Citrus Sinensis ID: 009253

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-------54

MAIYPLRLLHSPWSARSITSTLSTVGFSNKISAVNLLPLSCYRCPASSSSKSSPSVSHTLTRPTPNSSDDKWEPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSVRTRPGVTRPEMQTMVESEEILKMVDEFYTSVTLPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWKEKRFESKTIVESAISV

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEccccccccccccccccccHHHHHHHHHHHHcccccccccccccccEEEcccccccccccccEEEEEcccccccccccccHHHHHHHHHccccccEEEEEEEEcccccccccccccEEEEEEEcccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccEEEEEEEEEcccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccHHHHccccccccccccccHHHccEEcccccccccccccEEEEEEEEccccEEEccccEEEEEEEEcHHHHHHHHHHHHHHHHHHHccccHHHHHHHHccccccccccccccccEEccccccccccccccccccccccccHHHHHHHHHHHHHHcHHHHHHHHHccccHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccc

cEEEcccccccHHHHHcccccEEEEEEccccccccccccHcEEccccccccccccccccccccccccccccHccccccEEEEEEEEEccccccccccccccccccHHHHHHHHHHHcccccHHcccccccccHHHccccccccccccEEEEEEEEEccccccccHHHHHHHHHHHHHccccEEEEEEEEcccccccHHHccccEEEEEccHHcccccccccHHHHHHHHHHHHHHHHHHccccccHHccccccccccHHHHcccccccHHcccHHHccHHHHHHHHccccccccccccccccccccccccHHHccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHcccccccccccHHHEEEEEEEEccccEEEccEEEEEEEEEcHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHccccEEccccccccEEEEcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHccccccccc

maiyplrllhspwsarsitstlstvgfsnkisavnllplscyrcpassssksspsvshtltrptpnssddkwepvrkKKVALRVGYvgtdyrglqmqrdehsLSTIEGELETALFkaggiresnygNLQKIAWARssrtdkgvHSLATMICLkmeippdawkddpygidLAKRVnahlprnikvfsilpsqrsfdprrecnlrkysyllpaeviginsQLTAAEIDSHISDFNAILNEfegehpfhnyterskyrrkphktgrvskrakaSKDAVFSrveesegeedgfskveesdgeedlgiggeissddekanqnsmvsgvhqedccnqhanglkdqnsssvIRARWLYETDEADKLSASHFRKIFScscgklekslgfGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKhsrivlplapsevLFLRANsfsvrtrpgvtrpemqtMVESEEILKMVDEFYtsvtlpevskfldatkspwTEWIENLEKftsipneqLDEVRNAWQLWKEKRFESKTIVESAISV

MAIYPLRllhspwsaRSITSTLSTVGFSNKISAVNLLPLSCYRCPAssssksspsvshtltrptpnssddkwepvrkkkvalrvgyvgtdyrglqmqrdEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKvfsilpsqrsfdprRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPfhnyterskyrrkphktgrvskrakaskdavfsrveesegeedgfskveesdgeedLGIGGEISSDDEKANQNSMVSGVHQEDCCNQHanglkdqnsssVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFlransfsvrtrpgvtrpemqtmvESEEILKMVDEFYTSVTLPEVSKFLDATKSPWTEWIENLEkftsipneqlDEVRNAWQLWkekrfesktivesaisv

MAIYPLRLLHSPWSARSITSTLSTVGFSNKISAVNLLPLSCYRCPAssssksspsvsHTLTRPTPNSSDDKWEPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVeesdgeedlgiggeissDDEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSVRTRPGVTRPEMQTMVESEEILKMVDEFYTSVTLPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWKEKRFESKTIVESAISV

**IYPLRLLHSPWSARSITSTLSTVGFSNKISAVNLLPLSCYRC*********************************KKVALRVGYVGTDYRGLQMQ*****LSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFH*************************************************************************************************VIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSVRT**************SEEILKMVDEFYTSVTLPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWKEKRF************

********LH********************************************************************KVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDG*****************EISSD****************DCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSVRTRPGVTRPEMQTMVESEEILKMVDEFYTSVTLPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVR***********************

MAIYPLRLLHSPWSARSITSTLSTVGFSNKISAVNLLPLSCYR******************************PVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYTER*************************************************LGIGGEISSDDEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSVRTRPGVTRPEMQTMVESEEILKMVDEFYTSVTLPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWKEKRFES**********

MAIYPLRLLHSPWSARSITSTLSTVGFSNKISAVNLLPLSCYRCPA**************************EPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYTERS********************************************************S**EKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSVRTRPGVTRPEMQTMVESEEILKMVDEFYTSVTLPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWKEKRFESKT********

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		539	2.2.26 [Sep-21-2011]
O22928		510	Putative tRNA pseudouridi	yes	no	0.782	0.827	0.575	1e-141
Q6FV05		549	tRNA pseudouridine syntha	yes	no	0.617	0.606	0.301	1e-26
O94396		534	tRNA pseudouridine syntha	yes	no	0.651	0.657	0.279	2e-24
Q755C8		528	tRNA pseudouridine syntha	yes	no	0.244	0.25	0.409	2e-20
Q6CC39		528	tRNA pseudouridine syntha	yes	no	0.244	0.25	0.356	5e-20
Q12211		544	tRNA pseudouridine syntha	yes	no	0.226	0.224	0.410	3e-19
Q6CWQ8		553	tRNA pseudouridine syntha	yes	no	0.226	0.220	0.395	2e-18
Q4KM92		423	tRNA pseudouridine syntha	yes	no	0.320	0.408	0.294	2e-18
Q9Y606		427	tRNA pseudouridine syntha	yes	no	0.337	0.426	0.275	3e-18
Q9WU56		423	tRNA pseudouridine syntha	yes	no	0.320	0.408	0.294	3e-18

>sp\|O22928\|PUSH_ARATH Putative tRNA pseudouridine synthase OS=Arabidopsis thaliana GN=At2g30320 PE=3 SV=1	Back alignment and function desciption

 Score =  503 bits (1296), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 264/459 (57%), Positives = 321/459 (69%), Gaps = 37/459 (8%)

Query: 70  DKWEPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQ 129
           DKWE  RKKKV +R+GYVGTDYRGLQ+QRD+ S+ TIEGELE A++KAGGIR+SNYG+L 
Sbjct: 55  DKWESYRKKKVVIRIGYVGTDYRGLQIQRDDPSIKTIEGELEVAIYKAGGIRDSNYGDLH 114

Query: 130 KIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILP 189
           KI WARSSRTDKGVHSLAT I LKMEIP  AWKDDP G  LAK ++ HLP NI+VFS+LP
Sbjct: 115 KIGWARSSRTDKGVHSLATSISLKMEIPETAWKDDPQGTVLAKCISKHLPENIRVFSVLP 174

Query: 190 SQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYT 249
           S R FDPRREC LRKYSYLLP +V+GI +  T+ EID HI+DFN IL EFEGE+PFHNYT
Sbjct: 175 SNRRFDPRRECTLRKYSYLLPVDVLGIKNSFTSDEIDYHITDFNEILKEFEGEYPFHNYT 234

Query: 250 ERSKYRRK-----PHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIG 304
           +RS+YRRK       + GR  +  K+        ++ SE E   F +    +  E+    
Sbjct: 235 QRSRYRRKSEQKIKQRNGRPPREPKS--------IKASESE---FREENHIEIGEEEEEK 283

Query: 305 GEISSDDEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHF 364
                 DE                   H       NS    RA+WLYE DE DK+S +HF
Sbjct: 284 EVDGESDE-------------------HVVTPDSDNSQVYSRAKWLYEPDETDKISGAHF 324

Query: 365 RKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAK 424
           RK+F C  GKLE SLGFG+VEISI GESFMLHQIRKM+GTAVAVKR+LLPRDI+ LSL K
Sbjct: 325 RKVFRCRSGKLENSLGFGFVEISIWGESFMLHQIRKMIGTAVAVKRELLPRDIIRLSLNK 384

Query: 425 HSRIVLPLAPSEVLFLRANSFSVRTRPGVTRPEMQTMVESEEILKMVDEFYTSVTLPEVS 484
            +RIVLPLAPSEVL LR NSF VR  P   RP M+   ESEE+ K ++EFY +V +P+VS
Sbjct: 385 FTRIVLPLAPSEVLILRGNSFEVRRLP--ERPGMEATGESEEVEKEIEEFYRAVMVPQVS 442

Query: 485 KFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWK 523
            FLD+ KSPW EW+++L++   + +E+L++VR  W+ WK
Sbjct: 443 IFLDSEKSPWKEWVDHLDRNDGLIDEELEDVRKGWEEWK 481

Arabidopsis thaliana (taxid: 3702)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -

>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\|O94396\|PUS1_SCHPO tRNA pseudouridine synthase 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pus1 PE=1 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\|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\|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\|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\|Q4KM92\|TRUA_RAT tRNA pseudouridine synthase A, mitochondrial OS=Rattus norvegicus GN=Pus1 PE=2 SV=2	Back alignment and function description

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

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		539
147800604		602	hypothetical protein VITISV_034891 [Viti	0.944	0.845	0.633	1e-180
225434389		564	PREDICTED: putative tRNA pseudouridine s	0.936	0.895	0.640	1e-180
297745794		495	unnamed protein product [Vitis vinifera]	0.897	0.977	0.620	1e-172
224126927		445	predicted protein [Populus trichocarpa]	0.797	0.966	0.643	1e-166
356499004		516	PREDICTED: putative tRNA pseudouridine s	0.829	0.866	0.614	1e-164
356499006		453	PREDICTED: putative tRNA pseudouridine s	0.825	0.982	0.616	1e-162
357491367		501	Pseudouridylate synthase [Medicago trunc	0.818	0.880	0.623	1e-160
356577897		518	PREDICTED: putative tRNA pseudouridine s	0.829	0.862	0.597	1e-157
355430068		565	putative pseudouridine synthase family p	0.827	0.789	0.589	1e-152
357491363		483	Pseudouridylate synthase [Medicago trunc	0.849	0.948	0.542	1e-151

>gi\|147800604\|emb\|CAN68579.1\| hypothetical protein VITISV_034891 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  638 bits (1646), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 348/549 (63%), Positives = 401/549 (73%), Gaps = 40/549 (7%)

Query: 1   MAIYPLRLLHSPWSARSITSTLSTVGFSNKISAVNLLPLSCYRCPASSSSKSSPSVSHTL 60
           M +  LR    PW   + TS L    FSN      +LP     C +SSSS        T+
Sbjct: 1   MVVSSLRFPLFPWIISNHTSNLR---FSNP----RILPQWSLHCSSSSSS--------TV 45

Query: 61  TRPTPNSSDDKWEPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGI 120
           T   P+ S  KWE  RKKKV +RVGYVGT+YRGLQMQRDE SLSTIEGELETA+FKAGGI
Sbjct: 46  TESNPDQSVQKWESFRKKKVVMRVGYVGTNYRGLQMQRDESSLSTIEGELETAVFKAGGI 105

Query: 121 RESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPR 180
           R+SNYGNL KI W RSSRTDKGVHSLATMI LKMEIP +AWK+DP GI LA  VN HLP 
Sbjct: 106 RDSNYGNLHKIGWDRSSRTDKGVHSLATMISLKMEIPANAWKEDPNGIALANYVNFHLPN 165

Query: 181 NIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFE 240
           NIKVFSILPSQRSFD RREC+LR+YSYLLPAE+IGI S  +A+EID HI++FN ILN FE
Sbjct: 166 NIKVFSILPSQRSFDARRECDLRRYSYLLPAEIIGIKSNSSASEIDHHIAEFNDILNTFE 225

Query: 241 GEHPFHNYTERSKYRRK-PHK----TGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEES 295
           GEHPF NYT RSKYR++ P K     G V +RAK+S +A               S+ E S
Sbjct: 226 GEHPFQNYTIRSKYRKQFPAKQSPGNGGVFRRAKSSGEA-------------STSEFEVS 272

Query: 296 DGEEDLGIGGEISSD-DEKANQNSMVSGV---HQEDCCNQHANGLKDQNSSSVIRARWLY 351
           DGEE+ G+ G ISSD DE  NQNS  S     H     N +  GLK+Q+S  V+RARWL+
Sbjct: 273 DGEENSGVNGVISSDYDEGENQNSSESTSFVEHPVGSSNNNEKGLKEQSSKLVVRARWLH 332

Query: 352 ETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRK 411
             DE D++SASHFRKIF+CSCGKLEK LG  YVE+SI GESFMLHQIRKMVGTA+AVKR+
Sbjct: 333 GPDERDRISASHFRKIFNCSCGKLEKFLGLDYVELSICGESFMLHQIRKMVGTAIAVKRE 392

Query: 412 LLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSVRTRPG-VTRPEMQTMVESEEILKM 470
           LLPRDILTLSL K SRIVLPLAPSEVL LR NSFSVR +PG V RPEM T++ESEEILK 
Sbjct: 393 LLPRDILTLSLTKFSRIVLPLAPSEVLILRGNSFSVRKKPGNVKRPEMLTLMESEEILKS 452

Query: 471 VDEFYTSVTLPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWKEKRFESK 530
           VDEFYTSV LP+VSKFLD +KSPW +W+ENL   +SIP  +LD+VR AW+LWKE  F S+
Sbjct: 453 VDEFYTSVILPQVSKFLDPSKSPWHDWLENL-TLSSIPEAELDDVRTAWKLWKEN-FRSR 510

Query: 531 TIVESAISV 539
           T  E  +++
Sbjct: 511 TKCEDVLAL 519

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225434389\|ref\|XP_002276856.1\| PREDICTED: putative tRNA pseudouridine synthase-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297745794\|emb\|CBI15850.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224126927\|ref\|XP_002319961.1\| predicted protein [Populus trichocarpa] gi\|222858337\|gb\|EEE95884.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356499004\|ref\|XP_003518334.1\| PREDICTED: putative tRNA pseudouridine synthase-like [Glycine max]	Back alignment and taxonomy information

>gi\|356499006\|ref\|XP_003518335.1\| PREDICTED: putative tRNA pseudouridine synthase-like, partial [Glycine max]	Back alignment and taxonomy information

>gi\|357491367\|ref\|XP_003615971.1\| Pseudouridylate synthase [Medicago truncatula] gi\|355517306\|gb\|AES98929.1\| Pseudouridylate synthase [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356577897\|ref\|XP_003557058.1\| PREDICTED: putative tRNA pseudouridine synthase-like [Glycine max]	Back alignment and taxonomy information

>gi\|355430068\|gb\|AER92594.1\| putative pseudouridine synthase family protein [Linum usitatissimum]	Back alignment and taxonomy information

>gi\|357491363\|ref\|XP_003615969.1\| Pseudouridylate synthase [Medicago truncatula] gi\|355517304\|gb\|AES98927.1\| Pseudouridylate synthase [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		539
TAIR\|locus:2065748		510	AT2G30320 [Arabidopsis thalian	0.456	0.482	0.592	1.5e-138
DICTYBASE\|DDB_G0290987		596	pus1 "tRNA pseudouridylate syn	0.311	0.281	0.373	8.4e-32
DICTYBASE\|DDB_G0281619		504	DDB_G0281619 "tRNA pseudouridi	0.363	0.388	0.358	6.4e-30
TAIR\|locus:2012898		549	AT1G20370 [Arabidopsis thalian	0.246	0.242	0.344	3.3e-27
ZFIN\|ZDB-GENE-041212-26		412	pus1 "pseudouridine synthase 1	0.330	0.432	0.317	9.3e-26
UNIPROTKB\|G4N3B4		720	MGG_07663 "tRNA pseudouridine	0.144	0.108	0.444	8.6e-25
UNIPROTKB\|F1NZ90		405	PUS1 "tRNA pseudouridine synth	0.306	0.407	0.279	2.2e-24
TAIR\|locus:2199726		463	AT1G76120 [Arabidopsis thalian	0.224	0.261	0.375	3e-24
RGD\|1311871		423	Pus1 "pseudouridylate synthase	0.324	0.413	0.300	3.7e-24
UNIPROTKB\|Q4KM92		423	Pus1 "tRNA pseudouridine synth	0.324	0.413	0.300	3.7e-24

TAIR\|locus:2065748 AT2G30320 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 773 (277.2 bits), Expect = 1.5e-138, Sum P(2) = 1.5e-138
 Identities = 150/253 (59%), Positives = 184/253 (72%)

Query:    45 PAXXXXXXXXXXXHTLTRPTPNSSD----DKWEPVRKKKVALRVGYVGTDYRGLQMQRDE 100
             PA            + T  +P SSD    DKWE  RKKKV +R+GYVGTDYRGLQ+QRD+
Sbjct:    26 PALLRFSSSAAFQPSSTSLSPPSSDNFLADKWESYRKKKVVIRIGYVGTDYRGLQIQRDD 85

Query:   101 HSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDA 160
              S+ TIEGELE A++KAGGIR+SNYG+L KI WARSSRTDKGVHSLAT I LKMEIP  A
Sbjct:    86 PSIKTIEGELEVAIYKAGGIRDSNYGDLHKIGWARSSRTDKGVHSLATSISLKMEIPETA 145

Query:   161 WKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQL 220
             WKDDP G  LAK ++ HLP NI+VFS+LPS R FDPRREC LRKYSYLLP +V+GI +  
Sbjct:   146 WKDDPQGTVLAKCISKHLPENIRVFSVLPSNRRFDPRRECTLRKYSYLLPVDVLGIKNSF 205

Query:   221 TAAEIDSHISDFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKR-AKASKDAVFSRV 279
             T+ EID HI+DFN IL EFEGE+PFHNYT+RS+YRRK  +  ++ +R  +  ++    + 
Sbjct:   206 TSDEIDYHITDFNEILKEFEGEYPFHNYTQRSRYRRKSEQ--KIKQRNGRPPREPKSIKA 263

Query:   280 EESEGEEDGFSKV 292
              ESE  E+   ++
Sbjct:   264 SESEFREENHIEI 276

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

DICTYBASE\|DDB_G0290987 pus1 "tRNA pseudouridylate synthase" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0281619 DDB_G0281619 "tRNA pseudouridine synthase" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

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

ZFIN\|ZDB-GENE-041212-26 pus1 "pseudouridine synthase 1" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|G4N3B4 MGG_07663 "tRNA pseudouridine synthase 1" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NZ90 PUS1 "tRNA pseudouridine synthase" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

TAIR\|locus:2199726 AT1G76120 [Arabidopsis thaliana (taxid:3702)]	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

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O22928	PUSH_ARATH	5, ., 4, ., 9, 9, ., -	0.5751	0.7829	0.8274	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	5.4.99.12	0.737
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		539
PLN03078		513	PLN03078, PLN03078, Putative tRNA pseudouridine sy	0.0
cd02568		245	cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine sy	2e-62
TIGR00071		227	TIGR00071, hisT_truA, tRNA pseudouridine(38-40) sy	3e-28
COG0101		266	COG0101, TruA, Pseudouridylate synthase [Translati	5e-27
cd02568		245	cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine sy	2e-22
PRK00021		244	PRK00021, truA, tRNA pseudouridine synthase A; Val	3e-19
cd02570		239	cd02570, PseudoU_synth_EcTruA, Eukaryotic and bact	1e-17
cd00497		215	cd00497, PseudoU_synth_TruA_like, Pseudouridine sy	1e-17
cd02569		256	cd02569, PseudoU_synth_ScPus3, Pseudouridine synth	6e-14
cd02866		219	cd02866, PseudoU_synth_TruA_Archea, Archeal pseudo	7e-13
PRK14589		265	PRK14589, PRK14589, tRNA pseudouridine synthase AC	1e-12
COG0101		266	COG0101, TruA, Pseudouridylate synthase [Translati	1e-10
PRK14586		245	PRK14586, PRK14586, tRNA pseudouridine synthase AC	1e-10
PRK14588		272	PRK14588, PRK14588, tRNA pseudouridine synthase AC	9e-09
pfam01416		103	pfam01416, PseudoU_synth_1, tRNA pseudouridine syn	4e-08
cd02570		239	cd02570, PseudoU_synth_EcTruA, Eukaryotic and bact	2e-07
TIGR00071		227	TIGR00071, hisT_truA, tRNA pseudouridine(38-40) sy	2e-06
PRK00021		244	PRK00021, truA, tRNA pseudouridine synthase A; Val	4e-06
pfam01416		103	pfam01416, PseudoU_synth_1, tRNA pseudouridine syn	7e-05
PRK12434		245	PRK12434, PRK12434, tRNA pseudouridine synthase A;	8e-05
PRK14587		256	PRK14587, PRK14587, tRNA pseudouridine synthase AC	2e-04
cd00497		215	cd00497, PseudoU_synth_TruA_like, Pseudouridine sy	9e-04
PRK12434		245	PRK12434, PRK12434, tRNA pseudouridine synthase A;	0.001

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

 Score =  711 bits (1837), Expect = 0.0
 Identities = 329/522 (63%), Positives = 381/522 (72%), Gaps = 36/522 (6%)

Query: 9   LHSPWSARSITSTLSTVGFSNKISAVNLLPL-SCYRCPASSSSKSSPSVSHTLTRPTPNS 67
           L +PW      S+ S +   N      +L   S      SS+S S PS    LT  +   
Sbjct: 5   LRAPWPLWRFWSSTSLLRRVNP----RILRTSSSASSSPSSTSLSPPSSDPPLTDNSDQG 60

Query: 68  SDDKWEPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGN 127
              KWE  RKKKV LRVGYVGTDYRGLQ QRD  SLSTIEGELETA+FKAGGIRESNYGN
Sbjct: 61  GGMKWESARKKKVVLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNYGN 120

Query: 128 LQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSI 187
           L KI WARSSRTDKGVHSLATMI LKMEIP +AWKDDP GI LAK +N+HLP NI+VFSI
Sbjct: 121 LHKIGWARSSRTDKGVHSLATMISLKMEIPENAWKDDPDGIALAKFINSHLPDNIRVFSI 180

Query: 188 LPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHN 247
           LP+QRSFDPRREC+LRKYSYLLPAEVIGI S  ++ EID HIS+FN+ILN FEGEHPFHN
Sbjct: 181 LPAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFSSEEIDEHISEFNSILNGFEGEHPFHN 240

Query: 248 YTERSKYRRK-----PHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLG 302
           YT RSKYR+K       + G VS+RAK+SK+   S  EE+ GE                 
Sbjct: 241 YTARSKYRKKLPGKHKQRNGAVSRRAKSSKEMSSSESEENHGEIS--------------- 285

Query: 303 IGGEISSDDEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSAS 362
                  D+E  + +S+ SG       +++ + LK Q+S   IRARWL+E DE D++SAS
Sbjct: 286 -----EEDEEDLSFSSIPSGS-----SDENEDILKFQSSQVQIRARWLHEPDETDRISAS 335

Query: 363 HFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSL 422
           HFRKIF CSCGKLEKSLGF +VE+SI GESFMLHQIRKMVGTAVAVKR+LLPRDI+ LSL
Sbjct: 336 HFRKIFRCSCGKLEKSLGFDFVELSIWGESFMLHQIRKMVGTAVAVKRELLPRDIIRLSL 395

Query: 423 AKHSRIVLPLAPSEVLFLRANSFSVRTRPG-VTRPEMQTMVESEEILKMVDEFYTSVTLP 481
            K SRIVLPLAPSEVL LR NSFSVR +PG + RP M+TM ESEEILK V+EFY +V LP
Sbjct: 396 TKFSRIVLPLAPSEVLILRGNSFSVRKKPGNIKRPGMETMNESEEILKGVEEFYRAVMLP 455

Query: 482 EVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWK 523
           +VSKFLD +K PW EW+ENL++FTSIP+ QLDEVR AW++WK
Sbjct: 456 QVSKFLDPSKPPWKEWVENLDRFTSIPDAQLDEVRKAWKVWK 497

Length = 513

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

>gnl\|CDD\|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated	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\|211336 cd02569, PseudoU_synth_ScPus3, Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like	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\|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]	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\|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase	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\|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase	Back alignment and domain information

>gnl\|CDD\|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated	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\|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional	Back alignment and domain information

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		539
PLN03078		513	Putative tRNA pseudouridine synthase; Provisional	100.0
KOG2553		416	consensus Pseudouridylate synthase [Translation, r	100.0
PRK00021		244	truA tRNA pseudouridine synthase A; Validated	100.0
PRK12434		245	tRNA pseudouridine synthase A; Reviewed	100.0
COG0101		266	TruA Pseudouridylate synthase [Translation, riboso	100.0
cd02570		239	PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudou	100.0
cd02568		245	PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: P	100.0
PRK14588		272	tRNA pseudouridine synthase ACD; Provisional	100.0
PRK14589		265	tRNA pseudouridine synthase ACD; Provisional	100.0
TIGR00071		227	hisT_truA pseudouridylate synthase I. universal so	100.0
PRK14586		245	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	99.73
PF01416		105	PseudoU_synth_1: tRNA pseudouridine synthase; Inte	98.04
PF10105		187	DUF2344: Uncharacterized protein conserved in bact	94.1

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

Probab=100.00  E-value=7.2e-117  Score=941.23  Aligned_cols=511  Identities=65%  Similarity=0.978  Sum_probs=421.2

Q ss_pred             cccccccccCcccccccCCccccccccCcccccccCCcccccCCCCCC-CCCCCCCcccccCCCCCCCCCCcCccccceE
Q 009253            2 AIYPLRLLHSPWSARSITSTLSTVGFSNKISAVNLLPLSCYRCPASSS-SKSSPSVSHTLTRPTPNSSDDKWEPVRKKKV   80 (539)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~krkv   80 (539)
                      |++.+|+|++||++.+++++   +.+-+|    .+++.++..|.+.++ .++.++....++..+......+|++++|++|
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~---~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~krrv   73 (513)
T PLN03078          1 AVSFLRAPWPLWRFWSSTSL---LRRVNP----RILRTSSSASSSPSSTSLSPPSSDPPLTDNSDQGGGMKWESARKKKV   73 (513)
T ss_pred             Ccceecccccccccccchhh---hcccCc----ccccCccceecccccccCCCCCCCcccccccCCCCCCCcccccceEE
Confidence            57899999999999999994   445566    666666644555332 2222222222221122223339999999999


Q ss_pred             EEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCCCC
Q 009253           81 ALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDA  160 (539)
Q Consensus        81 al~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~~~  160 (539)
                      +|.|+|+||+|+|||+|++.+..+|||++||+||.++|+|.+.|+++++++.|+|||||||||||+||||||++.++...
T Consensus        74 aL~IaYdGt~Y~G~Q~Q~n~~~~~TVEg~LE~AL~k~~~I~e~n~~~~~ki~~~rAgRTDkGVHA~gQVvsf~l~~p~~~  153 (513)
T PLN03078         74 VLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNYGNLHKIGWARSSRTDKGVHSLATMISLKMEIPENA  153 (513)
T ss_pred             EEEEEEcCCCcceeeECCCCCCCCCHHHHHHHHHHHHhCccccccccccceeEEeeccCCcCccccccEEEEeccCcchh
Confidence            99999999999999999875456899999999999999999999999999999999999999999999999999887666


Q ss_pred             CCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCcchhhhhhhhHHHHHHHHhhcc
Q 009253          161 WKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFE  240 (539)
Q Consensus       161 ~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~~~~~~i~~~i~~~~~~l~~fe  240 (539)
                      |..++++..|+..||++||+||||++|.+|+++||||++|++|+|+|+||+++++.+..+....+++++++|++||++|+
T Consensus       154 ~~~d~~~~~L~~~LN~~LP~DIRVl~v~~V~~~FhAR~sc~sRtY~Y~iP~~~~~~k~~f~~~~~~~dI~kMneAl~~fi  233 (513)
T PLN03078        154 WKDDPDGIALAKFINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFSSEEIDEHISEFNSILNGFE  233 (513)
T ss_pred             ccccchHHHHHHHHHhcCCCCeEEEEEEECCCCcCCCCCCCceEEEEEEccccccCCCccchhhhHHHHHHHHHHHHhcc
Confidence            76677777799999999999999999999999999999999999999999987776666766666668999999999999


Q ss_pred             cccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCchhhhhccccc
Q 009253          241 GEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQNSMV  320 (539)
Q Consensus       241 GtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~  320 (539)
                      |+|||||||.+++|++..+  ||+++.++....+.+...+.+..+.      +..+++++.       .|+|+++..+..
T Consensus       234 GtHDFhNFT~r~~y~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~-------~~~e~~~~~~~~  298 (513)
T PLN03078        234 GEHPFHNYTARSKYRKKLP--GKHKQRNGAVSRRAKSSKEMSSSES------EENHGEISE-------EDEEDLSFSSIP  298 (513)
T ss_pred             cccCcccccCCCccCcccc--ccccccccccccccccccccccccc------ccccccccc-------chhhhhcccccc
Confidence            9999999999999998765  5555555433222111111110000      000111000       011111122222


Q ss_pred             cCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeCchhhHHHHH
Q 009253          321 SGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRK  400 (539)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~GqSFLlhQIRk  400 (539)
                      .+.     .+.+.+.++.+++.+.++++|+++++|+||++++|+|+|++|+|+++++..|.+||+|+|.|||||||||||
T Consensus       299 ~~~-----~~~~~~~~~~~~~~~~~~~~wl~e~d~~d~i~~s~~R~I~~~~~~~~~~~~g~~fv~i~I~GqSFmlhQIRK  373 (513)
T PLN03078        299 SGS-----SDENEDILKFQSSQVQIRARWLHEPDETDRISASHFRKIFRCSCGKLEKSLGFDFVELSIWGESFMLHQIRK  373 (513)
T ss_pred             ccc-----cccccccccccccchhhhhhhccCCccccccchhheEEEEEeecCCccccCCceEEEEEEEehhHHHHHHHH
Confidence            221     123345556666778889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHccCCCHHHHHHHHhccCCCCCCCCCCCCeeEeccccCCCCCCC-CCCCccccchhhHHHHHHHHHHHHhhc
Q 009253          401 MVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSVRTRPG-VTRPEMQTMVESEEILKMVDEFYTSVT  479 (539)
Q Consensus       401 MVG~avaV~rG~~p~~~i~~~L~~~~ri~iP~APa~GL~L~~v~f~~~nk~~-~~~~~~~~~~~~~~~~~~~e~Fk~~~i  479 (539)
                      |||++++|++|.+|++.|+.+|.++.++.+|+||++||||.+|+|+.||+.| ..+|+++.+++++++++.|++|++++|
T Consensus       374 MIG~~~aV~rg~~~~~~i~~~L~~~~r~~~P~AP~~GL~L~~~~F~~yn~~~~~~~p~~~~~~e~e~~~~~i~eF~~~~i  453 (513)
T PLN03078        374 MVGTAVAVKRELLPRDIIRLSLTKFSRIVLPLAPSEVLILRGNSFSVRKKPGNIKRPGMETMNESEEILKGVEEFYRAVM  453 (513)
T ss_pred             HHHHHHHHHhccCCHHHHHHHhccccccccccCCCcceEEEeeeccccccccccCCCCccccccHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999998999999999999999999999999876 688999999999999999999999999


Q ss_pred             hHhHHhhhhhccCcHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHhhhHHHhhhccC
Q 009253          480 LPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWKEKRFESKTIVESAISV  539 (539)
Q Consensus       480 ~p~I~~~l~~~~~~~~~W~e~l~~~~~~~~~~~~~~~~~~~~wk~~~~~~~~~~~~~~~~  539 (539)
                      ||+|+++++.++++|++|++||++|++||++||++||+||++||+++...|+.+.+|+++
T Consensus       454 ~p~i~~~~~~~~~~w~~w~~nl~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~  513 (513)
T PLN03078        454 LPQVSKFLDPSKPPWKEWVENLDRFTSIPDAQLDEVRKAWKVWKADYDRMKMARKSASSE  513 (513)
T ss_pred             hHHHHHHhccccchHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHhhhHHHHhhhcccccC
Confidence            999999999899999999999999999999999999999999999999999999999874

>KOG2553 consensus 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

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

>cd02570 PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like	Back alignment and domain information

>cd02568 PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: Pseudouridine synthase, PUS1/ PUS2 like	Back alignment and domain information

>PRK14588 tRNA pseudouridine synthase ACD; Provisional	Back alignment and domain information

>PRK14589 tRNA pseudouridine synthase ACD; Provisional	Back alignment and domain information

>TIGR00071 hisT_truA pseudouridylate synthase I	Back alignment and domain information

>PRK14586 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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		539
1vs3_A		249	Crystal Structure Of The Trna Pseudouridine Synthas		2e-04

>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust. Identities = 41/132 (31%), Positives = 58/132 (43%), Gaps = 23/132 (17%) Query: 78 KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSS 137 +++ L Y GT + GLQ R L T++GELE AL G L K A Sbjct: 2 RRLLLLCEYDGTLFAGLQ--RQGRGLRTVQGELERAL--------PGIGALPKAVAA--G 49 Query: 138 RTDKGVHSLATMICLKME--IPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFD 195 RTD GVH+LA + +E IP + + + +N LP ++KV F Sbjct: 50 RTDAGVHALAMPFHVDVESAIPVE---------KVPEALNRLLPEDLKVVGAREVAPDFH 100 Query: 196 PRRECNLRKYSY 207 R++ R Y Y Sbjct: 101 ARKDALWRAYRY 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		539
1vs3_A		249	TRNA pseudouridine synthase A; TRUA, tRNA modifica	4e-16
1dj0_A		264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	9e-16
1dj0_A		264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	6e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05

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

 Score = 77.1 bits (191), Expect = 4e-16
 Identities = 38/135 (28%), Positives = 56/135 (41%), Gaps = 25/135 (18%)

Query: 78  KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSS 137
           +++ L   Y GT + GLQ Q     L T++GELE AL   G                 + 
Sbjct: 2   RRLLLLCEYDGTLFAGLQRQG--RGLRTVQGELERALPGIGA-LPKAVA---------AG 49

Query: 138 RTDKGVHSLATMIC---LKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSF 194
           RTD GVH+LA M     ++  IP +            + +N  LP ++KV         F
Sbjct: 50  RTDAGVHALA-MPFHVDVESAIPVEKV---------PEALNRLLPEDLKVVGAREVAPDF 99

Query: 195 DPRRECNLRKYSYLL 209
             R++   R Y Y +
Sbjct: 100 HARKDALWRAYRYRI 114

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 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		539
1dj0_A		264	Pseudouridine synthase I; alpha/beta fold, RNA-bin	100.0
1vs3_A		249	TRNA pseudouridine synthase A; TRUA, tRNA modifica	100.0

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

Probab=100.00  E-value=4.9e-65  Score=512.58  Aligned_cols=241  Identities=22%  Similarity=0.332  Sum_probs=207.9

Q ss_pred             ccceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEec
Q 009253           76 RKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKME  155 (539)
Q Consensus        76 ~krkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~  155 (539)
                      +|++|+|.|+|+||+|+|||+|++   .+|||++||+||.++++         .++.|.+||||||||||+|||+||++.
T Consensus         2 Pm~r~~l~i~YdGt~y~GwQ~Q~~---~~TVq~~Le~AL~~~~~---------~~v~~~~agRTDaGVHA~gqv~~f~~~   69 (264)
T 1dj0_A            2 PVYKIALGIEYDGSKYYGWQRQNE---VRSVQEKLEKALSQVAN---------EPITVFCAGRTDAGVHGTGQVVHFETT   69 (264)
T ss_dssp             CCEEEEEEEEECCTTSSCSCCTTC---SSCHHHHHHHHHHHHHT---------SCCCEEESSCCCTTCEEEEEEEEEEES
T ss_pred             CccEEEEEEEEeCCCceeEEECcC---CCCHHHHHHHHHHHHhC---------CCeEEEEeccCCCCCchhhEEEEEEEC
Confidence            688999999999999999999986   48999999999999976         479999999999999999999999986


Q ss_pred             CCCCCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccC-----CcchhhhhhhhHH
Q 009253          156 IPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGIN-----SQLTAAEIDSHIS  230 (539)
Q Consensus       156 i~~~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~-----~~~~~~~i~~~i~  230 (539)
                      .+.       +...++..||++||+||+|+++.+|+.+||||++|.+|+|+|+|+.......     ......  ..|++
T Consensus        70 ~~~-------~~~~~~~~lN~~LP~dI~V~~~~~V~~~FhARf~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~--~lD~~  140 (264)
T 1dj0_A           70 ALR-------KDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYE--PLDAE  140 (264)
T ss_dssp             CCC-------CHHHHHHHHHHTSCTTEEEEEEEECCTTCCTTTTCCEEEEEEEEECSSSCCCTTTTSSEECCS--CCCHH
T ss_pred             CCC-------CHHHHHHHHHhhCCcCeEEEEEEeCCCCCCcccccccEEEEEEEccCCCCChhHcCceEeeCC--CCCHH
Confidence            331       3457899999999999999999999999999999999999999997643211     011112  23699


Q ss_pred             HHHHHHhhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCc
Q 009253          231 DFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSD  310 (539)
Q Consensus       231 ~~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~  310 (539)
                      +|+++++.|+|+|||+|||....     .                                                   
T Consensus       141 ~M~~aa~~l~G~HDF~~F~~~~~-----~---------------------------------------------------  164 (264)
T 1dj0_A          141 RMHRAAQCLLGENDFTSFRAVQC-----Q---------------------------------------------------  164 (264)
T ss_dssp             HHHHHHGGGCEEEECGGGCCTTC-----C---------------------------------------------------
T ss_pred             HHHHHHHHhcCcccHHHhccCCC-----C---------------------------------------------------
Confidence            99999999999999999986321     0                                                   


Q ss_pred             hhhhhccccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEe
Q 009253          311 DEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISG  390 (539)
Q Consensus       311 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~G  390 (539)
                                                                       ..+++|+|+++++.+     ..+++.|+|+|
T Consensus       165 -------------------------------------------------~~s~vR~I~~~~v~~-----~~~~i~~~i~g  190 (264)
T 1dj0_A          165 -------------------------------------------------SRTPWRNVMHINVTR-----HGPYVVVDIKA  190 (264)
T ss_dssp             -------------------------------------------------CSCCEEEEEEEEEEE-----ETTEEEEEEEE
T ss_pred             -------------------------------------------------CCCcEEEEEEEEEEE-----CCCEEEEEEEE
Confidence                                                             036689999998865     24799999999


Q ss_pred             CchhhHHHHHHHHHHHHHHccCCCHHHHHHHHhcc-CCCCCCCCCCCCeeEeccccCC
Q 009253          391 ESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKH-SRIVLPLAPSEVLFLRANSFSV  447 (539)
Q Consensus       391 qSFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~~~-~ri~iP~APa~GL~L~~v~f~~  447 (539)
                      +|||+||||+|||+|++||+|.++++.|+.+|... .+..+|+|||+||||.+|.|+.
T Consensus       191 ~~FL~~mVR~mvG~L~~vG~G~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~~  248 (264)
T 1dj0_A          191 NAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPD  248 (264)
T ss_dssp             SCCCTTHHHHHHHHHHHHHTTSSCTTHHHHHHHHCCGGGSCCCCCSTTEEEEEEECCG
T ss_pred             chHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhCCCcccCcCccCCCCcEEeeeccCc
Confidence            99999999999999999999999999999999754 4578999999999999999974

PyMOL of 1dj0

>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

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		539
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	8e-04

>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 = 37/186 (19%), Positives = 61/186 (32%), Gaps = 22/186 (11%)

Query: 77  KKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARS 136
             K+AL + Y G+ Y G Q Q +     +++ +LE AL +            + I    +
Sbjct: 3   VYKIALGIEYDGSKYYGWQRQNEVR---SVQEKLEKALSQVAN---------EPITVFCA 50

Query: 137 SRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDP 196
            RTD GVH    ++  +                    VNA+LP +I V  +      F  
Sbjct: 51  GRTDAGVHGTGQVVHFETTALRKDAAWTL-------GVNANLPGDIAVRWVKTVPDDFHA 103

Query: 197 RRECNL---RKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYTERSK 253
           R        R   Y        ++  +T           +       GE+ F ++     
Sbjct: 104 RFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQC 163

Query: 254 YRRKPH 259
             R P 
Sbjct: 164 QSRTPW 169

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		539
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=7.5e-62  Score=487.15  Aligned_cols=241  Identities=22%  Similarity=0.321  Sum_probs=204.7

Q ss_pred             ccceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEec
Q 009253           76 RKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKME  155 (539)
Q Consensus        76 ~krkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~  155 (539)
                      +++||||.|+|+||+|+|||+|++.   +||||+||+||.++++         +++.|.+||||||||||++|||+|++.
T Consensus         2 ~~~r~al~i~Y~Gt~f~G~Q~Q~~~---~TVq~~Le~aL~~~~~---------~~~~~~~agRTD~GVhA~~qv~~~~~~   69 (264)
T d1dj0a_           2 PVYKIALGIEYDGSKYYGWQRQNEV---RSVQEKLEKALSQVAN---------EPITVFCAGRTDAGVHGTGQVVHFETT   69 (264)
T ss_dssp             CCEEEEEEEEECCTTSSCSCCTTCS---SCHHHHHHHHHHHHHT---------SCCCEEESSCCCTTCEEEEEEEEEEES
T ss_pred             CcEEEEEEEEEECCCeeeEeECcCC---CCHHHHHHHHHHHhhC---------CCeEEEEeecccCCcceeeEEEEEeec
Confidence            5889999999999999999999874   8999999999999986         689999999999999999999999985


Q ss_pred             CCCCCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCc-----chhhhhhhhHH
Q 009253          156 IPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQ-----LTAAEIDSHIS  230 (539)
Q Consensus       156 i~~~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~-----~~~~~i~~~i~  230 (539)
                      ..       .+...+...||++||++|||+++.+|+.+||||++|.+|+|.|+++.........     .....  .+++
T Consensus        70 ~~-------~~~~~~~~~lN~~Lp~dI~i~~~~~v~~~F~aR~~a~~r~Y~Y~i~~~~~~~~~~~~~~~~~~~~--ld~~  140 (264)
T d1dj0a_          70 AL-------RKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEP--LDAE  140 (264)
T ss_dssp             CC-------CCHHHHHHHHHHTSCTTEEEEEEEECCTTCCTTTTCCEEEEEEEEECSSSCCCTTTTSSEECCSC--CCHH
T ss_pred             cc-------hhhhhhhcccccccccccccccceeccccccchhhhhhcccceeeccccccccccccccccccCC--cchH
Confidence            33       2346789999999999999999999999999999999999999998765432111     11122  3699


Q ss_pred             HHHHHHhhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCc
Q 009253          231 DFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSD  310 (539)
Q Consensus       231 ~~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~  310 (539)
                      +|+++++.|+|+|||+||+.....                                                        
T Consensus       141 ~m~~a~~~~~G~hdF~~F~~~~~~--------------------------------------------------------  164 (264)
T d1dj0a_         141 RMHRAAQCLLGENDFTSFRAVQCQ--------------------------------------------------------  164 (264)
T ss_dssp             HHHHHHGGGCEEEECGGGCCTTCC--------------------------------------------------------
T ss_pred             HHHHHHhhccCccccccccccccc--------------------------------------------------------
Confidence            999999999999999999753210                                                        


Q ss_pred             hhhhhccccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEe
Q 009253          311 DEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISG  390 (539)
Q Consensus       311 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~G  390 (539)
                                                                       ..+..|+|+.+.+..     ..+++.|+|+|
T Consensus       165 -------------------------------------------------~~~~~r~i~~~~~~~-----~~~~i~i~i~g  190 (264)
T d1dj0a_         165 -------------------------------------------------SRTPWRNVMHINVTR-----HGPYVVVDIKA  190 (264)
T ss_dssp             -------------------------------------------------CSCCEEEEEEEEEEE-----ETTEEEEEEEE
T ss_pred             -------------------------------------------------CCCccccccccccee-----cCcEEEEEech
Confidence                                                             013456677776654     35799999999


Q ss_pred             CchhhHHHHHHHHHHHHHHccCCCHHHHHHHHhcc-CCCCCCCCCCCCeeEeccccCC
Q 009253          391 ESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKH-SRIVLPLAPSEVLFLRANSFSV  447 (539)
Q Consensus       391 qSFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~~~-~ri~iP~APa~GL~L~~v~f~~  447 (539)
                      +|||+||||+|||++++|++|.++++.|+.+|..+ .....|+|||+||||++|.|+.
T Consensus       191 ~sFL~~qVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~~  248 (264)
T d1dj0a_         191 NAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPD  248 (264)
T ss_dssp             SCCCTTHHHHHHHHHHHHHTTSSCTTHHHHHHHHCCGGGSCCCCCSTTEEEEEEECCG
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHhcCCcccCccccCCCCCEEcccccCc
Confidence            99999999999999999999999999999999744 4567899999999999999974

PyMOL of d1dj0a_