Citrus Sinensis ID: 004125

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--

MATLADIGVSAALNILGAFIFLIAFAILRLQPFNDRVYFPKWYLKGLRDSPTHGGAFVRKFVNLDFRSYIRFLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVLVPVNWTNDTLDVAVKISNVTASDIDKLSISNVPLKSQRFWTHVVMAYAFTFWTCYVLLKEYEKVANLRLQFVASEKRRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHPNHYLTHQVVVNANKLAKLVKKKKKLQNWLDYYQLKYSRNNSKRPMMKTGFLGLWGEKVDGIDYHISEIEKLSKEIAEERERVVSDPKAIMPAAFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVYWQNLAIPYVSLSVRRLIMGVAFFFLTFFFMIPIAIVQSFASIEGIEKAVPFLKPVIEAKFIKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGSIIAGTAFEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLIIFHLKNFFLVKTEKDRVEAMDPGSLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFALAYVVFRHQIINVYNQRYESAAAFWPDVHRRIIAALIISQLLLMGLLSTKKAALSTPFLIALPVLTIWFHYFSKDRYESAFVKYPLQEAMMKDTLERAREPNLNLKGYLRNAYIHPVFKGEDDDDDALFNNEENENVLVLTKRQSRRNTPVPSKMSGASSPSLPEVVQEDPEP

cccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHccccHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEEcccccccccHHHHHHHHHHccccccEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEccHHHHHHHHHHccccccccEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHcccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

cccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEcHHHHHccccccccccccccccccccccccccccHHHHHHHHcccHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHcEcccccccHHccccccccccccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEEcccccccccHHHHHHHHHHHHccccEEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEEccHHHHHHHHHHHccccccEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHcHHHHHcccHHHHHHHccHHccccccHHHHHHHHHHcccccccccccccHHccccccccccccccccccccccccccccccccccccHHHccccccc

MATLADIGVSAALNILGAFIFLIAFAILRlqpfndrvyfpkwylkglrdspthggaFVRKFVNLDFRSYIRFLNwmpealkmpepeliehaglDSAVYLRIYLIGLKIFVPIALVAWSVLVPVNWTNDTLDVAVKIsnvtasdidklsisnvplksqRFWTHVVMAYAFTFWTCYVLLKEYEKVANLRLQFVasekrrpdqftvlvrnvppdpdesVSELVEHFFlvnhpnhyltHQVVVNANKLAKLVKKKKKLQNWLDYYQLKysrnnskrpmmktgflglwgekvdgidYHISEIEKLSKEIAEERervvsdpkaimPAAFVSFNSRWGAAVCAqtqqtrnptlwltewaseprdvywqnlaipyvSLSVRRLIMGVAFFFLTFFFMIPIAIVQSFASIEGIEKAVPFLKPVIEAKFIKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGSIIAGTAFEQLNSFLKQSAndipktigiaipkkATFFITYIMVDGWAGIAGEILMLKPLIIFHLKNfflvktekdrveamdpgslgfnsgepRIQFYFLLGLVYATVTPLLLPFIIVFFALAYVVFRHQIINVYNQRYESAAAFWPDVHRRIIAALIISQLLLMGLLSTkkaalstpfliALPVLTIWFHYFSKDRYESAFVKYPLQEAMMKDTLERarepnlnlkgylrnayihpvfkgedddddalfnneenENVLVLTKrqsrrntpvpskmsgasspslpevvqedpep

MATLADIGVSAALNILGAFIFLIAFAILRLQPFNDRVYFPKWYLKGLRDSPTHGGAFVRKFVNLDFRSYIRFLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVLVPVNWTNDTLDVAVKISnvtasdidklsisnvPLKSQRFWTHVVMAYAFTFWTCYVLLKEYEKVANLRLQFvasekrrpdqftvLVRNVPPDPDESVSELVEHFFLVNHPNHYLTHQVVVNANKLAKLVKKKKKLQNWLDYYQLkysrnnskrpmmKTGFLGLWGEKVDGIDYHISEIEKLSKEIAEERERVVSDPKAIMPAAFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVYWQNLAIPYVSLSVRRLIMGVAFFFLTFFFMIPIAIVQSFASIEGIEKAVPFLKPVIEAKFIKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGSIIAGTAFEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLIIFHLKNFFLVKTEKDRVEAMDPGSLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFALAYVVFRHQIINVYNQRYESAAAFWPDVHRRIIAALIISQLLLMGLLSTKKAALSTPFLIALPVLTIWFHYFSKDRYESAFVKYPLQEAMMKDTLERAREPNLNLKGYLRNAYIHPVFKGEDDDDDALFNNEENEnvlvltkrqsrrntpvpskmsgasspslpevvqedpep

MATLADIGVSAALNILGAFIFLIAFAILRLQPFNDRVYFPKWYLKGLRDSPTHGGAFVRKFVNLDFRSYIRFLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVLVPVNWTNDTLDVAVKISNVTASDIDKLSISNVPLKSQRFWTHVVMAYAFTFWTCYVLLKEYEKVANLRLQFVASEKRRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHPNHYLTHQvvvnanklaklvkkkkklQNWLDYYQLKYSRNNSKRPMMKTGFLGLWGEKVDGIDYHISEIEKLSKEIAEERERVVSDPKAIMPAAFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVYWQNLAIPYVSLSVRRLIMGVAfffltfffMIPIAIVQSFASIEGIEKAVPFLKPVIEAKFIKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGSIIAGTAFEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLIIFHLKNFFLVKTEKDRVEAMDPGSLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFALAYVVFRHQIINVYNQRYESAAAFWPDVHRRiiaaliisqlllmgllsTKKAALSTPFLIALPVLTIWFHYFSKDRYESAFVKYPLQEAMMKDTLERAREPNLNLKGYLRNAYIHPVFKGEDDDDDALFnneenenVLVLTKRQSRRNTPVPSKMSGASSPSLPEVVQEDPEP

****ADIGVSAALNILGAFIFLIAFAILRLQPFNDRVYFPKWYLKGLRDSPTHGGAFVRKFVNLDFRSYIRFLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVLVPVNWTNDTLDVAVKISNVTASDIDKLSISNVPLKSQRFWTHVVMAYAFTFWTCYVLLKEYEKVANLRLQFVASEKRRPDQFTVLVRN********VSELVEHFFLVNHPNHYLTHQVVVNANKL************WLDYYQLKYSR******MMKTGFLGLWGEKVDGIDYHISEIEKLSKEI******VVSDPKAIMPAAFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVYWQNLAIPYVSLSVRRLIMGVAFFFLTFFFMIPIAIVQSFASIEGIEKAVPFLKPVIEAKFIKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGSIIAGTAFEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLIIFHLKNFFLVKTEKDRVEA****SLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFALAYVVFRHQIINVYNQRYESAAAFWPDVHRRIIAALIISQLLLMGLLSTKKAALSTPFLIALPVLTIWFHYFSKDRYESAFVKYPLQEAMMKDTLERAREPNLNLKGYLRNAYIHPVFKG*****************************************************

MATLADIGVSAALNILGAFIFLIAFAILRLQPFNDRVYFPKWYLK********************FRSYIRFLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVLVPVNWTNDTLDVAVKISNVTASDIDKLSISNVPLKSQRFWTHVVMAYAFTFWTCYVLLKEYEKVANLRLQFVASEKRRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHPNHYLTHQVVVNANKLAKLVKKKKKLQNWLDYYQLKYSRNNSKRPMMKTGFLGLWGEKVDGIDYHISEIEKLSKEIAEERERVVSDPKAIMPAAFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVYWQNLAIPYVSLSVRRLIMGVAFFFLTFFFMIPIAIVQSFASIEGIEKAVPFLKPVIEAKFIKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGSIIAGTAFEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLIIFHLKNFFLVKTEKDRVEAMDPGSLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFALAYVVFRHQIINVYNQRYESAAAFWPDVHRRIIAALIISQLLLMGLLSTKKAALSTPFLIALPVLTIWFHYFSKDRYESAFVKYPL**************************YIH**********************************************************

**TLADIGVSAALNILGAFIFLIAFAILRLQPFNDRVYFPKWYLKGL****************LDFRSYIRFLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVLVPVNWTNDTLDVAVKISNVTASDIDKLSISNVPLKSQRFWTHVVMAYAFTFWTCYVLLKEYEKVANLRLQFVASEKRRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHPNHYLTHQVVVNANKLAKLVKKKKKLQNWLDYYQLKYSRNNSKRPMMKTGFLGLWGEKVDGIDYHISEIEKLSKEIAEERERVVSDPKAIMPAAFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVYWQNLAIPYVSLSVRRLIMGVAFFFLTFFFMIPIAIVQSFASIEGIEKAVPFLKPVIEAKFIKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGSIIAGTAFEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLIIFHLKNFFLVKTEKDRVEAMDPGSLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFALAYVVFRHQIINVYNQRYESAAAFWPDVHRRIIAALIISQLLLMGLLSTKKAALSTPFLIALPVLTIWFHYFSKDRYESAFVKYPLQEAMMKDTLERAREPNLNLKGYLRNAYIHPVFK******************************************************

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MATLADIGVSAALNILGAFIFLIAFAILRLQPFNDRVYFPKWYLKGLRDSPTHGGAFVRKFVNLDFRSYIRFLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVLVPVNWTNDTLDVAVKISNVTASDIDKLSISNVPLKSQRFWTHVVMAYAFTFWTCYVLLKEYEKVANLRLQFVASEKRRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHPNHYLTHQVVVNANKLAKLVKKKKKLQNWLDYYQLKYSRNNSKRPMMKTGFLGLWGEKVDGxxxxxxxxxxxxxxxxxxxxxVVSDPKAIMPAAFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVYWQNLAIPYVSLSVRRLIMGVAFFFLTFFFMIPIAIVQSFASIEGIEKAVPFLKPVIEAKFIKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGSIIAGTAFEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLIIFHLKNFFLVKTEKDRVEAMDPGSLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFALAYVVFRHQIINVYNQRYESAAAFWPDVHRRIIAALIISQLLLMGLLSTKKAALSTPFLIALPVLTIWFHYFSKDRYESAFVKYPLQEAMMKDTLERAREPNLNLKGYLRNAYIHPVFKGEDDDDDALFNNEENENVLVLTKRQSRRNTPVPSKMSGASSPSLPEVVQEDPEP

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		772	2.2.26 [Sep-21-2011]
Q09809		793	Uncharacterized membrane	yes	no	0.752	0.732	0.225	7e-39
Q09766		871	Uncharacterized membrane	no	no	0.764	0.677	0.227	1e-33
Q03516		953	Uncharacterized protein R	yes	no	0.760	0.615	0.228	6e-33
Q06538		782	Uncharacterized membrane	no	no	0.764	0.754	0.216	1e-31
Q12252		991	Phosphate metabolism prot	no	no	0.817	0.636	0.232	3e-29
O43022		865	Uncharacterized protein C	no	no	0.720	0.642	0.240	1e-26
Q91YT8		804	Transmembrane protein 63A	yes	no	0.667	0.640	0.222	9e-26
O94886		807	Transmembrane protein 63A	yes	no	0.667	0.638	0.224	1e-24
Q5R826		807	Transmembrane protein 63A	yes	no	0.667	0.638	0.219	5e-24
Q5T3F8		832	Transmembrane protein 63B	no	no	0.715	0.663	0.206	2e-21

>sp\|Q09809\|YAB9_SCHPO Uncharacterized membrane protein C2G11.09 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC2G11.09 PE=3 SV=2	Back alignment and function desciption

 Score =  162 bits (411), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 152/675 (22%), Positives = 288/675 (42%), Gaps = 94/675 (13%)

Query: 72  FLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVLVPVN------- 124
           +  W+ + + +P+  +   AGLD  V+L  + +G+K     +L+   +++PVN       
Sbjct: 68  YYKWLMDLVNIPDDVVQNCAGLDGYVFLLFFKMGIKFLSFASLLGVLIIMPVNKHFRGDA 127

Query: 125 WTNDTLDVAVKISNVTASDIDKLSISNVPLKSQR-------------------------- 158
           + N TL +  K     +S + K SI   P+ +                            
Sbjct: 128 FGNITLSMPAKSEYFFSSPLVKKSIVQSPIIANGSELNVGVLGPSLFNPIGNLSDIPGLP 187

Query: 159 ------FWTHVVMAYAFTFWTCYVLLKEYEKVANLRLQFVASEKRRPDQFTVLVRNVPPD 212
                  + +V+  Y  + +  YVL    + +A++R  ++A + R  D+ TV +  +P +
Sbjct: 188 QPGDGFLYLYVLFTYFISIFLLYVLFSSTKSIADIRQSYLARQNRLTDR-TVFISGLPNE 246

Query: 213 PDESVSELVEHFFLVNHPNHYLTHQVVVNANKLAKLVKKKKKLQNWLDYYQLKYSRNNSK 272
                +E ++ +F         +  +  N + +  L+ KK K    L+ Y   Y  N  K
Sbjct: 247 --LCSTENLKAYFDKLDVGSIDSLSICRNYSYMDILLSKKSKYVKKLEKYWSIYLSNCKK 304

Query: 273 ------------------------------------RPMMKTGFLGLWGEKVDGIDYHIS 296
                                                P++KT F G++G+K+D ID++ +
Sbjct: 305 LGISTLPPSNYLSPNRAELESTPEQLLEVPWQHHQCHPLIKTHFFGIFGQKIDAIDFYSA 364

Query: 297 EIEKLSKEIAEERERVVSDPKAIMPAAFVSFNSRWGAAVCAQTQQTRNPTLWL-TEWASE 355
           ++ K+S++I  E  R    P      AF++F S   A + AQT       + L  E A  
Sbjct: 365 KLYKISQQI--ENARSFDYPTT--GQAFITFESMATAQIVAQTHIDSKSLMGLHIELAPA 420

Query: 356 PRDVYWQNLAIPYVSLSVRRLIMGVAFFFLTFFFMIPIAIVQSFASIEGIEKAVPFLKPV 415
             D+ W N  I       +   + +  F +   + +P+  +  F +++ I +  P L  +
Sbjct: 421 ANDIQWHNTYIGRWHKFFQGWFITLVTFMIILLWTVPVGAIAVFINLDTIRRLWPELGRM 480

Query: 416 IE-AKFIKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFV 474
           IE   F+ S+++ FLP +   LF+   P +   +S  +G  S +  E  A  + Y + FV
Sbjct: 481 IEDLPFLNSLLRTFLPTLVYSLFISISPFLFRWLSSMQGLSSRAEEEIYAVGKNYAYLFV 540

Query: 475 NVFLGSIIAGTA--FEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEI 532
           N FL  +IAG+   +E     L +        +   +P +A FFI  I++ G      ++
Sbjct: 541 NFFLVYVIAGSTSIWE-----LAKDTTSFAHFLANRLPHQAQFFIDLIVLQGIGMFPLKL 595

Query: 533 LMLKPLIIFHLKNFFL-VKTEKDRVEAMDPGSLGFNSGEPRIQFYFLLGLVYATVTPLLL 591
           + L  L  + ++  F+       + E  D  S+G    +P   F  L+ L Y+ ++PL+L
Sbjct: 596 IQLGKLSSYFVRRSFVPYSIASKKFETPDSFSVGIFLPQP--MFIMLICLCYSIISPLIL 653

Query: 592 PFIIVFFALAYVVFRHQIINVYNQRYESAAAFWPDVHRRIIAALIISQLLLMGLLSTKKA 651
            F +++F + ++V+++++I        S    W  +  R+I   +I QL +MGL+S +KA
Sbjct: 654 VFGLIYFIIGFLVYKYELIYQMEHPQHSTGELWSTIFLRMIFGCVIMQLTMMGLMSLRKA 713

Query: 652 ALSTPFLIALPVLTI 666
              +  +  L   T+
Sbjct: 714 YWLSTVIFPLLCFTV 728

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp\|Q09766\|YA7D_SCHPO Uncharacterized membrane protein C24H6.13 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC24H6.13 PE=1 SV=1	Back alignment and function description

>sp\|Q03516\|RSN1_YEAST Uncharacterized protein RSN1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RSN1 PE=1 SV=1	Back alignment and function description

>sp\|Q06538\|YL241_YEAST Uncharacterized membrane protein YLR241W OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=YLR241W PE=1 SV=1	Back alignment and function description

>sp\|Q12252\|PHM7_YEAST Phosphate metabolism protein 7 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PHM7 PE=1 SV=1	Back alignment and function description

>sp\|O43022\|YGV8_SCHPO Uncharacterized protein C354.08c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC354.08c PE=4 SV=1	Back alignment and function description

>sp\|Q91YT8\|TM63A_MOUSE Transmembrane protein 63A OS=Mus musculus GN=Tmem63a PE=2 SV=1	Back alignment and function description

>sp\|O94886\|TM63A_HUMAN Transmembrane protein 63A OS=Homo sapiens GN=TMEM63A PE=2 SV=3	Back alignment and function description

>sp\|Q5R826\|TM63A_PONAB Transmembrane protein 63A OS=Pongo abelii GN=TMEM63A PE=2 SV=1	Back alignment and function description

>sp\|Q5T3F8\|TM63B_HUMAN Transmembrane protein 63B OS=Homo sapiens GN=TMEM63B PE=1 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		772
224115866		772	predicted protein [Populus trichocarpa]	0.997	0.997	0.826	0.0
343157312		772	early-responsive to dehydration-related	0.997	0.997	0.818	0.0
225444325		771	PREDICTED: uncharacterized membrane prot	0.997	0.998	0.796	0.0
255554789		773	conserved hypothetical protein [Ricinus	0.996	0.994	0.835	0.0
42567026		771	early-responsive to dehydration stress-r	0.988	0.989	0.798	0.0
225444327		766	PREDICTED: uncharacterized membrane prot	0.990	0.998	0.787	0.0
62319788		771	hypothetical protein [Arabidopsis thalia	0.988	0.989	0.796	0.0
224099861		771	predicted protein [Populus trichocarpa]	0.993	0.994	0.805	0.0
297799812		773	hypothetical protein ARALYDRAFT_492658 [	0.988	0.987	0.795	0.0
449455385		773	PREDICTED: uncharacterized membrane prot	1.0	0.998	0.808	0.0

>gi\|224115866\|ref\|XP_002317144.1\| predicted protein [Populus trichocarpa] gi\|222860209\|gb\|EEE97756.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score = 1289 bits (3336), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 638/772 (82%), Positives = 706/772 (91%), Gaps = 2/772 (0%)

Query: 1   MATLADIGVSAALNILGAFIFLIAFAILRLQPFNDRVYFPKWYLKGLRDSPTHGGAFVRK 60
           MATL DI VS ALN+LGAFIFL+AFAILR+QPFNDRVYFPKWYLKGLR S +H GAF R+
Sbjct: 1   MATLGDIAVSGALNLLGAFIFLLAFAILRIQPFNDRVYFPKWYLKGLRSSASHSGAFARR 60

Query: 61  FVNLDFRSYIRFLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVL 120
            VNLDFRSY RFLNWMPEALKMPEPELI+HAGLDSAVYLRIYL+GLKIFVPIA +AW++L
Sbjct: 61  IVNLDFRSYTRFLNWMPEALKMPEPELIDHAGLDSAVYLRIYLMGLKIFVPIAFLAWAIL 120

Query: 121 VPVNWTNDTLDVAVKISNVTASDIDKLSISNVPLKSQRFWTHVVMAYAFTFWTCYVLLKE 180
           VPVN+TNDTL+ A  +SNVTASDIDKLSISNVPLKSQRFW H+VMAYAFTFWTCYVLLKE
Sbjct: 121 VPVNYTNDTLEKAQLVSNVTASDIDKLSISNVPLKSQRFWAHIVMAYAFTFWTCYVLLKE 180

Query: 181 YEKVANLRLQFVASEKRRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHPNHYLTHQVVV 240
           YEK+A++RLQF++SE RRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHP+HYL HQVV 
Sbjct: 181 YEKIASMRLQFLSSEGRRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHPHHYLIHQVVC 240

Query: 241 NANKLAKLVKKKKKLQNWLDYYQLKYSRNNSKRPMMKTGFLGLWGEKVDGIDYHISEIEK 300
           NANKLA LVKKKK  QNWLDYYQLKY RN S+RP+ KTGFLGLWGEKVD ID+HISEI+K
Sbjct: 241 NANKLASLVKKKKSKQNWLDYYQLKYDRNQSQRPLKKTGFLGLWGEKVDAIDHHISEIKK 300

Query: 301 LSKEIAEERERVVSDPKAIMPAAFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVY 360
           LS+EI EERE+V+ DPK+IMPAAFVSF +RWGAAVCAQTQQ+RNPTLWLTEWA EPRDVY
Sbjct: 301 LSEEIEEEREKVLKDPKSIMPAAFVSFKTRWGAAVCAQTQQSRNPTLWLTEWAPEPRDVY 360

Query: 361 WQNLAIPYVSLSVRRLIMGVAFFFLTFFFMIPIAIVQSFASIEGIEKAVPFLKPVIEAKF 420
           W+NLAIPY+SLSVRRLI+GVAFFFLTFFFMIPIA VQ+ ASIEGIEK  PFLKP+IE KF
Sbjct: 361 WENLAIPYMSLSVRRLIIGVAFFFLTFFFMIPIASVQALASIEGIEKKAPFLKPIIEIKF 420

Query: 421 IKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGS 480
           IKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGF+S+SSLERR+ATRYY+F  +NVFLGS
Sbjct: 421 IKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFLSISSLERRSATRYYIFLIINVFLGS 480

Query: 481 IIAGTAFEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLII 540
           I+AG AFEQLNSF+ QSAN+IPKTIG+A+P KATFFITYIMVDGWAGIAGE+LMLKPLI+
Sbjct: 481 ILAGAAFEQLNSFINQSANEIPKTIGVAVPLKATFFITYIMVDGWAGIAGEVLMLKPLIL 540

Query: 541 FHLKNFFLVKTEKDRVEAMDPGSLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFAL 600
           +HLKNFFLVKTEKDR EAMDPGSLGFN+GEPRIQ YFLLGLVYATVTP+LLPFII+FFA 
Sbjct: 541 YHLKNFFLVKTEKDREEAMDPGSLGFNTGEPRIQLYFLLGLVYATVTPVLLPFIIIFFAF 600

Query: 601 AYVVFRHQIINVYNQRYESAAAFWPDVHRRIIAALIISQLLLMGLLSTKKAALSTPFLIA 660
           AYVVFRHQIINVYNQ YES AAFWPDVH R+I AL+ISQL L+GL+STK+AA S PFLIA
Sbjct: 601 AYVVFRHQIINVYNQEYESGAAFWPDVHGRVITALVISQLALLGLMSTKEAAQSAPFLIA 660

Query: 661 LPVLTIWFHYFSKDRYESAFVKYPLQEAMMKDTLERAREPNLNLKGYLRNAYIHPVFKGE 720
           LPVLTIWFH F   R++SAFVKYPLQEAMMKDTLERAR+PN NLK YL++AYIHPVFKG 
Sbjct: 661 LPVLTIWFHGFCNGRHKSAFVKYPLQEAMMKDTLERARDPNFNLKAYLQDAYIHPVFKGG 720

Query: 721 DDDDDALFNNE-ENENVLVLTKRQSRRNTPVPSKMSGASSPSLPEVVQE-DP 770
           DDD+D   + + E E+VLV TKRQSR+NTP PSK+SGASSPSL EVV+  DP
Sbjct: 721 DDDEDDDLSKKLETESVLVPTKRQSRKNTPAPSKISGASSPSLFEVVKNGDP 772

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|343157312\|gb\|AEL95439.1\| early-responsive to dehydration-related protein [Populus euphratica]	Back alignment and taxonomy information

>gi\|225444325\|ref\|XP_002264502.1\| PREDICTED: uncharacterized membrane protein C24H6.13 isoform 1 [Vitis vinifera] gi\|302144095\|emb\|CBI23200.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255554789\|ref\|XP_002518432.1\| conserved hypothetical protein [Ricinus communis] gi\|223542277\|gb\|EEF43819.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

>gi|42567026|ref|NP_193943.2| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|145333700|ref|NP_001078425.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|186512288|ref|NP_001119027.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|186512292|ref|NP_001119028.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|186512296|ref|NP_001119029.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|334186802|ref|NP_001190796.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|53828549|gb|AAU94384.1| At4g22120 [Arabidopsis thaliana] gi|57444911|gb|AAW50707.1| At4g22120 [Arabidopsis thaliana] gi|332659154|gb|AEE84554.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|332659155|gb|AEE84555.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|332659156|gb|AEE84556.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|332659157|gb|AEE84557.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|332659158|gb|AEE84558.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana] gi|332659159|gb|AEE84559.1| early-responsive to dehydration stress-related protein [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|225444327\|ref\|XP_002264591.1\| PREDICTED: uncharacterized membrane protein C24H6.13 isoform 2 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|62319788\|dbj\|BAD93792.1\| hypothetical protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|224099861\|ref\|XP_002334434.1\| predicted protein [Populus trichocarpa] gi\|222872071\|gb\|EEF09202.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|297799812\|ref\|XP_002867790.1\| hypothetical protein ARALYDRAFT_492658 [Arabidopsis lyrata subsp. lyrata] gi\|297313626\|gb\|EFH44049.1\| hypothetical protein ARALYDRAFT_492658 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|449455385\|ref\|XP_004145433.1\| PREDICTED: uncharacterized membrane protein C2G11.09-like [Cucumis sativus]	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		772
TAIR\|locus:2120673		771	AT4G22120 [Arabidopsis thalian	0.987	0.988	0.748	2.60000000198e-315
TAIR\|locus:2134882		772	AT4G04340 [Arabidopsis thalian	0.987	0.987	0.722	7.6e-302
TAIR\|locus:2008860		771	AT1G11960 "AT1G11960" [Arabido	0.987	0.988	0.694	1.7e-288
TAIR\|locus:2027119		769	AT1G62320 "AT1G62320" [Arabido	0.975	0.979	0.691	2.6e-285
TAIR\|locus:2089850		756	AT3G21620 "AT3G21620" [Arabido	0.962	0.982	0.691	1e-283
TAIR\|locus:2130130		761	AT4G15430 "AT4G15430" [Arabido	0.983	0.997	0.662	5.4e-276
TAIR\|locus:2140210		785	AT4G02900 [Arabidopsis thalian	0.990	0.974	0.627	3.6e-263
TAIR\|locus:2031735		806	AT1G32090 "AT1G32090" [Arabido	0.926	0.887	0.594	6e-238
TAIR\|locus:2102117		703	HYP1 "hypothetical protein 1"	0.822	0.903	0.311	3.3e-95
TAIR\|locus:2007126		711	AT1G69450 [Arabidopsis thalian	0.827	0.898	0.294	5.9e-89

TAIR\|locus:2120673 AT4G22120 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 3024 (1069.6 bits), Expect = 2.6e-315, P = 2.6e-315
 Identities = 573/766 (74%), Positives = 646/766 (84%)

Query:     1 MATLADIGVSAALNILGAFIFLIAFAILRLQPFNDRVYFPKWYLKGLRDSPTHGGAFVRK 60
             MATL DIGVSA +NIL AF+F I FA+LRLQPFNDRVYF KWYLKGLR SP  GGAF ++
Sbjct:     1 MATLQDIGVSAGINILSAFVFFIIFAVLRLQPFNDRVYFSKWYLKGLRSSPARGGAFAQR 60

Query:    61 FVNLDFRSYIRFLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVL 120
             FVNLDFRSY++FLNWMPEALKMPEPELI+HAGLDS VYLRIY +GLKIF PIA++AW+VL
Sbjct:    61 FVNLDFRSYMKFLNWMPEALKMPEPELIDHAGLDSVVYLRIYWLGLKIFTPIAVLAWAVL 120

Query:   121 VPVNWTNDTLDVAVKISNVTASDIDKLSISNVPLKSQRFWTHVVMAYAFTFWTCYVLLKE 180
             VPVNWTN+TL++A ++ NVT+SDIDKLS+SN+P  S RFWTH+VMAYAFT WTCYVL+KE
Sbjct:   121 VPVNWTNNTLEMAKQLRNVTSSDIDKLSVSNIPEYSMRFWTHIVMAYAFTIWTCYVLMKE 180

Query:   181 YEKVANLRLQFVASEKRRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHPNHYLTHQXXX 240
             YE +AN+RLQFVASE RRPDQFTVLVRNVPPD DESVSELVEHFFLVNHP+HYLTHQ   
Sbjct:   181 YETIANMRLQFVASEARRPDQFTVLVRNVPPDADESVSELVEHFFLVNHPDHYLTHQVVC 240

Query:   241 XXXXXXXXXXXXXXXQNWLDYYQLKYSRNNSKRPMMKTGFLGLWGEKVDGIDYHISEIEK 300
                            QNWLDYYQLKY+RNNS+R M+K GFLGLWG+KVD I+++I+EI+K
Sbjct:   241 NANKLADLVKKKKKLQNWLDYYQLKYARNNSQRIMVKLGFLGLWGQKVDAIEHYIAEIDK 300

Query:   301 LSKEIAEERERVVSDPKAIMPAAFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVY 360
             +SKEI++ERE VV+DPKAIMPAAFVSF +RW AAVCAQTQQTRNPT WLTEWA EPRDV+
Sbjct:   301 ISKEISKEREEVVNDPKAIMPAAFVSFKTRWAAAVCAQTQQTRNPTQWLTEWAPEPRDVF 360

Query:   361 WQNLAIPYVSLSVRRLIMGVAXXXXXXXXMIPIAIVQSFASIEGIEKAVPFLKPVIEAKF 420
             W NLAIPYVSL+VRRLIM VA        ++PIA VQS A+IEGI KA PFLK +++ KF
Sbjct:   361 WSNLAIPYVSLTVRRLIMHVAFFFLTFFFIVPIAFVQSLATIEGIVKAAPFLKFIVDDKF 420

Query:   421 IKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGS 480
             +KSVIQGFLPGIALKLFL FLP+ILMIMSKFEGF S+SSLERRAA RYY+FN VNVFL S
Sbjct:   421 MKSVIQGFLPGIALKLFLAFLPSILMIMSKFEGFTSISSLERRAAFRYYIFNLVNVFLAS 480

Query:   481 IIAGTAFEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLII 540
             +IAG AFEQLNSFL QSAN IPKTIG+AIP KATFFITYIMVDGWAG+AGEILMLKPLI+
Sbjct:   481 VIAGAAFEQLNSFLNQSANQIPKTIGVAIPMKATFFITYIMVDGWAGVAGEILMLKPLIM 540

Query:   541 FHLKNFFLVKTEKDRVEAMDPGSLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFAL 600
             FHLKN FLVKT+KDR EAMDPGS+GFN+GEPRIQ YFLLGLVYA VTP+LLPFI+VFFAL
Sbjct:   541 FHLKNAFLVKTDKDREEAMDPGSIGFNTGEPRIQLYFLLGLVYAPVTPMLLPFILVFFAL 600

Query:   601 AYVVFRHQIINVYNQRYESAAAFWPDVHRRXXXXXXXXXXXXXXXXXTKKAALSTPFLIA 660
             AY+V+RHQIINVYNQ YESAAAFWPDVH R                 TK AAL+ PFLIA
Sbjct:   601 AYIVYRHQIINVYNQEYESAAAFWPDVHGRVIAALVISQLLLMGLLGTKHAALAAPFLIA 660

Query:   661 LPVLTIWFHYFSKDRYESAFVKYPLQEAMMKDTLERAREPNLNLKGYLRNAYIHPVFKGE 720
             LPVLTI FH+F K RYE AF++YPLQEAMMKDTLE AREPNLNLKGYL+NAY+HPVFKG+
Sbjct:   661 LPVLTIGFHHFCKGRYEPAFIRYPLQEAMMKDTLETAREPNLNLKGYLQNAYVHPVFKGD 720

Query:   721 DDD---DDALFXXXXXXXVLVLTKRQSRRNTPVPSKMSGASSPSLP 763
             +DD   DD L        ++V TKRQSRRNTP PS +SG  SPSLP
Sbjct:   721 EDDYDIDDKL-GKFEDEAIIVPTKRQSRRNTPAPSIISGDDSPSLP 765

GO:0005886 "plasma membrane" evidence=ISM;IDA

GO:0016020 "membrane" evidence=IEA

TAIR\|locus:2134882 AT4G04340 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2008860 AT1G11960 "AT1G11960" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2027119 AT1G62320 "AT1G62320" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2089850 AT3G21620 "AT3G21620" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2130130 AT4G15430 "AT4G15430" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2140210 AT4G02900 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2031735 AT1G32090 "AT1G32090" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2102117 HYP1 "hypothetical protein 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2007126 AT1G69450 [Arabidopsis thaliana (taxid:3702)]	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

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		772
pfam02714		325	pfam02714, DUF221, Domain of unknown function DUF2	1e-117
COG5594		827	COG5594, COG5594, Uncharacterized integral membran	9e-74
pfam13967		151	pfam13967, RSN1_TM, Late exocytosis, associated wi	3e-44

>gnl\|CDD\|190398 pfam02714, DUF221, Domain of unknown function DUF221	Back alignment and domain information

 Score =  356 bits (917), Expect = e-117
 Identities = 121/326 (37%), Positives = 188/326 (57%), Gaps = 3/326 (0%)

Query: 323 AFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVYWQNLAIPYVSLSVRRLIMGVAF 382
           AFV+F S+  A + AQ  Q  NP  W T  A EPRD+ W+NL++      +RRLI+ +  
Sbjct: 1   AFVTFKSQAAAQMAAQALQHHNPLKWPTYLAPEPRDIIWENLSLSRWERWLRRLIVNLLL 60

Query: 383 FFLTFFFMIPIAIVQSFASIEGIEKAVPFLKPVIEA-KFIKSVIQGFLPGIALKLFLIFL 441
           F L  F+ IP+A V   +++E + K  PFLK +++    +  ++ G LP + L L +  L
Sbjct: 61  FLLIIFWAIPVAFVGLLSNLETLTKVWPFLKWILDLPPVLLGLVTGLLPTLLLSLLMALL 120

Query: 442 PTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFLGSIIAGTAFEQLNSFLKQSANDI 501
           P IL  +SK +G  S S +E    ++Y+ F  VNVFL   +A TA   +   +      I
Sbjct: 121 PIILRFLSKLQGHPSRSDVELSVQSKYFAFLVVNVFLVVTLASTASSLITEIIDN-PTSI 179

Query: 502 PKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLIIFHLKNFFLVKTEKDRVEAM-D 560
           P  +   +PK + FFI+YI++ G +G AGE+L L PLI+++++  FL KT +D+ E    
Sbjct: 180 PTLLATNLPKASNFFISYILLQGLSGAAGELLQLGPLILYYIRRKFLDKTPRDKWERYTT 239

Query: 561 PGSLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFALAYVVFRHQIINVYNQRYESA 620
           P S  + +  P     F +GL+Y+ + PL+LPF +V+F L Y V+++Q++ VY  +YES 
Sbjct: 240 PPSFDYGTVYPVFLLIFTIGLIYSVIAPLILPFGLVYFGLGYFVYKYQLLYVYVTKYESG 299

Query: 621 AAFWPDVHRRIIAALIISQLLLMGLL 646
             FWP    R++  L + QL L+GL 
Sbjct: 300 GLFWPRALNRLLVGLYLFQLCLIGLF 325

This family consists of hypothetical transmembrane proteins none of which have any function, the aligned region is at 538 residues at maximum length. Length = 325

>gnl\|CDD\|227881 COG5594, COG5594, Uncharacterized integral membrane protein [Function unknown]	Back alignment and domain information

>gnl\|CDD\|222479 pfam13967, RSN1_TM, Late exocytosis, associated with Golgi transport	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		772
KOG1134		728	consensus Uncharacterized conserved protein [Gener	100.0
COG5594		827	Uncharacterized integral membrane protein [Functio	100.0
PF02714		325	DUF221: Domain of unknown function DUF221; InterPr	100.0
PF13967		157	RSN1_TM: Late exocytosis, associated with Golgi tr	100.0
PF14703		85	DUF4463: Domain of unknown function (DUF4463)	99.02
PF04547		452	Anoctamin: Calcium-activated chloride channel; Int	98.98
KOG2513		647	consensus Protein required for meiotic chromosome	97.76
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	95.57
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	93.83
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	92.91
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	92.8
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	92.14
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	90.83
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	90.82
PLN03120		260	nucleic acid binding protein; Provisional	90.74
KOG0122		270	consensus Translation initiation factor 3, subunit	90.51
PF07810		111	TMC: TMC domain; InterPro: IPR012496 These sequenc	86.86
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	86.25
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	84.62
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	82.26
KOG2514		861	consensus Uncharacterized conserved protein [Funct	81.52
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	81.03
KOG0125		376	consensus Ataxin 2-binding protein (RRM superfamil	80.26

>KOG1134 consensus Uncharacterized conserved protein [General function prediction only]	Back alignment and domain information

Probab=100.00  E-value=1.1e-132  Score=1159.80  Aligned_cols=724  Identities=51%  Similarity=0.870  Sum_probs=674.7

Q ss_pred             CCchhhhHHHHHHHHHHHHHHHHHHHHHcCCCCCCceeccccccCCCCCCCCCCCccccccccccccccCcc-ccchhhh
Q 004125            1 MATLADIGVSAALNILGAFIFLIAFAILRLQPFNDRVYFPKWYLKGLRDSPTHGGAFVRKFVNLDFRSYIRF-LNWMPEA   79 (772)
Q Consensus         1 ~~~~~~~~~sl~in~~~~~~~~~~F~~LR~~p~~~~vY~Pr~~~~~~~~~p~~~~~~~~~~~~l~~~~~~~~-f~Wi~~~   79 (772)
                      ||+.++++.+..+|...+..++.+|.+++.+|+|++||.|+|++.+.+..|.....         ...+++. |+|++++
T Consensus         1 ~~~~~~~~~~s~~~~~~~~~~~~~~~~l~l~~~~~~vy~~~~~l~~~~~~~~~~~~---------~~~~~~~~~~Wl~~~   71 (728)
T KOG1134|consen    1 MATFESIGISSTLNLNSAFAFLFLFLFLRLQPRNFRVYLPIWSLKGLRSSPIESKV---------EPVPSSVNFGWLPAL   71 (728)
T ss_pred             CCccccccccccccchhhHHHHHHHHHHHhhhcceEEEEeeeeeccccCcCccccC---------CCCCCcccccchHHH
Confidence            78888899999999999999999999999999999999999999987655543211         1234455 9999999


Q ss_pred             cCCChhHHHHhhCchHHHHHHHHHHHHHHHHHHHHHHhhheeeeeecCCCccccccccCccCCccccccccCCCCCCcch
Q 004125           80 LKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVLVPVNWTNDTLDVAVKISNVTASDIDKLSISNVPLKSQRF  159 (772)
Q Consensus        80 ~~~~e~eil~~~GlDa~~fLrfl~~~~~if~~~~i~~~~iLlPvn~~~~~~~~~~~~~~~~~~~l~~lsisNv~~~s~~l  159 (772)
                      +|++|+|++++||+||++||||+++++++|+++++++++||+|||+++++.+..+      ..++|++|++|++.+|+++
T Consensus        72 ~k~~~~ei~~~~GlDa~~~L~~~~~~~~lf~~~~~l~~~illPVn~~~~~~~~~~------~~s~~~ls~snv~~~s~~l  145 (728)
T KOG1134|consen   72 LKIPDEEILEHAGLDAYVFLRFLKLGIKLFAVLSLLSVPILLPVNWTNGNLELGN------EDSLDKLSISNVQPGSSLL  145 (728)
T ss_pred             hcCCHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHhheEEeeEEEecCcccccc------cchhhhhhheeccCCCCCE
Confidence            9999999999999999999999999999999999999999999999999886431      1279999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcCCCCCcceEEEecCCCCCCcchHHHHHHhhhccCCCceeEEEEE
Q 004125          160 WTHVVMAYAFTFWTCYVLLKEYEKVANLRLQFVASEKRRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHPNHYLTHQVV  239 (772)
Q Consensus       160 w~h~i~~~~~t~~~~~~L~~ey~~~~~~R~~~l~s~~~~~~~~TVlV~~IP~~~~~~~~e~l~~~F~~~~p~~v~~v~i~  239 (772)
                      |+|++++|++++|+||++++||+++..+|+++++++.+++++.|++++++|+..+.+..+.++++|...+|+++.+++++
T Consensus       146 w~Hv~~~y~~~~~~~~~l~~e~~~~~~~R~~~l~~~~~~~~~~s~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~  225 (728)
T KOG1134|consen  146 WAHVFFTYLFTFFTLFILYREYKHVASIRQAYLASPKYRPDQSSVLVRNVPPPDGVSVSVIVRHFFSLNHPVKVRSHQVV  225 (728)
T ss_pred             EEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCcCccccchhhhcccCCCCCchhhHHhhhhhccCCceeehhHHH
Confidence            99999999999999999999999999999999999999999999999999976666778899999999999999999999


Q ss_pred             ecchhHHHHHHHHHHH-HHHHHHhHhhhhcCCCCCCcccccccCCCCccccHHHHHHHHHHHHHHHHHHHHhhhhcCCCC
Q 004125          240 VNANKLAKLVKKKKKL-QNWLDYYQLKYSRNNSKRPMMKTGFLGLWGEKVDGIDYHISEIEKLSKEIAEERERVVSDPKA  318 (772)
Q Consensus       240 ~~~~~L~~L~~~r~~~-~~~Le~~~~k~~r~~~~Rp~~r~g~~g~~g~kvDaI~~~~~~i~~L~~~I~~~r~~~~~~~~~  318 (772)
                      ||.+++.++.++++|+ ++++.+...+..++..+||++|.|+||++|+||||||||++|+++++++|+++|+...++  +
T Consensus       226 ~~~~~l~~l~~~~~k~~~~~l~~~~~~~~~~~~~rP~~k~~~~~l~gkkvdai~yy~~kl~~l~~~i~~~~~~~~~~--~  303 (728)
T KOG1134|consen  226 YNESKLSKLLSKLKKLRENKLYKEHKRLKSNPKKRPKRKLGFCGLFGKKVDAIDYYSEKLQELSEDIEELRESLYEE--K  303 (728)
T ss_pred             hhHHHHHHHHHHHHHHhHHHHHHhhhhhccccccCCcceeeeeeeecceecHHHHHHHHHHHHHHHHHHHHHHHHhc--C
Confidence            9999999999999999 666666665555554589999999999999999999999999999999999999998776  3


Q ss_pred             CCCeEEEEecCHHHHHHHHHhccCCCCCcceeeeCCCCCCeeecccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004125          319 IMPAAFVSFNSRWGAAVCAQTQQTRNPTLWLTEWASEPRDVYWQNLAIPYVSLSVRRLIMGVAFFFLTFFFMIPIAIVQS  398 (772)
Q Consensus       319 ~~~~AFVtF~s~~~A~~~~q~~~~~~p~~~~v~~APeP~DIiW~NL~~~~~~r~~R~~~~~~~~~~l~if~~iPva~v~~  398 (772)
                      ..|+|||||+|+++|+.|+|++++.++..|.++.||||+||+|+||.++..+|+.|+++++++++++++||++|+|+||+
T Consensus       304 ~~~~aFVtf~sr~~A~~~aq~~~~~~~~~w~~~~APeP~Di~W~nl~i~~~~~~~~~~~~~~~~~~li~f~~iPva~V~~  383 (728)
T KOG1134|consen  304 PLPAAFVTFKSRYGAAVAAQTQQSLNPTKWLTEFAPEPRDIYWDNLAISYVERYLRRFLVNVALFLLLFFWIIPVAFVQA  383 (728)
T ss_pred             CCceEEEEEEeeHHHHHHHHhhhcCCCCceEEEecCCcccceecccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhchhhhhhhcCcchhhhhchhHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhhcCCcchhHHHHHhhhhhhhhHHHHHHH
Q 004125          399 FASIEGIEKAVPFLKPVIEAKFIKSVIQGFLPGIALKLFLIFLPTILMIMSKFEGFISLSSLERRAATRYYLFNFVNVFL  478 (772)
Q Consensus       399 l~~l~~l~~~~p~l~~~~~~~~~~~li~g~LP~l~l~i~~~lLP~il~~ls~~eg~~S~S~~e~s~~~k~f~F~~vNvfl  478 (772)
                      ++|+++|++.+||++++.+.++++++|+|+||++++.++++++|.++++++++|||.|+|+.|++++.|||+|+++|+|+
T Consensus       384 l~nl~~l~~~~Pflk~i~~~~~i~~vI~gfLP~l~l~~~~~~lP~~l~~ls~~eG~~s~S~~e~~a~~k~~~F~~~nvFl  463 (728)
T KOG1134|consen  384 LTNLEGLSKVFPFLKPILEMKFISSVITGFLPTLALVIFLALLPPFLRYLSKLEGLISRSEEERSALNKYYIFLLVNVFL  463 (728)
T ss_pred             HHhhhhhhhccchhhhhhhcchHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHhcCccchhHHHHHHHHhHHHHHHhhhHH
Confidence            99999999999999999888999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhhHHHHHHHHhcccCCCHHHHHhhhcCchhHHHHHHHHHHHhhhhHHHHHhhHHHHHHHHHHhhhcCCHHHHhhh
Q 004125          479 GSIIAGTAFEQLNSFLKQSANDIPKTIGIAIPKKATFFITYIMVDGWAGIAGEILMLKPLIIFHLKNFFLVKTEKDRVEA  558 (772)
Q Consensus       479 v~~i~~s~~~~l~~~~~~p~~~i~~~L~~~lP~~s~FFi~yii~~~~~~~~~~Llr~~~li~~~~~~~~~~~T~re~~~~  558 (772)
                      +++++|++++++..++++| .+++..+|.++|++++||++|++++||+|.++|++|+++|+++++++.+..+|||++++.
T Consensus       464 ~~~l~~sa~~~~~~~l~~p-~~i~~~la~~lP~~a~Ff~~yii~~g~~g~~~ellrl~~Li~~~i~~~~~~~t~~~~~e~  542 (728)
T KOG1134|consen  464 VVTLSGSALRQLLSILSTP-RLIPKLLAAALPKQASFFITYIITSGWAGFAGELLRLVPLIIYLLKKLFLKSTPRDREER  542 (728)
T ss_pred             HhhhhHHHHHHHHHHhcCH-hHHHHHHhhhChhhHHHHHHHHHHhccchhhHHHhcchhHHHHHHHHHHcccchhhhhhh
Confidence            9999999999999999887 899999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC-CCCCcccchhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhhheeeeccCCCcccccHHHHHHHHHHHHHH
Q 004125          559 MDP-GSLGFNSGEPRIQFYFLLGLVYATVTPLLLPFIIVFFALAYVVFRHQIINVYNQRYESAAAFWPDVHRRIIAALII  637 (772)
Q Consensus       559 ~~~-~~f~~g~~y~~~ll~~~i~l~Ys~i~Plilpf~~~yF~l~y~v~Ky~llyvy~~~~esgG~~wp~~~~~~~~~l~i  637 (772)
                      ++| +.+++|..||+.+++++||++||++||+|+|||++||+++|+|||||++|||.++|||||++||.+|+++++|+++
T Consensus       543 ~~p~~~~~~g~~yP~~~~~f~i~i~YsviaPlILpF~lvyF~l~y~vyr~ql~yvy~~~yes~g~~wp~ih~~ii~~l~l  622 (728)
T KOG1134|consen  543 YEPLSSFYFGTIYPRILLIFTIGICYSVIAPLILPFGLVYFCLAYLVYRYQLIYVYNQKYESGGRFWPDIHRRIIFGLIL  622 (728)
T ss_pred             cCCccccchhhhccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhhheeecccccccccchHHHHHHHHHHHHH
Confidence            987 8899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHhhhhhhhccCchhHhhhcchhhhhcCCCc-chhhhhhcccCCCC
Q 004125          638 SQLLLMGLLSTKKAALSTPFLIALPVLTIWFHYFSKDRYESAFVKYPLQEAMMKDTLERAREPNL-NLKGYLRNAYIHPV  716 (772)
Q Consensus       638 ~q~~m~glf~lk~~~~~~~~~~~l~i~ti~f~~~~~~~~~~~~~~~pl~~a~~~d~~~~~~~~~~-~~~~~~~~~Y~~P~  716 (772)
                      ||++|+|+|++|+++..+.+++|++++|++||.+|+.+|.|.+.++|+++++.+|+.|+.++|+. +..+++.++|.||+
T Consensus       623 ~ql~l~gl~~~k~~~~~s~~~~~l~~lTi~~~~~c~~rf~p~f~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~p~  702 (728)
T KOG1134|consen  623 FQLILFGLFSLKKGAVASVLLFPLIVLTILFHIYCKGRFLPLFIAYPIEEAEVDDTLDEEREPNMENLYNYLKSAYVLPV  702 (728)
T ss_pred             HHHHHHHHHHhccccccchHHHHHHHHHHHHHHHHhhhccccccccchhhhhhccCCccccCCChhhccccccccccCcc
Confidence            99999999999999999999999999999999999999999999999999999999998777755 56788999999999


Q ss_pred             CCCCCCCchhhcccccccccccccccc
Q 004125          717 FKGEDDDDDALFNNEENENVLVLTKRQ  743 (772)
Q Consensus       717 l~~~~~~~~~~~~~~~~~~~~~~~~~~  743 (772)
                      +.+.+|+++ ..+..+++++++.||++
T Consensus       703 ~~~~~~~~~-~~~~~~~~~~~~~~~~~  728 (728)
T KOG1134|consen  703 FLSGSDSDG-SELSSEEKSPIVLTKRN  728 (728)
T ss_pred             ccccccccc-cccccccCCcHhhcCCC
Confidence            998875543 22233444777777763

>COG5594 Uncharacterized integral membrane protein [Function unknown]	Back alignment and domain information

>PF02714 DUF221: Domain of unknown function DUF221; InterPro: IPR003864 This domain is found in a family of hypothetical transmembrane proteins none of which have any known function, the aligned region is at 538 residues at maximum length	Back alignment and domain information

>PF13967 RSN1_TM: Late exocytosis, associated with Golgi transport	Back alignment and domain information

>PF14703 DUF4463: Domain of unknown function (DUF4463)	Back alignment and domain information

>PF04547 Anoctamin: Calcium-activated chloride channel; InterPro: IPR007632 This family contains the anoctamin/TMEM16 proteins which are thought to be calcium-dependent chloride channel []	Back alignment and domain information

>KOG2513 consensus Protein required for meiotic chromosome segregation [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>TIGR01659 sex-lethal sex-lethal family splicing factor	Back alignment and domain information

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>PLN03134 glycine-rich RNA-binding protein 4; Provisional	Back alignment and domain information

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor	Back alignment and domain information

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor	Back alignment and domain information

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family	Back alignment and domain information

>PLN03120 nucleic acid binding protein; Provisional	Back alignment and domain information

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF07810 TMC: TMC domain; InterPro: IPR012496 These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 (Q7TN63 from SWISSPROT) and EVIN2 (Q8IU68 from SWISSPROT) - this region is termed the TMC domain []	Back alignment and domain information

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family	Back alignment and domain information

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family	Back alignment and domain information

>KOG2514 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>TIGR01622 SF-CC1 splicing factor, CC1-like family	Back alignment and domain information

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [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

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		772
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04

>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

 Score = 48.7 bits (115), Expect = 8e-06
 Identities = 44/281 (15%), Positives = 93/281 (33%), Gaps = 77/281 (27%)

Query: 72  FLNWMPEALKMPEPELIEHAGLDSAVYLRIYLIGLKIFVPIALVAWSVLVPVNW---TND 128
            L +    L     +L       +    R+ +I   I   +A   W      NW     D
Sbjct: 307 LLKY----LDCRPQDLPREVLTTNP--RRLSIIAESIRDGLAT--WD-----NWKHVNCD 353

Query: 129 TLDVAVKIS--NVTASDI----DKLSI----SNVPLKSQRFWTHVVMAYAFTFWTCYVLL 178
            L   ++ S   +  ++     D+LS+    +++P          +++     W   V+ 
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTI--------LLS---LIW-FDVIK 401

Query: 179 KEYEKVANLRLQFVASEKRRPDQFTVLVRNVPPDPDESVSELVEHFFLVNHP--NHYLTH 236
            +   V N   ++   EK                P ES   +   +  +     N Y  H
Sbjct: 402 SDVMVVVNKLHKYSLVEK---------------QPKESTISIPSIYLELKVKLENEYALH 446

Query: 237 QVVVNANKLAKLVKKKKKLQNWLDYY-------QLKYSRNNSKRPMMKTGFLGL-W-GEK 287
           + +V+   + K       +  +LD Y        LK   +  +  + +  FL   +  +K
Sbjct: 447 RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK 506

Query: 288 V--DGIDYH--------ISEIEKLSKEIAE---ERERVVSD 315
           +  D   ++        + +++     I +   + ER+V+ 
Sbjct: 507 IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNA 547

PyMOL of 1vt4

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		772
2dnz_A		95	Probable RNA-binding protein 23; RNA recognition m	96.42
4fxv_A		99	ELAV-like protein 1; RNA recognition motif, putati	96.37
2lkz_A		95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	96.3
2jrs_A		108	RNA-binding protein 39; RNA binding motif of RBM39	96.09
3s8s_A		110	Histone-lysine N-methyltransferase SETD1A; chromat	96.01
1x5s_A		102	Cold-inducible RNA-binding protein; structure geno	95.87
3bs9_A		87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	95.86
3mdf_A		85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	95.8
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	95.79
2e5h_A		94	Zinc finger CCHC-type and RNA-binding motif- conta	95.77
1x5u_A		105	Splicing factor 3B subunit 4 (spliceosome associat	95.76
2dgs_A		99	DAZ-associated protein 1; RRM domain, structural g	95.76
1whw_A		99	Hypothetical protein riken cDNA 1200009A02; RNA re	95.71
3p5t_L		90	Cleavage and polyadenylation specificity factor S;	95.7
2lxi_A		91	RNA-binding protein 10; NMR {Homo sapiens}	95.62
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	95.59
2dnh_A		105	Bruno-like 5, RNA binding protein; RRM domain, RBD	95.57
2cpz_A		115	CUG triplet repeat RNA-binding protein 1; RRM doma	95.56
2dgo_A		115	Cytotoxic granule-associated RNA binding protein 1	95.53
2x1f_A		96	MRNA 3'-END-processing protein RNA15; transcriptio	95.51
4a8x_A		88	RNA-binding protein with serine-rich domain 1; tra	95.48
1x5t_A		96	Splicing factor 3B subunit 4; structure genomics,	95.46
2dgp_A		106	Bruno-like 4, RNA binding protein; RRM domain, str	95.46
2cq0_A		103	Eukaryotic translation initiation factor 3 subunit	95.45
3md1_A		83	Nuclear and cytoplasmic polyadenylated RNA-bindin	95.44
2fy1_A		116	RNA-binding motif protein, Y chromosome, family 1	95.38
2cqd_A		116	RNA-binding region containing protein 1; RNA recog	95.37
2dgv_A		92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	95.35
1p27_B		106	RNA-binding protein 8A; nuclear protein, mRNA spli	95.35
2do4_A		100	Squamous cell carcinoma antigen recognized by T- c	95.35
2cqi_A		103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	95.35
2cqc_A		95	Arginine/serine-rich splicing factor 10; RNA recog	95.34
4f25_A		115	Polyadenylate-binding protein 1; RRM fold, transla	95.31
2dnm_A		103	SRP46 splicing factor; RRM domain, RBD, structural	95.3
2cph_A		107	RNA binding motif protein 19; RNA recognition moti	95.27
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	95.27
2div_A		99	TRNA selenocysteine associated protein; structural	95.22
2cqg_A		103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	95.2
2khc_A		118	Testis-specific RNP-type RNA binding protein; RRM,	95.14
1wi8_A		104	EIF-4B, eukaryotic translation initiation factor 4	95.13
1oo0_B		110	CG8781-PA, drosophila Y14; RNA recognition motif,	95.11
1h2v_Z		156	20 kDa nuclear CAP binding protein; CAP-binding-co	95.1
2dhg_A		104	TRNA selenocysteine associated protein (SECP43); R	95.03
3ucg_A		89	Polyadenylate-binding protein 2; ferredoxin-like,	95.02
2cqb_A		102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	94.99
2la6_A		99	RNA-binding protein FUS; structural genomics, nort	94.97
3ex7_B		126	RNA-binding protein 8A; protein-RNA complex, mRNA	94.95
2ywk_A		95	Putative RNA-binding protein 11; RRM-domain, struc	94.95
2dng_A		103	Eukaryotic translation initiation factor 4H; RRM d	94.94
2d9p_A		103	Polyadenylate-binding protein 3; RRM domain, struc	94.9
2dnp_A		90	RNA-binding protein 14; RRM domain, RBD, structura	94.89
1x4h_A		111	RNA-binding protein 28; structural genomics, RRM d	94.84
2cpd_A		99	Apobec-1 stimulating protein; RNA recognition moti	94.8
2dnq_A		90	RNA-binding protein 4B; RRM domain,RBD, structural	94.75
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	94.74
2cpj_A		99	Non-POU domain-containing octamer-binding protein;	94.71
2kxn_B		129	Transformer-2 protein homolog beta; SR protein, RR	94.68
2cpf_A		98	RNA binding motif protein 19; RNA recognition moti	94.65
2dgx_A		96	KIAA0430 protein; RRM domain, structural genomics,	94.63
3ulh_A		107	THO complex subunit 4; nuclear protein, RNA bindin	94.62
2ku7_A		140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	94.62
2dgt_A		92	RNA-binding protein 30; RRM domain, structural gen	94.55
2err_A		109	Ataxin-2-binding protein 1; protein-RNA complex, R	94.51
3lqv_A		115	PRE-mRNA branch site protein P14; cysless mutant,	94.5
2cqp_A		98	RNA-binding protein 12; RNA recognition motif, RRM	94.49
2a3j_A		127	U1 small nuclear ribonucleoprotein A; computationa	94.43
1x4a_A		109	Splicing factor, arginine/serine-rich 1 (splicing	94.4
2ytc_A		85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	94.37
3ns6_A		100	Eukaryotic translation initiation factor 3 subuni;	94.35
1p1t_A		104	Cleavage stimulation factor, 64 kDa subunit; RNA r	94.34
1x4c_A		108	Splicing factor, arginine/serine-rich 1; structura	94.32
2kt5_A		124	RNA and export factor-binding protein 2; chaperone	94.27
1s79_A		103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	94.26
1x4e_A		85	RNA binding motif, single-stranded interacting pro	94.23
1uaw_A		77	Mouse-musashi-1; RNP-type structure, RNA binding p	94.16
2do0_A		114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	94.14
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	94.14
2cpe_A		113	RNA-binding protein EWS; RNA recognition motif, RR	94.1
3d2w_A		89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	94.09
1x5o_A		114	RNA binding motif, single-stranded interacting pro	94.08
1wf0_A		88	TDP-43, TAR DNA-binding protein-43; structural gen	94.03
1wf1_A		110	RNA-binding protein RALY; structural genomics, RRM	94.03
1x4g_A		109	Nucleolysin TIAR; structural genomics, RRM domain,	93.95
2cpi_A		111	CCR4-NOT transcription complex subunit 4; RNA reco	93.94
2ki2_A		90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	93.88
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	93.85
2fc8_A		102	NCL protein; structure genomics, RRM_1 domain, str	93.82
3r27_A		100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	93.8
1whx_A		111	Hypothetical protein riken cDNA 1200009A02; RNA re	93.78
2j76_E		100	EIF-4B, EIF4B, eukaryotic translation initiation f	93.73
1why_A		97	Hypothetical protein riken cDNA 1810017N16; RNA re	93.72
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	93.7
1wg5_A		104	Heterogeneous nuclear ribonucleoprotein H; structu	93.64
1wex_A		104	Hypothetical protein (riken cDNA 2810036L13); stru	93.63
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	93.62
2ek1_A		95	RNA-binding protein 12; RNA recognition motif, dim	93.62
2rs2_A		109	Musashi-1, RNA-binding protein musashi homolog 1;	93.58
2dgu_A		103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	93.54
2i2y_A		150	Fusion protein consists of immunoglobin G- binding	93.54
3n9u_C		156	Cleavage and polyadenylation specificity factor S;	93.51
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	93.44
2e44_A		96	Insulin-like growth factor 2 mRNA binding protein	93.43
2mss_A		75	Protein (musashi1); RNA-binding domain, RNA bindin	93.38
2f3j_A		177	RNA and export factor binding protein 2; RRM domai	93.36
1iqt_A		75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	93.33
2kvi_A		96	Nuclear polyadenylated RNA-binding protein 3; RNA-	93.31
2jvo_A		108	Nucleolar protein 3; nucleus, phosphorylation, rib	93.29
2dis_A		109	Unnamed protein product; structural genomics, RRM	93.28
1u6f_A		139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	93.27
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	93.25
2lea_A		135	Serine/arginine-rich splicing factor 2; SR protein	93.25
1nu4_A		97	U1A RNA binding domain; RNA recognition motif, U1	93.15
1rk8_A		165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	93.04
1x4f_A		112	Matrin 3; structural genomics, RRM domain, NPPSFA,	93.04
2kn4_A		158	Immunoglobulin G-binding protein G, splicing FACT	93.0
2jwn_A		124	Embryonic polyadenylate-binding protein 2-B; epabp	92.99
3beg_B		115	Splicing factor, arginine/serine-rich 1; kinase, S	92.92
1x4b_A		116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	92.83
1x4d_A		102	Matrin 3; structural genomics, RRM domain, NPPSFA,	92.79
2cpy_A		114	RNA-binding protein 12; RRM domain, structural gen	92.79
2dnl_A		114	Cytoplasmic polyadenylation element binding protei	92.76
2lmi_A		107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	92.73
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	92.62
2la4_A		101	Nuclear and cytoplasmic polyadenylated RNA-bindin	92.54
2hvz_A		101	Splicing factor, arginine/serine-rich 7; RRM, RNA	92.53
2xnq_A		97	Nuclear polyadenylated RNA-binding protein 3; tran	92.5
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	92.37
2m2b_A		131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	92.26
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	92.16
2dnn_A		109	RNA-binding protein 12; RRM domain, RBD, structura	92.11
2nlw_A		105	Eukaryotic translation initiation factor 3 subunit	92.03
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	91.92
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	91.89
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	91.64
2pe8_A		105	Splicing factor 45; RRM, protein binding; 2.00A {H	91.24
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	91.24
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	91.12
2diu_A		96	KIAA0430 protein; structural genomics, RRM domain,	91.06
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	91.04
2hgm_A		126	HNRPF protein, heterogeneous nuclear ribonucleopro	90.78
1wel_A		124	RNA-binding protein 12; structural genomics, NPPSF	90.76
3q2s_C		229	Cleavage and polyadenylation specificity factor S;	90.74
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	90.14
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	88.53
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	88.49
2wbr_A		89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	88.18
3pgw_S		437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	88.09
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	87.76
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	87.68
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	87.34
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	86.86
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	86.79
1jmt_A		104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	85.88
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	84.3
3s7r_A		87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	83.41
2dit_A		112	HIV TAT specific factor 1 variant; structural geno	83.22
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	83.15
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	82.17
2d9o_A		100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	81.94
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	81.45

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

Probab=96.42  E-value=0.029  Score=47.84  Aligned_cols=39  Identities=13%  Similarity=0.020  Sum_probs=29.5

Q ss_pred             CCeEEEEecCHHHHHHHHHhccCC--CCCcceeeeCCCCCC
Q 004125          320 MPAAFVSFNSRWGAAVCAQTQQTR--NPTLWLTEWASEPRD  358 (772)
Q Consensus       320 ~~~AFVtF~s~~~A~~~~q~~~~~--~p~~~~v~~APeP~D  358 (772)
                      .+.|||+|.+..+|..|.+.+...  +...+.|++|.++.+
T Consensus        47 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   87 (95)
T 2dnz_A           47 KGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLD   87 (95)
T ss_dssp             CSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCC
T ss_pred             eeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccC
Confidence            489999999999999999876543  345677777755443

PyMOL of 2dnz

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}	Back alignment and structure

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}	Back alignment and structure

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}	Back alignment and structure

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}	Back alignment and structure

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}	Back alignment and structure

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*	Back alignment and structure

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A	Back alignment and structure

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C	Back alignment and structure

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}	Back alignment and structure

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A	Back alignment and structure

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A	Back alignment and structure

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A	Back alignment and structure

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B	Back alignment and structure

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}	Back alignment and structure

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A	Back alignment and structure

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0	Back alignment and structure

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}	Back alignment and structure

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A	Back alignment and structure

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A	Back alignment and structure

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A	Back alignment and structure

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}	Back alignment and structure

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*	Back alignment and structure

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X	Back alignment and structure

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A	Back alignment and structure

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}	Back alignment and structure

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*	Back alignment and structure

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}	Back alignment and structure

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A	Back alignment and structure

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A	Back alignment and structure

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A	Back alignment and structure

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}	Back alignment and structure

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B	Back alignment and structure

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A	Back alignment and structure

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}	Back alignment and structure

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*	Back alignment and structure

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}	Back alignment and structure

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A	Back alignment and structure

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}	Back alignment and structure

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}	Back alignment and structure

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}	Back alignment and structure

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}	Back alignment and structure

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A	Back alignment and structure

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A	Back alignment and structure

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A	Back alignment and structure

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}	Back alignment and structure

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A	Back alignment and structure

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A	Back alignment and structure

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}	Back alignment and structure

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C	Back alignment and structure

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A	Back alignment and structure

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}	Back alignment and structure

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A	Back alignment and structure

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A	Back alignment and structure

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1	Back alignment and structure

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B	Back alignment and structure

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A	Back alignment and structure

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...	Back alignment and structure

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A	Back alignment and structure

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}	Back alignment and structure

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}	Back alignment and structure

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A	Back alignment and structure

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}	Back alignment and structure

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A	Back alignment and structure

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}	Back alignment and structure

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A	Back alignment and structure

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E	Back alignment and structure

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}	Back alignment and structure

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}	Back alignment and structure

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}	Back alignment and structure

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A	Back alignment and structure

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A	Back alignment and structure

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A	Back alignment and structure

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A	Back alignment and structure

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1	Back alignment and structure

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A	Back alignment and structure

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A	Back alignment and structure

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A	Back alignment and structure

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C	Back alignment and structure

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A	Back alignment and structure

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A	Back alignment and structure

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C	Back alignment and structure

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}	Back alignment and structure

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*	Back alignment and structure

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*	Back alignment and structure

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A	Back alignment and structure

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A	Back alignment and structure

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A	Back alignment and structure

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E	Back alignment and structure

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3	Back alignment and structure

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A	Back alignment and structure

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A	Back alignment and structure

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1	Back alignment and structure

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A	Back alignment and structure

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		772
d1x5ua1		93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	96.91
d1h2vz_		93	CBP20, 20KDa nuclear cap-binding protein {Human (H	96.78
d1b7fa1		82	Sex-lethal protein {Drosophila melanogaster [TaxId	96.76
d1rk8a_		88	RNA-binding protein 8 {Fruit fly (Drosophila melan	96.76
d1b7fa2		85	Sex-lethal protein {Drosophila melanogaster [TaxId	96.7
d1x5sa1		90	Cold-inducible RNA-binding protein {Human (Homo sa	96.58
d2b0ga1		83	Splicesomal U1A protein {Drosophila melanogaster [	96.51
d2cq0a1		90	Eukaryotic translation initiation factor 3 subunit	96.45
d2u2fa_		85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	96.42
d2cqga1		90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	96.35
d2cqia1		90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	96.35
d1l3ka1		84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	96.33
d1fxla1		82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	96.32
d2cqba1		89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	96.25
d1p1ta_		104	Cleavage stimulation factor, 64 kda subunit {Human	96.21
d2ghpa3		86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	96.16
d2cpza1		102	CUG triplet repeat RNA-binding protein 1 {Human (H	96.16
d1fxla2		85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	96.02
d2cq3a1		93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	95.99
d2cpja1		86	Non-POU domain-containing octamer-binding protein,	95.99
d1x4ha1		98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	95.93
d2cqda1		103	RNA-binding region containing protein 1 {Human (Ho	95.83
d1whwa_		99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	95.82
d1x4ga1		96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	95.79
d1no8a_		78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	95.71
d1cvja1		80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	95.71
d1nu4a_		91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	95.62
d1hd0a_		75	Heterogeneous nuclear ribonucleoprotein d0 {Human	95.53
d1whxa_		111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	95.51
d2ghpa1		81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	95.49
d1cvja2		89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	95.44
d2cpha1		94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	95.44
d2cpfa1		85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	95.36
d2cqpa1		86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	95.34
d1uawa_		77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	95.32
d2cqca1		83	Arginine/serine-rich splicing factor 10 {Human (Ho	95.31
d2f9da1		114	Pre-mRNA branch site protein p14 {Human (Homo sapi	95.3
d1zh5a2		85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	95.22
d1u6fa1		139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	95.16
d1x4ba1		103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	94.95
d1x4fa1		99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	94.92
d1x4aa1		95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	94.87
d1x0fa1		75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	94.85
d1wf0a_		88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	94.85
d2adca2		88	Polypyrimidine tract-binding protein {Human (Homo	94.82
d1wi8a_		104	Eukaryotic translation initiation factor 4B {Human	94.72
d1whya_		97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	94.62
d2adca1		109	Polypyrimidine tract-binding protein {Human (Homo	94.61
d2msta_		75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	94.6
d2cpia1		89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	94.55
d2cq4a1		101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	94.41
d2cpda1		86	APOBEC1 stimulating protein {Human (Homo sapiens)	94.38
d1l3ka2		79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	94.28
d2disa1		96	Hypothetical protein FLJ20273 {Human (Homo sapiens	94.25
d1x4ea1		72	RNA-binding motif, single-stranded-interacting pro	94.08
d2cq1a1		88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	94.0
d3begb1		87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	93.96
d1wg4a_		98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	93.79
d2cpea1		101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	93.56
d2cpxa1		102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	93.55
d1wg5a_		104	Heterogeneous nuclear ribonucleoprotein H' {Human	93.39
d1x5oa1		101	RNA-binding motif, single-stranded-interacting pro	93.33
d1wexa_		104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	93.2
d1weza_		102	Heterogeneous nuclear ribonucleoprotein H' {Human	93.2
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	92.42
d1fjeb1		91	Nucleolin {Golden hamster (Mesocricetus auratus) [	92.4
d2adba1		108	Polypyrimidine tract-binding protein {Human (Homo	90.24
d2cpya1		103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	89.27
d1x4da1		89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	88.61
d1wi6a1		75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	87.23
d1wf2a_		98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	86.36
d2ghpa2		75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	85.67
d2bz2a1		79	Negative elongation factor E, NELF-E {Human (Homo	84.66

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.91  E-value=0.0026  Score=52.80  Aligned_cols=39  Identities=15%  Similarity=0.031  Sum_probs=29.5

Q ss_pred             CCeEEEEecCHHHHHHHHHhccCC--CCCcceeeeC-CCCCC
Q 004125          320 MPAAFVSFNSRWGAAVCAQTQQTR--NPTLWLTEWA-SEPRD  358 (772)
Q Consensus       320 ~~~AFVtF~s~~~A~~~~q~~~~~--~p~~~~v~~A-PeP~D  358 (772)
                      .|.|||+|.+..+|..|.+.+...  +...+.+++| |..+|
T Consensus        51 kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~~n   92 (93)
T d1x5ua1          51 QGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKN   92 (93)
T ss_dssp             CSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSCC
T ss_pred             ccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCCC
Confidence            479999999999999999887654  3456778876 34433

PyMOL of d1x5ua1

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}	Back information, alignment and structure

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}	Back information, alignment and structure

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure