------------ccccCChHHHHHH
Confidence               667766554432                                                    1123689999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCccccCcEEEecCCCCcccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCcccee
Q 009530          249 VHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDGRHNLVK  328 (532)
Q Consensus       249 vhAYQSylwN~~~S~Ri~~~G~~~vv~GDLV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~v~  328 (532)
                      +|||||||||+++|+||+.+++..+++||+|...+....         +....                   +.......
T Consensus       195 v~AyQS~lfN~~ls~Ri~~~~~~~~~~GD~v~~~~~~~~---------~~~~~-------------------~~~~~~~~  246 (341)
T d1szwa_         195 LSAARSALFNQIVAERLKKADVNQVVDGDALQLAGRGSW---------FVATT-------------------EELAELQR  246 (341)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSSTTCCCTTCEEEETTSSCE---------EECCG-------------------GGHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCcccCCceeeecCCCcc---------cccch-------------------hhhHHHHh
Confidence            999999999999999999999888999999998654211         00000                   00000000


Q ss_pred             eehhhhhcCCCccccceeeecCCCCCCCCcchHHHHHHHHHhhcCCChhhhhhhhhhccccccccccccccccccceeEE
Q 009530          329 TVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWE  408 (532)
Q Consensus       329 ~lt~edi~~~~yti~DVvLPLPG~~v~yP~n~~~~~y~eiL~edGl~~~~~~~~~k~~~~~~l~G~YR~li~~P~dl~~~  408 (532)
                      .+...++        .+++||||+++.+|.+...+++++++++++...    ...+..+   ++|+||+++++|.|++|+
T Consensus       247 ~~~~~~~--------~~~~pl~G~~~~~~~~~~~~~e~~~l~~~~~~~----~~~~~~~---~~g~~R~~~~~p~dl~~~  311 (341)
T d1szwa_         247 RVNDKEL--------MITAALPGSGEWGTQREALAFEQAAVAAETELQ----ALLVREK---VEAARRAMLLYPQQLSWN  311 (341)
T ss_dssp             HHHTTSE--------EEEEEECCBSCCSCCHHHHHHHHHHTTTCHHHH----HHHHHTT---CBCEEEESEECCEEEEEE
T ss_pred             hhhcCce--------eeeeccCCCCCcCcchHHHHHHHHHhccchhHH----HHHHhCC---CCcccceeeeeccCCEEE
Confidence            1111121        388999999999999999999999988655432    2344555   899999999999999998


Q ss_pred             E
Q 009530          409 L  409 (532)
Q Consensus       409 ~  409 (532)
                      +
T Consensus       312 ~  312 (341)
T d1szwa_         312 W  312 (341)
T ss_dssp             E
T ss_pred             E
Confidence            5

PyMOL of d1szwa_