Citrus Sinensis ID: 003522

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-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810---

MLSILEVRYQLIMFILVSDDCTKFPFCIKNKSNCICKYIANIYIYTYTLLLGLWLTLVYFLKICSLLHQRYKDFSPCLIDGLLKVFFPGKSGEDLDADRNLKAMKKRSTLKLLLELYFIGIIEDSSIFINIIKDLTSIEHLKDRDTTQTNLTLLASFARQGRIFLGLPLSGPGQEIYEEFFKGLNITADQKKIFKKAFHTYYNAVQELLQAEHTSLRQMENENAKILNAKGELSEENSSSYEKLRKSYDHLYRNVSSLAEALDMQPPVMPEDVHTTRVTSGEDASPASGKDSSVPEPVWDDEETRAFYECLPDLRAFVPAVLLGEAEHKANEPSVKPLEQPTDPASEPDQGQLAAQDTAEVSADLGASPEGKSVEKGKDKEEKEKEKAKDPDKEKGKGKDKEEKDKEKAKDPDKEKGKEKDTERKVETEKEKLKGVEGTNLDALLQRLPGCVSRDLIDQLTVEFCYLNSKSNRKRLVRALFNVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIRFIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIRMANMLEILMRLKNVKNLDPRHVTLVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCESYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAETYWTHQKIVSGSGWLLLFLRLVVTTLTEALPRGNLIDF

ccHHHHHHHHHHHHHHHccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHcccccccccccccccHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccHHHHHHHcccccccccccccccHHHHHcccccccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccHHHHHHcccccEEEEccccccccHHHHHHHHHHHHHccccccHHHHHHHHHHHcHHHcccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHcccccHHHHHHHHHHcccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHcccccccccc

cccHHHHHHHHHHHHHHccccccccEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccccccccHHHHHHHHHcccHHcccccccHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHccHHHHHHccHHHcccccccccccccccccccccccHHHHHccccHHHHHHHcccccccccccccccccccHHHccccccccccHHHccHccccccccccccccccccccccccccccccHHHcccccHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccccHHHHHHHHHHHcccEEccccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHcccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHcccccccHHHHHEEcccccHHHHHHHHHHHHHHHHHccccccccc

MLSILEVRYQLIMFILVsddctkfpfciknksncICKYIANIYIYTYTLLLGLWLTLVYFLKICSLLHQRykdfspclidgllkvffpgksgedldADRNLKAMKKRSTLKLLLELYFIGIIEDSSIFINIIKDLtsiehlkdrdttqTNLTLLASFARQGRiflglplsgpgqEIYEEFFKGLNITADQKKIFKKAFHTYYNAVQELLQAEHTSLRQMENENAKILNakgelseenssSYEKLRKSYDHLYRNVSSLAealdmqppvmpedvhttrvtsgedaspasgkdssvpepvwddeetrAFYECLPDLRAFVPAVLLgeaehkanepsvkpleqptdpasepdqgqlaaQDTAEVSadlgaspegksvekgkDKEEKEkekakdpdkekgkgkdkeekdkekakdpdkekgkekdtERKVETEKEklkgvegtnLDALLQrlpgcvsrdlIDQLTVEFCYLNSKSNRKRLVRALFNvprtslellpYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIRFIGELCkfkiapaglVFSCLKACLDDFTHHNIDVACNLLETCgrflyrspeTSIRMANMLEILMRLknvknldprhvTLVENayylckppersarvskvrppLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCESYLLKCFMKvhkgkygqIHLIASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGElynyehvdssvIFDTLYLILVFGHGtaetywthqkivsgsGWLLLFLRLVVTTLTealprgnlidf

MLSILEVRYQLIMFILVSDDCTKFPFCIKNKSNCICKYIANIYIYTYTLLLGLWLTLVYFLKICSLLHQRYKDFSPCLIDGLLKVFFPGKSGEDLDADRNLKAMKKRSTLKLLLELYFIGIIEDSSIFINIIKDLTSIEHLKDRDTTQTNLTLLASFARQGRIFLGLPLSGPGQEIYEEFFKGLNITADQKKIFKKAFHTYYNAVQELLQAEHTSLRQMENENAKIlnakgelseenssSYEKLRKSYDHLYRNVSSLAEALDMQPPVMPEDVHTTRVTsgedaspasgkdssvpepvwDDEETRAFYECLPDLRAFVPAVLLGEAEHKANEPSVKPLEQPTDPASEPDQGQLAAQDTAEVSadlgaspegksvekgkdkeekekekakdpdkekgkgkdkeekdkekakdpdkekgkekdterkvetekeklkgvegtnldALLQRLPGCVSRDLIDQLTVEFCYlnsksnrkRLVRALFNvprtslellpYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIRFIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIRMANMLEILMRLKNVKNLDPRHVTLVENAyylckppersarvskvrpPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCESYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAETYWTHQKIVSGSGWLLLFLRLVVTTltealprgnlidf

MLSILEVRYQLIMFILVSDDCTKFPFCIKNKSNCICKyianiyiytytlllglwltlvyflKICSLLHQRYKDFSPCLIDGLLKVFFPGKSGEDLDADRNLKAMKKRSTLKLLLELYfigiiedssifiniiKDLTSIEHLKDRDTTQTNLTLLASFARQGRIFLGLPLSGPGQEIYEEFFKGLNITADQKKIFKKAFHTYYNAVQELLQAEHTSLRQMENENAKILNAKGELSEENSSSYEKLRKSYDHLYRNVSSLAEALDMQPPVMPEDVHTTRVTSGEDASPASGKDSSVPEPVWDDEETRAFYECLPDLRAFVPAVLLGEAEHKANEPSVKPLEQPTDPASEPDQGQLAAQDTAEVSADLGASPEGKSVekgkdkeekekekakdpdkekgkgkdkeekdkekakdpdkekgkekdTERKVETEKEKLKGVEGTNLDALLQRLPGCVSRDLIDQLTVEFCYLNSKSNRKRLVRALFNVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIRFIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIRMANMLEILMRLKNVKNLDPRHVTLVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCESYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAETYWTHQKIVSGSGWlllflrlvvttltEALPRGNLIDF

***ILEVRYQLIMFILVSDDCTKFPFCIKNKSNCICKYIANIYIYTYTLLLGLWLTLVYFLKICSLLHQRYKDFSPCLIDGLLKVFFPGK***************KRSTLKLLLELYFIGIIEDSSIFINIIKDLTSIEHLKDRDTTQTNLTLLASFARQGRIFLGLPLSGPGQEIYEEFFKGLNITADQKKIFKKAFHTYYNAVQELLQA*******************************************************************************************ETRAFYECLPDLRAFVPAVLLG******************************************************************************************************************TNLDALLQRLPGCVSRDLIDQLTVEFCYLNSKSNRKRLVRALFNVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIRFIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIRMANMLEILMRLKNVKNLDPRHVTLVENAYYLCKPP*****VSKVRPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCESYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAETYWTHQKIVSGSGWLLLFLRLVVTTLTEALP*******

*******RYQLIMFILVSDDCTKFPFCIKNKSNCICKYIANIYIYTYTLLLGLWLTLVYFLKICSLLHQRYKDFSPCLIDGLLKV*******************KKRSTLKLLLELYFIGIIEDSSIFINIIKDLTSIEHLKDRDTTQTNLTLLASFARQGRIFLGLPLSGP*************ITADQKKIFKKAFHTYYNAVQELLQAEHTSLRQMEN************************KSYDHLYRNVSSLAEALDMQPP************************************T*AFYECLPD*********************************************************************************************************************************ALLQRLPGCVSRDLIDQLTVEFCYLNSKSNRKRLVRALFNVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINK*******TKIRNIRFIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIRMANMLEILM***********HVTLVENAYYL******************QYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCESYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAETYW***KIVSGSGWLLLFLRLVVTTLTEALP*******

MLSILEVRYQLIMFILVSDDCTKFPFCIKNKSNCICKYIANIYIYTYTLLLGLWLTLVYFLKICSLLHQRYKDFSPCLIDGLLKVFFPGKSGEDLDADRNLKAMKKRSTLKLLLELYFIGIIEDSSIFINIIKDLTSIEHLKDRDTTQTNLTLLASFARQGRIFLGLPLSGPGQEIYEEFFKGLNITADQKKIFKKAFHTYYNAVQELLQAEHTSLRQMENENAKILNAK************KLRKSYDHLYRNVSSLAEALDMQPPVMPEDV***********************PVWDDEETRAFYECLPDLRAFVPAVLLGEAEH*********************************************************************************************************KGVEGTNLDALLQRLPGCVSRDLIDQLTVEFCYLNSKSNRKRLVRALFNVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIRFIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIRMANMLEILMRLKNVKNLDPRHVTLVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCESYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAETYWTHQKIVSGSGWLLLFLRLVVTTLTEALPRGNLIDF

*LSILEVRYQLIMFILVSDDCTKFPFCIKNKSNCICKYIANIYIYTYTLLLGLWLTLVYFLKICSLLHQRYKDFSPCLIDGLLKVFFPGKSGEDLDADRNLKAMKKRSTLKLLLELYFIGIIEDSSIFINIIKDLTSIEHLKDRDTTQTNLTLLASFARQGRIFLGLPLSGPGQEIYEEFFKGLNITADQKKIFKKAFHTYYNAVQELLQAEHTSLRQMENENAKILNAKGELSEENSSSYEKLRKSYDHLYRNVSSLAEALDMQPPV***************************EPVWDDEETRAFYECLPDLRAFVPAVLLGE***************************************************************************************************************EGTNLDALLQRLPGCVSRDLIDQLTVEFCYLNSKSNRKRLVRALFNVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIRFIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIRMANMLEILMRLKNVKNLDPRHVTLVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCESYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAETYWTHQKIVSGSGWLLLFLRLVVTTLTEALPRGNLI*F

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MLSILEVRYQLIMFILVSDDCTKFPFCIKNKSNCICKYIANIYIYTYTLLLGLWLTLVYFLKICSLLHQRYKDFSPCLIDGLLKVFFPGKSGEDLDADRNLKAMKKRSTLKLLLELYFIGIIEDSSIFINIIKDLTSIEHLKDRDTTQTNLTLLASFARQGRIFLGLPLSGPGQEIYEEFFKGLNITADQKKIFKKAFHTYxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxNSSSYEKLRKSYDHLYRNVSSLAEALDMQPPVMPEDVHTTRVTSGEDASPASGKDSSVPEPVWDDEETRAFYECLPDLRAFVPAVLLGEAEHKANEPSVKPLEQPTDPASEPDQGQLAAQDTAEVSADLGASPEGKSVEKGKDKEEKEKEKAKDPDKEKGKGKDKEEKDKEKAKDPDKEKGKEKDTERKVETEKEKLKGVEGTNLDALLQRLPGCVSRDLIDQLTVEFCYLNSKSNRKRLVRALFNVPRTSLELLPYYSRMVATLSTCMKDVSSMLxxxxxxxxxxxxxxxxxxxxxTKIRNIRFIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIRMANMLEILMRLKNVKNLDPRHVTLVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCESYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAETYWTHQKIVSGSGWLLLFLRLVVTTLTEALPRGNLIDF

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		813	2.2.26 [Sep-21-2011]
Q9HAU5		1272	Regulator of nonsense tra	yes	no	0.820	0.524	0.405	1e-135
O13824		1049	Nonsense-mediated mRNA de	yes	no	0.405	0.314	0.336	7e-52
P38798		1089	Nonsense-mediated mRNA de	yes	no	0.424	0.316	0.309	3e-44
F1QBY1		2876	Nipped-B-like protein B O	no	no	0.077	0.021	0.432	0.0004
Q6BU84		637	Pre-mRNA-splicing factor	no	no	0.248	0.317	0.223	0.0007

>sp\|Q9HAU5\|RENT2_HUMAN Regulator of nonsense transcripts 2 OS=Homo sapiens GN=UPF2 PE=1 SV=1	Back alignment and function desciption

 Score =  481 bits (1239), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 291/717 (40%), Positives = 413/717 (57%), Gaps = 50/717 (6%)

Query: 63  ICSLLHQRYKDFSPCLIDGLLKVFFPGKSGEDLDADRNLKAMKKRSTLKLLLELYFIGII 122
           +CSL HQRY DF+P L+    K F      E    ++     K R+ L+ + EL  +GI 
Sbjct: 225 LCSLFHQRYADFAPSLLQVWKKHF------EARKEEKTPNITKLRTDLRFIAELTIVGIF 278

Query: 123 EDSSIFINIIKDLTSIEHLKDRDTTQTNLTLLASFARQ-GRIFLGL---PLSGPGQEIYE 178
            D      I + L +I +  DR++  T+++++ SF R  G    GL    +    ++   
Sbjct: 279 TDKEGLSLIYEQLKNIINA-DRES-HTHVSVVISFCRHCGDDIAGLVPRKVKSAAEKFNL 336

Query: 179 EFFKGLNITADQKKIFKKAFHTYYNAVQELLQAEHTSLRQMENENAKILNAKGELSEENS 238
            F     I+ ++++ F+     Y+ ++ + L+ +H  L+  E +N +IL++KGELSE+  
Sbjct: 337 SFPPSEIISPEKQQPFQNLLKEYFTSLTKHLKRDHRELQNTERQNRRILHSKGELSEDRH 396

Query: 239 SSYEKLRKSYDHLYRNVSSLAEALDMQPPVMPEDVHTTRVTS-GEDA-SPASGKDSSVPE 296
             YE+   SY  L  N  SLA+ LD   P +P+D  T      G D  +P    +  +  
Sbjct: 397 KQYEEFAMSYQKLLANSQSLADLLDENMPDLPQDKPTPEEHGPGIDIFTPGKPGEYDLEG 456

Query: 297 PVWDDEETRAFYECLPDLRAFVPAVLLGEAEHKANEPSVKPLEQPTDPASEPDQGQLAAQ 356
            +W+DE+ R FYE L DL+AFVPA+L      K NE S +  E   D             
Sbjct: 457 GIWEDEDARNFYENLIDLKAFVPAILF-----KDNEKSCQNKESNKD------------- 498

Query: 357 DTAEVSADLGASPEGKSVEKGKDKEEKEKEKAKDPDKEKGKGKDKEEKDKEKAKDPDKEK 416
           DT E       S E K V    D E + +    + D  + +G D+       A+D  K+ 
Sbjct: 499 DTKEAKE----SKENKEVSSPDDLELELENLEINDDTLELEGGDE-------AEDLTKKL 547

Query: 417 GKEKDTERKVETEKEKLKGVEGTNLDALLQRLPGCVSRDLIDQLTVEFCY-LNSKSNRKR 475
             E++ E +  +    LK +    +DA LQ+LP CV+RDLID+  ++FC  +N+K+NRK+
Sbjct: 548 LDEQEQEDEEASTGSHLKLI----VDAFLQQLPNCVNRDLIDKAAMDFCMNMNTKANRKK 603

Query: 476 LVRALFNVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETK 535
           LVRALF VPR  L+LLP+Y+R+VATL  CM DV+  L  ML  +F F + KKDQ+NIETK
Sbjct: 604 LVRALFIVPRQRLDLLPFYARLVATLHPCMSDVAEDLCSMLRGDFRFHVRKKDQINIETK 663

Query: 536 IRNIRFIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIR 595
            + +RFIGEL KFK+        CLK  L DF+HH+I++AC LLETCGRFL+RSPE+ +R
Sbjct: 664 NKTVRFIGELTKFKMFTKNDTLHCLKMLLSDFSHHHIEMACTLLETCGRFLFRSPESHLR 723

Query: 596 MANMLEILMRLKNVKNLDPRHVTLVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDL 655
            + +LE +MR K   +LD R+VT+VENAYY C PP     V K RPPL +Y+RKLL+ DL
Sbjct: 724 TSVLLEQMMRKKQAMHLDARYVTMVENAYYYCNPPPAEKTVKKKRPPLQEYVRKLLYKDL 783

Query: 656 DKSSIEHVLRQLRKLPWSDCE--SYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAV 713
            K + E VLRQ+RKLPW D E   Y++ C + +   KY  IH +A+L AGL  Y ++  +
Sbjct: 784 SKVTTEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCVANLLAGLVLYQEDVGI 843

Query: 714 AVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFG 770
            VVD VLE+IRLG+E+N     QRR++  +FLGELYNY  V+S+VIF TLY    FG
Sbjct: 844 HVVDGVLEDIRLGMEVNQPKFNQRRISSAKFLGELYNYRMVESAVIFRTLYSFTSFG 900

Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC). Recruited by UPF3B associated with the EJC core at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF3B stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA.
Homo sapiens (taxid: 9606)

>sp\|O13824\|NMD2_SCHPO Nonsense-mediated mRNA decay protein 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=upf2 PE=1 SV=1	Back alignment and function description

>sp\|P38798\|NMD2_YEAST Nonsense-mediated mRNA decay protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NMD2 PE=1 SV=2	Back alignment and function description

>sp\|F1QBY1\|NIPLB_DANRE Nipped-B-like protein B OS=Danio rerio GN=nipblb PE=2 SV=1	Back alignment and function description

>sp\|Q6BU84\|CWC22_DEBHA Pre-mRNA-splicing factor CWC22 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=CWC22 PE=3 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		813
296086085		1193	unnamed protein product [Vitis vinifera]	0.851	0.580	0.850	0.0
359486551		1222	PREDICTED: regulator of nonsense transcr	0.851	0.566	0.850	0.0
255565870		824	Regulator of nonsense transcripts, putat	0.838	0.827	0.843	0.0
224109654		1194	predicted protein [Populus trichocarpa]	0.849	0.578	0.842	0.0
449452126		1195	PREDICTED: regulator of nonsense transcr	0.849	0.578	0.825	0.0
449524126		1144	PREDICTED: LOW QUALITY PROTEIN: regulato	0.849	0.604	0.815	0.0
356556505		1187	PREDICTED: regulator of nonsense transcr	0.848	0.581	0.787	0.0
124359836		1212	Initiation factor eIF-4 gamma, middle; U	0.851	0.570	0.798	0.0
242065844		1193	hypothetical protein SORBIDRAFT_04g02674	0.846	0.576	0.755	0.0
125540395		1190	hypothetical protein OsI_08170 [Oryza sa	0.842	0.575	0.760	0.0

>gi\|296086085\|emb\|CBI31526.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score = 1221 bits (3158), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 608/715 (85%), Positives = 645/715 (90%), Gaps = 23/715 (3%)

Query: 61  LKICSLLHQRYKDFSPCLIDGLLKVFFPGKSGEDLDADRNLKAMKKRSTLKLLLELYFIG 120
           ++ICSLLHQRYKDFSP LI GLLKVFFPGKSG++LD DRNLKAMKKRSTLKLLLELYF+G
Sbjct: 117 VQICSLLHQRYKDFSPSLIQGLLKVFFPGKSGDELDLDRNLKAMKKRSTLKLLLELYFVG 176

Query: 121 IIEDSSIFINIIKDLTSIEHLKDRDTTQTNLTLLASFARQGRIFLGLPLSGPGQEIYEEF 180
           ++EDS IFINIIKDLTSIEHLKDRDTTQTNL+LLASFARQGRIFLG PLSG  QEI+EEF
Sbjct: 177 VVEDSGIFINIIKDLTSIEHLKDRDTTQTNLSLLASFARQGRIFLGFPLSG--QEIHEEF 234

Query: 181 FKGLNITADQKKIFKKAFHTYYNAVQELLQAEHTSLRQMENENAKILNAKGELSEENSSS 240
           FKGLNITAD KKIF+KAFHTYY+A  ELLQAEHTSLRQME+ENAKILNAKGELS+EN SS
Sbjct: 235 FKGLNITADHKKIFRKAFHTYYDAAAELLQAEHTSLRQMEHENAKILNAKGELSDENVSS 294

Query: 241 YEKLRKSYDHLYRNVSSLAEALDMQPPVMPEDVHTTRVTSGEDASPASGKDSSVPEPVWD 300
           YEKLRKSYDHLYR VSSLAEALDMQPPVMPED HTTRVTSGED S  + K+SS  E VWD
Sbjct: 295 YEKLRKSYDHLYRGVSSLAEALDMQPPVMPEDGHTTRVTSGEDVSSPAAKESSALEAVWD 354

Query: 301 DEETRAFYECLPDLRAFVPAVLLGEAEHKANEPSVKPLEQPTDPASEPDQGQLAAQDTAE 360
           DE+TRAFYECLPDLRAFVPAVLLGEAE K NE S K  EQPTD A E DQ Q   QD AE
Sbjct: 355 DEDTRAFYECLPDLRAFVPAVLLGEAEPKVNEQSAKTQEQPTDLAPEADQSQSVNQDAAE 414

Query: 361 VSADLGASPEGKSVEKGKDKEEKEKEKAKDPDKEKGKGKDKEEKDKEKAKDPDKEKGKEK 420
           +S D  +  EG+S                       KGKDKEEK+KEK+KDPDKEKGKE+
Sbjct: 415 ISVDSCSPREGRS---------------------NEKGKDKEEKEKEKSKDPDKEKGKER 453

Query: 421 DTERKVETEKEKLKGVEGTNLDALLQRLPGCVSRDLIDQLTVEFCYLNSKSNRKRLVRAL 480
           D +RK E EKEKLKG+EGTNLD LLQRLPGCVSRDLIDQLTV+FCYLNSKSNRKRLVRAL
Sbjct: 454 DADRKGENEKEKLKGLEGTNLDGLLQRLPGCVSRDLIDQLTVDFCYLNSKSNRKRLVRAL 513

Query: 481 FNVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIR 540
           FNVPRTSLELLPYYSRMVATLSTCMKDVSSML+Q+LEEEFNFLINKKDQMNIETKIRNIR
Sbjct: 514 FNVPRTSLELLPYYSRMVATLSTCMKDVSSMLLQLLEEEFNFLINKKDQMNIETKIRNIR 573

Query: 541 FIGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIRMANML 600
           F+GELCKF+IAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPET++RMANML
Sbjct: 574 FLGELCKFRIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETTVRMANML 633

Query: 601 EILMRLKNVKNLDPRHVTLVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDLDKSSI 660
           EILMRLKNVKNLDPRH TLVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDLDKSSI
Sbjct: 634 EILMRLKNVKNLDPRHSTLVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDLDKSSI 693

Query: 661 EHVLRQLRKLPWSDCESYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVL 720
           EHVLRQLRKLPWS+CE YLLKCFMKVH+GKYGQIHLIASLT+GLSRYHD+FAV+VVDEVL
Sbjct: 694 EHVLRQLRKLPWSECEPYLLKCFMKVHRGKYGQIHLIASLTSGLSRYHDDFAVSVVDEVL 753

Query: 721 EEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAE 775
           EEIRLGLELNDYGMQQRR+AHMRFLGELYNYEHVDSSVIFDTLYLIL FGH TAE
Sbjct: 754 EEIRLGLELNDYGMQQRRIAHMRFLGELYNYEHVDSSVIFDTLYLILAFGHETAE 808

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359486551\|ref\|XP_002275646.2\| PREDICTED: regulator of nonsense transcripts 2-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255565870\|ref\|XP_002523924.1\| Regulator of nonsense transcripts, putative [Ricinus communis] gi\|223536854\|gb\|EEF38493.1\| Regulator of nonsense transcripts, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|224109654\|ref\|XP_002315268.1\| predicted protein [Populus trichocarpa] gi\|222864308\|gb\|EEF01439.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449452126\|ref\|XP_004143811.1\| PREDICTED: regulator of nonsense transcripts 2-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449524126\|ref\|XP_004169074.1\| PREDICTED: LOW QUALITY PROTEIN: regulator of nonsense transcripts 2-like, partial [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356556505\|ref\|XP_003546565.1\| PREDICTED: regulator of nonsense transcripts 2-like [Glycine max]	Back alignment and taxonomy information

>gi\|124359836\|gb\|ABD32424.2\| Initiation factor eIF-4 gamma, middle; Up-frameshift suppressor 2 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|242065844\|ref\|XP_002454211.1\| hypothetical protein SORBIDRAFT_04g026740 [Sorghum bicolor] gi\|241934042\|gb\|EES07187.1\| hypothetical protein SORBIDRAFT_04g026740 [Sorghum bicolor]	Back alignment and taxonomy information

>gi\|125540395\|gb\|EAY86790.1\| hypothetical protein OsI_08170 [Oryza sativa Indica Group]	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		813
TAIR\|locus:2056038		1181	AT2G39260 "AT2G39260" [Arabido	0.435	0.299	0.838	1.1e-275
UNIPROTKB\|E2RL95		1271	UPF2 "Uncharacterized protein"	0.423	0.270	0.529	3.8e-127
UNIPROTKB\|E2RLB0		1271	UPF2 "Uncharacterized protein"	0.423	0.270	0.529	3.8e-127
UNIPROTKB\|F1MQ83		1273	UPF2 "Uncharacterized protein"	0.423	0.270	0.529	1e-126
UNIPROTKB\|E1C0M6		1263	UPF2 "Uncharacterized protein"	0.423	0.272	0.529	2.1e-126
UNIPROTKB\|Q9HAU5		1272	UPF2 "Regulator of nonsense tr	0.423	0.270	0.529	3.4e-126
ZFIN\|ZDB-GENE-090715-1		1011	upf2 "UPF2 regulator of nonsen	0.430	0.346	0.518	3.4e-126
ASPGD\|ASPL0000002256		1170	nmdA [Emericella nidulans (tax	0.429	0.298	0.439	2.4e-95
FB\|FBgn0029992		1241	Upf2 "Upf2" [Drosophila melano	0.404	0.265	0.421	7.8e-86
DICTYBASE\|DDB_G0281623		1395	upf2 "eukaryotic initiation fa	0.425	0.248	0.357	3.9e-74

TAIR\|locus:2056038 AT2G39260 "AT2G39260" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1599 (567.9 bits), Expect = 1.1e-275, Sum P(2) = 1.1e-275
 Identities = 297/354 (83%), Positives = 333/354 (94%)

Query:   422 TERKVETEKEKLKGVEGTNLDALLQRLPGCVSRDLIDQLTVEFCYLNSKSNRKRLVRALF 481
             +E+K+E EKEK K ++  N + LLQRLPGCVSRDLIDQLTVE+CYLNSK+NRK+LV+ALF
Sbjct:   448 SEKKMEHEKEKGKSLDVANFERLLQRLPGCVSRDLIDQLTVEYCYLNSKTNRKKLVKALF 507

Query:   482 NVPRTSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIRF 541
             NVPRTSLELL YYSRMVATL++CMKD+ SML+QMLE+EFN L++KKDQMNIETKIRNIRF
Sbjct:   508 NVPRTSLELLAYYSRMVATLASCMKDIPSMLVQMLEDEFNSLVHKKDQMNIETKIRNIRF 567

Query:   542 IGELCKFKIAPAGLVFSCLKACLDDFTHHNIDVACNLLETCGRFLYRSPETSIRMANMLE 601
             IGELCKFKI PAGLVFSCLKACLD+FTHHNIDVACNLLETCGRFLYRSPET++RM NML+
Sbjct:   568 IGELCKFKIVPAGLVFSCLKACLDEFTHHNIDVACNLLETCGRFLYRSPETTLRMTNMLD 627

Query:   602 ILMRLKNVKNLDPRHVTLVENAYYLCKPPERSARVSKVRPPLHQYIRKLLFSDLDKSSIE 661
             ILMRLKNVKNLDPR  TLVENAYYLCKPPERSAR+SKVRPPLHQY+RKLLFSDLDK SI 
Sbjct:   628 ILMRLKNVKNLDPRQSTLVENAYYLCKPPERSARISKVRPPLHQYVRKLLFSDLDKDSIA 687

Query:   662 HVLRQLRKLPWSDCESYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVLE 721
             +VL+QLRKLPWS+CE Y+LKCFMKVHKGKYGQIHLIASLT+GLSR+HDEF VAVVDEVLE
Sbjct:   688 NVLKQLRKLPWSECEQYILKCFMKVHKGKYGQIHLIASLTSGLSRHHDEFVVAVVDEVLE 747

Query:   722 EIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAE 775
             EIR+GLELN+YG QQ+RLAHMRFLGELYNYEHVDSSVIF+TLYL L++GH T+E
Sbjct:   748 EIRVGLELNEYGAQQKRLAHMRFLGELYNYEHVDSSVIFETLYLTLLYGHDTSE 801

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0006412 "translation" evidence=ISS

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0019344 "cysteine biosynthetic process" evidence=RCA

UNIPROTKB\|E2RL95 UPF2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RLB0 UPF2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MQ83 UPF2 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E1C0M6 UPF2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9HAU5 UPF2 "Regulator of nonsense transcripts 2" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-090715-1 upf2 "UPF2 regulator of nonsense transcripts homolog (yeast)" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000002256 nmdA [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

FB\|FBgn0029992 Upf2 "Upf2" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0281623 upf2 "eukaryotic initiation factor 4 gamma, middle domain-containing protein" [Dictyostelium discoideum (taxid:44689)]	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

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	Sb04g026740.1	hypothetical protein (1194 aa)
		(Sorghum bicolor)
Predicted Functional Partners:
	Sb02g033940.1	hypothetical protein (1269 aa)	•	•	•	•	0.987
	Sb06g017380.1	hypothetical protein (505 aa)		•	•		0.854
	Sb01g030480.1	hypothetical protein (918 aa)			•		0.800
	Sb01g035510.1	hypothetical protein (867 aa)			•	•	0.452
	Sb04g025800.1	hypothetical protein (243 aa)			•	•	0.412

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		813
smart00543		200	smart00543, MIF4G, Middle domain of eukaryotic ini	5e-36
pfam02854		198	pfam02854, MIF4G, MIF4G domain	3e-34
pfam02854		198	pfam02854, MIF4G, MIF4G domain	8e-25
smart00543		200	smart00543, MIF4G, Middle domain of eukaryotic ini	1e-23
pfam08208		193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	8e-07
PRK14718		467	PRK14718, PRK14718, ribonuclease III; Provisional	8e-06
pfam10243		506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-05
pfam10243		506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-05
pfam10243		506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-05
PRK04195		482	PRK04195, PRK04195, replication factor C large sub	4e-05
pfam10243		506	pfam10243, MIP-T3, Microtubule-binding protein MIP	7e-05
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
pfam08208		193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	2e-04
PRK04195		482	PRK04195, PRK04195, replication factor C large sub	2e-04
TIGR02794		346	TIGR02794, tolA_full, TolA protein	2e-04
pfam07423		214	pfam07423, DUF1510, Protein of unknown function (D	3e-04
pfam07423		214	pfam07423, DUF1510, Protein of unknown function (D	4e-04
PRK13108		460	PRK13108, PRK13108, prolipoprotein diacylglyceryl	5e-04
pfam08208		193	pfam08208, RNA_polI_A34, DNA-directed RNA polymera	6e-04
pfam08432		182	pfam08432, DUF1742, Fungal protein of unknown func	6e-04
pfam10243		506	pfam10243, MIP-T3, Microtubule-binding protein MIP	7e-04
PRK04195		482	PRK04195, PRK04195, replication factor C large sub	7e-04
pfam08432		182	pfam08432, DUF1742, Fungal protein of unknown func	8e-04
PRK04195		482	PRK04195, PRK04195, replication factor C large sub	0.001
PRK04195		482	PRK04195, PRK04195, replication factor C large sub	0.001
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
pfam10243		506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.002
TIGR02794		346	TIGR02794, tolA_full, TolA protein	0.002
pfam14181		155	pfam14181, YqfQ, YqfQ-like protein	0.002
PRK09510		387	PRK09510, tolA, cell envelope integrity inner memb	0.002
PTZ00121		2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.003
TIGR02794		346	TIGR02794, tolA_full, TolA protein	0.003
COG4499		434	COG4499, COG4499, Predicted membrane protein [Func	0.003
smart00543		200	smart00543, MIF4G, Middle domain of eukaryotic ini	0.004

>gnl\|CDD\|214713 smart00543, MIF4G, Middle domain of eukaryotic initiation factor 4G (eIF4G)	Back alignment and domain information

 Score =  134 bits (339), Expect = 5e-36
 Identities = 48/198 (24%), Positives = 92/198 (46%), Gaps = 13/198 (6%)

Query: 445 LQRLPGCVSRDLIDQLTVEFCYLN--SKSNRKRLVRALFNVPRTSLELLPYYSRMVATLS 502
           ++ L   +S    + +  E   LN   K+ RK ++  +F         +P Y+R+ A L+
Sbjct: 4   VKGLINKLSPSNFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLN 63

Query: 503 TCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIRFIGELCKFKIAPAGLVFSCLKA 562
               D  S+L++ L+EEF   +  +++ + + ++  +RF+GEL  F++  + ++   LK 
Sbjct: 64  AKNPDFGSLLLERLQEEFEKGLESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKE 123

Query: 563 CLDDFT-------HHNIDVACNLLETCGRFLYRSPETSIRMANMLEILMRLKNVK---NL 612
            L+D T         +++   +LL TCG+ L R  ++   +  +LE L      K    L
Sbjct: 124 LLNDLTKLDPPRSDFSVECLLSLLPTCGKDLER-EKSPKLLDEILERLQDYLLKKDKTEL 182

Query: 613 DPRHVTLVENAYYLCKPP 630
             R   ++E    L K  
Sbjct: 183 SSRLRFMLELLIELRKNK 200

Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press). Length = 200

>gnl\|CDD\|217253 pfam02854, MIF4G, MIF4G domain	Back alignment and domain information

>gnl\|CDD\|217253 pfam02854, MIF4G, MIF4G domain	Back alignment and domain information

>gnl\|CDD\|214713 smart00543, MIF4G, Middle domain of eukaryotic initiation factor 4G (eIF4G)	Back alignment and domain information

>gnl\|CDD\|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34	Back alignment and domain information

>gnl\|CDD\|173181 PRK14718, PRK14718, ribonuclease III; Provisional	Back alignment and domain information

>gnl\|CDD\|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3	Back alignment and domain information

>gnl\|CDD\|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3	Back alignment and domain information

>gnl\|CDD\|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3	Back alignment and domain information

>gnl\|CDD\|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional	Back alignment and domain information

>gnl\|CDD\|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34	Back alignment and domain information

>gnl\|CDD\|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional	Back alignment and domain information

>gnl\|CDD\|234017 TIGR02794, tolA_full, TolA protein	Back alignment and domain information

>gnl\|CDD\|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)	Back alignment and domain information

>gnl\|CDD\|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)	Back alignment and domain information

>gnl\|CDD\|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase; Reviewed	Back alignment and domain information

>gnl\|CDD\|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit RPA34	Back alignment and domain information

>gnl\|CDD\|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)	Back alignment and domain information

>gnl\|CDD\|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3	Back alignment and domain information

>gnl\|CDD\|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional	Back alignment and domain information

>gnl\|CDD\|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)	Back alignment and domain information

>gnl\|CDD\|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional	Back alignment and domain information

>gnl\|CDD\|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3	Back alignment and domain information

>gnl\|CDD\|234017 TIGR02794, tolA_full, TolA protein	Back alignment and domain information

>gnl\|CDD\|222581 pfam14181, YqfQ, YqfQ-like protein	Back alignment and domain information

>gnl\|CDD\|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional	Back alignment and domain information

>gnl\|CDD\|173412 PTZ00121, PTZ00121, MAEBL; Provisional	Back alignment and domain information

>gnl\|CDD\|234017 TIGR02794, tolA_full, TolA protein	Back alignment and domain information

>gnl\|CDD\|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]	Back alignment and domain information

>gnl\|CDD\|214713 smart00543, MIF4G, Middle domain of eukaryotic initiation factor 4G (eIF4G)	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		813
KOG2051		1128	consensus Nonsense-mediated mRNA decay 2 protein [	100.0
smart00543		200	MIF4G Middle domain of eukaryotic initiation facto	99.83
PF02854		209	MIF4G: MIF4G domain; InterPro: IPR003890 This entr	99.69
PF02854		209	MIF4G: MIF4G domain; InterPro: IPR003890 This entr	99.47
smart00543		200	MIF4G Middle domain of eukaryotic initiation facto	99.44
KOG2140		739	consensus Uncharacterized conserved protein [Gener	97.95
KOG2051		1128	consensus Nonsense-mediated mRNA decay 2 protein [	97.9
KOG2141		822	consensus Protein involved in high osmolarity sign	97.5
KOG0401		970	consensus Translation initiation factor 4F, riboso	90.13
KOG2140		739	consensus Uncharacterized conserved protein [Gener	84.08

>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]	Back alignment and domain information

Probab=100.00  E-value=5.6e-174  Score=1499.23  Aligned_cols=740  Identities=44%  Similarity=0.682  Sum_probs=621.4

Q ss_pred             eeecCCCCchhhhhhccchhHhhhHHHHHHHHHHHhhhcccchHHHHHHHHHHhccccCchHHHHHHHhhhcCCCCCCCc
Q 003522           15 ILVSDDCTKFPFCIKNKSNCICKYIANIYIYTYTLLLGLWLTLVYFLKICSLLHQRYKDFSPCLIDGLLKVFFPGKSGED   94 (813)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~~l~ky~~ei~~~~~e~~~~~~~dI~aaVeI~S~LHQRy~~Ft~~Ll~~l~~~~~~~~~~~~   94 (813)
                      .|++.++|+|+++|.+||  |+|||+||++|++||++| .+||+|||++||++||||++||++|+.+|+++|..++    
T Consensus        44 ~~t~~~~dsli~els~ln--LsKyi~Ei~a~ivE~klK-~~dv~~~v~l~s~~h~~y~~Fs~~~lg~~~k~l~~~~----  116 (1128)
T KOG2051|consen   44 LLTAEQYDSLIKELSTLN--LSKYISEITAAIVEAKLK-CSDVPAAVELCSILHARYARFSTAFLGAFLKALECKK----  116 (1128)
T ss_pred             HHhhhhhHHHHHHHHhcc--HHHHHHHHHHHHHHHHHh-ccchHHHHHHHHHHHHHhccccHHHHHHHHHhcCCcc----
Confidence            478999999999999999  999999999999999999 6899999999999999999999999999999994332    


Q ss_pred             hhhhhhhhhhhhhhhhhhhhheeeeeeccChhhH---HHHHhhhhhcccccccCCCCcchHHHHHHHhh-ccccccCCCC
Q 003522           95 LDADRNLKAMKKRSTLKLLLELYFIGIIEDSSIF---INIIKDLTSIEHLKDRDTTQTNLTLLASFARQ-GRIFLGLPLS  170 (813)
Q Consensus        95 ~ekee~~ri~K~R~~LRll~EL~LvGV~~~~~~l---~~~lk~l~~~e~l~Dk~~~~~nL~ll~sF~K~-g~~~lG~~~~  170 (813)
                        .|+..|++|.|++||+++||++||||.+.+.+   ..+|+.++.+   +  +..|++++++.||||+ |+++.|+.|.
T Consensus       117 --~~k~~n~~klr~dlrl~aEL~~vGVf~~ke~l~~l~~~L~~li~~---~--~~~~~~v~~~~s~~r~~g~~~a~~~~~  189 (1128)
T KOG2051|consen  117 --YDKIGNITKLRSDLRLFAELYLVGVFDDKEGLSPLRKVLSILIQL---K--DIDHVNVSLIISFYRHCGGSTASIVPQ  189 (1128)
T ss_pred             --ccccccchhhhhhhHHHhhhhhheeeeccchhhhHHHHHHHHHhc---c--cCCccchhHHHHHhhhccccccccchH
Confidence              36889999999999999999999999877544   4455544442   3  3369999999999999 9999999886


Q ss_pred             CCCc--hh-hHhhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCChhhHHHHHHHHHH
Q 003522          171 GPGQ--EI-YEEFFKGLNITADQKKIFKKAFHTYYNAVQELLQAEHTSLRQMENENAKILNAKGELSEENSSSYEKLRKS  247 (813)
Q Consensus       171 ~~~~--~~-~~~~~~~~~is~e~q~~~r~ll~~Y~~al~~~l~~~hk~L~~~ek~n~~~~i~~Gel~eE~~~~ye~l~k~  247 (813)
                      .-..  +. ..+.+.+..|++++|+.|+.+|+.||+++++|+.++|+.+++++|+|+++++++|++++|+.+.|+++++.
T Consensus       190 ~~k~~a~~~~~~~p~~d~i~~dk~kt~~~l~k~y~~sL~~~~~~e~~~l~~~ek~~~r~~~~kgel~~er~~~~e~l~~~  269 (1128)
T KOG2051|consen  190 FRKMAAELFNGEVPSSDLISNDKKKTFQVLFKDYYDSLMSHLGKEHRELNDMEKENRRALFSKGELSDERTEGYEELQSG  269 (1128)
T ss_pred             HHHHHHHHhcccCCchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHH
Confidence            4110  00 01122334489999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCCccccccccCCCC-CCCCCCCCCCCCCCCCChhhhccccccccccccchhhhhhhh
Q 003522          248 YDHLYRNVSSLAEALDMQPPVMPEDVHTTRVTSGEDA-SPASGKDSSVPEPVWDDEETRAFYECLPDLRAFVPAVLLGEA  326 (813)
Q Consensus       248 yEkL~~~~~sLAe~L~~~mP~Lp~~~~~~~~~~g~~~-~~~~~~~~~~~~~iWeDEEtR~FYE~LpDL~~~VPa~Ll~~~  326 (813)
                      |+||++++++||++||++||+|+++.  ++...|++. .++.....+. .++|+||+||+|||+||||+++|||.+.+.+
T Consensus       270 ~dkL~~naisl~e~l~~~~p~l~e~s--~~~~~~~~~~~~~~~~s~~i-~~~wsDedtrafye~l~Dlr~~vpa~~~~~n  346 (1128)
T KOG2051|consen  270 LDKLLANAISLSELLGELMPELEEES--DEADPGEEASQMGKNGSLSI-EDLWSDEDTRAFYENLIDLRDFVPATNEGFN  346 (1128)
T ss_pred             HHHHHHHHHhHHHHhccccccccccc--ccCCccccccccccccccCc-ccccccHHHHHHHHhhhHHHHhcccccccch
Confidence            99999999999999999999999875  223334442 2222222233 3499999999999999999999998776654


Q ss_pred             ccccCCCCCCCCCCCCCCCCCCccchhhhchhhhhhcccCCCCCCCccccCCchhHHhhhhcCCCccccCCCCChhhhhh
Q 003522          327 EHKANEPSVKPLEQPTDPASEPDQGQLAAQDTAEVSADLGASPEGKSVEKGKDKEEKEKEKAKDPDKEKGKGKDKEEKDK  406 (813)
Q Consensus       327 ~~~~~~~~~~~~e~~~~~~~e~~~~~~~~~d~~e~~~~~~~~~~~~~~e~~~~~ee~e~~~~~~~~~~~~~g~d~ee~~~  406 (813)
                      +.+..+     .    ++..+.........++.++++++..+ ++...+   .+++..++         .+|+..++.++
T Consensus       347 ~~~e~e-----~----esn~~~~~~~~~~~~~~e~~~~~~~~-e~~~~~---~~~~~~~~---------~~~~~~~~~~~  404 (1128)
T KOG2051|consen  347 KSKEVE-----K----ESNSEAAMVWDDREQTTEVSSPSNFM-EGSIAE---MKEDLKES---------KGEDEKEELGK  404 (1128)
T ss_pred             hhhhhh-----h----hhhhhHHhhhcccccceeecCCCccc-cchhhh---hhhhhhhh---------hccchhhhcch
Confidence            322211     1    11111101000111222333322211 111111   11111111         11111121111


Q ss_pred             hhcCCCCcccCcccchhhhhhhhHhhhcCCcchhHHHHHhhCCCCCChhHHHHHHHHHhh-ccCchhHHHHHHHhhccCC
Q 003522          407 EKAKDPDKEKGKEKDTERKVETEKEKLKGVEGTNLDALLQRLPGCVSRDLIDQLTVEFCY-LNSKSNRKRLVRALFNVPR  485 (813)
Q Consensus       407 e~~~d~~~~~~~~~~~~~~~~~e~~~~~~~~~~~ld~fl~~Lp~~~nrd~ID~~aveF~~-lN~Ka~RkrLvk~l~~v~r  485 (813)
                      ++.            ....-+.+.....+...++++.|+.+||+|+|||.||++|++||. +|||++||||+|+||.+||
T Consensus       405 ~~~------------~~~~~~~~~~~~~~~~~~~~d~Fl~~L~~~vsrdliD~~a~ef~~nlNtKa~RkrLvKal~~vpr  472 (1128)
T KOG2051|consen  405 NKQ------------EQDLLESEGDLNTSQVVSNVDCFLLDLPNCVSRDLIDQAAIEFCSNLNTKANRKRLVKALFVVPR  472 (1128)
T ss_pred             hhh------------HHHHhhhhhhcchhhHHHHHHHHHccCcchHHHHHHHHHHHHHHHHhccHHHHHHHHHhhhcccc
Confidence            110            001111122222334557899999999999999999999999996 9999999999999999999


Q ss_pred             CCCCCchHHHHHHHHhcccchhhHHHHHHHHHHHHHHhhhhccccccchhhceeeeeeccccccccChhhHHHHHHHHhh
Q 003522          486 TSLELLPYYSRMVATLSTCMKDVSSMLIQMLEEEFNFLINKKDQMNIETKIRNIRFIGELCKFKIAPAGLVFSCLKACLD  565 (813)
Q Consensus       486 ~r~dlLP~YaR~vAtl~~~~~Dv~~~lv~~L~~~Fr~~~~kk~~~~~e~kiKnirfi~EL~KF~lvP~~~if~~lk~ll~  565 (813)
                      +|+|+||||+||||||++|||||+++||++|.++||+++|+|+|+++++|+|+||||||||||++||+++||||||+||+
T Consensus       473 t~ldllPyYsRlVAtl~~~M~dvat~lv~~L~~eFr~~~hkK~q~~ietk~~~VrfIsEL~KF~lv~~~~if~cLk~ll~  552 (1128)
T KOG2051|consen  473 TRLDLLPYYSRLVATLSKCMPDVATELVTMLRKEFRSHLHKKAQINIETKLKIVRFISELCKFQLVPKFEIFSCLKMLLN  552 (1128)
T ss_pred             hhhhhhhHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhHHhhhhhCccChHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCchHHHHHHHHhhhcccccCChhhHHHHHHHHHHHHHHhhccCCChhHHHHHHHhhhhcCCCccccccccCCCcHHH
Q 003522          566 DFTHHNIDVACNLLETCGRFLYRSPETSIRMANMLEILMRLKNVKNLDPRHVTLVENAYYLCKPPERSARVSKVRPPLHQ  645 (813)
Q Consensus       566 dfs~~nIei~c~llE~CGRfL~r~pet~~rm~~mLe~m~rkk~~~~L~~r~~~lieNa~y~~~PP~~~~~~~k~r~p~~~  645 (813)
                      ||+||||||+|+|||+|||||||+||||.||..|||+|||+|++++||+|+.++||||||+|+||+++++..|+|||+|+
T Consensus       553 dF~~hnIEm~c~lLE~~GrfLlr~pEt~lrM~~~Le~i~rkK~a~~lDsr~~~~iENay~~~~PPe~~~~~~k~r~p~~e  632 (1128)
T KOG2051|consen  553 DFTHHNIEMACVLLESCGRFLLRSPETKLRMRVFLEQIKRKKRASALDSRQATLIENAYYLCNPPERSKRLSKKRPPMQE  632 (1128)
T ss_pred             hcccccHHHHHHHHHhcchhhhcChhHHHHHHHHHHHHHHHHHHhhhchHHHHHHHHhHHhccChhhcccccccCCcHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCcccHHHHHHHHHcCCCCChh--HHHHHHHhcccccccccHHHHHHHHHHHhcccccchhhhhhhHHHHH
Q 003522          646 YIRKLLFSDLDKSSIEHVLRQLRKLPWSDCE--SYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVDEVLEEI  723 (813)
Q Consensus       646 fir~Li~~~L~~~~~~~vlk~lrKl~W~d~~--~~l~k~~~~~~k~ky~nI~~lA~ll~~L~~~~~~f~v~vVD~vlE~I  723 (813)
                      |||+|||.+|++.|++.++++||||||+|++  .|+++||++||+++|+||+++|++|+||++|||+|||+|||.|||+|
T Consensus       633 fiR~Li~~dL~k~tvd~~lkllRkl~W~D~e~~~yli~~~~k~w~iky~~i~~lA~llaGL~~y~~~fvi~VID~vlE~I  712 (1128)
T KOG2051|consen  633 FIRYLIRSDLSKDTVDRVLKLLRKLDWSDPEVKQYLISCFSKPWKIKYQNIHALASLLAGLSSYHPEFVIHVIDHVLEDI  712 (1128)
T ss_pred             HHHHHHHHHhccccHHHHHHHHHhcccccHHHHHHHHHHhhhhhccccccHHHHHHHHHHHHhhchhhhhhhHHHHHHHH
Confidence            9999999999999999999999999999975  79999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCCCchhHHHHHHHHHHHHHhhhcccCChhHHHHHHHHHhhcCCCCcCCcccccccccCCCccceeeehhhhhhhh
Q 003522          724 RLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAETYWTHQKIVSGSGWLLLFLRLVVTTLTE  803 (813)
Q Consensus       724 r~gLE~N~~~~nQrRia~vkyLgELYny~lv~s~vIfdtLY~ii~fGh~~~~~~~~~~~~~~~~~~~~fr~rl~~t~l~~  803 (813)
                      |.|||.|+|.+||||||+||||||||||+||||.|||+|||++|+|||++...+++     +|.|+|+|||||||++|++
T Consensus       713 r~glEin~~~~nQrriA~aryL~ELynfemvds~vIl~tLy~~i~~g~~~~~~~~~-----ldppddlFRirlV~~lL~t  787 (1128)
T KOG2051|consen  713 RPGLEINDYVSNQRRIALARYLGELYNFEMVDSDVILNTLYHLISLGHFENLTPSA-----LDPPDDLFRIRLVCMLLQT  787 (1128)
T ss_pred             HhhhhcCcHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHhcccccCCCCccc-----CCChHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999986645554     8999999999999999995


Q ss_pred             c---CCCCCC
Q 003522          804 A---LPRGNL  810 (813)
Q Consensus       804 ~---~~~~~~  810 (813)
                      |   |+||+-
T Consensus       788 c~~yf~rgs~  797 (1128)
T KOG2051|consen  788 CGPYFTRGST  797 (1128)
T ss_pred             cccccccchh
Confidence            5   788863

>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G)	Back alignment and domain information

>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain	Back alignment and domain information

>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain	Back alignment and domain information

>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G)	Back alignment and domain information

>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]	Back alignment and domain information

>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]	Back alignment and domain information

>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]	Back alignment and domain information

>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]	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		813
1uw4_B		248	The Structural Basis Of The Interaction Between Non		5e-34

>pdb|1UW4|B Chain B, The Structural Basis Of The Interaction Between Nonsense Mediated Decay Factors Upf2 And Upf3 Length = 248

Back alignment and structure

Iteration: 1

Score = 142 bits (359), Expect = 5e-34, Method: Compositional matrix adjust. Identities = 69/133 (51%), Positives = 91/133 (68%), Gaps = 2/133 (1%) Query: 640 RPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCE--SYLLKCFMKVHKGKYGQIHLI 697 RPPL +Y+RKLL+ DL K + E VLRQ+RKLPW D E Y++ C + + KY IH + Sbjct: 1 RPPLQEYVRKLLYKDLSKVTTEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCV 60 Query: 698 ASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSS 757 A+L AGL Y ++ + VVD VLE+IRLG+E+N QRR++ +FLGELYNY V+S+ Sbjct: 61 ANLLAGLVLYQEDVGIHVVDGVLEDIRLGMEVNQPKFNQRRISSAKFLGELYNYRMVESA 120 Query: 758 VIFDTLYLILVFG 770 VIF TLY FG Sbjct: 121 VIFRTLYSFTSFG 133

PyMOL of 1uw4

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		813
1uw4_B		248	UPF2, regulator of nonsense transcripts 2; nonsens	1e-56
1uw4_B		248	UPF2, regulator of nonsense transcripts 2; nonsens	8e-06
1hu3_A		260	EIF4GII; heat repeat, translation; 2.37A {Homo sap	5e-12
2vso_E		284	Eukaryotic initiation factor 4F subunit P150; acet	1e-08
3rk6_A		234	Polyadenylate-binding protein-interacting protein;	4e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
3lvg_D		190	LCB, clathrin light chain B; SELF assembly, coated	4e-04

>1uw4_B UPF2, regulator of nonsense transcripts 2; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: a.118.1.14 Length = 248	Back alignment and structure

 Score =  193 bits (492), Expect = 1e-56
 Identities = 68/140 (48%), Positives = 92/140 (65%), Gaps = 2/140 (1%)

Query: 640 RPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSD--CESYLLKCFMKVHKGKYGQIHLI 697
           RPPL +Y+RKLL+ DL K + E VLRQ+RKLPW D   + Y++ C + +   KY  IH +
Sbjct: 1   RPPLQEYVRKLLYKDLSKVTTEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCV 60

Query: 698 ASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSS 757
           A+L AGL  Y ++  + VVD VLE+IRLG+E+N     QRR++  +FLGELYNY  V+S+
Sbjct: 61  ANLLAGLVLYQEDVGIHVVDGVLEDIRLGMEVNQPKFNQRRISSAKFLGELYNYRMVESA 120

Query: 758 VIFDTLYLILVFGHGTAETY 777
           VIF TLY    FG     + 
Sbjct: 121 VIFRTLYSFTSFGVNPDGSP 140

PyMOL of 1uw4

>1uw4_B UPF2, regulator of nonsense transcripts 2; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: a.118.1.14 Length = 248	Back alignment and structure

>1hu3_A EIF4GII; heat repeat, translation; 2.37A {Homo sapiens} SCOP: a.118.1.14 Length = 260	Back alignment and structure

>2vso_E Eukaryotic initiation factor 4F subunit P150; acetylation, ATP-binding, phosphoprotein, protein biosynthesis, translation regulation; HET: AMP; 2.6A {Saccharomyces cerevisiae} PDB: 2vsx_E* Length = 284	Back alignment and structure

>3rk6_A Polyadenylate-binding protein-interacting protein; heat fold, PABP, EIF4A, EIF3, translation regulator; 2.00A {Homo sapiens} Length = 234	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

>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

>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

>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

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

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		813
d1uw4b_		248	a.118.1.14 (B:) Regulator of nonsense transcripts	2e-39
d1uw4b_		248	a.118.1.14 (B:) Regulator of nonsense transcripts	2e-20
d1h2vc1		262	a.118.1.14 (C:29-290) CBP80, 80KDa nuclear cap-bin	3e-24
d1hu3a_		243	a.118.1.14 (A:) Eukaryotic initiation factor eIF4G	6e-13

>d1uw4b_ a.118.1.14 (B:) Regulator of nonsense transcripts 2, UPF2 {Human (Homo sapiens) [TaxId: 9606]} Length = 248	Back information, alignment and structure


class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Regulator of nonsense transcripts 2, UPF2
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  143 bits (363), Expect = 2e-39
 Identities = 69/139 (49%), Positives = 92/139 (66%), Gaps = 2/139 (1%)

Query: 640 RPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCE--SYLLKCFMKVHKGKYGQIHLI 697
           RPPL +Y+RKLL+ DL K + E VLRQ+RKLPW D E   Y++ C + +   KY  IH +
Sbjct: 1   RPPLQEYVRKLLYKDLSKVTTEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCV 60

Query: 698 ASLTAGLSRYHDEFAVAVVDEVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSS 757
           A+L AGL  Y ++  + VVD VLE+IRLG+E+N     QRR++  +FLGELYNY  V+S+
Sbjct: 61  ANLLAGLVLYQEDVGIHVVDGVLEDIRLGMEVNQPKFNQRRISSAKFLGELYNYRMVESA 120

Query: 758 VIFDTLYLILVFGHGTAET 776
           VIF TLY    FG     +
Sbjct: 121 VIFRTLYSFTSFGVNPDGS 139

PyMOL of d1uw4b_

>d1uw4b_ a.118.1.14 (B:) Regulator of nonsense transcripts 2, UPF2 {Human (Homo sapiens) [TaxId: 9606]} Length = 248	Back information, alignment and structure

>d1h2vc1 a.118.1.14 (C:29-290) CBP80, 80KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 262	Back information, alignment and structure

>d1hu3a_ a.118.1.14 (A:) Eukaryotic initiation factor eIF4G {Human (Homo sapiens) [TaxId: 9606]} Length = 243	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		813
d1uw4b_		248	Regulator of nonsense transcripts 2, UPF2 {Human (	100.0
d1uw4b_		248	Regulator of nonsense transcripts 2, UPF2 {Human (	99.86
d1hu3a_		243	Eukaryotic initiation factor eIF4G {Human (Homo sa	99.48
d1h2vc1		262	CBP80, 80KDa nuclear cap-binding protein {Human (H	98.9
d1hu3a_		243	Eukaryotic initiation factor eIF4G {Human (Homo sa	97.37
d1h2vc1		262	CBP80, 80KDa nuclear cap-binding protein {Human (H	96.88

>d1uw4b_ a.118.1.14 (B:) Regulator of nonsense transcripts 2, UPF2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Regulator of nonsense transcripts 2, UPF2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=8.2e-36  Score=261.87  Aligned_cols=160  Identities=47%  Similarity=0.806  Sum_probs=153.0

Q ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCHH--HHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             9908899999988513845599999999719998736--89999873045455663999999999984003222025546
Q 003522          640 RPPLHQYIRKLLFSDLDKSSIEHVLRQLRKLPWSDCE--SYLLKCFMKVHKGKYGQIHLIASLTAGLSRYHDEFAVAVVD  717 (813)
Q Consensus       640 r~p~~~fir~Li~~~L~~~~~~~v~k~lrKl~W~d~~--~~l~~~~~~~~k~ky~nI~~lA~ll~~L~~~~~~f~v~vVD  717 (813)
                      |||+|+||||||+.+|++.+++.|+++++|++|+|++  .+++++++++|+++|++++..|.+++.|++++|+|++.+||
T Consensus         1 r~p~~~flr~li~n~Ls~~n~~~i~~~i~kl~~~n~e~~~~li~~i~~~~~~~~~~i~~yA~l~a~L~~~~~~f~~~~id   80 (248)
T d1uw4b_           1 RPPLQEYVRKLLYKDLSKVTTEKVLRQMRKLPWQDQEVKDYVICCMINIWNVKYNSIHCVANLLAGLVLYQEDVGIHVVD   80 (248)
T ss_dssp             CCHHHHHHHHHHHTTCSTTSHHHHHHHHHTSCTTSHHHHHHHHHHHHCGGGSCGGGHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98089999999986478857999999999779998799989999986250286467999999999999872799999999


Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEHH
Q ss_conf             68999885203799326779988979988743125688367999998885048899677323232236878641432004
Q 003522          718 EVLEEIRLGLELNDYGMQQRRLAHMRFLGELYNYEHVDSSVIFDTLYLILVFGHGTAETYWTHQKIVSGSGWLLLFLRLV  797 (813)
Q Consensus       718 ~vlE~Ir~gLE~N~~~~nQrRia~vkyLgELYny~lv~s~vIfd~Ly~ii~fGh~~~~~~~~~~~~~~~~~~~~fr~rl~  797 (813)
                      .+.|+++.|+|.|+++.+|||++.|+|+|||||++|+.+.+||+++|.+++|||+....+     .+.|+++|+|||+++
T Consensus        81 ~l~e~f~~~~e~~~~~~~~r~~~~v~figeLy~~~~v~~~~i~~~l~~Ll~~~~~~~~~~-----~~~d~~~d~~rIe~l  155 (248)
T d1uw4b_          81 GVLEDIRLGMEVNQPKFNQRRISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNPDGSP-----SSLDPPEHLFRIRLV  155 (248)
T ss_dssp             HHHHHHHHHHHHCCGGGHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTTCCTTSCC-----CSSSCTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCC-----CCCCCCCCHHHHHHH
T ss_conf             999999999987118899999989999999998745769999999999996578765555-----567987640579899


Q ss_pred             HHHHHHC
Q ss_conf             6452101
Q 003522          798 VTTLTEA  804 (813)
Q Consensus       798 ~t~l~~~  804 (813)
                      |++|.+|
T Consensus       156 ~~lL~t~  162 (248)
T d1uw4b_         156 CTILDTC  162 (248)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
T ss_conf             9999997

PyMOL of d1uw4b_

>d1uw4b_ a.118.1.14 (B:) Regulator of nonsense transcripts 2, UPF2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hu3a_ a.118.1.14 (A:) Eukaryotic initiation factor eIF4G {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1h2vc1 a.118.1.14 (C:29-290) CBP80, 80KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hu3a_ a.118.1.14 (A:) Eukaryotic initiation factor eIF4G {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1h2vc1 a.118.1.14 (C:29-290) CBP80, 80KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure